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biobtree.build fails on Linux ARM64

https://yikun.github.io/bioconductor-0301/report/biobtreeR/kunpeng1-buildsrc.html

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### Running command:
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###   /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD build --keep-empty-dirs --no-resave-data biobtreeR
###
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* checking for file ‘biobtreeR/DESCRIPTION’ ... OK
* preparing ‘biobtreeR’:
* checking DESCRIPTION meta-information ... OK
* installing the package to build vignettes
* creating vignettes ... ERROR
--- re-building ‘biobtreeR.Rmd’ using rmarkdown
trying URL 'https://github.com/tamerh/biobtree/releases/download/v1.8.0/biobtree_Linux_64bit.tar.gz'
Content type 'application/octet-stream' length 11081624 bytes (10.6 MB)
==================================================
downloaded 10.6 MB

biobtree
trying URL 'https://github.com/tamerh/biobtree/releases/download/v1.8.0/biobtree_Linux_64bit.tar.gz'
Content type 'application/octet-stream' length 11081624 bytes (10.6 MB)
==================================================
downloaded 10.6 MB

biobtree
sh: 1: /tmp/RtmpPigrdt/biobtree: Exec format error
Quitting from lines 67-68 (biobtreeR.Rmd) 
Error: processing vignette 'biobtreeR.Rmd' failed with diagnostics:
Built data couldn't found. Make sure data built or directory set correctly
--- failed re-building ‘biobtreeR.Rmd’

SUMMARY: processing the following file failed:
  ‘biobtreeR.Rmd’

Error: Vignette re-building failed.
Execution halted

GeneGA.build

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### Running command:
###
###   /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD build --keep-empty-dirs --no-resave-data GeneGA
###
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* checking for file ‘GeneGA/DESCRIPTION’ ... OK
* preparing ‘GeneGA’:
* checking DESCRIPTION meta-information ... OK
* installing the package to build vignettes
* creating vignettes ... ERROR
--- re-building ‘GeneGA.Rnw’ using Sweave
Loading required package: seqinr
Loading required package: hash
hash-2.2.6.2 provided by Decision Patterns

sh: 1: RNAfold: not found

Error: processing vignette 'GeneGA.Rnw' failed with diagnostics:
 chunk 3 
Error in system(paste("echo ", x, "|RNAfold", sep = ""), intern = T) : 
  error in running command

--- failed re-building ‘GeneGA.Rnw’

SUMMARY: processing the following file failed:
  ‘GeneGA.Rnw’

Error: Vignette re-building failed.
Execution halted

mait.build

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### Running command:
###
###   /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD build --keep-empty-dirs --no-resave-data MAIT
###
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* checking for file ‘MAIT/DESCRIPTION’ ... OK
* preparing ‘MAIT’:
* checking DESCRIPTION meta-information ... OK
* installing the package to build vignettes
* creating vignettes ... ERROR
--- re-building ‘MAIT_Vignette.Rnw’ using Sweave
Loading required package: CAMERA
Loading required package: Biobase
Loading required package: BiocGenerics

Attaching package: ‘BiocGenerics’

The following objects are masked from ‘package:stats’:

    IQR, mad, sd, var, xtabs

The following objects are masked from ‘package:base’:

    Filter, Find, Map, Position, Reduce, anyDuplicated, aperm, append,
    as.data.frame, basename, cbind, colnames, dirname, do.call,
    duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
    lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin,
    pmin.int, rank, rbind, rownames, sapply, setdiff, sort, table,
    tapply, union, unique, unsplit, which.max, which.min

Welcome to Bioconductor

    Vignettes contain introductory material; view with
    'browseVignettes()'. To cite Bioconductor, see
    'citation("Biobase")', and for packages 'citation("pkgname")'.

Loading required package: xcms
Loading required package: BiocParallel
Loading required package: MSnbase
Loading required package: mzR
Loading required package: Rcpp
Loading required package: S4Vectors
Loading required package: stats4

Attaching package: ‘S4Vectors’

The following objects are masked from ‘package:base’:

    I, expand.grid, unname

Loading required package: ProtGenerics

Attaching package: ‘ProtGenerics’

The following object is masked from ‘package:stats’:

    smooth


This is MSnbase version 2.25.2 
  Visit https://lgatto.github.io/MSnbase/ to get started.


Attaching package: ‘MSnbase’

The following object is masked from ‘package:base’:

    trimws


This is xcms version 3.21.2 


Attaching package: ‘xcms’

The following object is masked from ‘package:stats’:

    sigma

Loading required package: pls

Attaching package: ‘pls’

The following object is masked from ‘package:stats’:

    loadings


Attaching package: ‘MAIT’

The following objects are masked from ‘package:pls’:

    loadings, scores

The following object is masked from ‘package:mzR’:

    model

The following object is masked from ‘package:BiocGenerics’:

    plotPCA

The following object is masked from ‘package:stats’:

    loadings


Error: processing vignette 'MAIT_Vignette.Rnw' failed with diagnostics:
 chunk 2 (label = sampleProcessing) 
Error in library(faahKO) : there is no package called ‘faahKO’

--- failed re-building ‘MAIT_Vignette.Rnw’

SUMMARY: processing the following file failed:
  ‘MAIT_Vignette.Rnw’

Error: Vignette re-building failed.
Execution halted

sigPathway.install

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### Running command:
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###   /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD INSTALL sigPathway
###
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* installing to library ‘/home/biocbuild/bbs-3.17-bioc/R/library’
* installing *source* package ‘sigPathway’ ...
** using staged installation
** libs
using C compiler: ‘gcc (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0’
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG   -I/usr/local/include    -fPIC  -g -O2  -Wall -c calc_gene_set_internal.c -o calc_gene_set_internal.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG   -I/usr/local/include    -fPIC  -g -O2  -Wall -c calc_gene_set_stat.c -o calc_gene_set_stat.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG   -I/usr/local/include    -fPIC  -g -O2  -Wall -c calc_probe_stat.c -o calc_probe_stat.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG   -I/usr/local/include    -fPIC  -g -O2  -Wall -c calc_weights.c -o calc_weights.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG   -I/usr/local/include    -fPIC  -g -O2  -Wall -c matrix_fn.c -o matrix_fn.o
In file included from /home/biocbuild/bbs-3.17-bioc/R/include/R.h:78,
                 from sigPathway.h:18,
                 from matrix_fn.c:13:
matrix_fn.c: In function ‘matprod’:
matrix_fn.c:28:16: error: too few arguments to function ‘dgemm_’
   28 |       F77_CALL(dgemm)(transa, transb, &nrx, &ncy, &ncx, &one,
      |                ^~~~~
/home/biocbuild/bbs-3.17-bioc/R/include/R_ext/RS.h:77:25: note: in definition of macro ‘F77_CALL’
   77 | # define F77_CALL(x)    x ## _
      |                         ^
/home/biocbuild/bbs-3.17-bioc/R/include/R_ext/BLAS.h:207:10: note: declared here
  207 | F77_NAME(dgemm)(const char *transa, const char *transb, const int *m,
      |          ^~~~~
/home/biocbuild/bbs-3.17-bioc/R/include/R_ext/RS.h:77:25: note: in definition of macro ‘F77_CALL’
   77 | # define F77_CALL(x)    x ## _
      |                         ^
/home/biocbuild/bbs-3.17-bioc/R/include/R_ext/BLAS.h:207:1: note: in expansion of macro ‘F77_NAME’
  207 | F77_NAME(dgemm)(const char *transa, const char *transb, const int *m,
      | ^~~~~~~~
matrix_fn.c: In function ‘eigen’:
matrix_fn.c:65:12: error: too few arguments to function ‘dsyevr_’
   65 |   F77_CALL(dsyevr)(jobv, range, uplo, &n, rx, &n,
      |            ^~~~~~
/home/biocbuild/bbs-3.17-bioc/R/include/R_ext/RS.h:77:25: note: in definition of macro ‘F77_CALL’
   77 | # define F77_CALL(x)    x ## _
      |                         ^
/home/biocbuild/bbs-3.17-bioc/R/include/R_ext/Lapack.h:1270:10: note: declared here
 1270 | F77_NAME(dsyevr)(const char* jobz, const char* range, const char* uplo,
      |          ^~~~~~
/home/biocbuild/bbs-3.17-bioc/R/include/R_ext/RS.h:77:25: note: in definition of macro ‘F77_CALL’
   77 | # define F77_CALL(x)    x ## _
      |                         ^
/home/biocbuild/bbs-3.17-bioc/R/include/R_ext/Lapack.h:1270:1: note: in expansion of macro ‘F77_NAME’
 1270 | F77_NAME(dsyevr)(const char* jobz, const char* range, const char* uplo,
      | ^~~~~~~~
matrix_fn.c:77:12: error: too few arguments to function ‘dsyevr_’
   77 |   F77_CALL(dsyevr)(jobv, range, uplo, &n, rx, &n,
      |            ^~~~~~
matrix_fn.c:77:3: note: in expansion of macro ‘F77_CALL’
   77 |   F77_CALL(dsyevr)(jobv, range, uplo, &n, rx, &n,
      |   ^~~~~~~~
/home/biocbuild/bbs-3.17-bioc/R/include/R_ext/Lapack.h:1270:10: note: declared here
 1270 | F77_NAME(dsyevr)(const char* jobz, const char* range, const char* uplo,
      |          ^~~~~~
/home/biocbuild/bbs-3.17-bioc/R/include/R_ext/RS.h:77:25: note: in definition of macro ‘F77_CALL’
   77 | # define F77_CALL(x)    x ## _
      |                         ^
/home/biocbuild/bbs-3.17-bioc/R/include/R_ext/Lapack.h:1270:1: note: in expansion of macro ‘F77_NAME’
 1270 | F77_NAME(dsyevr)(const char* jobz, const char* range, const char* uplo,
      | ^~~~~~~~
make: *** [/home/biocbuild/bbs-3.17-bioc/R/etc/Makeconf:191: matrix_fn.o] Error 1
ERROR: compilation failed for package ‘sigPathway’
* removing ‘/home/biocbuild/bbs-3.17-bioc/R/library/sigPathway’

rsvg.install

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### Running command:
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###   /home/biocbuild/bbs-3.17-bioc/R/bin/Rscript -e "source('/home/biocbuild/BBS/utils/installNonTargetPkg.R');installNonTargetPkg('rsvg')"
###
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trying URL 'https://cran.rstudio.com/src/contrib/rsvg_2.4.0.tar.gz'
Content type 'application/x-gzip' length 258895 bytes (252 KB)
==================================================
downloaded 252 KB

* installing *source* package ‘rsvg’ ...
** package ‘rsvg’ successfully unpacked and MD5 sums checked
** using staged installation
Package librsvg-2.0 was not found in the pkg-config search path.
Perhaps you should add the directory containing `librsvg-2.0.pc'
to the PKG_CONFIG_PATH environment variable
No package 'librsvg-2.0' found
Using PKG_CFLAGS=
Using PKG_LIBS=-lrsvg
--------------------------- [ANTICONF] --------------------------------
Configuration failed to find the librsvg-2.0 library. Try installing:
 * deb: librsvg2-dev (Debian, Ubuntu, etc)
 * rpm: librsvg2-devel (Fedora, EPEL)
 * csw: librsvg_dev, sunx11_devel (Solaris)
 * brew: librsvg (OSX)
If librsvg-2.0 is already installed, check that 'pkg-config' is in your
PATH and PKG_CONFIG_PATH contains a librsvg-2.0.pc file. If pkg-config
is unavailable you can set INCLUDE_DIR and LIB_DIR manually via:
R CMD INSTALL --configure-vars='INCLUDE_DIR=... LIB_DIR=...'
-------------------------- [ERROR MESSAGE] ---------------------------
<stdin>:1:10: fatal error: librsvg/rsvg.h: No such file or directory
compilation terminated.
--------------------------------------------------------------------
ERROR: configuration failed for package ‘rsvg’
* removing ‘/home/biocbuild/bbs-3.17-bioc/R/library/rsvg’

The downloaded source packages are in
	‘/tmp/RtmpaI07Hu/downloaded_packages’
Updating HTML index of packages in '.Library'
Making 'packages.html' ... done
Warning message:
In install.packages(pkg, repos = .NON_TARGET_REPOS, dependencies = FALSE,  :
  installation of package ‘rsvg’ had non-zero exit status

lfa.install

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### Running command:
###
###   /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD INSTALL lfa
###
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* installing to library ‘/home/biocbuild/bbs-3.17-bioc/R/library’
* installing *source* package ‘lfa’ ...
** using staged installation
** libs
using C compiler: ‘gcc (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0’
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG   -I/usr/local/include    -fPIC  -g -O2  -Wall -c fastmat.c -o fastmat.o
In file included from /home/biocbuild/bbs-3.17-bioc/R/include/R.h:78,
                 from lfa.h:4,
                 from fastmat.c:1:
fastmat.c: In function ‘mv’:
fastmat.c:22:14: error: too few arguments to function ‘dgemv_’
   22 |     F77_CALL(dgemv)(&tr,dimA,dimA+1,&alpha,A,dimA,v,&one,&zero,ret,&one);
      |              ^~~~~
/home/biocbuild/bbs-3.17-bioc/R/include/R_ext/RS.h:77:25: note: in definition of macro ‘F77_CALL’
   77 | # define F77_CALL(x)    x ## _
      |                         ^
/home/biocbuild/bbs-3.17-bioc/R/include/R_ext/BLAS.h:107:10: note: declared here
  107 | F77_NAME(dgemv)(const char *trans, const int *m, const int *n,
      |          ^~~~~
/home/biocbuild/bbs-3.17-bioc/R/include/R_ext/RS.h:77:25: note: in definition of macro ‘F77_CALL’
   77 | # define F77_CALL(x)    x ## _
      |                         ^
/home/biocbuild/bbs-3.17-bioc/R/include/R_ext/BLAS.h:107:1: note: in expansion of macro ‘F77_NAME’
  107 | F77_NAME(dgemv)(const char *trans, const int *m, const int *n,
      | ^~~~~~~~
fastmat.c: In function ‘tmv’:
fastmat.c:48:14: error: too few arguments to function ‘dgemv_’
   48 |     F77_CALL(dgemv)(&tr,dimA,dimA+1,&alpha,A,dimA,v,&one,&zero,ret,&one);
      |              ^~~~~
/home/biocbuild/bbs-3.17-bioc/R/include/R_ext/RS.h:77:25: note: in definition of macro ‘F77_CALL’
   77 | # define F77_CALL(x)    x ## _
      |                         ^
/home/biocbuild/bbs-3.17-bioc/R/include/R_ext/BLAS.h:107:10: note: declared here
  107 | F77_NAME(dgemv)(const char *trans, const int *m, const int *n,
      |          ^~~~~
/home/biocbuild/bbs-3.17-bioc/R/include/R_ext/RS.h:77:25: note: in definition of macro ‘F77_CALL’
   77 | # define F77_CALL(x)    x ## _
      |                         ^
/home/biocbuild/bbs-3.17-bioc/R/include/R_ext/BLAS.h:107:1: note: in expansion of macro ‘F77_NAME’
  107 | F77_NAME(dgemv)(const char *trans, const int *m, const int *n,
      | ^~~~~~~~
make: *** [/home/biocbuild/bbs-3.17-bioc/R/etc/Makeconf:191: fastmat.o] Error 1
ERROR: compilation failed for package ‘lfa’
* removing ‘/home/biocbuild/bbs-3.17-bioc/R/library/lfa’

CancerInSilico.install

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### Running command:
###
###   /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD INSTALL CancerInSilico
###
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* installing to library ‘/home/biocbuild/bbs-3.17-bioc/R/library’
* installing *source* package ‘CancerInSilico’ ...
** using staged installation
** libs
using C++ compiler: ‘g++ (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0’
g++ -std=gnu++14  -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.17-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.17-bioc/R/library/BH/include' -I/usr/local/include    -fPIC  -g -O2  -Wall  -c RunModel.cpp -o RunModel.o
g++ -std=gnu++14  -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.17-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.17-bioc/R/library/BH/include' -I/usr/local/include    -fPIC  -g -O2  -Wall  -c RcppExports.cpp -o RcppExports.o
g++ -std=gnu++14  -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.17-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.17-bioc/R/library/BH/include' -I/usr/local/include    -fPIC  -g -O2  -Wall  -c CellModels/DrasdoHohmeModel.cpp -o CellModels/DrasdoHohmeModel.o
g++ -std=gnu++14  -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.17-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.17-bioc/R/library/BH/include' -I/usr/local/include    -fPIC  -g -O2  -Wall  -c OffLatticeModel/OffLatticeCell.cpp -o OffLatticeModel/OffLatticeCell.o
g++ -std=gnu++14  -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.17-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.17-bioc/R/library/BH/include' -I/usr/local/include    -fPIC  -g -O2  -Wall  -c OffLatticeModel/OffLatticeCellBasedModel.cpp -o OffLatticeModel/OffLatticeCellBasedModel.o
g++ -std=gnu++14  -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.17-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.17-bioc/R/library/BH/include' -I/usr/local/include    -fPIC  -g -O2  -Wall  -c OffLatticeModel/OffLatticeRadiusSolver.cpp -o OffLatticeModel/OffLatticeRadiusSolver.o
g++ -std=gnu++14  -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.17-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.17-bioc/R/library/BH/include' -I/usr/local/include    -fPIC  -g -O2  -Wall  -c Core/Cell.cpp -o Core/Cell.o
g++ -std=gnu++14  -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.17-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.17-bioc/R/library/BH/include' -I/usr/local/include    -fPIC  -g -O2  -Wall  -c Core/CellBasedModel.cpp -o Core/CellBasedModel.o
g++ -std=gnu++14  -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.17-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.17-bioc/R/library/BH/include' -I/usr/local/include    -fPIC  -g -O2  -Wall  -c Core/CellType.cpp -o Core/CellType.o
g++ -std=gnu++14  -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.17-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.17-bioc/R/library/BH/include' -I/usr/local/include    -fPIC  -g -O2  -Wall  -c Core/Drug.cpp -o Core/Drug.o
g++ -std=gnu++14  -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.17-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.17-bioc/R/library/BH/include' -I/usr/local/include    -fPIC  -g -O2  -Wall  -c Core/Random.cpp -o Core/Random.o
In file included from /home/biocbuild/bbs-3.17-bioc/R/library/BH/include/boost/mpl/aux_/na_assert.hpp:23,
                 from /home/biocbuild/bbs-3.17-bioc/R/library/BH/include/boost/mpl/arg.hpp:25,
                 from /home/biocbuild/bbs-3.17-bioc/R/library/BH/include/boost/mpl/placeholders.hpp:24,
                 from /home/biocbuild/bbs-3.17-bioc/R/library/BH/include/boost/iterator/iterator_categories.hpp:16,
                 from /home/biocbuild/bbs-3.17-bioc/R/library/BH/include/boost/iterator/iterator_concepts.hpp:10,
                 from /home/biocbuild/bbs-3.17-bioc/R/library/BH/include/boost/range/concepts.hpp:20,
                 from /home/biocbuild/bbs-3.17-bioc/R/library/BH/include/boost/range/size_type.hpp:20,
                 from /home/biocbuild/bbs-3.17-bioc/R/library/BH/include/boost/range/size.hpp:21,
                 from /home/biocbuild/bbs-3.17-bioc/R/library/BH/include/boost/random/hyperexponential_distribution.hpp:29,
                 from /home/biocbuild/bbs-3.17-bioc/R/library/BH/include/boost/random.hpp:70,
                 from Core/Random.cpp:3:
/home/biocbuild/bbs-3.17-bioc/R/library/BH/include/boost/mpl/assert.hpp:194:21: warning: unnecessary parentheses in declaration of ‘assert_arg’ [-Wparentheses]
  194 | failed ************ (Pred::************
      |                     ^~~~~~~~~~~~~~~~~~~
  195 |       assert_arg( void (*)(Pred), typename assert_arg_pred<Pred>::type )
      |       ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
  196 |     );
      |     ~                
/home/biocbuild/bbs-3.17-bioc/R/library/BH/include/boost/mpl/assert.hpp:194:21: note: remove parentheses
  194 | failed ************ (Pred::************
      |                     ^~~~~~~~~~~~~~~~~~~
      |                     -
  195 |       assert_arg( void (*)(Pred), typename assert_arg_pred<Pred>::type )
      |       ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
  196 |     );
      |     ~                
      |     -
/home/biocbuild/bbs-3.17-bioc/R/library/BH/include/boost/mpl/assert.hpp:199:21: warning: unnecessary parentheses in declaration of ‘assert_not_arg’ [-Wparentheses]
  199 | failed ************ (boost::mpl::not_<Pred>::************
      |                     ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
  200 |       assert_not_arg( void (*)(Pred), typename assert_arg_pred_not<Pred>::type )
      |       ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
  201 |     );
      |     ~                
/home/biocbuild/bbs-3.17-bioc/R/library/BH/include/boost/mpl/assert.hpp:199:21: note: remove parentheses
  199 | failed ************ (boost::mpl::not_<Pred>::************
      |                     ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
      |                     -
  200 |       assert_not_arg( void (*)(Pred), typename assert_arg_pred_not<Pred>::type )
      |       ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
  201 |     );
      |     ~                
      |     -
g++ -std=gnu++14  -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.17-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.17-bioc/R/library/BH/include' -I/usr/local/include    -fPIC  -g -O2  -Wall  -c test-runner.cpp -o test-runner.o
In file included from /usr/include/signal.h:328,
                 from Tests/catch.h:2070,
                 from test-runner.cpp:2:
Tests/catch.h:6473:33: error: size of array ‘altStackMem’ is not an integral constant-expression
 6473 |         static char altStackMem[SIGSTKSZ];
      |                                 ^~~~~~~~
Tests/catch.h:6524:45: error: size of array ‘altStackMem’ is not an integral constant-expression
 6524 |     char FatalConditionHandler::altStackMem[SIGSTKSZ] = {};
      |                                             ^~~~~~~~
make: *** [/home/biocbuild/bbs-3.17-bioc/R/etc/Makeconf:198: test-runner.o] Error 1
ERROR: compilation failed for package ‘CancerInSilico’
* removing ‘/home/biocbuild/bbs-3.17-bioc/R/library/CancerInSilico’

biobtreer.build

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD build --keep-empty-dirs --no-resave-data biobtreeR
###
##############################################################################
##############################################################################


* checking for file ‘biobtreeR/DESCRIPTION’ ... OK
* preparing ‘biobtreeR’:
* checking DESCRIPTION meta-information ... OK
* installing the package to build vignettes
* creating vignettes ... ERROR
--- re-building ‘biobtreeR.Rmd’ using rmarkdown
trying URL 'https://github.com/tamerh/biobtree/releases/download/v1.8.0/biobtree_Linux_64bit.tar.gz'
Content type 'application/octet-stream' length 11081624 bytes (10.6 MB)
==================================================
downloaded 10.6 MB

biobtree
trying URL 'https://github.com/tamerh/biobtree/releases/download/v1.8.0/biobtree_Linux_64bit.tar.gz'
Content type 'application/octet-stream' length 11081624 bytes (10.6 MB)
==================================================
downloaded 10.6 MB

biobtree
sh: 1: /tmp/RtmpPigrdt/biobtree: Exec format error
Quitting from lines 67-68 (biobtreeR.Rmd) 
Error: processing vignette 'biobtreeR.Rmd' failed with diagnostics:
Built data couldn't found. Make sure data built or directory set correctly
--- failed re-building ‘biobtreeR.Rmd’

SUMMARY: processing the following file failed:
  ‘biobtreeR.Rmd’

Error: Vignette re-building failed.
Execution halted

genotypeeval.check

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:genotypeeval.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/library --timings genotypeeval_1.31.1.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.17-bioc/meat/genotypeeval.Rcheck’
* using R Under development (unstable) (2023-01-14 r83615)
* using platform: aarch64-unknown-linux-gnu (64-bit)
* R was compiled by
    gcc (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0
    GNU Fortran (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0
* running under: Ubuntu 22.04.1 LTS
* using session charset: UTF-8
* checking for file ‘genotypeeval/DESCRIPTION’ ... OK
* this is package ‘genotypeeval’ version ‘1.31.1’
* checking package namespace information ... OK
* checking package dependencies ... ERROR
Package suggested but not available: ‘SNPlocs.Hsapiens.dbSNP141.GRCh38’

The suggested packages are required for a complete check.
Checking can be attempted without them by setting the environment
variable _R_CHECK_FORCE_SUGGESTS_ to a false value.

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
* DONE

Status: 1 ERROR
See
  ‘/home/biocbuild/bbs-3.17-bioc/meat/genotypeeval.Rcheck/00check.log’
for details.

DESeq2.check

https://yikun.github.io/bioconductor-0301/report/DESeq2/kunpeng1-checksrc.html

 mix <- unmix(norm.cts, pure, alpha=0.01)
Warning in sqrt(alpha * q) : NaNs produced
Error in optim(par = rep(1, ncol(pure)), fn = sumLossVST, gr = NULL, i,  : 
  L-BFGS-B needs finite values of 'fn'
Calls: unmix -> lapply -> lapply -> FUN -> optim
Execution halted

gapgom.build

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD build --keep-empty-dirs --no-resave-data GAPGOM
###
##############################################################################
##############################################################################


* checking for file ‘GAPGOM/DESCRIPTION’ ... OK
* preparing ‘GAPGOM’:
* checking DESCRIPTION meta-information ... OK
* installing the package to build vignettes
* creating vignettes ... ERROR
--- re-building ‘GAPGOM.Rmd’ using rmarkdown
Quitting from lines 130-142 (GAPGOM.Rmd) 
Error: processing vignette 'GAPGOM.Rmd' failed with diagnostics:
could not find function "ExpressionSet"
--- failed re-building ‘GAPGOM.Rmd’

--- re-building ‘benchmarks.Rmd’ using rmarkdown
--- finished re-building ‘benchmarks.Rmd’

SUMMARY: processing the following file failed:
  ‘GAPGOM.Rmd’

Error: Vignette re-building failed.
Execution halted

Rhisat2.install

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD INSTALL Rhisat2
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.17-bioc/R/library’
* installing *source* package ‘Rhisat2’ ...
** using staged installation
** libs
/usr/bin/g++ -O3 -m64 -msse2 -funroll-loops -g3 -DCOMPILER_OPTIONS="\"-O3 -m64 -msse2 -funroll-loops -g3 -std=c++11\"" -std=c++11 \
-fno-strict-aliasing -DHISAT2_VERSION="\"2.2.1\"" -DBUILD_HOST="\"kunpeng1\"" -DBUILD_TIME="\"Mon  6 Feb 02:48:28 UTC 2023\"" -DCOMPILER_VERSION="\"`/usr/bin/g++ -v 2>&1 | tail -1`\"" -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_GNU_SOURCE  -DBOWTIE_MM  -DUSESIMDE -DBOWTIE2 -DNDEBUG -Wall -DMASSIVE_DATA_RLCSA \
-I. -I third_party \
-o hisat2-build-s hisat2_build.cpp \
ccnt_lut.cpp ref_read.cpp alphabet.cpp shmem.cpp edit.cpp gfm.cpp reference.cpp ds.cpp multikey_qsort.cpp limit.cpp random_source.cpp tinythread.cpp diff_sample.cpp hisat2_build_main.cpp \
-lpthread 
g++: error: unrecognized command-line option ‘-m64’
g++: error: unrecognized command-line option ‘-msse2’
make: *** [Makefile:363: hisat2-build-s] Error 1
ERROR: compilation failed for package ‘Rhisat2’
* removing ‘/home/biocbuild/bbs-3.17-bioc/R/library/Rhisat2’

gmapR.install

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD INSTALL gmapR
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.17-bioc/R/library’
* installing *source* package ‘gmapR’ ...
** using staged installation
** libs
cd gstruct/; \
        CFLAGS="-g -O3" \
./configure --enable-static --disable-shared \
            --prefix=/home/biocbuild/bbs-3.17-bioc/meat/gmapR/src/../inst/usr --includedir=/home/biocbuild/bbs-3.17-bioc/meat/gmapR/src/../inst/usr/include/gstruct \
            --libdir=/home/biocbuild/bbs-3.17-bioc/meat/gmapR/src/../inst/usr/lib \
            --with-samtools-lib=/home/biocbuild/bbs-3.17-bioc/meat/gmapR/src/samtools \
	    --disable-maintainer-mode \
                    --disable-binaries
checking package version... 2017-01-01
checking whether to enable maintainer-specific portions of Makefiles... no
loading default site script ./config.site
checking CFLAGS... -g -O3
checking build system type... aarch64-unknown-linux-gnu
checking host system type... aarch64-unknown-linux-gnu
checking target system type... aarch64-unknown-linux-gnu
checking for gcc... gcc
checking whether the C compiler works... yes
checking for C compiler default output file name... a.out
checking for suffix of executables... 
checking whether we are cross compiling... no
checking for suffix of object files... o
checking whether we are using the GNU C compiler... yes
checking whether gcc accepts -g... yes
checking for gcc option to accept ISO C89... none needed
checking whether gcc understands -c and -o together... yes
checking for special C compiler options needed for large files... no
checking for _FILE_OFFSET_BITS value needed for large files... no
checking for a BSD-compatible install... /usr/bin/install -c
checking whether build environment is sane... yes
checking for a thread-safe mkdir -p... /usr/bin/mkdir -p
checking for gawk... gawk
checking whether make sets $(MAKE)... yes
checking for style of include used by make... GNU
checking whether make supports nested variables... yes
checking dependency style of gcc... gcc3
checking bindir... /home/biocbuild/bbs-3.17-bioc/meat/gmapR/src/../inst/usr/bin
checking whether to link statically... not specified so disabled by default
checking for a working version of perl... /usr/bin/perl
checking for gcc... (cached) gcc
checking whether we are using the GNU C compiler... (cached) yes
checking whether gcc accepts -g... (cached) yes
checking for gcc option to accept ISO C89... (cached) none needed
checking whether gcc understands -c and -o together... (cached) yes
checking how to print strings... printf
checking for a sed that does not truncate output... /usr/bin/sed
checking for grep that handles long lines and -e... /usr/bin/grep
checking for egrep... /usr/bin/grep -E
checking for fgrep... /usr/bin/grep -F
checking for ld used by gcc... /usr/bin/ld
checking if the linker (/usr/bin/ld) is GNU ld... yes
checking for BSD- or MS-compatible name lister (nm)... /usr/bin/nm -B
checking the name lister (/usr/bin/nm -B) interface... BSD nm
checking whether ln -s works... yes
checking the maximum length of command line arguments... 1572864
checking how to convert aarch64-unknown-linux-gnu file names to aarch64-unknown-linux-gnu format... func_convert_file_noop
checking how to convert aarch64-unknown-linux-gnu file names to toolchain format... func_convert_file_noop
checking for /usr/bin/ld option to reload object files... -r
checking for objdump... objdump
checking how to recognize dependent libraries... pass_all
checking for dlltool... no
checking how to associate runtime and link libraries... printf %s\n
checking for ar... ar
checking for archiver @FILE support... @
checking for strip... strip
checking for ranlib... ranlib
checking command to parse /usr/bin/nm -B output from gcc object... ok
checking for sysroot... no
checking for a working dd... /usr/bin/dd
checking how to truncate binary pipes... /usr/bin/dd bs=4096 count=1
checking for mt... mt
checking if mt is a manifest tool... no
checking how to run the C preprocessor... gcc -E
checking for ANSI C header files... yes
checking for sys/types.h... yes
checking for sys/stat.h... yes
checking for stdlib.h... yes
checking for string.h... yes
checking for memory.h... yes
checking for strings.h... yes
checking for inttypes.h... yes
checking for stdint.h... yes
checking for unistd.h... yes
checking for dlfcn.h... yes
checking for objdir... .libs
checking if gcc supports -fno-rtti -fno-exceptions... no
checking for gcc option to produce PIC... -fPIC -DPIC
checking if gcc PIC flag -fPIC -DPIC works... yes
checking if gcc static flag -static works... yes
checking if gcc supports -c -o file.o... yes
checking if gcc supports -c -o file.o... (cached) yes
checking whether the gcc linker (/usr/bin/ld) supports shared libraries... yes
checking dynamic linker characteristics... GNU/Linux ld.so
checking how to hardcode library paths into programs... immediate
checking whether stripping libraries is possible... yes
checking if libtool supports shared libraries... yes
checking whether to build shared libraries... no
checking whether to build static libraries... yes
checking for X... libraries , headers 
checking for gethostbyname... yes
checking for connect... yes
checking for remove... yes
checking for shmat... yes
checking for IceConnectionNumber in -lICE... yes
checking for qsub... no
checking gmap program directory... 
checking for get-genome... false
checking for iit_store... false
checking for iit_get... false
checking for gmap_build... false
checking for gmap... false
checking for gsnap... false
checking for sam_sort... false
checking for uniqscan... false
checking for rint in -lm... yes
checking for pthreads feature... not specified so enabled by default
checking for the pthreads library -lpthreads... no
checking whether pthreads work without any flags... yes
checking for joinable pthread attribute... PTHREAD_CREATE_JOINABLE
checking if more special flags are required for pthreads... no
checking for cc_r... gcc
checking for ANSI C header files... (cached) yes
checking for dirent.h that defines DIR... yes
checking for library containing opendir... none required
checking fcntl.h usability... yes
checking fcntl.h presence... yes
checking for fcntl.h... yes
checking limits.h usability... yes
checking limits.h presence... yes
checking for limits.h... yes
checking stddef.h usability... yes
checking stddef.h presence... yes
checking for stddef.h... yes
checking for stdlib.h... (cached) yes
checking for string.h... (cached) yes
checking for strings.h... (cached) yes
checking for unistd.h... (cached) yes
checking for sys/types.h... (cached) yes
checking whether byte ordering is bigendian... no
checking for an ANSI C-conforming const... yes
checking for working volatile... yes
checking for size_t... yes
checking for off_t... yes
checking for caddr_t... yes
checking size of unsigned long... 8
checking size of unsigned long long... 8
checking size of off_t... 8
checking for _LARGEFILE_SOURCE value needed for large files... no
checking for working mmap with MAP_FIXED... yes
checking for working mmap with MAP_VARIABLE... no
checking for MAP_FILE in mmap... yes
checking for MAP_VARIABLE in mmap... no
checking for MAP_SHARED in mmap... yes
checking for MAP_PRIVATE in mmap... yes
checking for MAP_FAILED in mmap... yes
checking for MADV_DONTNEED in madvise... yes
checking for MADV_WILLNEED in madvise... yes
checking for MADV_RANDOM in madvise... yes
checking for MADV_SEQUENTIAL in madvise... yes
checking for ceil... yes
checking for floor... yes
checking for index... yes
checking for log... yes
checking for madvise... yes
checking for memcpy... yes
checking for memmove... yes
checking for memset... yes
checking for munmap... yes
checking for pow... yes
checking for rint... yes
checking for stat64... yes
checking for strtoul... yes
checking for sysconf... yes
checking for sysctl... no
checking for sigaction... yes
checking for struct stat64... no
checking for pagesize via sysconf... yes
checking for pagesize via sysctl... no
checking whether fopen accepts "b" mode... yes
checking whether fopen accepts "t" mode... yes
checking for builtin popcount/clz/ctz features... not specified so enabled by default
./configure: line 16917: ACX_BUILTIN_POPCOUNT: command not found
checking for bsr instruction in assembly... yes
checking whether sse2 is enabled... not specified so enabled by default
checking compiler is defective and requires an immediate in sse2 shift commands... yes
checking whether ssse3 is enabled... not specified so enabled by default
checking whether sse4.1 is enabled... not specified so enabled by default
checking whether sse4.2 is enabled... not specified so enabled by default
checking whether avx is enabled... not specified so enabled by default
checking whether avx2 is enabled... not specified so enabled by default
checking whether simd is enabled... not specified so enabled by default
checking gmapdb... /home/biocbuild/bbs-3.17-bioc/meat/gmapR/src/../inst/usr/share
checking whether to make binaries... disabled
checking for zlib support... enabled
checking zlib.h usability... yes
checking zlib.h presence... yes
checking for zlib.h... yes
checking for gzopen in -lz... yes
checking for gzeof in -lz... yes
checking for gzgetc in -lz... yes
checking for gzgets in -lz... yes
checking for gzclose in -lz... yes
checking if zlib package is complete... working
checking for gzbuffer in -lz... yes
checking for samtools program... checking for samtools library... provided by --with-samtools-lib
checking that generated files are newer than configure... done
configure: creating ./config.status
config.status: creating Makefile
config.status: creating src/Makefile
config.status: creating lib/gstruct-1.0.pc
config.status: creating src/config.h
config.status: executing depfiles commands
config.status: executing libtool commands
configure: WARNING:

WARNING: You don't seem to have gsnap specified.

checking Standard compiler and flags to be used... gcc -g -O3
checking Standard linker flags to be used... 
checking pthread compiler flags to be used... 
checking popcnt compiler flags to be used... 
checking SIMD features available on computer... 
checking SIMD compiler flags to be used... 
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I/home/biocbuild/bbs-3.17-bioc/meat/gmapR/src/../inst/usr/include  -I/usr/local/include    -fPIC  -g -O2  -Wall -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -DBGZF_CACHE -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -c samtools/bgzf.c -o samtools/bgzf.o
samtools/bgzf.c: In function ‘worker_aux’:
samtools/bgzf.c:412:16: warning: variable ‘tmp’ set but not used [-Wunused-but-set-variable]
  412 |         int i, tmp, stop = 0;
      |                ^~~
samtools/bgzf.c: In function ‘bgzf_close’:
samtools/bgzf.c:592:18: warning: variable ‘count’ set but not used [-Wunused-but-set-variable]
  592 |         int ret, count, block_length;
      |                  ^~~~~
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I/home/biocbuild/bbs-3.17-bioc/meat/gmapR/src/../inst/usr/include  -I/usr/local/include    -fPIC  -g -O2  -Wall -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -DBGZF_CACHE -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -c samtools/kstring.c -o samtools/kstring.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I/home/biocbuild/bbs-3.17-bioc/meat/gmapR/src/../inst/usr/include  -I/usr/local/include    -fPIC  -g -O2  -Wall -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -DBGZF_CACHE -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -c samtools/bam_aux.c -o samtools/bam_aux.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I/home/biocbuild/bbs-3.17-bioc/meat/gmapR/src/../inst/usr/include  -I/usr/local/include    -fPIC  -g -O2  -Wall -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -DBGZF_CACHE -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -c samtools/bam.c -o samtools/bam.o
samtools/bam.c: In function ‘bam_header_write’:
samtools/bam.c:128:9: warning: ‘strncpy’ output truncated before terminating nul copying 4 bytes from a string of the same length [-Wstringop-truncation]
  128 |         strncpy(buf, "BAM\001", 4);
      |         ^~~~~~~~~~~~~~~~~~~~~~~~~~
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I/home/biocbuild/bbs-3.17-bioc/meat/gmapR/src/../inst/usr/include  -I/usr/local/include    -fPIC  -g -O2  -Wall -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -DBGZF_CACHE -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -c samtools/bam_import.c -o samtools/bam_import.o
In file included from /usr/include/aarch64-linux-gnu/bits/libc-header-start.h:33,
                 from /usr/include/limits.h:26,
                 from /usr/lib/gcc/aarch64-linux-gnu/11/include/limits.h:203,
                 from /usr/lib/gcc/aarch64-linux-gnu/11/include/syslimits.h:7,
                 from /usr/lib/gcc/aarch64-linux-gnu/11/include/limits.h:34,
                 from /usr/include/zconf.h:418,
                 from /usr/include/zlib.h:34,
                 from samtools/bam_import.c:3:
/usr/include/features.h:194:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
  194 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
      |   ^~~~~~~
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I/home/biocbuild/bbs-3.17-bioc/meat/gmapR/src/../inst/usr/include  -I/usr/local/include    -fPIC  -g -O2  -Wall -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -DBGZF_CACHE -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -c samtools/sam.c -o samtools/sam.o
In file included from /usr/include/aarch64-linux-gnu/bits/libc-header-start.h:33,
                 from /usr/include/string.h:26,
                 from samtools/sam.c:3:
/usr/include/features.h:194:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
  194 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
      |   ^~~~~~~
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I/home/biocbuild/bbs-3.17-bioc/meat/gmapR/src/../inst/usr/include  -I/usr/local/include    -fPIC  -g -O2  -Wall -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -DBGZF_CACHE -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -c samtools/bam_index.c -o samtools/bam_index.o
samtools/bam_index.c: In function ‘bam_index_core’:
samtools/bam_index.c:178:42: warning: overflow in conversion from ‘uint32_t’ {aka ‘unsigned int’} to ‘int32_t’ {aka ‘int’} changes value from ‘last_bin = 4294967295’ to ‘-1’ [-Woverflow]
  178 |         save_bin = save_tid = last_tid = last_bin = 0xffffffffu;
      |                                          ^~~~~~~~
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I/home/biocbuild/bbs-3.17-bioc/meat/gmapR/src/../inst/usr/include  -I/usr/local/include    -fPIC  -g -O2  -Wall -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -DBGZF_CACHE -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -c samtools/bam_pileup.c -o samtools/bam_pileup.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I/home/biocbuild/bbs-3.17-bioc/meat/gmapR/src/../inst/usr/include  -I/usr/local/include    -fPIC  -g -O2  -Wall -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -DBGZF_CACHE -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -c samtools/bam_lpileup.c -o samtools/bam_lpileup.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I/home/biocbuild/bbs-3.17-bioc/meat/gmapR/src/../inst/usr/include  -I/usr/local/include    -fPIC  -g -O2  -Wall -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -DBGZF_CACHE -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -c samtools/bam_md.c -o samtools/bam_md.o
samtools/bam_md.c: In function ‘bam_prob_realn_core’:
samtools/bam_md.c:214:35: warning: writing 1 byte into a region of size 0 [-Wstringop-overflow=]
  214 |                         *(bq - 3) = 'Z';
      |                         ~~~~~~~~~~^~~~~
samtools/bam_md.c:198:19: note: at offset -2 into destination object of size [0, 9223372036854775807] allocated by ‘bam_aux_get’
  198 |         if ((bq = bam_aux_get(b, "BQ")) != 0) ++bq;
      |                   ^~~~~~~~~~~~~~~~~~~~
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I/home/biocbuild/bbs-3.17-bioc/meat/gmapR/src/../inst/usr/include  -I/usr/local/include    -fPIC  -g -O2  -Wall -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -DBGZF_CACHE -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -c samtools/razf.c -o samtools/razf.o
samtools/razf.c: In function ‘razf_open_w’:
samtools/razf.c:178:9: warning: ‘strncpy’ output truncated before terminating nul copying 4 bytes from a string of the same length [-Wstringop-truncation]
  178 |         strncpy((char*)rz->header->extra, "RAZF", 4);
      |         ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I/home/biocbuild/bbs-3.17-bioc/meat/gmapR/src/../inst/usr/include  -I/usr/local/include    -fPIC  -g -O2  -Wall -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -DBGZF_CACHE -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -c samtools/faidx.c -o samtools/faidx.o
samtools/faidx.c: In function ‘fai_load0’:
samtools/faidx.c:309:5: warning: this ‘else’ clause does not guard... [-Wmisleading-indentation]
  309 |     else
      |     ^~~~
samtools/faidx.c:312:9: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘else’
  312 |         if (fp == 0) {
      |         ^~
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I/home/biocbuild/bbs-3.17-bioc/meat/gmapR/src/../inst/usr/include  -I/usr/local/include    -fPIC  -g -O2  -Wall -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -DBGZF_CACHE -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -c samtools/knetfile.c -o samtools/knetfile.o
In file included from /usr/include/time.h:25,
                 from samtools/knetfile.c:33:
/usr/include/features.h:194:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
  194 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
      |   ^~~~~~~
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I/home/biocbuild/bbs-3.17-bioc/meat/gmapR/src/../inst/usr/include  -I/usr/local/include    -fPIC  -g -O2  -Wall -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -DBGZF_CACHE -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -c samtools/bam_sort.c -o samtools/bam_sort.o
In file included from /usr/include/aarch64-linux-gnu/bits/libc-header-start.h:33,
                 from /usr/include/stdlib.h:26,
                 from samtools/bam_sort.c:3:
/usr/include/features.h:194:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
  194 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
      |   ^~~~~~~
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I/home/biocbuild/bbs-3.17-bioc/meat/gmapR/src/../inst/usr/include  -I/usr/local/include    -fPIC  -g -O2  -Wall -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -DBGZF_CACHE -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -c samtools/sam_header.c -o samtools/sam_header.o
In file included from /usr/include/aarch64-linux-gnu/bits/libc-header-start.h:33,
                 from /usr/include/stdio.h:27,
                 from samtools/sam_header.c:3:
/usr/include/features.h:194:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
  194 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
      |   ^~~~~~~
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I/home/biocbuild/bbs-3.17-bioc/meat/gmapR/src/../inst/usr/include  -I/usr/local/include    -fPIC  -g -O2  -Wall -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -DBGZF_CACHE -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -c samtools/bam_reheader.c -o samtools/bam_reheader.o
samtools/bam_reheader.c: In function ‘bam_reheader’:
samtools/bam_reheader.c:12:23: warning: variable ‘old’ set but not used [-Wunused-but-set-variable]
   12 |         bam_header_t *old;
      |                       ^~~
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I/home/biocbuild/bbs-3.17-bioc/meat/gmapR/src/../inst/usr/include  -I/usr/local/include    -fPIC  -g -O2  -Wall -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -DBGZF_CACHE -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -c samtools/kprobaln.c -o samtools/kprobaln.o
samtools/kprobaln.c: In function ‘kpa_glocal’:
samtools/kprobaln.c:78:28: warning: variable ‘is_diff’ set but not used [-Wunused-but-set-variable]
   78 |         int bw, bw2, i, k, is_diff = 0, is_backward = 1, Pr;
      |                            ^~~~~~~
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I/home/biocbuild/bbs-3.17-bioc/meat/gmapR/src/../inst/usr/include  -I/usr/local/include    -fPIC  -g -O2  -Wall -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -DBGZF_CACHE -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -c samtools/samtools_patch.c -o samtools/samtools_patch.o
ar -crus samtools/libbam.a samtools/bgzf.o samtools/kstring.o samtools/bam_aux.o samtools/bam.o samtools/bam_import.o samtools/sam.o samtools/bam_index.o samtools/bam_pileup.o samtools/bam_lpileup.o samtools/bam_md.o samtools/razf.o samtools/faidx.o samtools/knetfile.o samtools/bam_sort.o samtools/sam_header.o samtools/bam_reheader.o samtools/kprobaln.o samtools/samtools_patch.o
ar: `u' modifier ignored since `D' is the default (see `U')
cd gstruct; \
make install
make[1]: Entering directory '/home/biocbuild/bbs-3.17-bioc/meat/gmapR/src/gstruct'
Making install in src
make[2]: Entering directory '/home/biocbuild/bbs-3.17-bioc/meat/gmapR/src/gstruct/src'
/bin/bash ../libtool  --tag=CC   --mode=compile gcc -DHAVE_CONFIG_H -I.        -I. -fPIC -DTARGET=\"aarch64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.17-bioc/meat/gmapR/src/../inst/usr/share\" -g -O3 -MT libgstruct_1.0_la-except.lo -MD -MP -MF .deps/libgstruct_1.0_la-except.Tpo -c -o libgstruct_1.0_la-except.lo `test -f 'except.c' || echo './'`except.c
libtool: compile:  gcc -DHAVE_CONFIG_H -I. -I. -fPIC -DTARGET=\"aarch64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.17-bioc/meat/gmapR/src/../inst/usr/share\" -g -O3 -MT libgstruct_1.0_la-except.lo -MD -MP -MF .deps/libgstruct_1.0_la-except.Tpo -c except.c -o libgstruct_1.0_la-except.o
mv -f .deps/libgstruct_1.0_la-except.Tpo .deps/libgstruct_1.0_la-except.Plo
/bin/bash ../libtool  --tag=CC   --mode=compile gcc -DHAVE_CONFIG_H -I.        -I. -fPIC -DTARGET=\"aarch64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.17-bioc/meat/gmapR/src/../inst/usr/share\" -g -O3 -MT libgstruct_1.0_la-assert.lo -MD -MP -MF .deps/libgstruct_1.0_la-assert.Tpo -c -o libgstruct_1.0_la-assert.lo `test -f 'assert.c' || echo './'`assert.c
libtool: compile:  gcc -DHAVE_CONFIG_H -I. -I. -fPIC -DTARGET=\"aarch64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.17-bioc/meat/gmapR/src/../inst/usr/share\" -g -O3 -MT libgstruct_1.0_la-assert.lo -MD -MP -MF .deps/libgstruct_1.0_la-assert.Tpo -c assert.c -o libgstruct_1.0_la-assert.o
mv -f .deps/libgstruct_1.0_la-assert.Tpo .deps/libgstruct_1.0_la-assert.Plo
/bin/bash ../libtool  --tag=CC   --mode=compile gcc -DHAVE_CONFIG_H -I.        -I. -fPIC -DTARGET=\"aarch64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.17-bioc/meat/gmapR/src/../inst/usr/share\" -g -O3 -MT libgstruct_1.0_la-mem.lo -MD -MP -MF .deps/libgstruct_1.0_la-mem.Tpo -c -o libgstruct_1.0_la-mem.lo `test -f 'mem.c' || echo './'`mem.c
libtool: compile:  gcc -DHAVE_CONFIG_H -I. -I. -fPIC -DTARGET=\"aarch64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.17-bioc/meat/gmapR/src/../inst/usr/share\" -g -O3 -MT libgstruct_1.0_la-mem.lo -MD -MP -MF .deps/libgstruct_1.0_la-mem.Tpo -c mem.c -o libgstruct_1.0_la-mem.o
mv -f .deps/libgstruct_1.0_la-mem.Tpo .deps/libgstruct_1.0_la-mem.Plo
/bin/bash ../libtool  --tag=CC   --mode=compile gcc -DHAVE_CONFIG_H -I.        -I. -fPIC -DTARGET=\"aarch64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.17-bioc/meat/gmapR/src/../inst/usr/share\" -g -O3 -MT libgstruct_1.0_la-intlist.lo -MD -MP -MF .deps/libgstruct_1.0_la-intlist.Tpo -c -o libgstruct_1.0_la-intlist.lo `test -f 'intlist.c' || echo './'`intlist.c
libtool: compile:  gcc -DHAVE_CONFIG_H -I. -I. -fPIC -DTARGET=\"aarch64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.17-bioc/meat/gmapR/src/../inst/usr/share\" -g -O3 -MT libgstruct_1.0_la-intlist.lo -MD -MP -MF .deps/libgstruct_1.0_la-intlist.Tpo -c intlist.c -o libgstruct_1.0_la-intlist.o
mv -f .deps/libgstruct_1.0_la-intlist.Tpo .deps/libgstruct_1.0_la-intlist.Plo
/bin/bash ../libtool  --tag=CC   --mode=compile gcc -DHAVE_CONFIG_H -I.        -I. -fPIC -DTARGET=\"aarch64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.17-bioc/meat/gmapR/src/../inst/usr/share\" -g -O3 -MT libgstruct_1.0_la-list.lo -MD -MP -MF .deps/libgstruct_1.0_la-list.Tpo -c -o libgstruct_1.0_la-list.lo `test -f 'list.c' || echo './'`list.c
libtool: compile:  gcc -DHAVE_CONFIG_H -I. -I. -fPIC -DTARGET=\"aarch64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.17-bioc/meat/gmapR/src/../inst/usr/share\" -g -O3 -MT libgstruct_1.0_la-list.lo -MD -MP -MF .deps/libgstruct_1.0_la-list.Tpo -c list.c -o libgstruct_1.0_la-list.o
mv -f .deps/libgstruct_1.0_la-list.Tpo .deps/libgstruct_1.0_la-list.Plo
/bin/bash ../libtool  --tag=CC   --mode=compile gcc -DHAVE_CONFIG_H -I.        -I. -fPIC -DTARGET=\"aarch64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.17-bioc/meat/gmapR/src/../inst/usr/share\" -g -O3 -MT libgstruct_1.0_la-littleendian.lo -MD -MP -MF .deps/libgstruct_1.0_la-littleendian.Tpo -c -o libgstruct_1.0_la-littleendian.lo `test -f 'littleendian.c' || echo './'`littleendian.c
libtool: compile:  gcc -DHAVE_CONFIG_H -I. -I. -fPIC -DTARGET=\"aarch64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.17-bioc/meat/gmapR/src/../inst/usr/share\" -g -O3 -MT libgstruct_1.0_la-littleendian.lo -MD -MP -MF .deps/libgstruct_1.0_la-littleendian.Tpo -c littleendian.c -o libgstruct_1.0_la-littleendian.o
littleendian.c: In function ‘Littleendian_write_uint’:
littleendian.c:17:3: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result]
   17 |   write(fd,buf,4);
      |   ^~~~~~~~~~~~~~~
mv -f .deps/libgstruct_1.0_la-littleendian.Tpo .deps/libgstruct_1.0_la-littleendian.Plo
/bin/bash ../libtool  --tag=CC   --mode=compile gcc -DHAVE_CONFIG_H -I.        -I. -fPIC -DTARGET=\"aarch64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.17-bioc/meat/gmapR/src/../inst/usr/share\" -g -O3 -MT libgstruct_1.0_la-bigendian.lo -MD -MP -MF .deps/libgstruct_1.0_la-bigendian.Tpo -c -o libgstruct_1.0_la-bigendian.lo `test -f 'bigendian.c' || echo './'`bigendian.c
libtool: compile:  gcc -DHAVE_CONFIG_H -I. -I. -fPIC -DTARGET=\"aarch64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.17-bioc/meat/gmapR/src/../inst/usr/share\" -g -O3 -MT libgstruct_1.0_la-bigendian.lo -MD -MP -MF .deps/libgstruct_1.0_la-bigendian.Tpo -c bigendian.c -o libgstruct_1.0_la-bigendian.o
bigendian.c: In function ‘Bigendian_write_uint’:
bigendian.c:296:3: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result]
  296 |   write(fd,buf,4);
      |   ^~~~~~~~~~~~~~~
bigendian.c: In function ‘Bigendian_fileio_read_uint’:
bigendian.c:457:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result]
  457 |   read(fd,buf,4);
      |   ^~~~~~~~~~~~~~
bigendian.c: In function ‘Bigendian_fileio_read_uint8’:
bigendian.c:758:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result]
  758 |   read(fd,buf,8);
      |   ^~~~~~~~~~~~~~
mv -f .deps/libgstruct_1.0_la-bigendian.Tpo .deps/libgstruct_1.0_la-bigendian.Plo
/bin/bash ../libtool  --tag=CC   --mode=compile gcc -DHAVE_CONFIG_H -I.        -I. -fPIC -DTARGET=\"aarch64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.17-bioc/meat/gmapR/src/../inst/usr/share\" -g -O3 -MT libgstruct_1.0_la-interval.lo -MD -MP -MF .deps/libgstruct_1.0_la-interval.Tpo -c -o libgstruct_1.0_la-interval.lo `test -f 'interval.c' || echo './'`interval.c
libtool: compile:  gcc -DHAVE_CONFIG_H -I. -I. -fPIC -DTARGET=\"aarch64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.17-bioc/meat/gmapR/src/../inst/usr/share\" -g -O3 -MT libgstruct_1.0_la-interval.lo -MD -MP -MF .deps/libgstruct_1.0_la-interval.Tpo -c interval.c -o libgstruct_1.0_la-interval.o
mv -f .deps/libgstruct_1.0_la-interval.Tpo .deps/libgstruct_1.0_la-interval.Plo
/bin/bash ../libtool  --tag=CC   --mode=compile gcc -DHAVE_CONFIG_H -I.        -I. -fPIC -DTARGET=\"aarch64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.17-bioc/meat/gmapR/src/../inst/usr/share\" -g -O3 -MT libgstruct_1.0_la-uintlist.lo -MD -MP -MF .deps/libgstruct_1.0_la-uintlist.Tpo -c -o libgstruct_1.0_la-uintlist.lo `test -f 'uintlist.c' || echo './'`uintlist.c
libtool: compile:  gcc -DHAVE_CONFIG_H -I. -I. -fPIC -DTARGET=\"aarch64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.17-bioc/meat/gmapR/src/../inst/usr/share\" -g -O3 -MT libgstruct_1.0_la-uintlist.lo -MD -MP -MF .deps/libgstruct_1.0_la-uintlist.Tpo -c uintlist.c -o libgstruct_1.0_la-uintlist.o
mv -f .deps/libgstruct_1.0_la-uintlist.Tpo .deps/libgstruct_1.0_la-uintlist.Plo
/bin/bash ../libtool  --tag=CC   --mode=compile gcc -DHAVE_CONFIG_H -I.        -I. -fPIC -DTARGET=\"aarch64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.17-bioc/meat/gmapR/src/../inst/usr/share\" -g -O3 -MT libgstruct_1.0_la-stopwatch.lo -MD -MP -MF .deps/libgstruct_1.0_la-stopwatch.Tpo -c -o libgstruct_1.0_la-stopwatch.lo `test -f 'stopwatch.c' || echo './'`stopwatch.c
libtool: compile:  gcc -DHAVE_CONFIG_H -I. -I. -fPIC -DTARGET=\"aarch64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.17-bioc/meat/gmapR/src/../inst/usr/share\" -g -O3 -MT libgstruct_1.0_la-stopwatch.lo -MD -MP -MF .deps/libgstruct_1.0_la-stopwatch.Tpo -c stopwatch.c -o libgstruct_1.0_la-stopwatch.o
mv -f .deps/libgstruct_1.0_la-stopwatch.Tpo .deps/libgstruct_1.0_la-stopwatch.Plo
/bin/bash ../libtool  --tag=CC   --mode=compile gcc -DHAVE_CONFIG_H -I.        -I. -fPIC -DTARGET=\"aarch64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.17-bioc/meat/gmapR/src/../inst/usr/share\" -g -O3 -MT libgstruct_1.0_la-access.lo -MD -MP -MF .deps/libgstruct_1.0_la-access.Tpo -c -o libgstruct_1.0_la-access.lo `test -f 'access.c' || echo './'`access.c
libtool: compile:  gcc -DHAVE_CONFIG_H -I. -I. -fPIC -DTARGET=\"aarch64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.17-bioc/meat/gmapR/src/../inst/usr/share\" -g -O3 -MT libgstruct_1.0_la-access.lo -MD -MP -MF .deps/libgstruct_1.0_la-access.Tpo -c access.c -o libgstruct_1.0_la-access.o
access.c: In function ‘Access_file_exists_p’:
access.c:59:7: warning: implicit declaration of function ‘stat64’; did you mean ‘stat’? [-Wimplicit-function-declaration]
   59 |   if (stat64(filename,&sb) == 0) {
      |       ^~~~~~
      |       stat
In file included from access.c:39:
access.c: In function ‘Access_allocated’:
littleendian.h:18:29: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result]
   18 | #define FREAD_UINTS(a,n,fp) fread(a,sizeof(unsigned int),n,fp)
      |                             ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
access.c:125:3: note: in expansion of macro ‘FREAD_UINTS’
  125 |   FREAD_UINTS(memory,(*len)/eltsize,fp);
      |   ^~~~~~~~~~~
mv -f .deps/libgstruct_1.0_la-access.Tpo .deps/libgstruct_1.0_la-access.Plo
/bin/bash ../libtool  --tag=CC   --mode=compile gcc -DHAVE_CONFIG_H -I.        -I. -fPIC -DTARGET=\"aarch64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.17-bioc/meat/gmapR/src/../inst/usr/share\" -g -O3 -MT libgstruct_1.0_la-iit-read.lo -MD -MP -MF .deps/libgstruct_1.0_la-iit-read.Tpo -c -o libgstruct_1.0_la-iit-read.lo `test -f 'iit-read.c' || echo './'`iit-read.c
libtool: compile:  gcc -DHAVE_CONFIG_H -I. -I. -fPIC -DTARGET=\"aarch64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.17-bioc/meat/gmapR/src/../inst/usr/share\" -g -O3 -MT libgstruct_1.0_la-iit-read.lo -MD -MP -MF .deps/libgstruct_1.0_la-iit-read.Tpo -c iit-read.c -o libgstruct_1.0_la-iit-read.o
In file included from iit-read.c:12:
iit-read.c: In function ‘IIT_read_divint’:
littleendian.h:15:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result]
   15 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp)
      |                         ^~~~~~~~~~~~~~~~~~~~~~~~~
iit-read.c:2353:5: note: in expansion of macro ‘FREAD_INT’
 2353 |     FREAD_INT(&version,fp);
      |     ^~~~~~~~~
iit-read.c: In function ‘IIT_read’:
littleendian.h:15:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result]
   15 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp)
      |                         ^~~~~~~~~~~~~~~~~~~~~~~~~
iit-read.c:2619:5: note: in expansion of macro ‘FREAD_INT’
 2619 |     FREAD_INT(&new->version,fp);
      |     ^~~~~~~~~
iit-read.c: In function ‘read_tree’:
iit-read.c:1731:9: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result]
 1731 |         fread(&(new->nodes[divno][i].value),sizeof(unsigned int),1,fp);
      |         ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
iit-read.c:1732:9: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result]
 1732 |         fread(&(new->nodes[divno][i].a),sizeof(int),1,fp);
      |         ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
iit-read.c:1733:9: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result]
 1733 |         fread(&(new->nodes[divno][i].b),sizeof(int),1,fp);
      |         ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
iit-read.c:1734:9: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result]
 1734 |         fread(&(new->nodes[divno][i].leftindex),sizeof(int),1,fp);
      |         ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
iit-read.c:1735:9: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result]
 1735 |         fread(&(new->nodes[divno][i].rightindex),sizeof(int),1,fp);
      |         ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
iit-read.c: In function ‘read_intervals’:
iit-read.c:1816:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result]
 1816 |       fread(&(new->intervals[divno][i].low),sizeof(unsigned int),1,fp);
      |       ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
iit-read.c:1817:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result]
 1817 |       fread(&(new->intervals[divno][i].high),sizeof(unsigned int),1,fp);
      |       ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
iit-read.c:1819:9: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result]
 1819 |         fread(&(new->intervals[divno][i].sign),sizeof(int),1,fp);
      |         ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
iit-read.c:1823:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result]
 1823 |       fread(&(new->intervals[divno][i].type),sizeof(int),1,fp);
      |       ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from iit-read.c:12:
iit-read.c: In function ‘read_words’:
littleendian.h:20:27: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result]
   20 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp)
      |                           ^~~~~~~~~~~~~~~~~~~~~~~~~~~
iit-read.c:1907:5: note: in expansion of macro ‘FREAD_UINT8’
 1907 |     FREAD_UINT8(&length8,fp);
      |     ^~~~~~~~~~~
littleendian.h:16:26: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result]
   16 | #define FREAD_UINT(p,fp) fread(p,sizeof(unsigned int),1,fp)
      |                          ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
iit-read.c:1913:5: note: in expansion of macro ‘FREAD_UINT’
 1913 |     FREAD_UINT(&length,fp);
      |     ^~~~~~~~~~
iit-read.c: In function ‘read_annotations’:
iit-read.c:2257:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result]
 2257 |   read(new->fd,new->labelorder,new->total_nintervals*sizeof(int));
      |   ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
iit-read.c:2263:5: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result]
 2263 |     read(new->fd,new->labelpointers8,(new->total_nintervals+1)*sizeof(UINT8));
      |     ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
iit-read.c:2268:5: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result]
 2268 |     read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(unsigned int));
      |     ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
iit-read.c:2279:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result]
 2279 |   read(new->fd,new->labels,new->label_length*sizeof(char));
      |   ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
iit-read.c:2285:5: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result]
 2285 |     read(new->fd,new->annotpointers8,(new->total_nintervals+1)*sizeof(UINT8));
      |     ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
iit-read.c:2290:5: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result]
 2290 |     read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(unsigned int));
      |     ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
iit-read.c:2301:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result]
 2301 |   read(new->fd,new->annotations,new->annot_length*sizeof(char));
      |   ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from iit-read.c:12:
iit-read.c: In function ‘IIT_debug’:
littleendian.h:15:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result]
   15 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp)
      |                         ^~~~~~~~~~~~~~~~~~~~~~~~~
iit-read.c:3019:5: note: in expansion of macro ‘FREAD_INT’
 3019 |     FREAD_INT(&new->version,fp);
      |     ^~~~~~~~~
iit-read.c: In function ‘read_words_debug’:
littleendian.h:20:27: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result]
   20 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp)
      |                           ^~~~~~~~~~~~~~~~~~~~~~~~~~~
iit-read.c:2030:5: note: in expansion of macro ‘FREAD_UINT8’
 2030 |     FREAD_UINT8(&length8,fp);
      |     ^~~~~~~~~~~
littleendian.h:16:26: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result]
   16 | #define FREAD_UINT(p,fp) fread(p,sizeof(unsigned int),1,fp)
      |                          ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
iit-read.c:2035:5: note: in expansion of macro ‘FREAD_UINT’
 2035 |     FREAD_UINT(&length,fp);
      |     ^~~~~~~~~~
mv -f .deps/libgstruct_1.0_la-iit-read.Tpo .deps/libgstruct_1.0_la-iit-read.Plo
/bin/bash ../libtool  --tag=CC   --mode=compile gcc -DHAVE_CONFIG_H -I.        -I. -fPIC -DTARGET=\"aarch64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.17-bioc/meat/gmapR/src/../inst/usr/share\" -g -O3 -MT libgstruct_1.0_la-chrom.lo -MD -MP -MF .deps/libgstruct_1.0_la-chrom.Tpo -c -o libgstruct_1.0_la-chrom.lo `test -f 'chrom.c' || echo './'`chrom.c
libtool: compile:  gcc -DHAVE_CONFIG_H -I. -I. -fPIC -DTARGET=\"aarch64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.17-bioc/meat/gmapR/src/../inst/usr/share\" -g -O3 -MT libgstruct_1.0_la-chrom.lo -MD -MP -MF .deps/libgstruct_1.0_la-chrom.Tpo -c chrom.c -o libgstruct_1.0_la-chrom.o
chrom.c: In function ‘Chrom_from_string’:
chrom.c:108:12: warning: comparison between pointer and zero character constant [-Wpointer-compare]
  108 |   while (p != '\0' && *p >= '0' && *p <= '9') {
      |            ^~
chrom.c:108:10: note: did you mean to dereference the pointer?
  108 |   while (p != '\0' && *p >= '0' && *p <= '9') {
      |          ^
mv -f .deps/libgstruct_1.0_la-chrom.Tpo .deps/libgstruct_1.0_la-chrom.Plo
/bin/bash ../libtool  --tag=CC   --mode=compile gcc -DHAVE_CONFIG_H -I.        -I. -fPIC -DTARGET=\"aarch64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.17-bioc/meat/gmapR/src/../inst/usr/share\" -g -O3 -MT libgstruct_1.0_la-genomicpos.lo -MD -MP -MF .deps/libgstruct_1.0_la-genomicpos.Tpo -c -o libgstruct_1.0_la-genomicpos.lo `test -f 'genomicpos.c' || echo './'`genomicpos.c
libtool: compile:  gcc -DHAVE_CONFIG_H -I. -I. -fPIC -DTARGET=\"aarch64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.17-bioc/meat/gmapR/src/../inst/usr/share\" -g -O3 -MT libgstruct_1.0_la-genomicpos.lo -MD -MP -MF .deps/libgstruct_1.0_la-genomicpos.Tpo -c genomicpos.c -o libgstruct_1.0_la-genomicpos.o
mv -f .deps/libgstruct_1.0_la-genomicpos.Tpo .deps/libgstruct_1.0_la-genomicpos.Plo
/bin/bash ../libtool  --tag=CC   --mode=compile gcc -DHAVE_CONFIG_H -I.        -I. -fPIC -DTARGET=\"aarch64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.17-bioc/meat/gmapR/src/../inst/usr/share\" -g -O3 -MT libgstruct_1.0_la-md5.lo -MD -MP -MF .deps/libgstruct_1.0_la-md5.Tpo -c -o libgstruct_1.0_la-md5.lo `test -f 'md5.c' || echo './'`md5.c
libtool: compile:  gcc -DHAVE_CONFIG_H -I. -I. -fPIC -DTARGET=\"aarch64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.17-bioc/meat/gmapR/src/../inst/usr/share\" -g -O3 -MT libgstruct_1.0_la-md5.lo -MD -MP -MF .deps/libgstruct_1.0_la-md5.Tpo -c md5.c -o libgstruct_1.0_la-md5.o
mv -f .deps/libgstruct_1.0_la-md5.Tpo .deps/libgstruct_1.0_la-md5.Plo
/bin/bash ../libtool  --tag=CC   --mode=compile gcc -DHAVE_CONFIG_H -I.        -I. -fPIC -DTARGET=\"aarch64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.17-bioc/meat/gmapR/src/../inst/usr/share\" -g -O3 -MT libgstruct_1.0_la-sequence.lo -MD -MP -MF .deps/libgstruct_1.0_la-sequence.Tpo -c -o libgstruct_1.0_la-sequence.lo `test -f 'sequence.c' || echo './'`sequence.c
libtool: compile:  gcc -DHAVE_CONFIG_H -I. -I. -fPIC -DTARGET=\"aarch64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.17-bioc/meat/gmapR/src/../inst/usr/share\" -g -O3 -MT libgstruct_1.0_la-sequence.lo -MD -MP -MF .deps/libgstruct_1.0_la-sequence.Tpo -c sequence.c -o libgstruct_1.0_la-sequence.o
mv -f .deps/libgstruct_1.0_la-sequence.Tpo .deps/libgstruct_1.0_la-sequence.Plo
/bin/bash ../libtool  --tag=CC   --mode=compile gcc -DHAVE_CONFIG_H -I.        -I. -fPIC -DTARGET=\"aarch64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.17-bioc/meat/gmapR/src/../inst/usr/share\" -g -O3 -MT libgstruct_1.0_la-genome.lo -MD -MP -MF .deps/libgstruct_1.0_la-genome.Tpo -c -o libgstruct_1.0_la-genome.lo `test -f 'genome.c' || echo './'`genome.c
libtool: compile:  gcc -DHAVE_CONFIG_H -I. -I. -fPIC -DTARGET=\"aarch64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.17-bioc/meat/gmapR/src/../inst/usr/share\" -g -O3 -MT libgstruct_1.0_la-genome.lo -MD -MP -MF .deps/libgstruct_1.0_la-genome.Tpo -c genome.c -o libgstruct_1.0_la-genome.o
genome.c: In function ‘fill_buffer’:
genome.c:1218:7: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result]
 1218 |       read(this->fd,gbuffer1,length);
      |       ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
genome.c: In function ‘genomecomp_read_current’:
genome.c:329:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result]
  329 |   read(this->fd,buffer,4);
      |   ^~~~~~~~~~~~~~~~~~~~~~~
genome.c: In function ‘Genome_fill_buffer_simple’:
genome.c:1374:7: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result]
 1374 |       read(this->fd,gbuffer1,length);
      |       ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
genome.c: In function ‘Genome_fill_buffer_simple_alt’:
genome.c:1451:7: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result]
 1451 |       read(this->fd,gbuffer1,length);
      |       ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
genome.c: In function ‘Genome_get_char’:
genome.c:1554:7: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result]
 1554 |       read(this->fd,gbuffer1,/*length*/1);
      |       ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
genome.c: In function ‘Genome_ntcounts’:
genome.c:1710:7: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result]
 1710 |       read(this->fd,gbuffer,length);
      |       ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~
mv -f .deps/libgstruct_1.0_la-genome.Tpo .deps/libgstruct_1.0_la-genome.Plo
/bin/bash ../libtool  --tag=CC   --mode=compile gcc -DHAVE_CONFIG_H -I.        -I. -fPIC -DTARGET=\"aarch64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.17-bioc/meat/gmapR/src/../inst/usr/share\" -g -O3 -MT libgstruct_1.0_la-uinttable.lo -MD -MP -MF .deps/libgstruct_1.0_la-uinttable.Tpo -c -o libgstruct_1.0_la-uinttable.lo `test -f 'uinttable.c' || echo './'`uinttable.c
libtool: compile:  gcc -DHAVE_CONFIG_H -I. -I. -fPIC -DTARGET=\"aarch64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.17-bioc/meat/gmapR/src/../inst/usr/share\" -g -O3 -MT libgstruct_1.0_la-uinttable.lo -MD -MP -MF .deps/libgstruct_1.0_la-uinttable.Tpo -c uinttable.c -o libgstruct_1.0_la-uinttable.o
mv -f .deps/libgstruct_1.0_la-uinttable.Tpo .deps/libgstruct_1.0_la-uinttable.Plo
/bin/bash ../libtool  --tag=CC   --mode=compile gcc -DHAVE_CONFIG_H -I.        -I. -fPIC -DTARGET=\"aarch64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.17-bioc/meat/gmapR/src/../inst/usr/share\" -g -O3 -MT libgstruct_1.0_la-table.lo -MD -MP -MF .deps/libgstruct_1.0_la-table.Tpo -c -o libgstruct_1.0_la-table.lo `test -f 'table.c' || echo './'`table.c
libtool: compile:  gcc -DHAVE_CONFIG_H -I. -I. -fPIC -DTARGET=\"aarch64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.17-bioc/meat/gmapR/src/../inst/usr/share\" -g -O3 -MT libgstruct_1.0_la-table.lo -MD -MP -MF .deps/libgstruct_1.0_la-table.Tpo -c table.c -o libgstruct_1.0_la-table.o
mv -f .deps/libgstruct_1.0_la-table.Tpo .deps/libgstruct_1.0_la-table.Plo
/bin/bash ../libtool  --tag=CC   --mode=compile gcc -DHAVE_CONFIG_H -I.        -I. -fPIC -DTARGET=\"aarch64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.17-bioc/meat/gmapR/src/../inst/usr/share\" -g -O3 -MT libgstruct_1.0_la-chrnum.lo -MD -MP -MF .deps/libgstruct_1.0_la-chrnum.Tpo -c -o libgstruct_1.0_la-chrnum.lo `test -f 'chrnum.c' || echo './'`chrnum.c
libtool: compile:  gcc -DHAVE_CONFIG_H -I. -I. -fPIC -DTARGET=\"aarch64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.17-bioc/meat/gmapR/src/../inst/usr/share\" -g -O3 -MT libgstruct_1.0_la-chrnum.lo -MD -MP -MF .deps/libgstruct_1.0_la-chrnum.Tpo -c chrnum.c -o libgstruct_1.0_la-chrnum.o
mv -f .deps/libgstruct_1.0_la-chrnum.Tpo .deps/libgstruct_1.0_la-chrnum.Plo
/bin/bash ../libtool  --tag=CC   --mode=compile gcc -DHAVE_CONFIG_H -I.        -I. -fPIC -DTARGET=\"aarch64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.17-bioc/meat/gmapR/src/../inst/usr/share\" -g -O3 -MT libgstruct_1.0_la-bamread.lo -MD -MP -MF .deps/libgstruct_1.0_la-bamread.Tpo -c -o libgstruct_1.0_la-bamread.lo `test -f 'bamread.c' || echo './'`bamread.c
libtool: compile:  gcc -DHAVE_CONFIG_H -I. -I. -fPIC -DTARGET=\"aarch64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.17-bioc/meat/gmapR/src/../inst/usr/share\" -g -O3 -MT libgstruct_1.0_la-bamread.lo -MD -MP -MF .deps/libgstruct_1.0_la-bamread.Tpo -c bamread.c -o libgstruct_1.0_la-bamread.o
mv -f .deps/libgstruct_1.0_la-bamread.Tpo .deps/libgstruct_1.0_la-bamread.Plo
/bin/bash ../libtool  --tag=CC   --mode=compile gcc -DHAVE_CONFIG_H -I.        -I. -fPIC -DTARGET=\"aarch64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.17-bioc/meat/gmapR/src/../inst/usr/share\" -g -O3 -MT libgstruct_1.0_la-samread.lo -MD -MP -MF .deps/libgstruct_1.0_la-samread.Tpo -c -o libgstruct_1.0_la-samread.lo `test -f 'samread.c' || echo './'`samread.c
libtool: compile:  gcc -DHAVE_CONFIG_H -I. -I. -fPIC -DTARGET=\"aarch64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.17-bioc/meat/gmapR/src/../inst/usr/share\" -g -O3 -MT libgstruct_1.0_la-samread.lo -MD -MP -MF .deps/libgstruct_1.0_la-samread.Tpo -c samread.c -o libgstruct_1.0_la-samread.o
mv -f .deps/libgstruct_1.0_la-samread.Tpo .deps/libgstruct_1.0_la-samread.Plo
/bin/bash ../libtool  --tag=CC   --mode=compile gcc -DHAVE_CONFIG_H -I.        -I. -fPIC -DTARGET=\"aarch64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.17-bioc/meat/gmapR/src/../inst/usr/share\" -g -O3 -MT libgstruct_1.0_la-parserange.lo -MD -MP -MF .deps/libgstruct_1.0_la-parserange.Tpo -c -o libgstruct_1.0_la-parserange.lo `test -f 'parserange.c' || echo './'`parserange.c
libtool: compile:  gcc -DHAVE_CONFIG_H -I. -I. -fPIC -DTARGET=\"aarch64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.17-bioc/meat/gmapR/src/../inst/usr/share\" -g -O3 -MT libgstruct_1.0_la-parserange.lo -MD -MP -MF .deps/libgstruct_1.0_la-parserange.Tpo -c parserange.c -o libgstruct_1.0_la-parserange.o
mv -f .deps/libgstruct_1.0_la-parserange.Tpo .deps/libgstruct_1.0_la-parserange.Plo
/bin/bash ../libtool  --tag=CC   --mode=compile gcc -DHAVE_CONFIG_H -I.        -I. -fPIC -DTARGET=\"aarch64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.17-bioc/meat/gmapR/src/../inst/usr/share\" -g -O3 -MT libgstruct_1.0_la-tableuint.lo -MD -MP -MF .deps/libgstruct_1.0_la-tableuint.Tpo -c -o libgstruct_1.0_la-tableuint.lo `test -f 'tableuint.c' || echo './'`tableuint.c
libtool: compile:  gcc -DHAVE_CONFIG_H -I. -I. -fPIC -DTARGET=\"aarch64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.17-bioc/meat/gmapR/src/../inst/usr/share\" -g -O3 -MT libgstruct_1.0_la-tableuint.lo -MD -MP -MF .deps/libgstruct_1.0_la-tableuint.Tpo -c tableuint.c -o libgstruct_1.0_la-tableuint.o
mv -f .deps/libgstruct_1.0_la-tableuint.Tpo .deps/libgstruct_1.0_la-tableuint.Plo
/bin/bash ../libtool  --tag=CC   --mode=compile gcc -DHAVE_CONFIG_H -I.        -I. -fPIC -DTARGET=\"aarch64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.17-bioc/meat/gmapR/src/../inst/usr/share\" -g -O3 -MT libgstruct_1.0_la-iit-write.lo -MD -MP -MF .deps/libgstruct_1.0_la-iit-write.Tpo -c -o libgstruct_1.0_la-iit-write.lo `test -f 'iit-write.c' || echo './'`iit-write.c
libtool: compile:  gcc -DHAVE_CONFIG_H -I. -I. -fPIC -DTARGET=\"aarch64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.17-bioc/meat/gmapR/src/../inst/usr/share\" -g -O3 -MT libgstruct_1.0_la-iit-write.lo -MD -MP -MF .deps/libgstruct_1.0_la-iit-write.Tpo -c iit-write.c -o libgstruct_1.0_la-iit-write.o
mv -f .deps/libgstruct_1.0_la-iit-write.Tpo .deps/libgstruct_1.0_la-iit-write.Plo
/bin/bash ../libtool  --tag=CC   --mode=compile gcc -DHAVE_CONFIG_H -I.        -I. -fPIC -DTARGET=\"aarch64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.17-bioc/meat/gmapR/src/../inst/usr/share\" -g -O3 -MT libgstruct_1.0_la-ucharlist.lo -MD -MP -MF .deps/libgstruct_1.0_la-ucharlist.Tpo -c -o libgstruct_1.0_la-ucharlist.lo `test -f 'ucharlist.c' || echo './'`ucharlist.c
libtool: compile:  gcc -DHAVE_CONFIG_H -I. -I. -fPIC -DTARGET=\"aarch64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.17-bioc/meat/gmapR/src/../inst/usr/share\" -g -O3 -MT libgstruct_1.0_la-ucharlist.lo -MD -MP -MF .deps/libgstruct_1.0_la-ucharlist.Tpo -c ucharlist.c -o libgstruct_1.0_la-ucharlist.o
mv -f .deps/libgstruct_1.0_la-ucharlist.Tpo .deps/libgstruct_1.0_la-ucharlist.Plo
/bin/bash ../libtool  --tag=CC   --mode=compile gcc -DHAVE_CONFIG_H -I.        -I. -fPIC -DTARGET=\"aarch64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.17-bioc/meat/gmapR/src/../inst/usr/share\" -g -O3 -MT libgstruct_1.0_la-matchpool.lo -MD -MP -MF .deps/libgstruct_1.0_la-matchpool.Tpo -c -o libgstruct_1.0_la-matchpool.lo `test -f 'matchpool.c' || echo './'`matchpool.c
libtool: compile:  gcc -DHAVE_CONFIG_H -I. -I. -fPIC -DTARGET=\"aarch64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.17-bioc/meat/gmapR/src/../inst/usr/share\" -g -O3 -MT libgstruct_1.0_la-matchpool.lo -MD -MP -MF .deps/libgstruct_1.0_la-matchpool.Tpo -c matchpool.c -o libgstruct_1.0_la-matchpool.o
mv -f .deps/libgstruct_1.0_la-matchpool.Tpo .deps/libgstruct_1.0_la-matchpool.Plo
/bin/bash ../libtool  --tag=CC   --mode=compile gcc -DHAVE_CONFIG_H -I.        -I. -fPIC -DTARGET=\"aarch64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.17-bioc/meat/gmapR/src/../inst/usr/share\" -g -O3 -MT libgstruct_1.0_la-mismatchpool.lo -MD -MP -MF .deps/libgstruct_1.0_la-mismatchpool.Tpo -c -o libgstruct_1.0_la-mismatchpool.lo `test -f 'mismatchpool.c' || echo './'`mismatchpool.c
libtool: compile:  gcc -DHAVE_CONFIG_H -I. -I. -fPIC -DTARGET=\"aarch64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.17-bioc/meat/gmapR/src/../inst/usr/share\" -g -O3 -MT libgstruct_1.0_la-mismatchpool.lo -MD -MP -MF .deps/libgstruct_1.0_la-mismatchpool.Tpo -c mismatchpool.c -o libgstruct_1.0_la-mismatchpool.o
mv -f .deps/libgstruct_1.0_la-mismatchpool.Tpo .deps/libgstruct_1.0_la-mismatchpool.Plo
/bin/bash ../libtool  --tag=CC   --mode=compile gcc -DHAVE_CONFIG_H -I.        -I. -fPIC -DTARGET=\"aarch64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.17-bioc/meat/gmapR/src/../inst/usr/share\" -g -O3 -MT libgstruct_1.0_la-tally.lo -MD -MP -MF .deps/libgstruct_1.0_la-tally.Tpo -c -o libgstruct_1.0_la-tally.lo `test -f 'tally.c' || echo './'`tally.c
libtool: compile:  gcc -DHAVE_CONFIG_H -I. -I. -fPIC -DTARGET=\"aarch64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.17-bioc/meat/gmapR/src/../inst/usr/share\" -g -O3 -MT libgstruct_1.0_la-tally.lo -MD -MP -MF .deps/libgstruct_1.0_la-tally.Tpo -c tally.c -o libgstruct_1.0_la-tally.o
mv -f .deps/libgstruct_1.0_la-tally.Tpo .deps/libgstruct_1.0_la-tally.Plo
/bin/bash ../libtool  --tag=CC   --mode=compile gcc -DHAVE_CONFIG_H -I.        -I. -fPIC -DTARGET=\"aarch64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.17-bioc/meat/gmapR/src/../inst/usr/share\" -g -O3 -MT libgstruct_1.0_la-translation.lo -MD -MP -MF .deps/libgstruct_1.0_la-translation.Tpo -c -o libgstruct_1.0_la-translation.lo `test -f 'translation.c' || echo './'`translation.c
libtool: compile:  gcc -DHAVE_CONFIG_H -I. -I. -fPIC -DTARGET=\"aarch64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.17-bioc/meat/gmapR/src/../inst/usr/share\" -g -O3 -MT libgstruct_1.0_la-translation.lo -MD -MP -MF .deps/libgstruct_1.0_la-translation.Tpo -c translation.c -o libgstruct_1.0_la-translation.o
mv -f .deps/libgstruct_1.0_la-translation.Tpo .deps/libgstruct_1.0_la-translation.Plo
/bin/bash ../libtool  --tag=CC   --mode=compile gcc -DHAVE_CONFIG_H -I.        -I. -fPIC -DTARGET=\"aarch64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.17-bioc/meat/gmapR/src/../inst/usr/share\" -g -O3 -MT libgstruct_1.0_la-expr.lo -MD -MP -MF .deps/libgstruct_1.0_la-expr.Tpo -c -o libgstruct_1.0_la-expr.lo `test -f 'expr.c' || echo './'`expr.c
libtool: compile:  gcc -DHAVE_CONFIG_H -I. -I. -fPIC -DTARGET=\"aarch64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.17-bioc/meat/gmapR/src/../inst/usr/share\" -g -O3 -MT libgstruct_1.0_la-expr.lo -MD -MP -MF .deps/libgstruct_1.0_la-expr.Tpo -c expr.c -o libgstruct_1.0_la-expr.o
mv -f .deps/libgstruct_1.0_la-expr.Tpo .deps/libgstruct_1.0_la-expr.Plo
/bin/bash ../libtool  --tag=CC   --mode=compile gcc -DHAVE_CONFIG_H -I.        -I. -fPIC -DTARGET=\"aarch64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.17-bioc/meat/gmapR/src/../inst/usr/share\" -g -O3 -MT libgstruct_1.0_la-bamtally.lo -MD -MP -MF .deps/libgstruct_1.0_la-bamtally.Tpo -c -o libgstruct_1.0_la-bamtally.lo `test -f 'bamtally.c' || echo './'`bamtally.c
libtool: compile:  gcc -DHAVE_CONFIG_H -I. -I. -fPIC -DTARGET=\"aarch64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.17-bioc/meat/gmapR/src/../inst/usr/share\" -g -O3 -MT libgstruct_1.0_la-bamtally.lo -MD -MP -MF .deps/libgstruct_1.0_la-bamtally.Tpo -c bamtally.c -o libgstruct_1.0_la-bamtally.o
bamtally.c:7453:14: error: unknown type name ‘__m128i’
 7453 |              __m128i *passing_counts, int nreps, int nmult) {
      |              ^~~~~~~
bamtally.c:8190:21: error: unknown type name ‘__m128i’
 8190 | get_passing_counts (__m128i *passing_counts, int readlength, Bamline_T *bamlines, int nreps, int minimum_quality_score) {
      |                     ^~~~~~~
bamtally.c: In function ‘Bamtally_run’:
bamtally.c:8372:3: error: unknown type name ‘__m128i’
 8372 |   __m128i *passing_counts;
      |   ^~~~~~~
bamtally.c:8543:13: warning: implicit declaration of function ‘revise_read’; did you mean ‘revise_read_lh’? [-Wimplicit-function-declaration]
 8543 |             revise_read(alloc_tallies,chrstart,chrend,chrpos_low,chrpos_high,Bamline_flag(bamline_rep),
      |             ^~~~~~~~~~~
      |             revise_read_lh
bamtally.c:8551:31: error: ‘__m128i’ undeclared (first use in this function)
 8551 |             passing_counts = (__m128i *) _mm_malloc((nvectors + 1) * sizeof(__m128i),16);
      |                               ^~~~~~~
bamtally.c:8551:31: note: each undeclared identifier is reported only once for each function it appears in
bamtally.c:8551:40: error: expected expression before ‘)’ token
 8551 |             passing_counts = (__m128i *) _mm_malloc((nvectors + 1) * sizeof(__m128i),16);
      |                                        ^
bamtally.c:8552:13: warning: implicit declaration of function ‘get_passing_counts’ [-Wimplicit-function-declaration]
 8552 |             get_passing_counts(passing_counts,readlength,&(bamlines[linei_start]),nreps,minimum_quality_score);
      |             ^~~~~~~~~~~~~~~~~~
bamtally.c:8559:13: warning: implicit declaration of function ‘_mm_free’; did you mean ‘Mem_free’? [-Wimplicit-function-declaration]
 8559 |             _mm_free(passing_counts);
      |             ^~~~~~~~
      |             Mem_free
bamtally.c:8792:40: error: expected expression before ‘)’ token
 8792 |             passing_counts = (__m128i *) _mm_malloc((nvectors + 1) * sizeof(__m128i),16);
      |                                        ^
bamtally.c: In function ‘Bamtally_expr’:
bamtally.c:8986:3: error: unknown type name ‘__m128i’
 8986 |   __m128i *passing_counts;
      |   ^~~~~~~
bamtally.c:9152:31: error: ‘__m128i’ undeclared (first use in this function)
 9152 |             passing_counts = (__m128i *) _mm_malloc((nvectors + 1) * sizeof(__m128i),16);
      |                               ^~~~~~~
bamtally.c:9152:40: error: expected expression before ‘)’ token
 9152 |             passing_counts = (__m128i *) _mm_malloc((nvectors + 1) * sizeof(__m128i),16);
      |                                        ^
bamtally.c:9381:40: error: expected expression before ‘)’ token
 9381 |             passing_counts = (__m128i *) _mm_malloc((nvectors + 1) * sizeof(__m128i),16);
      |                                        ^
make[2]: *** [Makefile:1014: libgstruct_1.0_la-bamtally.lo] Error 1
make[2]: Leaving directory '/home/biocbuild/bbs-3.17-bioc/meat/gmapR/src/gstruct/src'
make[1]: *** [Makefile:440: install-recursive] Error 1
make[1]: Leaving directory '/home/biocbuild/bbs-3.17-bioc/meat/gmapR/src/gstruct'
make: *** [Makefile:50: gstruct] Error 2
ERROR: compilation failed for package ‘gmapR’
* removing ‘/home/biocbuild/bbs-3.17-bioc/R/library/gmapR’

cosmiq.install

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD INSTALL cosmiq
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.17-bioc/R/library’
ERROR: dependency ‘faahKO’ is not available for package ‘cosmiq’
* removing ‘/home/biocbuild/bbs-3.17-bioc/R/library/cosmiq’

Rbwa.install

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD INSTALL Rbwa
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.17-bioc/R/library’
* installing *source* package ‘Rbwa’ ...
** using staged installation
** libs
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG   -I/usr/local/include    -fPIC  -g -Wall -O2 -c utils.c -o utils.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG   -I/usr/local/include    -fPIC  -g -Wall -O2 -c kthread.c -o kthread.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG   -I/usr/local/include    -fPIC  -g -Wall -O2 -c kstring.c -o kstring.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG   -I/usr/local/include    -fPIC  -g -Wall -O2 -c ksw.c -o ksw.o
ksw.c:29:10: fatal error: emmintrin.h: No such file or directory
   29 | #include <emmintrin.h>
      |          ^~~~~~~~~~~~~
compilation terminated.
make: *** [/home/biocbuild/bbs-3.17-bioc/R/etc/Makeconf:191: ksw.o] Error 1
ERROR: compilation failed for package ‘Rbwa’
* removing ‘/home/biocbuild/bbs-3.17-bioc/R/library/Rbwa’

lpsymphony.install

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD INSTALL lpsymphony
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.17-bioc/R/library’
* installing *source* package ‘lpsymphony’ ...
** using staged installation
configure: loading site script /home/biocbuild/bbs-3.17-bioc/meat/lpsymphony/src/SYMPHONY/share/config.site
checking build system type... ./config.guess: unable to guess system type

This script, last modified 2007-05-17, has failed to recognize
the operating system you are using. It is advised that you
download the most up to date version of the config scripts from

  http://savannah.gnu.org/cgi-bin/viewcvs/*checkout*/config/config/config.guess
and
  http://savannah.gnu.org/cgi-bin/viewcvs/*checkout*/config/config/config.sub

If the version you run (./config.guess) is already up to date, please
send the following data and any information you think might be
pertinent to <[email protected]> in order to provide the needed
information to handle your system.

config.guess timestamp = 2007-05-17

uname -m = aarch64
uname -r = 5.15.0-58-generic
uname -s = Linux
uname -v = #64-Ubuntu SMP Thu Jan 5 12:06:43 UTC 2023

/usr/bin/uname -p = aarch64
/bin/uname -X     = 

hostinfo               = 
/bin/universe          = 
/usr/bin/arch -k       = 
/bin/arch              = aarch64
/usr/bin/oslevel       = 
/usr/convex/getsysinfo = 

UNAME_MACHINE = aarch64
UNAME_RELEASE = 5.15.0-58-generic
UNAME_SYSTEM  = Linux
UNAME_VERSION = #64-Ubuntu SMP Thu Jan 5 12:06:43 UTC 2023
configure: error: cannot guess build type; you must specify one
** libs
using C++ compiler: ‘g++ (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0’
make[1]: Entering directory '/home/biocbuild/bbs-3.17-bioc/meat/lpsymphony/src/SYMPHONY'
make[1]: *** No targets specified and no makefile found.  Stop.
make[1]: Leaving directory '/home/biocbuild/bbs-3.17-bioc/meat/lpsymphony/src/SYMPHONY'
make: *** [Makevars:13: SYMPHONY.ts] Error 2
ERROR: compilation failed for package ‘lpsymphony’
* removing ‘/home/biocbuild/bbs-3.17-bioc/R/library/lpsymphony’

ChIC.install

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD INSTALL ChIC
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.17-bioc/R/library’
ERROR: dependency ‘spp’ is not available for package ‘ChIC’
* removing ‘/home/biocbuild/bbs-3.17-bioc/R/library/ChIC’

GEOquery.build

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD build --keep-empty-dirs --no-resave-data GEOquery
###
##############################################################################
##############################################################################


* checking for file ‘GEOquery/DESCRIPTION’ ... OK
* preparing ‘GEOquery’:
* checking DESCRIPTION meta-information ... OK
* installing the package to build vignettes
* creating vignettes ... ERROR
--- re-building ‘GEOquery.Rmd’ using rmarkdown
Quitting from lines 135-139 (GEOquery.Rmd) 
Error: processing vignette 'GEOquery.Rmd' failed with diagnostics:
Timeout was reached: [] Operation timed out after 120000 milliseconds with 917504 out of 8480960 bytes received
--- failed re-building ‘GEOquery.Rmd’

SUMMARY: processing the following file failed:
  ‘GEOquery.Rmd’

Error: Vignette re-building failed.
Execution halted

iClusterPlus.install

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD INSTALL iClusterPlus
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.17-bioc/R/library’
* installing *source* package ‘iClusterPlus’ ...
** using staged installation
 This package has only been tested with gfortran.
 So some checks are needed.
 R_HOME is /home/biocbuild/bbs-3.17-bioc/R
Attempting to determine R_ARCH...
R_ARCH is 
Attempting to detect how R was configured for Fortran 90....
  R configured for gfortran; Good!
configure: creating ./config.status
config.status: creating src/Makevars
** libs
using C compiler: ‘gcc (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0’
using Fortran compiler: ‘GNU Fortran (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0’
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG   -I/usr/local/include    -fPIC  -g -O2  -Wall -c iClusterBayes.c -o iClusterBayes.o
In file included from /home/biocbuild/bbs-3.17-bioc/R/include/R.h:78,
                 from iClusterBayes.c:7:
iClusterBayes.c: In function ‘rmvnormal’:
iClusterBayes.c:87:12: error: too few arguments to function ‘dpotrf_’
   87 |   F77_CALL(dpotrf)(uplo,n,tempcov,n,&info);
      |            ^~~~~~
/home/biocbuild/bbs-3.17-bioc/R/include/R_ext/RS.h:77:25: note: in definition of macro ‘F77_CALL’
   77 | # define F77_CALL(x)    x ## _
      |                         ^
/home/biocbuild/bbs-3.17-bioc/R/include/R_ext/Lapack.h:825:10: note: declared here
  825 | F77_NAME(dpotrf)(const char* uplo, const int* n,
      |          ^~~~~~
/home/biocbuild/bbs-3.17-bioc/R/include/R_ext/RS.h:77:25: note: in definition of macro ‘F77_CALL’
   77 | # define F77_CALL(x)    x ## _
      |                         ^
/home/biocbuild/bbs-3.17-bioc/R/include/R_ext/Lapack.h:825:1: note: in expansion of macro ‘F77_NAME’
  825 | F77_NAME(dpotrf)(const char* uplo, const int* n,
      | ^~~~~~~~
iClusterBayes.c:103:12: error: too few arguments to function ‘dgemv_’
  103 |   F77_CALL(dgemv)(transN,n,n,&ONE,tempcov,n,zvec,&incx, &ZERO,vec, &incy);
      |            ^~~~~
/home/biocbuild/bbs-3.17-bioc/R/include/R_ext/RS.h:77:25: note: in definition of macro ‘F77_CALL’
   77 | # define F77_CALL(x)    x ## _
      |                         ^
/home/biocbuild/bbs-3.17-bioc/R/include/R_ext/BLAS.h:107:10: note: declared here
  107 | F77_NAME(dgemv)(const char *trans, const int *m, const int *n,
      |          ^~~~~
/home/biocbuild/bbs-3.17-bioc/R/include/R_ext/RS.h:77:25: note: in definition of macro ‘F77_CALL’
   77 | # define F77_CALL(x)    x ## _
      |                         ^
/home/biocbuild/bbs-3.17-bioc/R/include/R_ext/BLAS.h:107:1: note: in expansion of macro ‘F77_NAME’
  107 | F77_NAME(dgemv)(const char *trans, const int *m, const int *n,
      | ^~~~~~~~
iClusterBayes.c: In function ‘bvsNormal’:
iClusterBayes.c:166:12: error: too few arguments to function ‘dgemm_’
  166 |   F77_CALL(dgemm)(transT,transN,&k1,&k1,n,&ONE,C1Z,n,C1Z,n,&ZERO,ZtZ,&k1);
      |            ^~~~~
/home/biocbuild/bbs-3.17-bioc/R/include/R_ext/RS.h:77:25: note: in definition of macro ‘F77_CALL’
   77 | # define F77_CALL(x)    x ## _
      |                         ^
/home/biocbuild/bbs-3.17-bioc/R/include/R_ext/BLAS.h:207:10: note: declared here
  207 | F77_NAME(dgemm)(const char *transa, const char *transb, const int *m,
      |          ^~~~~
/home/biocbuild/bbs-3.17-bioc/R/include/R_ext/RS.h:77:25: note: in definition of macro ‘F77_CALL’
   77 | # define F77_CALL(x)    x ## _
      |                         ^
/home/biocbuild/bbs-3.17-bioc/R/include/R_ext/BLAS.h:207:1: note: in expansion of macro ‘F77_NAME’
  207 | F77_NAME(dgemm)(const char *transa, const char *transb, const int *m,
      | ^~~~~~~~
iClusterBayes.c:171:12: error: too few arguments to function ‘dgemm_’
  171 |   F77_CALL(dgemm)(transT,transN,&k1,p,n,&ONE,C1Z,n,X,n,&ZERO,ZtX,&k1);
      |            ^~~~~
/home/biocbuild/bbs-3.17-bioc/R/include/R_ext/RS.h:77:25: note: in definition of macro ‘F77_CALL’
   77 | # define F77_CALL(x)    x ## _
      |                         ^
/home/biocbuild/bbs-3.17-bioc/R/include/R_ext/BLAS.h:207:10: note: declared here
  207 | F77_NAME(dgemm)(const char *transa, const char *transb, const int *m,
      |          ^~~~~
/home/biocbuild/bbs-3.17-bioc/R/include/R_ext/RS.h:77:25: note: in definition of macro ‘F77_CALL’
   77 | # define F77_CALL(x)    x ## _
      |                         ^
/home/biocbuild/bbs-3.17-bioc/R/include/R_ext/BLAS.h:207:1: note: in expansion of macro ‘F77_NAME’
  207 | F77_NAME(dgemm)(const char *transa, const char *transb, const int *m,
      | ^~~~~~~~
iClusterBayes.c:197:12: error: too few arguments to function ‘dgemm_’
  197 |   F77_CALL(dgemm)(transN,transT,n,p, &k1,&ONE,C1Z,n,alphaBeta,p,&ZERO,meanX,n);
      |            ^~~~~
/home/biocbuild/bbs-3.17-bioc/R/include/R_ext/RS.h:77:25: note: in definition of macro ‘F77_CALL’
   77 | # define F77_CALL(x)    x ## _
      |                         ^
/home/biocbuild/bbs-3.17-bioc/R/include/R_ext/BLAS.h:207:10: note: declared here
  207 | F77_NAME(dgemm)(const char *transa, const char *transb, const int *m,
      |          ^~~~~
/home/biocbuild/bbs-3.17-bioc/R/include/R_ext/RS.h:77:25: note: in definition of macro ‘F77_CALL’
   77 | # define F77_CALL(x)    x ## _
      |                         ^
/home/biocbuild/bbs-3.17-bioc/R/include/R_ext/BLAS.h:207:1: note: in expansion of macro ‘F77_NAME’
  207 | F77_NAME(dgemm)(const char *transa, const char *transb, const int *m,
      | ^~~~~~~~
iClusterBayes.c:249:14: error: too few arguments to function ‘dgemv_’
  249 |     F77_CALL(dgemv)(transN,&k1,&k1,&ONE,beta_invV,&k1,ZtXj,&incx, &ZERO,beta_m, &incy);
      |              ^~~~~
/home/biocbuild/bbs-3.17-bioc/R/include/R_ext/RS.h:77:25: note: in definition of macro ‘F77_CALL’
   77 | # define F77_CALL(x)    x ## _
      |                         ^
/home/biocbuild/bbs-3.17-bioc/R/include/R_ext/BLAS.h:107:10: note: declared here
  107 | F77_NAME(dgemv)(const char *trans, const int *m, const int *n,
      |          ^~~~~
/home/biocbuild/bbs-3.17-bioc/R/include/R_ext/RS.h:77:25: note: in definition of macro ‘F77_CALL’
   77 | # define F77_CALL(x)    x ## _
      |                         ^
/home/biocbuild/bbs-3.17-bioc/R/include/R_ext/BLAS.h:107:1: note: in expansion of macro ‘F77_NAME’
  107 | F77_NAME(dgemv)(const char *trans, const int *m, const int *n,
      | ^~~~~~~~
iClusterBayes.c:293:12: error: too few arguments to function ‘dgemm_’
  293 |   F77_CALL(dgemm)(transN,transT,n,p, &k1,&ONE,C1Z,n,alphaBeta2,p,&ZERO,meanX,n);
      |            ^~~~~
/home/biocbuild/bbs-3.17-bioc/R/include/R_ext/RS.h:77:25: note: in definition of macro ‘F77_CALL’
   77 | # define F77_CALL(x)    x ## _
      |                         ^
/home/biocbuild/bbs-3.17-bioc/R/include/R_ext/BLAS.h:207:10: note: declared here
  207 | F77_NAME(dgemm)(const char *transa, const char *transb, const int *m,
      |          ^~~~~
/home/biocbuild/bbs-3.17-bioc/R/include/R_ext/RS.h:77:25: note: in definition of macro ‘F77_CALL’
   77 | # define F77_CALL(x)    x ## _
      |                         ^
/home/biocbuild/bbs-3.17-bioc/R/include/R_ext/BLAS.h:207:1: note: in expansion of macro ‘F77_NAME’
  207 | F77_NAME(dgemm)(const char *transa, const char *transb, const int *m,
      | ^~~~~~~~
iClusterBayes.c:306:12: error: too few arguments to function ‘dgemm_’
  306 |   F77_CALL(dgemm)(transN,transT,n,p, &k1,&ONE,C1Z,n,alphaBeta2,p,&ZERO,meanX_p,n);
      |            ^~~~~
/home/biocbuild/bbs-3.17-bioc/R/include/R_ext/RS.h:77:25: note: in definition of macro ‘F77_CALL’
   77 | # define F77_CALL(x)    x ## _
      |                         ^
/home/biocbuild/bbs-3.17-bioc/R/include/R_ext/BLAS.h:207:10: note: declared here
  207 | F77_NAME(dgemm)(const char *transa, const char *transb, const int *m,
      |          ^~~~~
/home/biocbuild/bbs-3.17-bioc/R/include/R_ext/RS.h:77:25: note: in definition of macro ‘F77_CALL’
   77 | # define F77_CALL(x)    x ## _
      |                         ^
/home/biocbuild/bbs-3.17-bioc/R/include/R_ext/BLAS.h:207:1: note: in expansion of macro ‘F77_NAME’
  207 | F77_NAME(dgemm)(const char *transa, const char *transb, const int *m,
      | ^~~~~~~~
iClusterBayes.c: In function ‘bvsPoisson’:
iClusterBayes.c:422:12: error: too few arguments to function ‘dgemm_’
  422 |   F77_CALL(dgemm)(transT,transN,&k1,&k1,n,&ONE,C1Z,n,C1Z,n,&ZERO,ZtZ,&k1);
      |            ^~~~~
/home/biocbuild/bbs-3.17-bioc/R/include/R_ext/RS.h:77:25: note: in definition of macro ‘F77_CALL’
   77 | # define F77_CALL(x)    x ## _
      |                         ^
/home/biocbuild/bbs-3.17-bioc/R/include/R_ext/BLAS.h:207:10: note: declared here
  207 | F77_NAME(dgemm)(const char *transa, const char *transb, const int *m,
      |          ^~~~~
/home/biocbuild/bbs-3.17-bioc/R/include/R_ext/RS.h:77:25: note: in definition of macro ‘F77_CALL’
   77 | # define F77_CALL(x)    x ## _
      |                         ^
/home/biocbuild/bbs-3.17-bioc/R/include/R_ext/BLAS.h:207:1: note: in expansion of macro ‘F77_NAME’
  207 | F77_NAME(dgemm)(const char *transa, const char *transb, const int *m,
      | ^~~~~~~~
iClusterBayes.c:465:12: error: too few arguments to function ‘dgemm_’
  465 |   F77_CALL(dgemm)(transN,transT,n,p, &k1,&ONE,C1Z,n,alphaBeta2,p,&ZERO,ZtBeta,n);
      |            ^~~~~
/home/biocbuild/bbs-3.17-bioc/R/include/R_ext/RS.h:77:25: note: in definition of macro ‘F77_CALL’
   77 | # define F77_CALL(x)    x ## _
      |                         ^
/home/biocbuild/bbs-3.17-bioc/R/include/R_ext/BLAS.h:207:10: note: declared here
  207 | F77_NAME(dgemm)(const char *transa, const char *transb, const int *m,
      |          ^~~~~
/home/biocbuild/bbs-3.17-bioc/R/include/R_ext/RS.h:77:25: note: in definition of macro ‘F77_CALL’
   77 | # define F77_CALL(x)    x ## _
      |                         ^
/home/biocbuild/bbs-3.17-bioc/R/include/R_ext/BLAS.h:207:1: note: in expansion of macro ‘F77_NAME’
  207 | F77_NAME(dgemm)(const char *transa, const char *transb, const int *m,
      | ^~~~~~~~
iClusterBayes.c:480:12: error: too few arguments to function ‘dgemm_’
  480 |   F77_CALL(dgemm)(transN,transT,n,p, &k1,&ONE,C1Z,n,alphaBeta2,p,&ZERO,ZtBeta_p,n);
      |            ^~~~~
/home/biocbuild/bbs-3.17-bioc/R/include/R_ext/RS.h:77:25: note: in definition of macro ‘F77_CALL’
   77 | # define F77_CALL(x)    x ## _
      |                         ^
/home/biocbuild/bbs-3.17-bioc/R/include/R_ext/BLAS.h:207:10: note: declared here
  207 | F77_NAME(dgemm)(const char *transa, const char *transb, const int *m,
      |          ^~~~~
/home/biocbuild/bbs-3.17-bioc/R/include/R_ext/RS.h:77:25: note: in definition of macro ‘F77_CALL’
   77 | # define F77_CALL(x)    x ## _
      |                         ^
/home/biocbuild/bbs-3.17-bioc/R/include/R_ext/BLAS.h:207:1: note: in expansion of macro ‘F77_NAME’
  207 | F77_NAME(dgemm)(const char *transa, const char *transb, const int *m,
      | ^~~~~~~~
iClusterBayes.c:501:13: error: too few arguments to function ‘dgemv_’
  501 |    F77_CALL(dgemv)(transN,&k1,&k1,&ONE,invSigma0,&k1,tempab,&incx, &ZERO,invSigmaBeta0, &incy);
      |             ^~~~~
/home/biocbuild/bbs-3.17-bioc/R/include/R_ext/RS.h:77:25: note: in definition of macro ‘F77_CALL’
   77 | # define F77_CALL(x)    x ## _
      |                         ^
/home/biocbuild/bbs-3.17-bioc/R/include/R_ext/BLAS.h:107:10: note: declared here
  107 | F77_NAME(dgemv)(const char *trans, const int *m, const int *n,
      |          ^~~~~
/home/biocbuild/bbs-3.17-bioc/R/include/R_ext/RS.h:77:25: note: in definition of macro ‘F77_CALL’
   77 | # define F77_CALL(x)    x ## _
      |                         ^
/home/biocbuild/bbs-3.17-bioc/R/include/R_ext/BLAS.h:107:1: note: in expansion of macro ‘F77_NAME’
  107 | F77_NAME(dgemv)(const char *trans, const int *m, const int *n,
      | ^~~~~~~~
iClusterBayes.c:505:13: error: too few arguments to function ‘dgemv_’
  505 |    F77_CALL(dgemv)(transN,&k1,&k1,&ONE,invSigma0,&k1,tempab_p,&incx, &ZERO,invSigmaBeta0, &incy);
      |             ^~~~~
/home/biocbuild/bbs-3.17-bioc/R/include/R_ext/RS.h:77:25: note: in definition of macro ‘F77_CALL’
   77 | # define F77_CALL(x)    x ## _
      |                         ^
/home/biocbuild/bbs-3.17-bioc/R/include/R_ext/BLAS.h:107:10: note: declared here
  107 | F77_NAME(dgemv)(const char *trans, const int *m, const int *n,
      |          ^~~~~
/home/biocbuild/bbs-3.17-bioc/R/include/R_ext/RS.h:77:25: note: in definition of macro ‘F77_CALL’
   77 | # define F77_CALL(x)    x ## _
      |                         ^
/home/biocbuild/bbs-3.17-bioc/R/include/R_ext/BLAS.h:107:1: note: in expansion of macro ‘F77_NAME’
  107 | F77_NAME(dgemv)(const char *trans, const int *m, const int *n,
      | ^~~~~~~~
iClusterBayes.c:548:16: error: too few arguments to function ‘dgemv_’
  548 |       F77_CALL(dgemv)(transN,n,&k1,&ONE,C1Z,n,beta_m,&incx,&ZERO,Zbeta,&incy);
      |                ^~~~~
/home/biocbuild/bbs-3.17-bioc/R/include/R_ext/RS.h:77:25: note: in definition of macro ‘F77_CALL’
   77 | # define F77_CALL(x)    x ## _
      |                         ^
/home/biocbuild/bbs-3.17-bioc/R/include/R_ext/BLAS.h:107:10: note: declared here
  107 | F77_NAME(dgemv)(const char *trans, const int *m, const int *n,
      |          ^~~~~
/home/biocbuild/bbs-3.17-bioc/R/include/R_ext/RS.h:77:25: note: in definition of macro ‘F77_CALL’
   77 | # define F77_CALL(x)    x ## _
      |                         ^
/home/biocbuild/bbs-3.17-bioc/R/include/R_ext/BLAS.h:107:1: note: in expansion of macro ‘F77_NAME’
  107 | F77_NAME(dgemv)(const char *trans, const int *m, const int *n,
      | ^~~~~~~~
iClusterBayes.c:551:16: error: too few arguments to function ‘dgemv_’
  551 |       F77_CALL(dgemv)(transN,n,&k1,&ONE,C1Z,n,beta_p,&incx,&ZERO,Zbeta_p,&incy);
      |                ^~~~~
/home/biocbuild/bbs-3.17-bioc/R/include/R_ext/RS.h:77:25: note: in definition of macro ‘F77_CALL’
   77 | # define F77_CALL(x)    x ## _
      |                         ^
/home/biocbuild/bbs-3.17-bioc/R/include/R_ext/BLAS.h:107:10: note: declared here
  107 | F77_NAME(dgemv)(const char *trans, const int *m, const int *n,
      |          ^~~~~
/home/biocbuild/bbs-3.17-bioc/R/include/R_ext/RS.h:77:25: note: in definition of macro ‘F77_CALL’
   77 | # define F77_CALL(x)    x ## _
      |                         ^
/home/biocbuild/bbs-3.17-bioc/R/include/R_ext/BLAS.h:107:1: note: in expansion of macro ‘F77_NAME’
  107 | F77_NAME(dgemv)(const char *trans, const int *m, const int *n,
      | ^~~~~~~~
iClusterBayes.c:570:16: error: too few arguments to function ‘dgemv_’
  570 |       F77_CALL(dgemv)(transN,&k1,&k1,&ONE,invSigma0,&k1,tempab,&incx, &ZERO,invSigmaBeta0, &incy);
      |                ^~~~~
/home/biocbuild/bbs-3.17-bioc/R/include/R_ext/RS.h:77:25: note: in definition of macro ‘F77_CALL’
   77 | # define F77_CALL(x)    x ## _
      |                         ^
/home/biocbuild/bbs-3.17-bioc/R/include/R_ext/BLAS.h:107:10: note: declared here
  107 | F77_NAME(dgemv)(const char *trans, const int *m, const int *n,
      |          ^~~~~
/home/biocbuild/bbs-3.17-bioc/R/include/R_ext/RS.h:77:25: note: in definition of macro ‘F77_CALL’
   77 | # define F77_CALL(x)    x ## _
      |                         ^
/home/biocbuild/bbs-3.17-bioc/R/include/R_ext/BLAS.h:107:1: note: in expansion of macro ‘F77_NAME’
  107 | F77_NAME(dgemv)(const char *trans, const int *m, const int *n,
      | ^~~~~~~~
iClusterBayes.c:574:16: error: too few arguments to function ‘dgemv_’
  574 |       F77_CALL(dgemv)(transN,&k1,&k1,&ONE,invSigma0,&k1,tempab_p,&incx, &ZERO,invSigmaBeta0, &incy);
      |                ^~~~~
/home/biocbuild/bbs-3.17-bioc/R/include/R_ext/RS.h:77:25: note: in definition of macro ‘F77_CALL’
   77 | # define F77_CALL(x)    x ## _
      |                         ^
/home/biocbuild/bbs-3.17-bioc/R/include/R_ext/BLAS.h:107:10: note: declared here
  107 | F77_NAME(dgemv)(const char *trans, const int *m, const int *n,
      |          ^~~~~
/home/biocbuild/bbs-3.17-bioc/R/include/R_ext/RS.h:77:25: note: in definition of macro ‘F77_CALL’
   77 | # define F77_CALL(x)    x ## _
      |                         ^
/home/biocbuild/bbs-3.17-bioc/R/include/R_ext/BLAS.h:107:1: note: in expansion of macro ‘F77_NAME’
  107 | F77_NAME(dgemv)(const char *trans, const int *m, const int *n,
      | ^~~~~~~~
iClusterBayes.c: In function ‘bvsBinom’:
iClusterBayes.c:670:12: error: too few arguments to function ‘dgemm_’
  670 |   F77_CALL(dgemm)(transT,transN,&k1,&k1,n,&ONE,C1Z,n,C1Z,n,&ZERO,ZtZ,&k1);
      |            ^~~~~
/home/biocbuild/bbs-3.17-bioc/R/include/R_ext/RS.h:77:25: note: in definition of macro ‘F77_CALL’
   77 | # define F77_CALL(x)    x ## _
      |                         ^
/home/biocbuild/bbs-3.17-bioc/R/include/R_ext/BLAS.h:207:10: note: declared here
  207 | F77_NAME(dgemm)(const char *transa, const char *transb, const int *m,
      |          ^~~~~
/home/biocbuild/bbs-3.17-bioc/R/include/R_ext/RS.h:77:25: note: in definition of macro ‘F77_CALL’
   77 | # define F77_CALL(x)    x ## _
      |                         ^
/home/biocbuild/bbs-3.17-bioc/R/include/R_ext/BLAS.h:207:1: note: in expansion of macro ‘F77_NAME’
  207 | F77_NAME(dgemm)(const char *transa, const char *transb, const int *m,
      | ^~~~~~~~
iClusterBayes.c:713:12: error: too few arguments to function ‘dgemm_’
  713 |   F77_CALL(dgemm)(transN,transT,n,p, &k1,&ONE,C1Z,n,alphaBeta2,p,&ZERO,ZtBeta,n);
      |            ^~~~~
/home/biocbuild/bbs-3.17-bioc/R/include/R_ext/RS.h:77:25: note: in definition of macro ‘F77_CALL’
   77 | # define F77_CALL(x)    x ## _
      |                         ^
/home/biocbuild/bbs-3.17-bioc/R/include/R_ext/BLAS.h:207:10: note: declared here
  207 | F77_NAME(dgemm)(const char *transa, const char *transb, const int *m,
      |          ^~~~~
/home/biocbuild/bbs-3.17-bioc/R/include/R_ext/RS.h:77:25: note: in definition of macro ‘F77_CALL’
   77 | # define F77_CALL(x)    x ## _
      |                         ^
/home/biocbuild/bbs-3.17-bioc/R/include/R_ext/BLAS.h:207:1: note: in expansion of macro ‘F77_NAME’
  207 | F77_NAME(dgemm)(const char *transa, const char *transb, const int *m,
      | ^~~~~~~~
iClusterBayes.c:728:12: error: too few arguments to function ‘dgemm_’
  728 |   F77_CALL(dgemm)(transN,transT,n,p, &k1,&ONE,C1Z,n,alphaBeta2,p,&ZERO,ZtBeta_p,n);
      |            ^~~~~
/home/biocbuild/bbs-3.17-bioc/R/include/R_ext/RS.h:77:25: note: in definition of macro ‘F77_CALL’
   77 | # define F77_CALL(x)    x ## _
      |                         ^
/home/biocbuild/bbs-3.17-bioc/R/include/R_ext/BLAS.h:207:10: note: declared here
  207 | F77_NAME(dgemm)(const char *transa, const char *transb, const int *m,
      |          ^~~~~
/home/biocbuild/bbs-3.17-bioc/R/include/R_ext/RS.h:77:25: note: in definition of macro ‘F77_CALL’
   77 | # define F77_CALL(x)    x ## _
      |                         ^
/home/biocbuild/bbs-3.17-bioc/R/include/R_ext/BLAS.h:207:1: note: in expansion of macro ‘F77_NAME’
  207 | F77_NAME(dgemm)(const char *transa, const char *transb, const int *m,
      | ^~~~~~~~
iClusterBayes.c:754:13: error: too few arguments to function ‘dgemv_’
  754 |    F77_CALL(dgemv)(transN,&k1,&k1,&ONE,invSigma0,&k1,tempab,&incx, &ZERO,invSigmaBeta0, &incy);
      |             ^~~~~
/home/biocbuild/bbs-3.17-bioc/R/include/R_ext/RS.h:77:25: note: in definition of macro ‘F77_CALL’
   77 | # define F77_CALL(x)    x ## _
      |                         ^
/home/biocbuild/bbs-3.17-bioc/R/include/R_ext/BLAS.h:107:10: note: declared here
  107 | F77_NAME(dgemv)(const char *trans, const int *m, const int *n,
      |          ^~~~~
/home/biocbuild/bbs-3.17-bioc/R/include/R_ext/RS.h:77:25: note: in definition of macro ‘F77_CALL’
   77 | # define F77_CALL(x)    x ## _
      |                         ^
/home/biocbuild/bbs-3.17-bioc/R/include/R_ext/BLAS.h:107:1: note: in expansion of macro ‘F77_NAME’
  107 | F77_NAME(dgemv)(const char *trans, const int *m, const int *n,
      | ^~~~~~~~
iClusterBayes.c:757:13: error: too few arguments to function ‘dgemv_’
  757 |    F77_CALL(dgemv)(transN,&k1,&k1,&ONE,invSigma0,&k1,tempab_p,&incx, &ZERO,invSigmaBeta0, &incy);
      |             ^~~~~
/home/biocbuild/bbs-3.17-bioc/R/include/R_ext/RS.h:77:25: note: in definition of macro ‘F77_CALL’
   77 | # define F77_CALL(x)    x ## _
      |                         ^
/home/biocbuild/bbs-3.17-bioc/R/include/R_ext/BLAS.h:107:10: note: declared here
  107 | F77_NAME(dgemv)(const char *trans, const int *m, const int *n,
      |          ^~~~~
/home/biocbuild/bbs-3.17-bioc/R/include/R_ext/RS.h:77:25: note: in definition of macro ‘F77_CALL’
   77 | # define F77_CALL(x)    x ## _
      |                         ^
/home/biocbuild/bbs-3.17-bioc/R/include/R_ext/BLAS.h:107:1: note: in expansion of macro ‘F77_NAME’
  107 | F77_NAME(dgemv)(const char *trans, const int *m, const int *n,
      | ^~~~~~~~
iClusterBayes.c:800:16: error: too few arguments to function ‘dgemv_’
  800 |       F77_CALL(dgemv)(transN,n,&k1,&ONE,C1Z,n,beta_m,&incx,&ZERO,Zbeta,&incy);
      |                ^~~~~
/home/biocbuild/bbs-3.17-bioc/R/include/R_ext/RS.h:77:25: note: in definition of macro ‘F77_CALL’
   77 | # define F77_CALL(x)    x ## _
      |                         ^
/home/biocbuild/bbs-3.17-bioc/R/include/R_ext/BLAS.h:107:10: note: declared here
  107 | F77_NAME(dgemv)(const char *trans, const int *m, const int *n,
      |          ^~~~~
/home/biocbuild/bbs-3.17-bioc/R/include/R_ext/RS.h:77:25: note: in definition of macro ‘F77_CALL’
   77 | # define F77_CALL(x)    x ## _
      |                         ^
/home/biocbuild/bbs-3.17-bioc/R/include/R_ext/BLAS.h:107:1: note: in expansion of macro ‘F77_NAME’
  107 | F77_NAME(dgemv)(const char *trans, const int *m, const int *n,
      | ^~~~~~~~
iClusterBayes.c:803:16: error: too few arguments to function ‘dgemv_’
  803 |       F77_CALL(dgemv)(transN,n,&k1,&ONE,C1Z,n,beta_p,&incx,&ZERO,Zbeta_p,&incy);
      |                ^~~~~
/home/biocbuild/bbs-3.17-bioc/R/include/R_ext/RS.h:77:25: note: in definition of macro ‘F77_CALL’
   77 | # define F77_CALL(x)    x ## _
      |                         ^
/home/biocbuild/bbs-3.17-bioc/R/include/R_ext/BLAS.h:107:10: note: declared here
  107 | F77_NAME(dgemv)(const char *trans, const int *m, const int *n,
      |          ^~~~~
/home/biocbuild/bbs-3.17-bioc/R/include/R_ext/RS.h:77:25: note: in definition of macro ‘F77_CALL’
   77 | # define F77_CALL(x)    x ## _
      |                         ^
/home/biocbuild/bbs-3.17-bioc/R/include/R_ext/BLAS.h:107:1: note: in expansion of macro ‘F77_NAME’
  107 | F77_NAME(dgemv)(const char *trans, const int *m, const int *n,
      | ^~~~~~~~
iClusterBayes.c:827:16: error: too few arguments to function ‘dgemv_’
  827 |       F77_CALL(dgemv)(transN,&k1,&k1,&ONE,invSigma0,&k1,tempab,&incx, &ZERO,invSigmaBeta0, &incy);
      |                ^~~~~
/home/biocbuild/bbs-3.17-bioc/R/include/R_ext/RS.h:77:25: note: in definition of macro ‘F77_CALL’
   77 | # define F77_CALL(x)    x ## _
      |                         ^
/home/biocbuild/bbs-3.17-bioc/R/include/R_ext/BLAS.h:107:10: note: declared here
  107 | F77_NAME(dgemv)(const char *trans, const int *m, const int *n,
      |          ^~~~~
/home/biocbuild/bbs-3.17-bioc/R/include/R_ext/RS.h:77:25: note: in definition of macro ‘F77_CALL’
   77 | # define F77_CALL(x)    x ## _
      |                         ^
/home/biocbuild/bbs-3.17-bioc/R/include/R_ext/BLAS.h:107:1: note: in expansion of macro ‘F77_NAME’
  107 | F77_NAME(dgemv)(const char *trans, const int *m, const int *n,
      | ^~~~~~~~
iClusterBayes.c:831:16: error: too few arguments to function ‘dgemv_’
  831 |       F77_CALL(dgemv)(transN,&k1,&k1,&ONE,invSigma0,&k1,tempab_p,&incx, &ZERO,invSigmaBeta0, &incy);
      |                ^~~~~
/home/biocbuild/bbs-3.17-bioc/R/include/R_ext/RS.h:77:25: note: in definition of macro ‘F77_CALL’
   77 | # define F77_CALL(x)    x ## _
      |                         ^
/home/biocbuild/bbs-3.17-bioc/R/include/R_ext/BLAS.h:107:10: note: declared here
  107 | F77_NAME(dgemv)(const char *trans, const int *m, const int *n,
      |          ^~~~~
/home/biocbuild/bbs-3.17-bioc/R/include/R_ext/RS.h:77:25: note: in definition of macro ‘F77_CALL’
   77 | # define F77_CALL(x)    x ## _
      |                         ^
/home/biocbuild/bbs-3.17-bioc/R/include/R_ext/BLAS.h:107:1: note: in expansion of macro ‘F77_NAME’
  107 | F77_NAME(dgemv)(const char *trans, const int *m, const int *n,
      | ^~~~~~~~
iClusterBayes.c: In function ‘mcmcBayes’:
iClusterBayes.c:1212:28: warning: variable ‘Zdraw’ set but not used [-Wunused-but-set-variable]
 1212 |   int i,j,h,n,k,ID,Zburnin,Zdraw,ndt,nk,thin,nthin,remainder,ty0,p0,ty1,p1,ty2,p2,ty3,p3,ty4,p4,ty5,p5,betaBurnin,betaDraw,p0k,p1k,p2k,p3k,p4k,p5k;
      |                            ^~~~~
iClusterBayes.c:1212:20: warning: variable ‘Zburnin’ set but not used [-Wunused-but-set-variable]
 1212 |   int i,j,h,n,k,ID,Zburnin,Zdraw,ndt,nk,thin,nthin,remainder,ty0,p0,ty1,p1,ty2,p2,ty3,p3,ty4,p4,ty5,p5,betaBurnin,betaDraw,p0k,p1k,p2k,p3k,p4k,p5k;
      |                    ^~~~~~~
make: *** [/home/biocbuild/bbs-3.17-bioc/R/etc/Makeconf:191: iClusterBayes.o] Error 1
ERROR: compilation failed for package ‘iClusterPlus’
* removing ‘/home/biocbuild/bbs-3.17-bioc/R/library/iClusterPlus’

Basilisk.build fails due to old (?!) version of conda

https://yikun.github.io/bioconductor-0301/report/basilisk/kunpeng1-buildsrc.html

R CMD build basilisk fails with:

==> WARNING: A newer version of conda exists. <==
  current version: 4.12.0
  latest version: 23.1.0

Please update conda by running

    $ conda update -n base -c defaults conda


Quitting from lines 294-313 (motivation.Rmd) 
Error: processing vignette 'motivation.Rmd' failed with diagnostics:
one node produced an error: '/tmp/RtmpCFB0iC/Rbuild65fce678e0ba4/basilisk/vignettes/basilisk-vignette-test2/bin/python' was not built with a shared library.
reticulate can only bind to copies of Python built with '--enable-shared'.
--- failed re-building ‘motivation.Rmd’

SUMMARY: processing the following file failed:
  ‘motivation.Rmd’

Error: Vignette re-building failed.

NetPathMiner.install

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD INSTALL NetPathMiner
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.17-bioc/R/library’
* installing *source* package ‘NetPathMiner’ ...
** using staged installation
'config' variable 'CPP' is defunct
checking for gcc... gcc
checking whether the C compiler works... yes
checking for C compiler default output file name... a.out
checking for suffix of executables... 
checking whether we are cross compiling... no
checking for suffix of object files... o
checking whether we are using the GNU C compiler... yes
checking whether gcc accepts -g... yes
checking for gcc option to accept ISO C89... none needed
checking how to run the C preprocessor... gcc -E
checking for xmlParseFile in -lxml2... yes
checking for readSBML in -lsbml... yes
untarring boost include tree...
libSBML found, finding configuration...
pkg-config tool found
libsbml.pc found. Using pkg-config to extract it.
checking for xml2-config... /usr/bin/xml2-config
configure: creating ./config.status
config.status: creating src/Makevars
** libs
using C compiler: ‘gcc (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0’
using C++ compiler: ‘g++ (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0’
g++ -std=gnu++14  -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I. -I/usr/local/include -DHAVE_XML -I/usr/include/libxml2 -DHAVE_SBML -I/usr/include/libxml2  -I/usr/local/include    -fPIC  -g -O2  -Wall  -c PathRanker.cpp -o PathRanker.o
In file included from ./boost/mpl/aux_/na_assert.hpp:23,
                 from ./boost/mpl/arg.hpp:25,
                 from ./boost/mpl/placeholders.hpp:24,
                 from ./boost/iterator/iterator_categories.hpp:17,
                 from ./boost/graph/graph_traits.hpp:25,
                 from ./boost/graph/graph_utility.hpp:29,
                 from PathRanker.cpp:27:
./boost/mpl/assert.hpp:187:21: warning: unnecessary parentheses in declaration of ‘assert_arg’ [-Wparentheses]
  187 | failed ************ (Pred::************
      |                     ^~~~~~~~~~~~~~~~~~~
  188 |       assert_arg( void (*)(Pred), typename assert_arg_pred<Pred>::type )
      |       ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
  189 |     );
      |     ~                
./boost/mpl/assert.hpp:187:21: note: remove parentheses
  187 | failed ************ (Pred::************
      |                     ^~~~~~~~~~~~~~~~~~~
      |                     -
  188 |       assert_arg( void (*)(Pred), typename assert_arg_pred<Pred>::type )
      |       ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
  189 |     );
      |     ~                
      |     -
./boost/mpl/assert.hpp:192:21: warning: unnecessary parentheses in declaration of ‘assert_not_arg’ [-Wparentheses]
  192 | failed ************ (boost::mpl::not_<Pred>::************
      |                     ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
  193 |       assert_not_arg( void (*)(Pred), typename assert_arg_pred_not<Pred>::type )
      |       ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
  194 |     );
      |     ~                
./boost/mpl/assert.hpp:192:21: note: remove parentheses
  192 | failed ************ (boost::mpl::not_<Pred>::************
      |                     ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
      |                     -
  193 |       assert_not_arg( void (*)(Pred), typename assert_arg_pred_not<Pred>::type )
      |       ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
  194 |     );
      |     ~                
      |     -
In file included from ./boost/smart_ptr/detail/shared_count.hpp:30,
                 from ./boost/smart_ptr/shared_ptr.hpp:32,
                 from ./boost/shared_ptr.hpp:17,
                 from ./boost/property_map/vector_property_map.hpp:14,
                 from ./boost/property_map/property_map.hpp:844,
                 from ./boost/graph/properties.hpp:19,
                 from ./boost/graph/graph_utility.hpp:30,
                 from PathRanker.cpp:27:
./boost/smart_ptr/detail/sp_counted_impl.hpp:81:41: error: ‘boost::detail::sp_typeinfo’ has not been declared
   81 |     virtual void * get_deleter( detail::sp_typeinfo const & )
      |                                         ^~~~~~~~~~~
./boost/smart_ptr/detail/sp_counted_impl.hpp:156:41: error: ‘boost::detail::sp_typeinfo’ has not been declared
  156 |     virtual void * get_deleter( detail::sp_typeinfo const & ti )
      |                                         ^~~~~~~~~~~
./boost/smart_ptr/detail/sp_counted_impl.hpp: In member function ‘virtual void* boost::detail::sp_counted_impl_pd<P, D>::get_deleter(const int&)’:
./boost/smart_ptr/detail/sp_counted_impl.hpp:158:39: error: expected primary-expression before ‘)’ token
  158 |         return ti == BOOST_SP_TYPEID(D)? &reinterpret_cast<char&>( del ): 0;
      |                                       ^
./boost/smart_ptr/detail/sp_counted_impl.hpp:158:22: error: there are no arguments to ‘BOOST_SP_TYPEID’ that depend on a template parameter, so a declaration of ‘BOOST_SP_TYPEID’ must be available [-fpermissive]
  158 |         return ti == BOOST_SP_TYPEID(D)? &reinterpret_cast<char&>( del ): 0;
      |                      ^~~~~~~~~~~~~~~
./boost/smart_ptr/detail/sp_counted_impl.hpp:158:22: note: (if you use ‘-fpermissive’, G++ will accept your code, but allowing the use of an undeclared name is deprecated)
./boost/smart_ptr/detail/sp_counted_impl.hpp: At global scope:
./boost/smart_ptr/detail/sp_counted_impl.hpp:235:41: error: ‘boost::detail::sp_typeinfo’ has not been declared
  235 |     virtual void * get_deleter( detail::sp_typeinfo const & ti )
      |                                         ^~~~~~~~~~~
./boost/smart_ptr/detail/sp_counted_impl.hpp: In member function ‘virtual void* boost::detail::sp_counted_impl_pda<P, D, A>::get_deleter(const int&)’:
./boost/smart_ptr/detail/sp_counted_impl.hpp:237:41: error: expected primary-expression before ‘)’ token
  237 |         return ti == BOOST_SP_TYPEID( D )? &reinterpret_cast<char&>( d_ ): 0;
      |                                         ^
./boost/smart_ptr/detail/sp_counted_impl.hpp:237:22: error: there are no arguments to ‘BOOST_SP_TYPEID’ that depend on a template parameter, so a declaration of ‘BOOST_SP_TYPEID’ must be available [-fpermissive]
  237 |         return ti == BOOST_SP_TYPEID( D )? &reinterpret_cast<char&>( d_ ): 0;
      |                      ^~~~~~~~~~~~~~~
In file included from ./boost/smart_ptr/shared_ptr.hpp:32,
                 from ./boost/shared_ptr.hpp:17,
                 from ./boost/property_map/vector_property_map.hpp:14,
                 from ./boost/property_map/property_map.hpp:844,
                 from ./boost/graph/properties.hpp:19,
                 from ./boost/graph/graph_utility.hpp:30,
                 from PathRanker.cpp:27:
./boost/smart_ptr/detail/shared_count.hpp: At global scope:
./boost/smart_ptr/detail/shared_count.hpp:446:25: error: ‘sp_typeinfo’ has not been declared
  446 |     void * get_deleter( sp_typeinfo const & ti ) const
      |                         ^~~~~~~~~~~
./boost/smart_ptr/detail/shared_count.hpp: In member function ‘void* boost::detail::shared_count::get_deleter(const int&) const’:
./boost/smart_ptr/detail/shared_count.hpp:448:39: error: cannot convert ‘const int’ to ‘const sp_typeinfo_&’ {aka ‘const std::type_info&’}
  448 |         return pi_? pi_->get_deleter( ti ): 0;
      |                                       ^~
      |                                       |
      |                                       const int
In file included from ./boost/smart_ptr/detail/sp_counted_base.hpp:60,
                 from ./boost/smart_ptr/detail/shared_count.hpp:29,
                 from ./boost/smart_ptr/shared_ptr.hpp:32,
                 from ./boost/shared_ptr.hpp:17,
                 from ./boost/property_map/vector_property_map.hpp:14,
                 from ./boost/property_map/property_map.hpp:844,
                 from ./boost/graph/properties.hpp:19,
                 from ./boost/graph/graph_utility.hpp:30,
                 from PathRanker.cpp:27:
/usr/include/boost/smart_ptr/detail/sp_counted_base_sync.hpp:119:54: note:   initializing argument 1 of ‘virtual void* boost::detail::sp_counted_base::get_deleter(const sp_typeinfo_&)’
  119 |     virtual void * get_deleter( sp_typeinfo_ const & ti ) = 0;
      |                                 ~~~~~~~~~~~~~~~~~~~~~^~
In file included from ./boost/shared_ptr.hpp:17,
                 from ./boost/property_map/vector_property_map.hpp:14,
                 from ./boost/property_map/property_map.hpp:844,
                 from ./boost/graph/properties.hpp:19,
                 from ./boost/graph/graph_utility.hpp:30,
                 from PathRanker.cpp:27:
./boost/smart_ptr/shared_ptr.hpp: At global scope:
./boost/smart_ptr/shared_ptr.hpp:700:50: error: ‘boost::detail::sp_typeinfo’ has not been declared
  700 |     void * _internal_get_deleter( boost::detail::sp_typeinfo const & ti ) const BOOST_NOEXCEPT
      |                                                  ^~~~~~~~~~~
In file included from ./boost/shared_ptr.hpp:17,
                 from ./boost/property_map/vector_property_map.hpp:14,
                 from ./boost/property_map/property_map.hpp:844,
                 from ./boost/graph/properties.hpp:19,
                 from ./boost/graph/graph_utility.hpp:30,
                 from PathRanker.cpp:27:
./boost/smart_ptr/shared_ptr.hpp: In function ‘D* boost::detail::basic_get_deleter(const boost::shared_ptr<U>&)’:
./boost/smart_ptr/shared_ptr.hpp:892:71: error: expected primary-expression before ‘)’ token
  892 |     return static_cast<D *>( p._internal_get_deleter(BOOST_SP_TYPEID(D)) );
      |                                                                       ^
./boost/smart_ptr/shared_ptr.hpp:892:54: error: there are no arguments to ‘BOOST_SP_TYPEID’ that depend on a template parameter, so a declaration of ‘BOOST_SP_TYPEID’ must be available [-fpermissive]
  892 |     return static_cast<D *>( p._internal_get_deleter(BOOST_SP_TYPEID(D)) );
      |                                                      ^~~~~~~~~~~~~~~
In file included from ./boost/shared_array.hpp:17,
                 from ./boost/graph/detail/d_ary_heap.hpp:20,
                 from ./boost/graph/named_function_params.hpp:24,
                 from ./boost/graph/depth_first_search.hpp:21,
                 from ./boost/graph/graph_utility.hpp:32,
                 from PathRanker.cpp:27:
./boost/smart_ptr/shared_array.hpp: At global scope:
./boost/smart_ptr/shared_array.hpp:223:50: error: ‘boost::detail::sp_typeinfo’ has not been declared
  223 |     void * _internal_get_deleter( boost::detail::sp_typeinfo const & ti ) const
      |                                                  ^~~~~~~~~~~
./boost/smart_ptr/shared_array.hpp: In function ‘D* boost::get_deleter(const boost::shared_array<T>&)’:
./boost/smart_ptr/shared_array.hpp:283:74: error: expected primary-expression before ‘)’ token
  283 |     return static_cast< D * >( p._internal_get_deleter( BOOST_SP_TYPEID(D) ) );
      |                                                                          ^
./boost/smart_ptr/shared_array.hpp:283:57: error: there are no arguments to ‘BOOST_SP_TYPEID’ that depend on a template parameter, so a declaration of ‘BOOST_SP_TYPEID’ must be available [-fpermissive]
  283 |     return static_cast< D * >( p._internal_get_deleter( BOOST_SP_TYPEID(D) ) );
      |                                                         ^~~~~~~~~~~~~~~
make: *** [/home/biocbuild/bbs-3.17-bioc/R/etc/Makeconf:198: PathRanker.o] Error 1
ERROR: compilation failed for package ‘NetPathMiner’
* removing ‘/home/biocbuild/bbs-3.17-bioc/R/library/NetPathMiner’

https://yikun.github.io/bioconductor-0301/report/NetPathMiner/kunpeng1-install.html

DEqMS.build

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD build --keep-empty-dirs --no-resave-data DEqMS
###
##############################################################################
##############################################################################


* checking for file ‘DEqMS/DESCRIPTION’ ... OK
* preparing ‘DEqMS’:
* checking DESCRIPTION meta-information ... OK
* installing the package to build vignettes
* creating vignettes ... ERROR
--- re-building ‘DEqMS-package-vignette.Rmd’ using rmarkdown
trying URL 'https://ftp.ebi.ac.uk/pride-archive/2016/06/PXD004163/Yan_miR_Protein_table.flatprottable.txt'
Content type 'text/plain; charset=UTF-8' length 3515045 bytes (3.4 MB)
==================================================
downloaded 3.4 MB

trying URL 'https://ftp.ebi.ac.uk/pride-archive/2014/09/PXD000279/proteomebenchmark.zip'
Content type 'application/zip' length 38428469 bytes (36.6 MB)

downloaded 437 KB

Quitting from lines 227-230 (DEqMS-package-vignette.Rmd) 
Error: processing vignette 'DEqMS-package-vignette.Rmd' failed with diagnostics:
download from 'https://ftp.ebi.ac.uk/pride-archive/2014/09/PXD000279/proteomebenchmark.zip' failed
--- failed re-building ‘DEqMS-package-vignette.Rmd’

SUMMARY: processing the following file failed:
  ‘DEqMS-package-vignette.Rmd’

Error: Vignette re-building failed.
Execution halted

bsseq.check

https://yikun.github.io/bioconductor-0301/report/bsseq/kunpeng1-checksrc.html

Build ERROR

xxx=`grep -l "Status: ERROR" /home/biocbuild/public_html/BBS/3.17/bioc/products-in/kunpeng1/buildsrc/* | xargs -L 1 basename | cut -d '-' -f1 | sed "s/.........$//g"`
for i in $xxx
do
    echo $i""  > /tmp/report.txt
    echo "" >> /tmp/report.txt
    echo '```' >> /tmp/report.txt
    cat /home/biocbuild/public_html/BBS/3.17/bioc/products-in/kunpeng1/buildsrc/$i".buildsrc-out.txt" >> /tmp/report.txt
    echo '```' >> /tmp/report.txt
    # hub issue create -F

    if grep -q "not available for package" /tmp/report.txt
    then
        echo 'Skip '$i, due to not available for package `grep "not available for package" /tmp/report.txt`
    else
        echo 'Issue '$i: https://yikun.github.io/bioconductor-0208/report/$i/kunpeng1-buildsrc.html
    fi
done

LowMACA.build

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD build --keep-empty-dirs --no-resave-data LowMACA
###
##############################################################################
##############################################################################


* checking for file ‘LowMACA/DESCRIPTION’ ... OK
* preparing ‘LowMACA’:
* checking DESCRIPTION meta-information ... OK
* installing the package to build vignettes
* creating vignettes ... ERROR
--- re-building ‘LowMACA.Rmd’ using rmarkdown
JobId: clustalo-R20230227-145726-0995-78167370-p1m
FINISHED
Creating result file: /tmp/RtmpuIRBhu/webClustal.out.txt
Creating result file: /tmp/RtmpuIRBhu/webClustal.sequence.txt
Creating result file: /tmp/RtmpuIRBhu/webClustal.aln-clustal.clustal
Creating result file: /tmp/RtmpuIRBhu/webClustal.phylotree.ph
Creating result file: /tmp/RtmpuIRBhu/webClustal.pim.pim
Creating result file: /tmp/RtmpuIRBhu/webClustal.submission.params
Quitting from lines 176-178 (LowMACA.Rmd) 
Error: processing vignette 'LowMACA.Rmd' failed with diagnostics:
Error in the HTTP2 framing layer
--- failed re-building ‘LowMACA.Rmd’

SUMMARY: processing the following file failed:
  ‘LowMACA.Rmd’

Error: Vignette re-building failed.
Execution halted

LEA.install

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD INSTALL LEA
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.17-bioc/R/library’
* installing *source* package ‘LEA’ ...
** using staged installation
** libs
using C compiler: ‘gcc (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0’
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I.  -I/usr/local/include    -fPIC  -g -O2  -Wall -c R_LFMM.c -o R_LFMM.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I.  -I/usr/local/include    -fPIC  -g -O2  -Wall -c R_crossEntropy.c -o R_crossEntropy.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I.  -I/usr/local/include    -fPIC  -g -O2  -Wall -c R_createDataSet.c -o R_createDataSet.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I.  -I/usr/local/include    -fPIC  -g -O2  -Wall -c R_sNMF.c -o R_sNMF.o
In file included from sNMF/sNMF.h:13,
                 from R_sNMF.c:24:
sNMF/../bituint/bituint.h:212:2: error: #error Unsupported architecture
  212 | #error Unsupported architecture
      |  ^~~~~
sNMF/../bituint/bituint.h:223:23: error: unknown type name ‘bituint’; did you mean ‘uint’?
  223 | void init_mat_bituint(bituint ** dat, int N, int Mc, int *Mp);
      |                       ^~~~~~~
      |                       uint
In file included from R_sNMF.c:24:
sNMF/sNMF.h:62:9: error: unknown type name ‘bituint’
   62 |         bituint *X;             /**< @brief the data matrix (of size nxMp) */
      |         ^~~~~~~
sNMF/sNMF.h:63:9: error: unknown type name ‘bituint’
   63 |         bituint *Xi;             /**< @brief the init data matrix (of size nxMpi) */
      |         ^~~~~~~
make: *** [/home/biocbuild/bbs-3.17-bioc/R/etc/Makeconf:191: R_sNMF.o] Error 1
ERROR: compilation failed for package ‘LEA’
* removing ‘/home/biocbuild/bbs-3.17-bioc/R/library/LEA’

Rbec.install

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD INSTALL Rbec
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.17-bioc/R/library’
* installing *source* package ‘Rbec’ ...
** using staged installation
** libs
using C++ compiler: ‘g++ (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0’
g++ -std=gnu++14  -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.17-bioc/R/library/Rcpp/include' -I/usr/local/include    -fPIC  -g -O2  -Wall  -c RcppExports.cpp -o RcppExports.o
In file included from ../inst/include/Rbec.h:7,
                 from RcppExports.cpp:4:
../inst/include/Rbec_RcppExports.h:14:14: warning: ‘void Rbec::{anonymous}::validateSignature(const char*)’ defined but not used [-Wunused-function]
   14 |         void validateSignature(const char* sig) {
      |              ^~~~~~~~~~~~~~~~~
g++ -std=gnu++14  -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.17-bioc/R/library/Rcpp/include' -I/usr/local/include    -fPIC  -g -O2  -Wall  -c kmer_dist.cpp -o kmer_dist.o
kmer_dist.cpp: In function ‘Rcpp::NumericVector kmer_dist(std::vector<std::__cxx11::basic_string<char> >, std::vector<std::__cxx11::basic_string<char> >, int)’:
kmer_dist.cpp:33:16: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare]
   33 |   for(int i=0;i<nseqs;i++) {
      |               ~^~~~~~
g++ -std=gnu++14  -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.17-bioc/R/library/Rcpp/include' -I/usr/local/include    -fPIC  -g -O2  -Wall  -c rcpp_test.cpp -o rcpp_test.o
rcpp_test.cpp:3:10: fatal error: emmintrin.h: No such file or directory
    3 | #include "emmintrin.h"
      |          ^~~~~~~~~~~~~
compilation terminated.
make: *** [/home/biocbuild/bbs-3.17-bioc/R/etc/Makeconf:198: rcpp_test.o] Error 1
ERROR: compilation failed for package ‘Rbec’
* removing ‘/home/biocbuild/bbs-3.17-bioc/R/library/Rbec’

FLAMES.install

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD INSTALL FLAMES
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.17-bioc/R/library’
* installing *source* package ‘FLAMES’ ...
** using staged installation
** libs
using C compiler: ‘gcc (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0’
using C++ compiler: ‘g++ (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0’
using C++17
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.17-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.17-bioc/R/library/Rhtslib/include' -I'/home/biocbuild/bbs-3.17-bioc/R/library/zlibbioc/include' -I/usr/local/include    -fPIC  -g -O2  -Wall -c RcppExports.cpp -o RcppExports.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.17-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.17-bioc/R/library/Rhtslib/include' -I'/home/biocbuild/bbs-3.17-bioc/R/library/zlibbioc/include' -I/usr/local/include    -fPIC  -g -O2  -Wall -c RcppFunctions.cpp -o RcppFunctions.o
In file included from main-functions/../utility/fastq_utils.h:7,
                 from main-functions/match_cell_barcode.h:13,
                 from RcppFunctions.cpp:7:
/home/biocbuild/bbs-3.17-bioc/R/library/Rhtslib/include/htslib/kseq.h:185:19: warning: ‘int kseq_read(kseq_t*)’ defined but not used [-Wunused-function]
  185 |         SCOPE int kseq_read(kseq_t *seq) \
      |                   ^~~~~~~~~
/home/biocbuild/bbs-3.17-bioc/R/library/Rhtslib/include/htslib/kseq.h:185:19: note: in definition of macro ‘__KSEQ_READ’
  185 |         SCOPE int kseq_read(kseq_t *seq) \
      |                   ^~~~~~~~~
/home/biocbuild/bbs-3.17-bioc/R/library/Rhtslib/include/htslib/kseq.h:240:35: note: in expansion of macro ‘KSEQ_INIT2’
  240 | #define KSEQ_INIT(type_t, __read) KSEQ_INIT2(static, type_t, __read)
      |                                   ^~~~~~~~~~
main-functions/../utility/fastq_utils.h:12:1: note: in expansion of macro ‘KSEQ_INIT’
   12 | KSEQ_INIT(gzFile, gzread)
      | ^~~~~~~~~
/home/biocbuild/bbs-3.17-bioc/R/library/Rhtslib/include/htslib/kseq.h:171:20: warning: ‘void kseq_destroy(kseq_t*)’ defined but not used [-Wunused-function]
  171 |         SCOPE void kseq_destroy(kseq_t *ks)                                                                     \
      |                    ^~~~~~~~~~~~
/home/biocbuild/bbs-3.17-bioc/R/library/Rhtslib/include/htslib/kseq.h:171:20: note: in definition of macro ‘__KSEQ_BASIC’
  171 |         SCOPE void kseq_destroy(kseq_t *ks)                                                                     \
      |                    ^~~~~~~~~~~~
/home/biocbuild/bbs-3.17-bioc/R/library/Rhtslib/include/htslib/kseq.h:240:35: note: in expansion of macro ‘KSEQ_INIT2’
  240 | #define KSEQ_INIT(type_t, __read) KSEQ_INIT2(static, type_t, __read)
      |                                   ^~~~~~~~~~
main-functions/../utility/fastq_utils.h:12:1: note: in expansion of macro ‘KSEQ_INIT’
   12 | KSEQ_INIT(gzFile, gzread)
      | ^~~~~~~~~
/home/biocbuild/bbs-3.17-bioc/R/library/Rhtslib/include/htslib/kseq.h:165:23: warning: ‘kseq_t* kseq_init(gzFile)’ defined but not used [-Wunused-function]
  165 |         SCOPE kseq_t *kseq_init(type_t fd)                                                                      \
      |                       ^~~~~~~~~
/home/biocbuild/bbs-3.17-bioc/R/library/Rhtslib/include/htslib/kseq.h:165:23: note: in definition of macro ‘__KSEQ_BASIC’
  165 |         SCOPE kseq_t *kseq_init(type_t fd)                                                                      \
      |                       ^~~~~~~~~
/home/biocbuild/bbs-3.17-bioc/R/library/Rhtslib/include/htslib/kseq.h:240:35: note: in expansion of macro ‘KSEQ_INIT2’
  240 | #define KSEQ_INIT(type_t, __read) KSEQ_INIT2(static, type_t, __read)
      |                                   ^~~~~~~~~~
main-functions/../utility/fastq_utils.h:12:1: note: in expansion of macro ‘KSEQ_INIT’
   12 | KSEQ_INIT(gzFile, gzread)
      | ^~~~~~~~~
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.17-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.17-bioc/R/library/Rhtslib/include' -I'/home/biocbuild/bbs-3.17-bioc/R/library/zlibbioc/include' -I/usr/local/include    -fPIC  -g -O2  -Wall -c main-functions/match_cell_barcode.cpp -o main-functions/match_cell_barcode.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.17-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.17-bioc/R/library/Rhtslib/include' -I'/home/biocbuild/bbs-3.17-bioc/R/library/zlibbioc/include' -I/usr/local/include    -fPIC  -g -O2  -Wall -c utility/edit_dist.cpp -o utility/edit_dist.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.17-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.17-bioc/R/library/Rhtslib/include' -I'/home/biocbuild/bbs-3.17-bioc/R/library/zlibbioc/include' -I/usr/local/include    -fPIC  -g -O2  -Wall -c utility/fastq_utils.cpp -o utility/fastq_utils.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.17-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.17-bioc/R/library/Rhtslib/include' -I'/home/biocbuild/bbs-3.17-bioc/R/library/zlibbioc/include' -I/usr/local/include    -fPIC  -g -O2  -Wall -c utility/ssw/ssw_cpp.cpp -o utility/ssw/ssw_cpp.o
In file included from utility/ssw/ssw_cpp.cpp:6:
utility/ssw/ssw.h:19:10: fatal error: sse2neon.h: No such file or directory
   19 | #include "sse2neon.h"
      |          ^~~~~~~~~~~~
compilation terminated.
make: *** [/home/biocbuild/bbs-3.17-bioc/R/etc/Makeconf:198: utility/ssw/ssw_cpp.o] Error 1
ERROR: compilation failed for package ‘FLAMES’
* removing ‘/home/biocbuild/bbs-3.17-bioc/R/library/FLAMES’

genbankr.build

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD build --keep-empty-dirs --no-resave-data genbankr
###
##############################################################################
##############################################################################


* checking for file ‘genbankr/DESCRIPTION’ ... OK
* preparing ‘genbankr’:
* checking DESCRIPTION meta-information ... OK
* installing the package to build vignettes
* creating vignettes ... ERROR
--- re-building ‘genbankr.Rmd’ using rmarkdown
Quitting from lines 95-97 (genbankr.Rmd) 
Error: processing vignette 'genbankr.Rmd' failed with diagnostics:
unable to find an inherited method for function 'resource' for signature '"GenBankFile"'
--- failed re-building ‘genbankr.Rmd’

SUMMARY: processing the following file failed:
  ‘genbankr.Rmd’

Error: Vignette re-building failed.
Execution halted

SAIGEgds.install

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD INSTALL SAIGEgds
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.17-bioc/R/library’
* installing *source* package ‘SAIGEgds’ ...
** using staged installation
** libs
using C++ compiler: ‘g++ (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0’
using C++11
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.17-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.17-bioc/R/library/RcppArmadillo/include' -I'/home/biocbuild/bbs-3.17-bioc/R/library/RcppParallel/include' -I/usr/local/include    -fPIC  -g -O2  -Wall -c SPATest.cpp -o SPATest.o
SPATest.cpp:42:15: error: ‘COREARRAY_TARGET_CLONES’ does not name a type
   42 | inline static COREARRAY_TARGET_CLONES
      |               ^~~~~~~~~~~~~~~~~~~~~~~
SPATest.cpp:56:15: error: ‘COREARRAY_TARGET_CLONES’ does not name a type
   56 | inline static COREARRAY_TARGET_CLONES
      |               ^~~~~~~~~~~~~~~~~~~~~~~
SPATest.cpp:71:15: error: ‘COREARRAY_TARGET_CLONES’ does not name a type
   71 | inline static COREARRAY_TARGET_CLONES
      |               ^~~~~~~~~~~~~~~~~~~~~~~
SPATest.cpp:93:9: error: expected initializer before ‘getroot_K1’
   93 |         getroot_K1(const double g_pos, const double g_neg,
      |         ^~~~~~~~~~
SPATest.cpp:140:9: error: expected initializer before ‘getroot_K1_fast’
  140 |         getroot_K1_fast(const double g_pos, const double g_neg, double &root,
      |         ^~~~~~~~~~~~~~~
SPATest.cpp:189:9: error: expected initializer before ‘get_saddle_prob’
  189 |         get_saddle_prob(double t, size_t n_g, const double mu[], const double g[],
      |         ^~~~~~~~~~~~~~~
SPATest.cpp:212:9: error: expected initializer before ‘get_saddle_prob_fast’
  212 |         get_saddle_prob_fast(double t, size_t n_nonzero, const double mu[],
      |         ^~~~~~~~~~~~~~~~~~~~
SPATest.cpp:238:9: error: expected initializer before ‘Saddle_Prob’
  238 |         Saddle_Prob(double q, double m1, double var1, size_t n_g, const double mu[],
      |         ^~~~~~~~~~~
SPATest.cpp:300:9: error: expected initializer before ‘Saddle_Prob_Fast’
  300 |         Saddle_Prob_Fast(double q, double m1, double var1, size_t n_g,
      |         ^~~~~~~~~~~~~~~~
make: *** [/home/biocbuild/bbs-3.17-bioc/R/etc/Makeconf:198: SPATest.o] Error 1
ERROR: compilation failed for package ‘SAIGEgds’
* removing ‘/home/biocbuild/bbs-3.17-bioc/R/library/SAIGEgds’

flowClust.install

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD INSTALL flowClust
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.17-bioc/R/library’
* installing *source* package ‘flowClust’ ...
** using staged installation
configure: Using bundled GSL.
configure: Searching for the compilers specified by R.
checking for gcc... gcc
checking whether the C compiler works... yes
checking for C compiler default output file name... a.out
checking for suffix of executables... 
checking whether we are cross compiling... no
checking for suffix of object files... o
checking whether we are using the GNU C compiler... yes
checking whether gcc accepts -g... yes
checking for gcc option to accept ISO C89... none needed
checking how to run the C preprocessor... gcc -E
untarring gsl...
configure: Preparing to compile GSL.
configure: Configuring bundled GSL.
checking for a BSD-compatible install... /usr/bin/install -c
checking whether build environment is sane... yes
checking for a thread-safe mkdir -p... /usr/bin/mkdir -p
checking for gawk... gawk
checking whether make sets $(MAKE)... yes
checking whether to enable maintainer-specific portions of Makefiles... no
checking whether make sets $(MAKE)... (cached) yes
checking build system type... ./config.guess: unable to guess system type

This script, last modified 2007-05-17, has failed to recognize
the operating system you are using. It is advised that you
download the most up to date version of the config scripts from

  http://savannah.gnu.org/cgi-bin/viewcvs/*checkout*/config/config/config.guess
and
  http://savannah.gnu.org/cgi-bin/viewcvs/*checkout*/config/config/config.sub

If the version you run (./config.guess) is already up to date, please
send the following data and any information you think might be
pertinent to <[email protected]> in order to provide the needed
information to handle your system.

config.guess timestamp = 2007-05-17

uname -m = aarch64
uname -r = 5.15.0-58-generic
uname -s = Linux
uname -v = #64-Ubuntu SMP Thu Jan 5 12:06:43 UTC 2023

/usr/bin/uname -p = aarch64
/bin/uname -X     = 

hostinfo               = 
/bin/universe          = 
/usr/bin/arch -k       = 
/bin/arch              = aarch64
/usr/bin/oslevel       = 
/usr/convex/getsysinfo = 

UNAME_MACHINE = aarch64
UNAME_RELEASE = 5.15.0-58-generic
UNAME_SYSTEM  = Linux
UNAME_VERSION = #64-Ubuntu SMP Thu Jan 5 12:06:43 UTC 2023
configure: error: cannot guess build type; you must specify one
cp: will not overwrite just-created 'gsl/test.h' with 'roots/test.h'
cp: will not overwrite just-created 'gsl/error.h' with 'specfunc/error.h'
cp: will not overwrite just-created 'gsl/view.h' with 'vector/view.h'
make: *** No rule to make target 'install'.  Stop.
cp: cannot create directory '/home/biocbuild/bbs-3.17-bioc/meat/flowClust/src/gslbuild/include': No such file or directory
configure: Using the following compilation and linking flags for flowClust
configure:    PKG_CFLAGS= -I/home/biocbuild/bbs-3.17-bioc/meat/flowClust/src/gslbuild/include
configure:    PKG_LIBS=
configure:    FLOWCLUST_DEFS=-DGSL_MAJOR=1 -DGSL_MINOR=13 -DGSL_STATIC
configure: Compiling using GSL version: '1.13.0'.
configure: Using bundled GSL: 'yes'.
configure: creating ./config.status
config.status: creating src/Makevars
** libs
using C compiler: ‘gcc (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0’
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG   -I/usr/local/include   -I/home/biocbuild/bbs-3.17-bioc/meat/flowClust/src/gslbuild/include -DGSL_MAJOR=1 -DGSL_MINOR=13 -DGSL_STATIC -fPIC  -g -O2  -Wall -c BoxCox.c -o BoxCox.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG   -I/usr/local/include   -I/home/biocbuild/bbs-3.17-bioc/meat/flowClust/src/gslbuild/include -DGSL_MAJOR=1 -DGSL_MINOR=13 -DGSL_STATIC -fPIC  -g -O2  -Wall -c BoxCoxPriors.c -o BoxCoxPriors.o
BoxCoxPriors.c: In function ‘BoxCoxGradientPriors’:
BoxCoxPriors.c:57:23: warning: unused variable ‘rowZ’ [-Wunused-variable]
   57 |         rowPrecision, rowZ, rowLambda0;
      |                       ^~~~
BoxCoxPriors.c:33:31: warning: unused variable ‘kappa0’ [-Wunused-variable]
   33 |         double *nu0 = p->nu0, kappa0 = p->kappa0;
      |                               ^~~~~~
BoxCoxPriors.c:32:14: warning: unused variable ‘itersolve’ [-Wunused-variable]
   32 |         int *itersolve = p->itersolve;
      |              ^~~~~~~~~
BoxCoxPriors.c:31:13: warning: unused variable ‘iter’ [-Wunused-variable]
   31 |         int iter = p->iter;
      |             ^~~~
BoxCoxPriors.c:28:13: warning: unused variable ‘model’ [-Wunused-variable]
   28 |         int model = *p->model;
      |             ^~~~~
BoxCoxPriors.c:23:21: warning: unused variable ‘SumZlogY’ [-Wunused-variable]
   23 |         gsl_vector *SumZlogY = p->SumZlogY;
      |                     ^~~~~~~~
BoxCoxPriors.c:15:21: warning: unused variable ‘Precision’ [-Wunused-variable]
   15 |         gsl_matrix *Precision = p->Precision; // will be updated
      |                     ^~~~~~~~~
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG   -I/usr/local/include   -I/home/biocbuild/bbs-3.17-bioc/meat/flowClust/src/gslbuild/include -DGSL_MAJOR=1 -DGSL_MINOR=13 -DGSL_STATIC -fPIC  -g -O2  -Wall -c Nu.c -o Nu.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG   -I/usr/local/include   -I/home/biocbuild/bbs-3.17-bioc/meat/flowClust/src/gslbuild/include -DGSL_MAJOR=1 -DGSL_MINOR=13 -DGSL_STATIC -fPIC  -g -O2  -Wall -c flowClust.c -o flowClust.o
flowClust.c: In function ‘flowClust’:
flowClust.c:48:9: warning: unused variable ‘matrixZUY2’ [-Wunused-variable]
   48 |         matrixZUY2;
      |         ^~~~~~~~~~
flowClust.c:46:55: warning: unused variable ‘subRowZUY2’ [-Wunused-variable]
   46 |         rowYTransS, rowZUY, subRowZUY, rowZ, rowZUY2, subRowZUY2;
      |                                                       ^~~~~~~~~~
flowClust.c:46:46: warning: unused variable ‘rowZUY2’ [-Wunused-variable]
   46 |         rowYTransS, rowZUY, subRowZUY, rowZ, rowZUY2, subRowZUY2;
      |                                              ^~~~~~~
flowClust.c: In function ‘ECMUpdateSigmaG2’:
flowClust.c:1111:13: warning: unused variable ‘i’ [-Wunused-variable]
 1111 |         int i=0;
      |             ^
At top level:
flowClust.c:10:27: warning: ‘CEntries’ defined but not used [-Wunused-const-variable=]
   10 | static const R_CMethodDef CEntries[] = { { "flowClust", (DL_FUNC) & flowClust,
      |                           ^~~~~~~~
flowClust.c: In function ‘flowClust’:
flowClust.c:702:34: warning: ‘s3’ may be used uninitialized in this function [-Wmaybe-uninitialized]
  702 |                         status = gsl_min_fminimizer_set(s3, &F3, *nu, *nuLow, *nuUp);
      |                                  ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
flowClust.c:647:57: warning: ‘s2’ may be used uninitialized in this function [-Wmaybe-uninitialized]
  647 |                                                 nu_hi = gsl_root_fsolver_x_upper(s2);
      |                                                         ^~~~~~~~~~~~~~~~~~~~~~~~~~~~
flowClust.c:348:56: warning: ‘s’ may be used uninitialized in this function [-Wmaybe-uninitialized]
  348 |                                                 x_hi = gsl_root_fsolver_x_upper(s);
      |                                                        ^~~~~~~~~~~~~~~~~~~~~~~~~~~
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG   -I/usr/local/include   -I/home/biocbuild/bbs-3.17-bioc/meat/flowClust/src/gslbuild/include -DGSL_MAJOR=1 -DGSL_MINOR=13 -DGSL_STATIC -fPIC  -g -O2  -Wall -c flowClustGaussian.c -o flowClustGaussian.o
flowClustGaussian.c: In function ‘flowClustGaussian’:
flowClustGaussian.c:207:56: warning: ‘s’ may be used uninitialized in this function [-Wmaybe-uninitialized]
  207 |                                                 x_hi = gsl_root_fsolver_x_upper(s);
      |                                                        ^~~~~~~~~~~~~~~~~~~~~~~~~~~
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG   -I/usr/local/include   -I/home/biocbuild/bbs-3.17-bioc/meat/flowClust/src/gslbuild/include -DGSL_MAJOR=1 -DGSL_MINOR=13 -DGSL_STATIC -fPIC  -g -O2  -Wall -c ranMVNT.c -o ranMVNT.o
gcc -shared -L/home/biocbuild/bbs-3.17-bioc/R/lib -L/usr/local/lib -o flowClust.so BoxCox.o BoxCoxPriors.o Nu.o flowClust.o flowClustGaussian.o ranMVNT.o -L/home/biocbuild/bbs-3.17-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.17-bioc/R/library/00LOCK-flowClust/00new/flowClust/libs
** R
** data
** inst
** byte-compile and prepare package for lazy loading
Creating a new generic function for ‘Map’ in package ‘flowClust’
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
Error: package or namespace load failed for ‘flowClust’ in dyn.load(file, DLLpath = DLLpath, ...):
 unable to load shared object '/home/biocbuild/bbs-3.17-bioc/R/library/00LOCK-flowClust/00new/flowClust/libs/flowClust.so':
  /home/biocbuild/bbs-3.17-bioc/R/library/00LOCK-flowClust/00new/flowClust/libs/flowClust.so: undefined symbol: gsl_min_fminimizer_brent
Error: loading failed
Execution halted
ERROR: loading failed
* removing ‘/home/biocbuild/bbs-3.17-bioc/R/library/flowClust’

maftools.build

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD build --keep-empty-dirs --no-resave-data maftools
###
##############################################################################
##############################################################################


* checking for file ‘maftools/DESCRIPTION’ ... OK
* preparing ‘maftools’:
* checking DESCRIPTION meta-information ... OK
* cleaning src
* installing the package to build vignettes
* creating vignettes ... ERROR
--- re-building ‘cancer_hotspots.Rmd’ using rmarkdown
--- finished re-building ‘cancer_hotspots.Rmd’

--- re-building ‘cnv_analysis.Rmd’ using rmarkdown
Could not fetch https://user-images.githubusercontent.com/8164062/160853684-85021668-a515-4e3d-8ccb-dddf992098d9.png
HttpExceptionRequest Request {
  host                 = "user-images.githubusercontent.com"
  port                 = 443
  secure               = True
  requestHeaders       = []
  path                 = "/8164062/160853684-85021668-a515-4e3d-8ccb-dddf992098d9.png"
  queryString          = ""
  method               = "GET"
  proxy                = Nothing
  rawBody              = False
  redirectCount        = 10
  responseTimeout      = ResponseTimeoutDefault
  requestVersion       = HTTP/1.1
}
 ResponseTimeout
Error: processing vignette 'cnv_analysis.Rmd' failed with diagnostics:
pandoc document conversion failed with error 61
--- failed re-building ‘cnv_analysis.Rmd’

--- re-building ‘maftools.Rmd’ using rmarkdown
Warning in doTryCatch(return(expr), name, parentenv, handler) :
  "axes" is not a graphical parameter
Warning in doTryCatch(return(expr), name, parentenv, handler) :
  "axes" is not a graphical parameter
Warning in doTryCatch(return(expr), name, parentenv, handler) :
  "axes" is not a graphical parameter
--- finished re-building ‘maftools.Rmd’

--- re-building ‘oncoplots.Rmd’ using rmarkdown
--- finished re-building ‘oncoplots.Rmd’

SUMMARY: processing the following file failed:
  ‘cnv_analysis.Rmd’

Error: Vignette re-building failed.
Execution halted

CiteFuse.install

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD INSTALL CiteFuse
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.17-bioc/R/library’
* installing *source* package ‘CiteFuse’ ...
** using staged installation
** R
** data
** inst
** byte-compile and prepare package for lazy loading
Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) : 
  there is no package called ‘propr’
Calls: <Anonymous> ... loadNamespace -> withRestarts -> withOneRestart -> doWithOneRestart
Execution halted
ERROR: lazy loading failed for package ‘CiteFuse’
* removing ‘/home/biocbuild/bbs-3.17-bioc/R/library/CiteFuse’

GeneAccord.build

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD build --keep-empty-dirs --no-resave-data GeneAccord
###
##############################################################################
##############################################################################


* checking for file ‘GeneAccord/DESCRIPTION’ ... OK
* preparing ‘GeneAccord’:
* checking DESCRIPTION meta-information ... OK
* installing the package to build vignettes
* creating vignettes ... ERROR
--- re-building ‘GeneAccord.Rmd’ using rmarkdown
Quitting from lines 225-228 (GeneAccord.Rmd) 
Error: processing vignette 'GeneAccord.Rmd' failed with diagnostics:
'length = 2' in coercion to 'logical(1)'
--- failed re-building ‘GeneAccord.Rmd’

SUMMARY: processing the following file failed:
  ‘GeneAccord.Rmd’

Error: Vignette re-building failed.
Execution halted

msa.install

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD INSTALL msa
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.17-bioc/R/library’
* installing *source* package ‘msa’ ...
** using staged installation
** libs

make[1]: Leaving directory '/home/biocbuild/bbs-3.17-bioc/meat/msa/src/Muscle'
----------------------------------------
---------------- MUSCLE ----------------
----------------------------------------
--------- Compilation finished ---------
----------------------------------------
make --file=msaMakefile --directory=ClustalW
make[1]: Entering directory '/home/biocbuild/bbs-3.17-bioc/meat/msa/src/ClustalW'
./configure; \
cd src; \
export PKG_CXXFLAGS="-DHAVE_CONFIG_H -I.  -Wno-deprecated -Wno-unused-result"; \
/home/biocbuild/bbs-3.17-bioc/R/bin/R CMD SHLIB -o libClustalW.so pairwise/FullPairwiseAlign.cpp pairwise/FastPairwiseAlign.cpp fileInput/MSFFileParser.cpp fileInput/FileReader.cpp fileInput/PIRFileParser.cpp fileInput/RSFFileParser.cpp fileInput/GDEFileParser.cpp fileInput/InFileStream.cpp fileInput/ClustalFileParser.cpp fileInput/PearsonFileParser.cpp fileInput/FileParser.cpp fileInput/EMBLFileParser.cpp tree/UPGMA/RootedClusterTree.cpp tree/UPGMA/UPGMAAlgorithm.cpp tree/UPGMA/Node.cpp tree/UPGMA/RootedGuideTree.cpp tree/UPGMA/RootedTreeOutput.cpp tree/Tree.cpp tree/ClusterTree.cpp tree/TreeInterface.cpp tree/UnRootedClusterTree.cpp tree/ClusterTreeOutput.cpp tree/RandomGenerator.cpp tree/NJTree.cpp tree/AlignmentSteps.cpp interface/CommandLineParser.cpp substitutionMatrix/SubMatrix.cpp multipleAlign/Iteration.cpp multipleAlign/MSA.cpp multipleAlign/MyersMillerProfileAlign.cpp multipleAlign/ProfileStandard.cpp multipleAlign/ProfileWithSub.cpp multipleAlign/ProfileBase.cpp multipleAlign/LowScoreSegProfile.cpp general/OutputFile.cpp general/UserParameters.cpp general/Utility.cpp general/InvalidCombination.cpp general/DebugLog.cpp general/ClustalWResources.cpp general/VectorOutOfRange.cpp general/SymMatrix.cpp general/Stats.cpp Help.cpp alignment/Alignment.cpp alignment/AlignmentOutput.cpp alignment/ObjectiveScore.cpp alignment/Sequence.cpp Clustal.cpp RClustalWMain.cpp RClustalW.cpp && \
ar rcs libClustalW.a pairwise/FullPairwiseAlign.o pairwise/FastPairwiseAlign.o fileInput/MSFFileParser.o fileInput/FileReader.o fileInput/PIRFileParser.o fileInput/RSFFileParser.o fileInput/GDEFileParser.o fileInput/InFileStream.o fileInput/ClustalFileParser.o fileInput/PearsonFileParser.o fileInput/FileParser.o fileInput/EMBLFileParser.o tree/UPGMA/RootedClusterTree.o tree/UPGMA/UPGMAAlgorithm.o tree/UPGMA/Node.o tree/UPGMA/RootedGuideTree.o tree/UPGMA/RootedTreeOutput.o tree/Tree.o tree/ClusterTree.o tree/TreeInterface.o tree/UnRootedClusterTree.o tree/ClusterTreeOutput.o tree/RandomGenerator.o tree/NJTree.o tree/AlignmentSteps.o interface/CommandLineParser.o substitutionMatrix/SubMatrix.o multipleAlign/Iteration.o multipleAlign/MSA.o multipleAlign/MyersMillerProfileAlign.o multipleAlign/ProfileStandard.o multipleAlign/ProfileWithSub.o multipleAlign/ProfileBase.o multipleAlign/LowScoreSegProfile.o general/OutputFile.o general/UserParameters.o general/Utility.o general/InvalidCombination.o general/DebugLog.o general/ClustalWResources.o general/VectorOutOfRange.o general/SymMatrix.o general/Stats.o Help.o alignment/Alignment.o alignment/AlignmentOutput.o alignment/ObjectiveScore.o alignment/Sequence.o Clustal.o RClustalWMain.o RClustalW.o && \
cp libClustalW.a ../../
checking build system type... ./config.guess: unable to guess system type

This script, last modified 2009-06-10, has failed to recognize
the operating system you are using. It is advised that you
download the most up to date version of the config scripts from

  http://git.savannah.gnu.org/gitweb/?p=config.git;a=blob_plain;f=config.guess;hb=HEAD
and
  http://git.savannah.gnu.org/gitweb/?p=config.git;a=blob_plain;f=config.sub;hb=HEAD

If the version you run (./config.guess) is already up to date, please
send the following data and any information you think might be
pertinent to <[email protected]> in order to provide the needed
information to handle your system.

config.guess timestamp = 2009-06-10

uname -m = aarch64
uname -r = 5.15.0-58-generic
uname -s = Linux
uname -v = #64-Ubuntu SMP Thu Jan 5 12:06:43 UTC 2023

/usr/bin/uname -p = aarch64
/bin/uname -X     =

hostinfo               =
/bin/universe          =
/usr/bin/arch -k       =
/bin/arch              = aarch64
/usr/bin/oslevel       =
/usr/convex/getsysinfo =

UNAME_MACHINE = aarch64
UNAME_RELEASE = 5.15.0-58-generic
UNAME_SYSTEM  = Linux
UNAME_VERSION = #64-Ubuntu SMP Thu Jan 5 12:06:43 UTC 2023
configure: error: cannot guess build type; you must specify one
using C++ compiler: ‘g++ (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0’
make[2]: Entering directory '/home/biocbuild/bbs-3.17-bioc/meat/msa/src/ClustalW/src'
g++ -std=gnu++14  -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.17-bioc/R/library/Rcpp/include' -I/usr/local/include   -DHAVE_CONFIG_H -I.  -Wno-deprecated -Wno-unused-result -fPIC  -g -O2  -Wall  -c pairwise/FullPairwiseAlign.cpp -o pairwise/FullPairwiseAlign.o
pairwise/FullPairwiseAlign.cpp:7:14: fatal error: config.h: No such file or directory
    7 |     #include "config.h"
      |              ^~~~~~~~~~
compilation terminated.
make[2]: *** [/home/biocbuild/bbs-3.17-bioc/R/etc/Makeconf:198: pairwise/FullPairwiseAlign.o] Error 1
make[2]: Leaving directory '/home/biocbuild/bbs-3.17-bioc/meat/msa/src/ClustalW/src'
make[1]: *** [msaMakefile:8: clustalw] Error 1
make[1]: Leaving directory '/home/biocbuild/bbs-3.17-bioc/meat/msa/src/ClustalW'
make: *** [Makevars:28: build_clustalw] Error 2
ERROR: compilation failed for package ‘msa’
* removing ‘/home/biocbuild/bbs-3.17-bioc/R/library/msa’

Rbowtie2.install

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD INSTALL Rbowtie2
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.17-bioc/R/library’
* installing *source* package ‘Rbowtie2’ ...
** using staged installation
** libs
mkdir -p ../inst
(cd	adapterremoval && (make CXX="g++ -std=gnu++11" -f Makefile))
make[1]: Entering directory '/home/biocbuild/bbs-3.17-bioc/meat/Rbowtie2/src/adapterremoval'
g++ -std=gnu++11 -O3 -pthread -DNDEBUG  -c adapterset.cc 
g++ -std=gnu++11 -O3 -pthread -DNDEBUG  -c alignment.cc 
g++ -std=gnu++11 -O3 -pthread -DNDEBUG  -c argparse.cc 
g++ -std=gnu++11 -O3 -pthread -DNDEBUG  -c debug.cc 
g++ -std=gnu++11 -O3 -pthread -DNDEBUG  -c demultiplex.cc 
g++ -std=gnu++11 -O3 -pthread -DNDEBUG  -c fastq.cc 
g++ -std=gnu++11 -O3 -pthread -DNDEBUG  -c fastq_enc.cc 
g++ -std=gnu++11 -O3 -pthread -DNDEBUG  -c fastq_io.cc 
g++ -std=gnu++11 -O3 -pthread -DNDEBUG  -c linereader.cc 
g++ -std=gnu++11 -O3 -pthread -DNDEBUG  -c linereader_joined.cc 
g++ -std=gnu++11 -O3 -pthread -DNDEBUG  -c main_adapter_id.cc 
g++ -std=gnu++11 -O3 -pthread -DNDEBUG  -c main_adapter_rm.cc 
g++ -std=gnu++11 -O3 -pthread -DNDEBUG  -c main_demultiplex.cc 
g++ -std=gnu++11 -O3 -pthread -DNDEBUG  -c scheduler.cc 
g++ -std=gnu++11 -O3 -pthread -DNDEBUG  -c strutils.cc 
g++ -std=gnu++11 -O3 -pthread -DNDEBUG  -c threads.cc 
g++ -std=gnu++11 -O3 -pthread -DNDEBUG  -c timer.cc 
g++ -std=gnu++11 -O3 -pthread -DNDEBUG  -c trimmed_reads.cc 
g++ -std=gnu++11 -O3 -pthread -DNDEBUG  -c userconfig.cc 
g++ -std=gnu++11 -O3 -pthread -DNDEBUG  -c main.cc 
g++ -std=gnu++11 -O3 -pthread -DNDEBUG   -o AdapterRemoval adapterset.o alignment.o argparse.o debug.o demultiplex.o fastq.o fastq_enc.o fastq_io.o linereader.o linereader_joined.o main_adapter_id.o main_adapter_rm.o main_demultiplex.o scheduler.o strutils.o threads.o timer.o trimmed_reads.o userconfig.o main.o
mv AdapterRemoval ../../inst/
make[1]: Leaving directory '/home/biocbuild/bbs-3.17-bioc/meat/Rbowtie2/src/adapterremoval'
(cd	adapterremoval && (make clean_o -f Makefile))
make[1]: Entering directory '/home/biocbuild/bbs-3.17-bioc/meat/Rbowtie2/src/adapterremoval'
rm -f *.o
make[1]: Leaving directory '/home/biocbuild/bbs-3.17-bioc/meat/Rbowtie2/src/adapterremoval'
(cd bowtie2-2.4.4 && (make CXX="g++" -f Makefile))
make[1]: Entering directory '/home/biocbuild/bbs-3.17-bioc/meat/Rbowtie2/src/bowtie2-2.4.4'
g++ -O3  -funroll-loops -g3 -DCOMPILER_OPTIONS="\"-O3  -funroll-loops -g3 -std=c++11 -fopenmp-simd -DNO_SPINLOCK -DWITH_QUEUELOCK=1\"" -std=c++11 -fopenmp-simd -DNO_SPINLOCK -DWITH_QUEUELOCK=1 \
	-fno-strict-aliasing -DBOWTIE2_VERSION="\"`cat BOWTIE2_VERSION`\"" -DBUILD_HOST="\"${HOSTNAME:-`hostname`}\"" -DBUILD_TIME="\"`date -u`\"" -DCOMPILER_VERSION="\"`g++ -v 2>&1 | tail -1`\"" -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_GNU_SOURCE  -DBOWTIE_MM  -DBOWTIE2 -DNDEBUG -Wall \
	-Ithird_party \
	-o bowtie2-build-s bt2_build.cpp \
	ccnt_lut.cpp ref_read.cpp alphabet.cpp shmem.cpp edit.cpp bt2_locks.cpp bt2_idx.cpp bt2_io.cpp bt2_util.cpp reference.cpp ds.cpp multikey_qsort.cpp limit.cpp random_source.cpp diff_sample.cpp bowtie_build_main.cpp \
	 -lpthread -lz
g++ -O3  -funroll-loops -g3 -DCOMPILER_OPTIONS="\"-O3  -funroll-loops -g3 -std=c++11 -fopenmp-simd -DNO_SPINLOCK -DWITH_QUEUELOCK=1\"" -std=c++11 -fopenmp-simd -DNO_SPINLOCK -DWITH_QUEUELOCK=1 \
	-fno-strict-aliasing -DBOWTIE2_VERSION="\"`cat BOWTIE2_VERSION`\"" -DBUILD_HOST="\"${HOSTNAME:-`hostname`}\"" -DBUILD_TIME="\"`date -u`\"" -DCOMPILER_VERSION="\"`g++ -v 2>&1 | tail -1`\"" -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_GNU_SOURCE  -DBOWTIE_MM  -DBOWTIE2 -DBOWTIE_64BIT_INDEX -DNDEBUG -Wall \
	-Ithird_party \
	-o bowtie2-build-l bt2_build.cpp \
	ccnt_lut.cpp ref_read.cpp alphabet.cpp shmem.cpp edit.cpp bt2_locks.cpp bt2_idx.cpp bt2_io.cpp bt2_util.cpp reference.cpp ds.cpp multikey_qsort.cpp limit.cpp random_source.cpp diff_sample.cpp bowtie_build_main.cpp \
	 -lpthread -lz
g++ -O3  -funroll-loops -g3 -DCOMPILER_OPTIONS="\"-O3  -funroll-loops -g3 -std=c++11 -fopenmp-simd -DNO_SPINLOCK -DWITH_QUEUELOCK=1\"" -std=c++11 -fopenmp-simd -DNO_SPINLOCK -DWITH_QUEUELOCK=1 \
	-fno-strict-aliasing -DBOWTIE2_VERSION="\"`cat BOWTIE2_VERSION`\"" -DBUILD_HOST="\"${HOSTNAME:-`hostname`}\"" -DBUILD_TIME="\"`date -u`\"" -DCOMPILER_VERSION="\"`g++ -v 2>&1 | tail -1`\"" -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_GNU_SOURCE  -DBOWTIE_MM  -DBOWTIE2 -DNDEBUG -Wall \
	-Ithird_party \
	-o bowtie2-align-s bt2_search.cpp \
	ccnt_lut.cpp ref_read.cpp alphabet.cpp shmem.cpp edit.cpp bt2_locks.cpp bt2_idx.cpp bt2_io.cpp bt2_util.cpp reference.cpp ds.cpp multikey_qsort.cpp limit.cpp random_source.cpp qual.cpp pat.cpp sam.cpp read_qseq.cpp aligner_seed_policy.cpp aligner_seed.cpp aligner_seed2.cpp aligner_sw.cpp aligner_sw_driver.cpp aligner_cache.cpp aligner_result.cpp ref_coord.cpp mask.cpp pe.cpp aln_sink.cpp dp_framer.cpp scoring.cpp presets.cpp unique.cpp simple_func.cpp random_util.cpp aligner_bt.cpp sse_util.cpp aligner_swsse.cpp outq.cpp aligner_swsse_loc_i16.cpp aligner_swsse_ee_i16.cpp aligner_swsse_loc_u8.cpp aligner_swsse_ee_u8.cpp aligner_driver.cpp bowtie_main.cpp \
	 -lpthread -lz
In file included from aligner_sw.h:73,
                 from bt2_search.cpp:54:
sse_wrap.h:31:10: fatal error: simde/x86/sse2.h: No such file or directory
   31 | #include "simde/x86/sse2.h"
      |          ^~~~~~~~~~~~~~~~~~
compilation terminated.
In file included from aligner_sw.h:73,
                 from aligner_sw.cpp:25:
sse_wrap.h:31:10: fatal error: simde/x86/sse2.h: No such file or directory
   31 | #include "simde/x86/sse2.h"
      |          ^~~~~~~~~~~~~~~~~~
compilation terminated.
In file included from aligner_sw.h:73,
                 from aligner_sw_driver.h:81,
                 from aligner_sw_driver.cpp:47:
sse_wrap.h:31:10: fatal error: simde/x86/sse2.h: No such file or directory
   31 | #include "simde/x86/sse2.h"
      |          ^~~~~~~~~~~~~~~~~~
compilation terminated.
In file included from sse_util.h:27,
                 from aligner_bt.h:31,
                 from aligner_bt.cpp:20:
sse_wrap.h:31:10: fatal error: simde/x86/sse2.h: No such file or directory
   31 | #include "simde/x86/sse2.h"
      |          ^~~~~~~~~~~~~~~~~~
compilation terminated.
In file included from sse_util.h:27,
                 from sse_util.cpp:20:
sse_wrap.h:31:10: fatal error: simde/x86/sse2.h: No such file or directory
   31 | #include "simde/x86/sse2.h"
      |          ^~~~~~~~~~~~~~~~~~
compilation terminated.
In file included from sse_util.h:27,
                 from aligner_swsse.h:28,
                 from aligner_swsse.cpp:22:
sse_wrap.h:31:10: fatal error: simde/x86/sse2.h: No such file or directory
   31 | #include "simde/x86/sse2.h"
      |          ^~~~~~~~~~~~~~~~~~
compilation terminated.
In file included from aligner_sw.h:73,
                 from aligner_swsse_loc_i16.cpp:56:
sse_wrap.h:31:10: fatal error: simde/x86/sse2.h: No such file or directory
   31 | #include "simde/x86/sse2.h"
      |          ^~~~~~~~~~~~~~~~~~
compilation terminated.
In file included from aligner_sw.h:73,
                 from aligner_swsse_ee_i16.cpp:56:
sse_wrap.h:31:10: fatal error: simde/x86/sse2.h: No such file or directory
   31 | #include "simde/x86/sse2.h"
      |          ^~~~~~~~~~~~~~~~~~
compilation terminated.
In file included from aligner_sw.h:73,
                 from aligner_swsse_loc_u8.cpp:56:
sse_wrap.h:31:10: fatal error: simde/x86/sse2.h: No such file or directory
   31 | #include "simde/x86/sse2.h"
      |          ^~~~~~~~~~~~~~~~~~
compilation terminated.
In file included from aligner_sw.h:73,
                 from aligner_swsse_ee_u8.cpp:56:
sse_wrap.h:31:10: fatal error: simde/x86/sse2.h: No such file or directory
   31 | #include "simde/x86/sse2.h"
      |          ^~~~~~~~~~~~~~~~~~
compilation terminated.
make[1]: *** [Makefile:339: bowtie2-align-s] Error 1
make[1]: Leaving directory '/home/biocbuild/bbs-3.17-bioc/meat/Rbowtie2/src/bowtie2-2.4.4'
make: *** [Makefile:12: all] Error 2
ERROR: compilation failed for package ‘Rbowtie2’
* removing ‘/home/biocbuild/bbs-3.17-bioc/R/library/Rbowtie2’

NetPathMiner.install

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD INSTALL NetPathMiner
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.17-bioc/R/library’
* installing *source* package ‘NetPathMiner’ ...
** using staged installation
'config' variable 'CPP' is defunct
checking for gcc... gcc
checking whether the C compiler works... yes
checking for C compiler default output file name... a.out
checking for suffix of executables... 
checking whether we are cross compiling... no
checking for suffix of object files... o
checking whether we are using the GNU C compiler... yes
checking whether gcc accepts -g... yes
checking for gcc option to accept ISO C89... none needed
checking how to run the C preprocessor... gcc -E
checking for xmlParseFile in -lxml2... yes
checking for readSBML in -lsbml... yes
untarring boost include tree...
libSBML found, finding configuration...
pkg-config tool found
libsbml.pc found. Using pkg-config to extract it.
checking for xml2-config... /usr/bin/xml2-config
configure: creating ./config.status
config.status: creating src/Makevars
** libs
using C compiler: ‘gcc (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0’
using C++ compiler: ‘g++ (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0’
g++ -std=gnu++14  -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG   -I/usr/local/include   -I . -I/usr/local/include -DHAVE_XML -I/usr/include/libxml2 -DHAVE_SBML -I/usr/include/libxml2 -fPIC  -g -O2  -Wall  -c PathRanker.cpp -o PathRanker.o
PathRanker.cpp:18: warning: ignoring ‘#pragma clang diagnostic’ [-Wunknown-pragmas]
   18 | #pragma clang diagnostic push
      | 
PathRanker.cpp:19: warning: ignoring ‘#pragma clang diagnostic’ [-Wunknown-pragmas]
   19 | #pragma clang diagnostic ignored "-Wunused-local-typedef"
      | 
PathRanker.cpp:29: warning: ignoring ‘#pragma clang diagnostic’ [-Wunknown-pragmas]
   29 | #pragma clang diagnostic pop
      | 
PathRanker.cpp:17:32: warning: unknown option after ‘#pragma GCC diagnostic’ kind [-Wpragmas]
   17 | #pragma GCC diagnostic ignored "-Wunused-local-typedef"
      |                                ^~~~~~~~~~~~~~~~~~~~~~~~
PathRanker.cpp:17:32: note: did you mean ‘-Wunused-local-typedefs’?
In file included from ./boost/tuple/tuple.hpp:33,
                 from ./boost/graph/graph_utility.hpp:19,
                 from PathRanker.cpp:23:
./boost/tuple/detail/tuple_basic.hpp: In function ‘typename boost::tuples::access_traits<typename boost::tuples::element<N, boost::tuples::cons<HT, TT> >::type>::const_type boost::tuples::get(const boost::tuples::cons<HT, TT>&)’:
./boost/tuple/detail/tuple_basic.hpp:228:45: warning: typedef ‘cons_element’ locally defined but not used [-Wunused-local-typedefs]
  228 |   typedef BOOST_DEDUCED_TYPENAME impl::type cons_element;
      |                                             ^~~~~~~~~~~~
In file included from ./boost/mpl/aux_/na_assert.hpp:23,
                 from ./boost/mpl/arg.hpp:25,
                 from ./boost/mpl/placeholders.hpp:24,
                 from ./boost/iterator/iterator_categories.hpp:17,
                 from ./boost/graph/graph_traits.hpp:25,
                 from ./boost/graph/graph_utility.hpp:29,
                 from PathRanker.cpp:23:
./boost/mpl/assert.hpp: At global scope:
./boost/mpl/assert.hpp:187:21: warning: unnecessary parentheses in declaration of ‘assert_arg’ [-Wparentheses]
  187 | failed ************ (Pred::************
      |                     ^~~~~~~~~~~~~~~~~~~
  188 |       assert_arg( void (*)(Pred), typename assert_arg_pred<Pred>::type )
      |       ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
  189 |     );
      |     ~                
./boost/mpl/assert.hpp:187:21: note: remove parentheses
  187 | failed ************ (Pred::************
      |                     ^~~~~~~~~~~~~~~~~~~
      |                     -
  188 |       assert_arg( void (*)(Pred), typename assert_arg_pred<Pred>::type )
      |       ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
  189 |     );
      |     ~                
      |     -
./boost/mpl/assert.hpp:192:21: warning: unnecessary parentheses in declaration of ‘assert_not_arg’ [-Wparentheses]
  192 | failed ************ (boost::mpl::not_<Pred>::************
      |                     ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
  193 |       assert_not_arg( void (*)(Pred), typename assert_arg_pred_not<Pred>::type )
      |       ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
  194 |     );
      |     ~                
./boost/mpl/assert.hpp:192:21: note: remove parentheses
  192 | failed ************ (boost::mpl::not_<Pred>::************
      |                     ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
      |                     -
  193 |       assert_not_arg( void (*)(Pred), typename assert_arg_pred_not<Pred>::type )
      |       ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
  194 |     );
      |     ~                
      |     -
In file included from ./boost/mpl/aux_/integral_wrapper.hpp:22,
                 from ./boost/mpl/int.hpp:20,
                 from ./boost/type_traits/detail/template_arity_spec.hpp:10,
                 from ./boost/type_traits/detail/type_trait_def.hpp:14,
                 from ./boost/type_traits/add_const.hpp:16,
                 from ./boost/type_traits/cv_traits.hpp:15,
                 from ./boost/tuple/detail/tuple_basic.hpp:38,
                 from ./boost/tuple/tuple.hpp:33,
                 from ./boost/graph/graph_utility.hpp:19,
                 from PathRanker.cpp:23:
./boost/concept_check.hpp: In function ‘void boost::function_requires(Model*)’:
./boost/concept/detail/general.hpp:71:20: warning: typedef ‘boost_concept_check45’ locally defined but not used [-Wunused-local-typedefs]
   71 |       BOOST_PP_CAT(boost_concept_check,__LINE__)
      |                    ^~~~~~~~~~~~~~~~~~~
./boost/preprocessor/cat.hpp:29:34: note: in definition of macro ‘BOOST_PP_CAT_I’
   29 | #    define BOOST_PP_CAT_I(a, b) a ## b
      |                                  ^
./boost/concept/detail/general.hpp:71:7: note: in expansion of macro ‘BOOST_PP_CAT’
   71 |       BOOST_PP_CAT(boost_concept_check,__LINE__)
      |       ^~~~~~~~~~~~
./boost/concept/assert.hpp:44:5: note: in expansion of macro ‘BOOST_CONCEPT_ASSERT_FN’
   44 |     BOOST_CONCEPT_ASSERT_FN(void(*)ModelInParens)
      |     ^~~~~~~~~~~~~~~~~~~~~~~
./boost/concept_check.hpp:45:7: note: in expansion of macro ‘BOOST_CONCEPT_ASSERT’
   45 |       BOOST_CONCEPT_ASSERT((Model));
      |       ^~~~~~~~~~~~~~~~~~~~
./boost/concept_check.hpp: In destructor ‘boost::AdaptableGenerator<Func, Return>::~AdaptableGenerator()’:
./boost/concept/detail/general.hpp:71:20: warning: typedef ‘boost_concept_check453’ locally defined but not used [-Wunused-local-typedefs]
   71 |       BOOST_PP_CAT(boost_concept_check,__LINE__)
      |                    ^~~~~~~~~~~~~~~~~~~
./boost/preprocessor/cat.hpp:29:34: note: in definition of macro ‘BOOST_PP_CAT_I’
   29 | #    define BOOST_PP_CAT_I(a, b) a ## b
      |                                  ^
./boost/concept/detail/general.hpp:71:7: note: in expansion of macro ‘BOOST_PP_CAT’
   71 |       BOOST_PP_CAT(boost_concept_check,__LINE__)
      |       ^~~~~~~~~~~~
./boost/concept/assert.hpp:44:5: note: in expansion of macro ‘BOOST_CONCEPT_ASSERT_FN’
   44 |     BOOST_CONCEPT_ASSERT_FN(void(*)ModelInParens)
      |     ^~~~~~~~~~~~~~~~~~~~~~~
./boost/concept_check.hpp:453:11: note: in expansion of macro ‘BOOST_CONCEPT_ASSERT’
  453 |           BOOST_CONCEPT_ASSERT((Convertible<result_type, Return>));
      |           ^~~~~~~~~~~~~~~~~~~~
./boost/concept_check.hpp: In destructor ‘boost::AdaptableUnaryFunction<Func, Return, Arg>::~AdaptableUnaryFunction()’:
./boost/concept/detail/general.hpp:71:20: warning: typedef ‘boost_concept_check465’ locally defined but not used [-Wunused-local-typedefs]
   71 |       BOOST_PP_CAT(boost_concept_check,__LINE__)
      |                    ^~~~~~~~~~~~~~~~~~~
./boost/preprocessor/cat.hpp:29:34: note: in definition of macro ‘BOOST_PP_CAT_I’
   29 | #    define BOOST_PP_CAT_I(a, b) a ## b
      |                                  ^
./boost/concept/detail/general.hpp:71:7: note: in expansion of macro ‘BOOST_PP_CAT’
   71 |       BOOST_PP_CAT(boost_concept_check,__LINE__)
      |       ^~~~~~~~~~~~
./boost/concept/assert.hpp:44:5: note: in expansion of macro ‘BOOST_CONCEPT_ASSERT_FN’
   44 |     BOOST_CONCEPT_ASSERT_FN(void(*)ModelInParens)
      |     ^~~~~~~~~~~~~~~~~~~~~~~
./boost/concept_check.hpp:465:11: note: in expansion of macro ‘BOOST_CONCEPT_ASSERT’
  465 |           BOOST_CONCEPT_ASSERT((Convertible<result_type, Return>));
      |           ^~~~~~~~~~~~~~~~~~~~
./boost/concept/detail/general.hpp:71:20: warning: typedef ‘boost_concept_check466’ locally defined but not used [-Wunused-local-typedefs]
   71 |       BOOST_PP_CAT(boost_concept_check,__LINE__)
      |                    ^~~~~~~~~~~~~~~~~~~
./boost/preprocessor/cat.hpp:29:34: note: in definition of macro ‘BOOST_PP_CAT_I’
   29 | #    define BOOST_PP_CAT_I(a, b) a ## b
      |                                  ^
./boost/concept/detail/general.hpp:71:7: note: in expansion of macro ‘BOOST_PP_CAT’
   71 |       BOOST_PP_CAT(boost_concept_check,__LINE__)
      |       ^~~~~~~~~~~~
./boost/concept/assert.hpp:44:5: note: in expansion of macro ‘BOOST_CONCEPT_ASSERT_FN’
   44 |     BOOST_CONCEPT_ASSERT_FN(void(*)ModelInParens)
      |     ^~~~~~~~~~~~~~~~~~~~~~~
./boost/concept_check.hpp:466:11: note: in expansion of macro ‘BOOST_CONCEPT_ASSERT’
  466 |           BOOST_CONCEPT_ASSERT((Convertible<Arg, argument_type>));
      |           ^~~~~~~~~~~~~~~~~~~~
./boost/concept_check.hpp: In destructor ‘boost::AdaptableBinaryFunction<Func, Return, First, Second>::~AdaptableBinaryFunction()’:
./boost/concept/detail/general.hpp:71:20: warning: typedef ‘boost_concept_check484’ locally defined but not used [-Wunused-local-typedefs]
   71 |       BOOST_PP_CAT(boost_concept_check,__LINE__)
      |                    ^~~~~~~~~~~~~~~~~~~
./boost/preprocessor/cat.hpp:29:34: note: in definition of macro ‘BOOST_PP_CAT_I’
   29 | #    define BOOST_PP_CAT_I(a, b) a ## b
      |                                  ^
./boost/concept/detail/general.hpp:71:7: note: in expansion of macro ‘BOOST_PP_CAT’
   71 |       BOOST_PP_CAT(boost_concept_check,__LINE__)
      |       ^~~~~~~~~~~~
./boost/concept/assert.hpp:44:5: note: in expansion of macro ‘BOOST_CONCEPT_ASSERT_FN’
   44 |     BOOST_CONCEPT_ASSERT_FN(void(*)ModelInParens)
      |     ^~~~~~~~~~~~~~~~~~~~~~~
./boost/concept_check.hpp:484:11: note: in expansion of macro ‘BOOST_CONCEPT_ASSERT’
  484 |           BOOST_CONCEPT_ASSERT((Convertible<result_type, Return>));
      |           ^~~~~~~~~~~~~~~~~~~~
./boost/concept/detail/general.hpp:71:20: warning: typedef ‘boost_concept_check485’ locally defined but not used [-Wunused-local-typedefs]
   71 |       BOOST_PP_CAT(boost_concept_check,__LINE__)
      |                    ^~~~~~~~~~~~~~~~~~~
./boost/preprocessor/cat.hpp:29:34: note: in definition of macro ‘BOOST_PP_CAT_I’
   29 | #    define BOOST_PP_CAT_I(a, b) a ## b
      |                                  ^
./boost/concept/detail/general.hpp:71:7: note: in expansion of macro ‘BOOST_PP_CAT’
   71 |       BOOST_PP_CAT(boost_concept_check,__LINE__)
      |       ^~~~~~~~~~~~
./boost/concept/assert.hpp:44:5: note: in expansion of macro ‘BOOST_CONCEPT_ASSERT_FN’
   44 |     BOOST_CONCEPT_ASSERT_FN(void(*)ModelInParens)
      |     ^~~~~~~~~~~~~~~~~~~~~~~
./boost/concept_check.hpp:485:11: note: in expansion of macro ‘BOOST_CONCEPT_ASSERT’
  485 |           BOOST_CONCEPT_ASSERT((Convertible<First, first_argument_type>));
      |           ^~~~~~~~~~~~~~~~~~~~
./boost/concept/detail/general.hpp:71:20: warning: typedef ‘boost_concept_check486’ locally defined but not used [-Wunused-local-typedefs]
   71 |       BOOST_PP_CAT(boost_concept_check,__LINE__)
      |                    ^~~~~~~~~~~~~~~~~~~
./boost/preprocessor/cat.hpp:29:34: note: in definition of macro ‘BOOST_PP_CAT_I’
   29 | #    define BOOST_PP_CAT_I(a, b) a ## b
      |                                  ^
./boost/concept/detail/general.hpp:71:7: note: in expansion of macro ‘BOOST_PP_CAT’
   71 |       BOOST_PP_CAT(boost_concept_check,__LINE__)
      |       ^~~~~~~~~~~~
./boost/concept/assert.hpp:44:5: note: in expansion of macro ‘BOOST_CONCEPT_ASSERT_FN’
   44 |     BOOST_CONCEPT_ASSERT_FN(void(*)ModelInParens)
      |     ^~~~~~~~~~~~~~~~~~~~~~~
./boost/concept_check.hpp:486:11: note: in expansion of macro ‘BOOST_CONCEPT_ASSERT’
  486 |           BOOST_CONCEPT_ASSERT((Convertible<Second, second_argument_type>));
      |           ^~~~~~~~~~~~~~~~~~~~
./boost/concept_check.hpp: In destructor ‘boost::InputIterator<TT>::~InputIterator()’:
./boost/concept/detail/general.hpp:71:20: warning: typedef ‘boost_concept_check517’ locally defined but not used [-Wunused-local-typedefs]
   71 |       BOOST_PP_CAT(boost_concept_check,__LINE__)
      |                    ^~~~~~~~~~~~~~~~~~~
./boost/preprocessor/cat.hpp:29:34: note: in definition of macro ‘BOOST_PP_CAT_I’
   29 | #    define BOOST_PP_CAT_I(a, b) a ## b
      |                                  ^
./boost/concept/detail/general.hpp:71:7: note: in expansion of macro ‘BOOST_PP_CAT’
   71 |       BOOST_PP_CAT(boost_concept_check,__LINE__)
      |       ^~~~~~~~~~~~
./boost/concept/assert.hpp:44:5: note: in expansion of macro ‘BOOST_CONCEPT_ASSERT_FN’
   44 |     BOOST_CONCEPT_ASSERT_FN(void(*)ModelInParens)
      |     ^~~~~~~~~~~~~~~~~~~~~~~
./boost/concept_check.hpp:517:9: note: in expansion of macro ‘BOOST_CONCEPT_ASSERT’
  517 |         BOOST_CONCEPT_ASSERT((SignedInteger<difference_type>));
      |         ^~~~~~~~~~~~~~~~~~~~
./boost/concept/detail/general.hpp:71:20: warning: typedef ‘boost_concept_check518’ locally defined but not used [-Wunused-local-typedefs]
   71 |       BOOST_PP_CAT(boost_concept_check,__LINE__)
      |                    ^~~~~~~~~~~~~~~~~~~
./boost/preprocessor/cat.hpp:29:34: note: in definition of macro ‘BOOST_PP_CAT_I’
   29 | #    define BOOST_PP_CAT_I(a, b) a ## b
      |                                  ^
./boost/concept/detail/general.hpp:71:7: note: in expansion of macro ‘BOOST_PP_CAT’
   71 |       BOOST_PP_CAT(boost_concept_check,__LINE__)
      |       ^~~~~~~~~~~~
./boost/concept/assert.hpp:44:5: note: in expansion of macro ‘BOOST_CONCEPT_ASSERT_FN’
   44 |     BOOST_CONCEPT_ASSERT_FN(void(*)ModelInParens)
      |     ^~~~~~~~~~~~~~~~~~~~~~~
./boost/concept_check.hpp:518:9: note: in expansion of macro ‘BOOST_CONCEPT_ASSERT’
  518 |         BOOST_CONCEPT_ASSERT((Convertible<iterator_category, std::input_iterator_tag>));
      |         ^~~~~~~~~~~~~~~~~~~~
./boost/concept_check.hpp: In destructor ‘boost::ForwardIterator<TT>::~ForwardIterator()’:
./boost/concept/detail/general.hpp:71:20: warning: typedef ‘boost_concept_check548’ locally defined but not used [-Wunused-local-typedefs]
   71 |       BOOST_PP_CAT(boost_concept_check,__LINE__)
      |                    ^~~~~~~~~~~~~~~~~~~
./boost/preprocessor/cat.hpp:29:34: note: in definition of macro ‘BOOST_PP_CAT_I’
   29 | #    define BOOST_PP_CAT_I(a, b) a ## b
      |                                  ^
./boost/concept/detail/general.hpp:71:7: note: in expansion of macro ‘BOOST_PP_CAT’
   71 |       BOOST_PP_CAT(boost_concept_check,__LINE__)
      |       ^~~~~~~~~~~~
./boost/concept/assert.hpp:44:5: note: in expansion of macro ‘BOOST_CONCEPT_ASSERT_FN’
   44 |     BOOST_CONCEPT_ASSERT_FN(void(*)ModelInParens)
      |     ^~~~~~~~~~~~~~~~~~~~~~~
./boost/concept_check.hpp:548:11: note: in expansion of macro ‘BOOST_CONCEPT_ASSERT’
  548 |           BOOST_CONCEPT_ASSERT((Convertible<
      |           ^~~~~~~~~~~~~~~~~~~~
./boost/concept_check.hpp: In destructor ‘boost::BidirectionalIterator<TT>::~BidirectionalIterator()’:
./boost/concept/detail/general.hpp:71:20: warning: typedef ‘boost_concept_check576’ locally defined but not used [-Wunused-local-typedefs]
   71 |       BOOST_PP_CAT(boost_concept_check,__LINE__)
      |                    ^~~~~~~~~~~~~~~~~~~
./boost/preprocessor/cat.hpp:29:34: note: in definition of macro ‘BOOST_PP_CAT_I’
   29 | #    define BOOST_PP_CAT_I(a, b) a ## b
      |                                  ^
./boost/concept/detail/general.hpp:71:7: note: in expansion of macro ‘BOOST_PP_CAT’
   71 |       BOOST_PP_CAT(boost_concept_check,__LINE__)
      |       ^~~~~~~~~~~~
./boost/concept/assert.hpp:44:5: note: in expansion of macro ‘BOOST_CONCEPT_ASSERT_FN’
   44 |     BOOST_CONCEPT_ASSERT_FN(void(*)ModelInParens)
      |     ^~~~~~~~~~~~~~~~~~~~~~~
./boost/concept_check.hpp:576:11: note: in expansion of macro ‘BOOST_CONCEPT_ASSERT’
  576 |           BOOST_CONCEPT_ASSERT((Convertible<
      |           ^~~~~~~~~~~~~~~~~~~~
./boost/concept_check.hpp: In destructor ‘boost::RandomAccessIterator<TT>::~RandomAccessIterator()’:
./boost/concept/detail/general.hpp:71:20: warning: typedef ‘boost_concept_check606’ locally defined but not used [-Wunused-local-typedefs]
   71 |       BOOST_PP_CAT(boost_concept_check,__LINE__)
      |                    ^~~~~~~~~~~~~~~~~~~
./boost/preprocessor/cat.hpp:29:34: note: in definition of macro ‘BOOST_PP_CAT_I’
   29 | #    define BOOST_PP_CAT_I(a, b) a ## b
      |                                  ^
./boost/concept/detail/general.hpp:71:7: note: in expansion of macro ‘BOOST_PP_CAT’
   71 |       BOOST_PP_CAT(boost_concept_check,__LINE__)
      |       ^~~~~~~~~~~~
./boost/concept/assert.hpp:44:5: note: in expansion of macro ‘BOOST_CONCEPT_ASSERT_FN’
   44 |     BOOST_CONCEPT_ASSERT_FN(void(*)ModelInParens)
      |     ^~~~~~~~~~~~~~~~~~~~~~~
./boost/concept_check.hpp:606:11: note: in expansion of macro ‘BOOST_CONCEPT_ASSERT’
  606 |           BOOST_CONCEPT_ASSERT((Convertible<
      |           ^~~~~~~~~~~~~~~~~~~~
./boost/concept_check.hpp: In destructor ‘boost::Container<C>::~Container()’:
./boost/concept/detail/general.hpp:71:20: warning: typedef ‘boost_concept_check653’ locally defined but not used [-Wunused-local-typedefs]
   71 |       BOOST_PP_CAT(boost_concept_check,__LINE__)
      |                    ^~~~~~~~~~~~~~~~~~~
./boost/preprocessor/cat.hpp:29:34: note: in definition of macro ‘BOOST_PP_CAT_I’
   29 | #    define BOOST_PP_CAT_I(a, b) a ## b
      |                                  ^
./boost/concept/detail/general.hpp:71:7: note: in expansion of macro ‘BOOST_PP_CAT’
   71 |       BOOST_PP_CAT(boost_concept_check,__LINE__)
      |       ^~~~~~~~~~~~
./boost/concept/assert.hpp:44:5: note: in expansion of macro ‘BOOST_CONCEPT_ASSERT_FN’
   44 |     BOOST_CONCEPT_ASSERT_FN(void(*)ModelInParens)
      |     ^~~~~~~~~~~~~~~~~~~~~~~
./boost/concept_check.hpp:653:11: note: in expansion of macro ‘BOOST_CONCEPT_ASSERT’
  653 |           BOOST_CONCEPT_ASSERT((InputIterator<const_iterator>));
      |           ^~~~~~~~~~~~~~~~~~~~
./boost/concept_check.hpp: In destructor ‘boost::Mutable_Container<C>::~Mutable_Container()’:
./boost/concept/detail/general.hpp:71:20: warning: typedef ‘boost_concept_check680’ locally defined but not used [-Wunused-local-typedefs]
   71 |       BOOST_PP_CAT(boost_concept_check,__LINE__)
      |                    ^~~~~~~~~~~~~~~~~~~
./boost/preprocessor/cat.hpp:29:34: note: in definition of macro ‘BOOST_PP_CAT_I’
   29 | #    define BOOST_PP_CAT_I(a, b) a ## b
      |                                  ^
./boost/concept/detail/general.hpp:71:7: note: in expansion of macro ‘BOOST_PP_CAT’
   71 |       BOOST_PP_CAT(boost_concept_check,__LINE__)
      |       ^~~~~~~~~~~~
./boost/concept/assert.hpp:44:5: note: in expansion of macro ‘BOOST_CONCEPT_ASSERT_FN’
   44 |     BOOST_CONCEPT_ASSERT_FN(void(*)ModelInParens)
      |     ^~~~~~~~~~~~~~~~~~~~~~~
./boost/concept_check.hpp:680:11: note: in expansion of macro ‘BOOST_CONCEPT_ASSERT’
  680 |           BOOST_CONCEPT_ASSERT((
      |           ^~~~~~~~~~~~~~~~~~~~
./boost/concept/detail/general.hpp:71:20: warning: typedef ‘boost_concept_check683’ locally defined but not used [-Wunused-local-typedefs]
   71 |       BOOST_PP_CAT(boost_concept_check,__LINE__)
      |                    ^~~~~~~~~~~~~~~~~~~
./boost/preprocessor/cat.hpp:29:34: note: in definition of macro ‘BOOST_PP_CAT_I’
   29 | #    define BOOST_PP_CAT_I(a, b) a ## b
      |                                  ^
./boost/concept/detail/general.hpp:71:7: note: in expansion of macro ‘BOOST_PP_CAT’
   71 |       BOOST_PP_CAT(boost_concept_check,__LINE__)
      |       ^~~~~~~~~~~~
./boost/concept/assert.hpp:44:5: note: in expansion of macro ‘BOOST_CONCEPT_ASSERT_FN’
   44 |     BOOST_CONCEPT_ASSERT_FN(void(*)ModelInParens)
      |     ^~~~~~~~~~~~~~~~~~~~~~~
./boost/concept_check.hpp:683:11: note: in expansion of macro ‘BOOST_CONCEPT_ASSERT’
  683 |           BOOST_CONCEPT_ASSERT((InputIterator<iterator>));
      |           ^~~~~~~~~~~~~~~~~~~~
./boost/concept_check.hpp: In destructor ‘boost::ForwardContainer<C>::~ForwardContainer()’:
./boost/concept/detail/general.hpp:71:20: warning: typedef ‘boost_concept_check700’ locally defined but not used [-Wunused-local-typedefs]
   71 |       BOOST_PP_CAT(boost_concept_check,__LINE__)
      |                    ^~~~~~~~~~~~~~~~~~~
./boost/preprocessor/cat.hpp:29:34: note: in definition of macro ‘BOOST_PP_CAT_I’
   29 | #    define BOOST_PP_CAT_I(a, b) a ## b
      |                                  ^
./boost/concept/detail/general.hpp:71:7: note: in expansion of macro ‘BOOST_PP_CAT’
   71 |       BOOST_PP_CAT(boost_concept_check,__LINE__)
      |       ^~~~~~~~~~~~
./boost/concept/assert.hpp:44:5: note: in expansion of macro ‘BOOST_CONCEPT_ASSERT_FN’
   44 |     BOOST_CONCEPT_ASSERT_FN(void(*)ModelInParens)
      |     ^~~~~~~~~~~~~~~~~~~~~~~
./boost/concept_check.hpp:700:11: note: in expansion of macro ‘BOOST_CONCEPT_ASSERT’
  700 |           BOOST_CONCEPT_ASSERT((
      |           ^~~~~~~~~~~~~~~~~~~~
./boost/concept_check.hpp: In destructor ‘boost::Mutable_ForwardContainer<C>::~Mutable_ForwardContainer()’:
./boost/concept/detail/general.hpp:71:20: warning: typedef ‘boost_concept_check713’ locally defined but not used [-Wunused-local-typedefs]
   71 |       BOOST_PP_CAT(boost_concept_check,__LINE__)
      |                    ^~~~~~~~~~~~~~~~~~~
./boost/preprocessor/cat.hpp:29:34: note: in definition of macro ‘BOOST_PP_CAT_I’
   29 | #    define BOOST_PP_CAT_I(a, b) a ## b
      |                                  ^
./boost/concept/detail/general.hpp:71:7: note: in expansion of macro ‘BOOST_PP_CAT’
   71 |       BOOST_PP_CAT(boost_concept_check,__LINE__)
      |       ^~~~~~~~~~~~
./boost/concept/assert.hpp:44:5: note: in expansion of macro ‘BOOST_CONCEPT_ASSERT_FN’
   44 |     BOOST_CONCEPT_ASSERT_FN(void(*)ModelInParens)
      |     ^~~~~~~~~~~~~~~~~~~~~~~
./boost/concept_check.hpp:713:11: note: in expansion of macro ‘BOOST_CONCEPT_ASSERT’
  713 |           BOOST_CONCEPT_ASSERT((
      |           ^~~~~~~~~~~~~~~~~~~~
./boost/concept_check.hpp: In destructor ‘boost::ReversibleContainer<C>::~ReversibleContainer()’:
./boost/concept/detail/general.hpp:71:20: warning: typedef ‘boost_concept_check729’ locally defined but not used [-Wunused-local-typedefs]
   71 |       BOOST_PP_CAT(boost_concept_check,__LINE__)
      |                    ^~~~~~~~~~~~~~~~~~~
./boost/preprocessor/cat.hpp:29:34: note: in definition of macro ‘BOOST_PP_CAT_I’
   29 | #    define BOOST_PP_CAT_I(a, b) a ## b
      |                                  ^
./boost/concept/detail/general.hpp:71:7: note: in expansion of macro ‘BOOST_PP_CAT’
   71 |       BOOST_PP_CAT(boost_concept_check,__LINE__)
      |       ^~~~~~~~~~~~
./boost/concept/assert.hpp:44:5: note: in expansion of macro ‘BOOST_CONCEPT_ASSERT_FN’
   44 |     BOOST_CONCEPT_ASSERT_FN(void(*)ModelInParens)
      |     ^~~~~~~~~~~~~~~~~~~~~~~
./boost/concept_check.hpp:729:11: note: in expansion of macro ‘BOOST_CONCEPT_ASSERT’
  729 |           BOOST_CONCEPT_ASSERT((
      |           ^~~~~~~~~~~~~~~~~~~~
./boost/concept/detail/general.hpp:71:20: warning: typedef ‘boost_concept_check733’ locally defined but not used [-Wunused-local-typedefs]
   71 |       BOOST_PP_CAT(boost_concept_check,__LINE__)
      |                    ^~~~~~~~~~~~~~~~~~~
./boost/preprocessor/cat.hpp:29:34: note: in definition of macro ‘BOOST_PP_CAT_I’
   29 | #    define BOOST_PP_CAT_I(a, b) a ## b
      |                                  ^
./boost/concept/detail/general.hpp:71:7: note: in expansion of macro ‘BOOST_PP_CAT’
   71 |       BOOST_PP_CAT(boost_concept_check,__LINE__)
      |       ^~~~~~~~~~~~
./boost/concept/assert.hpp:44:5: note: in expansion of macro ‘BOOST_CONCEPT_ASSERT_FN’
   44 |     BOOST_CONCEPT_ASSERT_FN(void(*)ModelInParens)
      |     ^~~~~~~~~~~~~~~~~~~~~~~
./boost/concept_check.hpp:733:11: note: in expansion of macro ‘BOOST_CONCEPT_ASSERT’
  733 |           BOOST_CONCEPT_ASSERT((BidirectionalIterator<const_reverse_iterator>));
      |           ^~~~~~~~~~~~~~~~~~~~
./boost/concept_check.hpp: In destructor ‘boost::Mutable_ReversibleContainer<C>::~Mutable_ReversibleContainer()’:
./boost/concept/detail/general.hpp:71:20: warning: typedef ‘boost_concept_check755’ locally defined but not used [-Wunused-local-typedefs]
   71 |       BOOST_PP_CAT(boost_concept_check,__LINE__)
      |                    ^~~~~~~~~~~~~~~~~~~
./boost/preprocessor/cat.hpp:29:34: note: in definition of macro ‘BOOST_PP_CAT_I’
   29 | #    define BOOST_PP_CAT_I(a, b) a ## b
      |                                  ^
./boost/concept/detail/general.hpp:71:7: note: in expansion of macro ‘BOOST_PP_CAT’
   71 |       BOOST_PP_CAT(boost_concept_check,__LINE__)
      |       ^~~~~~~~~~~~
./boost/concept/assert.hpp:44:5: note: in expansion of macro ‘BOOST_CONCEPT_ASSERT_FN’
   44 |     BOOST_CONCEPT_ASSERT_FN(void(*)ModelInParens)
      |     ^~~~~~~~~~~~~~~~~~~~~~~
./boost/concept_check.hpp:755:11: note: in expansion of macro ‘BOOST_CONCEPT_ASSERT’
  755 |           BOOST_CONCEPT_ASSERT((Mutable_BidirectionalIterator<iterator>));
      |           ^~~~~~~~~~~~~~~~~~~~
./boost/concept/detail/general.hpp:71:20: warning: typedef ‘boost_concept_check756’ locally defined but not used [-Wunused-local-typedefs]
   71 |       BOOST_PP_CAT(boost_concept_check,__LINE__)
      |                    ^~~~~~~~~~~~~~~~~~~
./boost/preprocessor/cat.hpp:29:34: note: in definition of macro ‘BOOST_PP_CAT_I’
   29 | #    define BOOST_PP_CAT_I(a, b) a ## b
      |                                  ^
./boost/concept/detail/general.hpp:71:7: note: in expansion of macro ‘BOOST_PP_CAT’
   71 |       BOOST_PP_CAT(boost_concept_check,__LINE__)
      |       ^~~~~~~~~~~~
./boost/concept/assert.hpp:44:5: note: in expansion of macro ‘BOOST_CONCEPT_ASSERT_FN’
   44 |     BOOST_CONCEPT_ASSERT_FN(void(*)ModelInParens)
      |     ^~~~~~~~~~~~~~~~~~~~~~~
./boost/concept_check.hpp:756:11: note: in expansion of macro ‘BOOST_CONCEPT_ASSERT’
  756 |           BOOST_CONCEPT_ASSERT((Mutable_BidirectionalIterator<reverse_iterator>));
      |           ^~~~~~~~~~~~~~~~~~~~
./boost/concept_check.hpp: In destructor ‘boost::RandomAccessContainer<C>::~RandomAccessContainer()’:
./boost/concept/detail/general.hpp:71:20: warning: typedef ‘boost_concept_check773’ locally defined but not used [-Wunused-local-typedefs]
   71 |       BOOST_PP_CAT(boost_concept_check,__LINE__)
      |                    ^~~~~~~~~~~~~~~~~~~
./boost/preprocessor/cat.hpp:29:34: note: in definition of macro ‘BOOST_PP_CAT_I’
   29 | #    define BOOST_PP_CAT_I(a, b) a ## b
      |                                  ^
./boost/concept/detail/general.hpp:71:7: note: in expansion of macro ‘BOOST_PP_CAT’
   71 |       BOOST_PP_CAT(boost_concept_check,__LINE__)
      |       ^~~~~~~~~~~~
./boost/concept/assert.hpp:44:5: note: in expansion of macro ‘BOOST_CONCEPT_ASSERT_FN’
   44 |     BOOST_CONCEPT_ASSERT_FN(void(*)ModelInParens)
      |     ^~~~~~~~~~~~~~~~~~~~~~~
./boost/concept_check.hpp:773:11: note: in expansion of macro ‘BOOST_CONCEPT_ASSERT’
  773 |           BOOST_CONCEPT_ASSERT((
      |           ^~~~~~~~~~~~~~~~~~~~
./boost/concept_check.hpp: In destructor ‘boost::Mutable_RandomAccessContainer<C>::~Mutable_RandomAccessContainer()’:
./boost/concept/detail/general.hpp:71:20: warning: typedef ‘boost_concept_check800’ locally defined but not used [-Wunused-local-typedefs]
   71 |       BOOST_PP_CAT(boost_concept_check,__LINE__)
      |                    ^~~~~~~~~~~~~~~~~~~
./boost/preprocessor/cat.hpp:29:34: note: in definition of macro ‘BOOST_PP_CAT_I’
   29 | #    define BOOST_PP_CAT_I(a, b) a ## b
      |                                  ^
./boost/concept/detail/general.hpp:71:7: note: in expansion of macro ‘BOOST_PP_CAT’
   71 |       BOOST_PP_CAT(boost_concept_check,__LINE__)
      |       ^~~~~~~~~~~~
./boost/concept/assert.hpp:44:5: note: in expansion of macro ‘BOOST_CONCEPT_ASSERT_FN’
   44 |     BOOST_CONCEPT_ASSERT_FN(void(*)ModelInParens)
      |     ^~~~~~~~~~~~~~~~~~~~~~~
./boost/concept_check.hpp:800:11: note: in expansion of macro ‘BOOST_CONCEPT_ASSERT’
  800 |           BOOST_CONCEPT_ASSERT((Mutable_RandomAccessIterator<typename self::iterator>));
      |           ^~~~~~~~~~~~~~~~~~~~
./boost/concept/detail/general.hpp:71:20: warning: typedef ‘boost_concept_check801’ locally defined but not used [-Wunused-local-typedefs]
   71 |       BOOST_PP_CAT(boost_concept_check,__LINE__)
      |                    ^~~~~~~~~~~~~~~~~~~
./boost/preprocessor/cat.hpp:29:34: note: in definition of macro ‘BOOST_PP_CAT_I’
   29 | #    define BOOST_PP_CAT_I(a, b) a ## b
      |                                  ^
./boost/concept/detail/general.hpp:71:7: note: in expansion of macro ‘BOOST_PP_CAT’
   71 |       BOOST_PP_CAT(boost_concept_check,__LINE__)
      |       ^~~~~~~~~~~~
./boost/concept/assert.hpp:44:5: note: in expansion of macro ‘BOOST_CONCEPT_ASSERT_FN’
   44 |     BOOST_CONCEPT_ASSERT_FN(void(*)ModelInParens)
      |     ^~~~~~~~~~~~~~~~~~~~~~~
./boost/concept_check.hpp:801:11: note: in expansion of macro ‘BOOST_CONCEPT_ASSERT’
  801 |           BOOST_CONCEPT_ASSERT((Mutable_RandomAccessIterator<typename self::reverse_iterator>));
      |           ^~~~~~~~~~~~~~~~~~~~
./boost/concept_check.hpp: In destructor ‘boost::AssociativeContainer<C>::~AssociativeContainer()’:
./boost/concept/detail/general.hpp:71:20: warning: typedef ‘boost_concept_check905’ locally defined but not used [-Wunused-local-typedefs]
   71 |       BOOST_PP_CAT(boost_concept_check,__LINE__)
      |                    ^~~~~~~~~~~~~~~~~~~
./boost/preprocessor/cat.hpp:29:34: note: in definition of macro ‘BOOST_PP_CAT_I’
   29 | #    define BOOST_PP_CAT_I(a, b) a ## b
      |                                  ^
./boost/concept/detail/general.hpp:71:7: note: in expansion of macro ‘BOOST_PP_CAT’
   71 |       BOOST_PP_CAT(boost_concept_check,__LINE__)
      |       ^~~~~~~~~~~~
./boost/concept/assert.hpp:44:5: note: in expansion of macro ‘BOOST_CONCEPT_ASSERT_FN’
   44 |     BOOST_CONCEPT_ASSERT_FN(void(*)ModelInParens)
      |     ^~~~~~~~~~~~~~~~~~~~~~~
./boost/concept_check.hpp:905:11: note: in expansion of macro ‘BOOST_CONCEPT_ASSERT’
  905 |           BOOST_CONCEPT_ASSERT((BinaryPredicate<key_compare,key_type,key_type>));
      |           ^~~~~~~~~~~~~~~~~~~~
./boost/concept/detail/general.hpp:71:20: warning: typedef ‘boost_concept_check908’ locally defined but not used [-Wunused-local-typedefs]
   71 |       BOOST_PP_CAT(boost_concept_check,__LINE__)
      |                    ^~~~~~~~~~~~~~~~~~~
./boost/preprocessor/cat.hpp:29:34: note: in definition of macro ‘BOOST_PP_CAT_I’
   29 | #    define BOOST_PP_CAT_I(a, b) a ## b
      |                                  ^
./boost/concept/detail/general.hpp:71:7: note: in expansion of macro ‘BOOST_PP_CAT’
   71 |       BOOST_PP_CAT(boost_concept_check,__LINE__)
      |       ^~~~~~~~~~~~
./boost/concept/assert.hpp:44:5: note: in expansion of macro ‘BOOST_CONCEPT_ASSERT_FN’
   44 |     BOOST_CONCEPT_ASSERT_FN(void(*)ModelInParens)
      |     ^~~~~~~~~~~~~~~~~~~~~~~
./boost/concept_check.hpp:908:11: note: in expansion of macro ‘BOOST_CONCEPT_ASSERT’
  908 |           BOOST_CONCEPT_ASSERT((BinaryPredicate<value_compare,value_type_,value_type_>));
      |           ^~~~~~~~~~~~~~~~~~~~
In file included from ./boost/smart_ptr/detail/shared_count.hpp:30,
                 from ./boost/smart_ptr/shared_ptr.hpp:32,
                 from ./boost/shared_ptr.hpp:17,
                 from ./boost/property_map/vector_property_map.hpp:14,
                 from ./boost/property_map/property_map.hpp:844,
                 from ./boost/graph/properties.hpp:19,
                 from ./boost/graph/graph_utility.hpp:30,
                 from PathRanker.cpp:23:
./boost/smart_ptr/detail/sp_counted_impl.hpp: At global scope:
./boost/smart_ptr/detail/sp_counted_impl.hpp:81:41: error: ‘boost::detail::sp_typeinfo’ has not been declared
   81 |     virtual void * get_deleter( detail::sp_typeinfo const & )
      |                                         ^~~~~~~~~~~
./boost/smart_ptr/detail/sp_counted_impl.hpp:156:41: error: ‘boost::detail::sp_typeinfo’ has not been declared
  156 |     virtual void * get_deleter( detail::sp_typeinfo const & ti )
      |                                         ^~~~~~~~~~~
./boost/smart_ptr/detail/sp_counted_impl.hpp: In member function ‘virtual void* boost::detail::sp_counted_impl_pd<P, D>::get_deleter(const int&)’:
./boost/smart_ptr/detail/sp_counted_impl.hpp:158:39: error: expected primary-expression before ‘)’ token
  158 |         return ti == BOOST_SP_TYPEID(D)? &reinterpret_cast<char&>( del ): 0;
      |                                       ^
./boost/smart_ptr/detail/sp_counted_impl.hpp:158:22: error: there are no arguments to ‘BOOST_SP_TYPEID’ that depend on a template parameter, so a declaration of ‘BOOST_SP_TYPEID’ must be available [-fpermissive]
  158 |         return ti == BOOST_SP_TYPEID(D)? &reinterpret_cast<char&>( del ): 0;
      |                      ^~~~~~~~~~~~~~~
./boost/smart_ptr/detail/sp_counted_impl.hpp:158:22: note: (if you use ‘-fpermissive’, G++ will accept your code, but allowing the use of an undeclared name is deprecated)
./boost/smart_ptr/detail/sp_counted_impl.hpp: At global scope:
./boost/smart_ptr/detail/sp_counted_impl.hpp:235:41: error: ‘boost::detail::sp_typeinfo’ has not been declared
  235 |     virtual void * get_deleter( detail::sp_typeinfo const & ti )
      |                                         ^~~~~~~~~~~
./boost/smart_ptr/detail/sp_counted_impl.hpp: In member function ‘virtual void* boost::detail::sp_counted_impl_pda<P, D, A>::get_deleter(const int&)’:
./boost/smart_ptr/detail/sp_counted_impl.hpp:237:41: error: expected primary-expression before ‘)’ token
  237 |         return ti == BOOST_SP_TYPEID( D )? &reinterpret_cast<char&>( d_ ): 0;
      |                                         ^
./boost/smart_ptr/detail/sp_counted_impl.hpp:237:22: error: there are no arguments to ‘BOOST_SP_TYPEID’ that depend on a template parameter, so a declaration of ‘BOOST_SP_TYPEID’ must be available [-fpermissive]
  237 |         return ti == BOOST_SP_TYPEID( D )? &reinterpret_cast<char&>( d_ ): 0;
      |                      ^~~~~~~~~~~~~~~
In file included from ./boost/smart_ptr/shared_ptr.hpp:32,
                 from ./boost/shared_ptr.hpp:17,
                 from ./boost/property_map/vector_property_map.hpp:14,
                 from ./boost/property_map/property_map.hpp:844,
                 from ./boost/graph/properties.hpp:19,
                 from ./boost/graph/graph_utility.hpp:30,
                 from PathRanker.cpp:23:
./boost/smart_ptr/detail/shared_count.hpp: At global scope:
./boost/smart_ptr/detail/shared_count.hpp:323:33: warning: ‘template<class> class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
  323 |     explicit shared_count( std::auto_ptr<Y> & r ): pi_( new sp_counted_impl_p<Y>( r.get() ) )
      |                                 ^~~~~~~~
In file included from /usr/include/c++/11/memory:76,
                 from ./boost/config/no_tr1/memory.hpp:21,
                 from ./boost/smart_ptr/shared_ptr.hpp:27,
                 from ./boost/shared_ptr.hpp:17,
                 from ./boost/property_map/vector_property_map.hpp:14,
                 from ./boost/property_map/property_map.hpp:844,
                 from ./boost/graph/properties.hpp:19,
                 from ./boost/graph/graph_utility.hpp:30,
                 from PathRanker.cpp:23:
/usr/include/c++/11/bits/unique_ptr.h:57:28: note: declared here
   57 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
In file included from ./boost/smart_ptr/shared_ptr.hpp:32,
                 from ./boost/shared_ptr.hpp:17,
                 from ./boost/property_map/vector_property_map.hpp:14,
                 from ./boost/property_map/property_map.hpp:844,
                 from ./boost/graph/properties.hpp:19,
                 from ./boost/graph/graph_utility.hpp:30,
                 from PathRanker.cpp:23:
./boost/smart_ptr/detail/shared_count.hpp:446:25: error: ‘sp_typeinfo’ has not been declared
  446 |     void * get_deleter( sp_typeinfo const & ti ) const
      |                         ^~~~~~~~~~~
./boost/smart_ptr/detail/shared_count.hpp: In member function ‘void* boost::detail::shared_count::get_deleter(const int&) const’:
./boost/smart_ptr/detail/shared_count.hpp:448:39: error: cannot convert ‘const int’ to ‘const sp_typeinfo_&’ {aka ‘const std::type_info&’}
  448 |         return pi_? pi_->get_deleter( ti ): 0;
      |                                       ^~
      |                                       |
      |                                       const int
In file included from ./boost/smart_ptr/detail/sp_counted_base.hpp:60,
                 from ./boost/smart_ptr/detail/shared_count.hpp:29,
                 from ./boost/smart_ptr/shared_ptr.hpp:32,
                 from ./boost/shared_ptr.hpp:17,
                 from ./boost/property_map/vector_property_map.hpp:14,
                 from ./boost/property_map/property_map.hpp:844,
                 from ./boost/graph/properties.hpp:19,
                 from ./boost/graph/graph_utility.hpp:30,
                 from PathRanker.cpp:23:
/usr/include/boost/smart_ptr/detail/sp_counted_base_sync.hpp:119:54: note:   initializing argument 1 of ‘virtual void* boost::detail::sp_counted_base::get_deleter(const sp_typeinfo_&)’
  119 |     virtual void * get_deleter( sp_typeinfo_ const & ti ) = 0;
      |                                 ~~~~~~~~~~~~~~~~~~~~~^~
In file included from ./boost/shared_ptr.hpp:17,
                 from ./boost/property_map/vector_property_map.hpp:14,
                 from ./boost/property_map/property_map.hpp:844,
                 from ./boost/graph/properties.hpp:19,
                 from ./boost/graph/graph_utility.hpp:30,
                 from PathRanker.cpp:23:
./boost/smart_ptr/shared_ptr.hpp: At global scope:
./boost/smart_ptr/shared_ptr.hpp:247:65: warning: ‘template<class> class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
  247 | template< class T, class R > struct sp_enable_if_auto_ptr< std::auto_ptr< T >, R >
      |                                                                 ^~~~~~~~
In file included from /usr/include/c++/11/memory:76,
                 from ./boost/config/no_tr1/memory.hpp:21,
                 from ./boost/smart_ptr/shared_ptr.hpp:27,
                 from ./boost/shared_ptr.hpp:17,
                 from ./boost/property_map/vector_property_map.hpp:14,
                 from ./boost/property_map/property_map.hpp:844,
                 from ./boost/graph/properties.hpp:19,
                 from ./boost/graph/graph_utility.hpp:30,
                 from PathRanker.cpp:23:
/usr/include/c++/11/bits/unique_ptr.h:57:28: note: declared here
   57 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
In file included from ./boost/shared_ptr.hpp:17,
                 from ./boost/property_map/vector_property_map.hpp:14,
                 from ./boost/property_map/property_map.hpp:844,
                 from ./boost/graph/properties.hpp:19,
                 from ./boost/graph/graph_utility.hpp:30,
                 from PathRanker.cpp:23:
./boost/smart_ptr/shared_ptr.hpp:446:31: warning: ‘template<class> class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
  446 |     explicit shared_ptr( std::auto_ptr<Y> & r ): px(r.get()), pn()
      |                               ^~~~~~~~
In file included from /usr/include/c++/11/memory:76,
                 from ./boost/config/no_tr1/memory.hpp:21,
                 from ./boost/smart_ptr/shared_ptr.hpp:27,
                 from ./boost/shared_ptr.hpp:17,
                 from ./boost/property_map/vector_property_map.hpp:14,
                 from ./boost/property_map/property_map.hpp:844,
                 from ./boost/graph/properties.hpp:19,
                 from ./boost/graph/graph_utility.hpp:30,
                 from PathRanker.cpp:23:
/usr/include/c++/11/bits/unique_ptr.h:57:28: note: declared here
   57 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
In file included from ./boost/shared_ptr.hpp:17,
                 from ./boost/property_map/vector_property_map.hpp:14,
                 from ./boost/property_map/property_map.hpp:844,
                 from ./boost/graph/properties.hpp:19,
                 from ./boost/graph/graph_utility.hpp:30,
                 from PathRanker.cpp:23:
./boost/smart_ptr/shared_ptr.hpp:459:22: warning: ‘template<class> class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
  459 |     shared_ptr( std::auto_ptr<Y> && r ): px(r.get()), pn()
      |                      ^~~~~~~~
In file included from /usr/include/c++/11/memory:76,
                 from ./boost/config/no_tr1/memory.hpp:21,
                 from ./boost/smart_ptr/shared_ptr.hpp:27,
                 from ./boost/shared_ptr.hpp:17,
                 from ./boost/property_map/vector_property_map.hpp:14,
                 from ./boost/property_map/property_map.hpp:844,
                 from ./boost/graph/properties.hpp:19,
                 from ./boost/graph/graph_utility.hpp:30,
                 from PathRanker.cpp:23:
/usr/include/c++/11/bits/unique_ptr.h:57:28: note: declared here
   57 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
In file included from ./boost/shared_ptr.hpp:17,
                 from ./boost/property_map/vector_property_map.hpp:14,
                 from ./boost/property_map/property_map.hpp:844,
                 from ./boost/graph/properties.hpp:19,
                 from ./boost/graph/graph_utility.hpp:30,
                 from PathRanker.cpp:23:
./boost/smart_ptr/shared_ptr.hpp:525:34: warning: ‘template<class> class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
  525 |     shared_ptr & operator=( std::auto_ptr<Y> & r )
      |                                  ^~~~~~~~
In file included from /usr/include/c++/11/memory:76,
                 from ./boost/config/no_tr1/memory.hpp:21,
                 from ./boost/smart_ptr/shared_ptr.hpp:27,
                 from ./boost/shared_ptr.hpp:17,
                 from ./boost/property_map/vector_property_map.hpp:14,
                 from ./boost/property_map/property_map.hpp:844,
                 from ./boost/graph/properties.hpp:19,
                 from ./boost/graph/graph_utility.hpp:30,
                 from PathRanker.cpp:23:
/usr/include/c++/11/bits/unique_ptr.h:57:28: note: declared here
   57 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
In file included from ./boost/shared_ptr.hpp:17,
                 from ./boost/property_map/vector_property_map.hpp:14,
                 from ./boost/property_map/property_map.hpp:844,
                 from ./boost/graph/properties.hpp:19,
                 from ./boost/graph/graph_utility.hpp:30,
                 from PathRanker.cpp:23:
./boost/smart_ptr/shared_ptr.hpp:534:34: warning: ‘template<class> class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
  534 |     shared_ptr & operator=( std::auto_ptr<Y> && r )
      |                                  ^~~~~~~~
In file included from /usr/include/c++/11/memory:76,
                 from ./boost/config/no_tr1/memory.hpp:21,
                 from ./boost/smart_ptr/shared_ptr.hpp:27,
                 from ./boost/shared_ptr.hpp:17,
                 from ./boost/property_map/vector_property_map.hpp:14,
                 from ./boost/property_map/property_map.hpp:844,
                 from ./boost/graph/properties.hpp:19,
                 from ./boost/graph/graph_utility.hpp:30,
                 from PathRanker.cpp:23:
/usr/include/c++/11/bits/unique_ptr.h:57:28: note: declared here
   57 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
In file included from ./boost/shared_ptr.hpp:17,
                 from ./boost/property_map/vector_property_map.hpp:14,
                 from ./boost/property_map/property_map.hpp:844,
                 from ./boost/graph/properties.hpp:19,
                 from ./boost/graph/graph_utility.hpp:30,
                 from PathRanker.cpp:23:
./boost/smart_ptr/shared_ptr.hpp:700:50: error: ‘boost::detail::sp_typeinfo’ has not been declared
  700 |     void * _internal_get_deleter( boost::detail::sp_typeinfo const & ti ) const BOOST_NOEXCEPT
      |                                                  ^~~~~~~~~~~
In file included from ./boost/shared_ptr.hpp:17,
                 from ./boost/property_map/vector_property_map.hpp:14,
                 from ./boost/property_map/property_map.hpp:844,
                 from ./boost/graph/properties.hpp:19,
                 from ./boost/graph/graph_utility.hpp:30,
                 from PathRanker.cpp:23:
./boost/smart_ptr/shared_ptr.hpp: In member function ‘boost::shared_ptr<T>& boost::shared_ptr<T>::operator=(std::auto_ptr<_Up>&&)’:
./boost/smart_ptr/shared_ptr.hpp:536:38: warning: ‘template<class> class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
  536 |         this_type( static_cast< std::auto_ptr<Y> && >( r ) ).swap( *this );
      |                                      ^~~~~~~~
In file included from /usr/include/c++/11/memory:76,
                 from ./boost/config/no_tr1/memory.hpp:21,
                 from ./boost/smart_ptr/shared_ptr.hpp:27,
                 from ./boost/shared_ptr.hpp:17,
                 from ./boost/property_map/vector_property_map.hpp:14,
                 from ./boost/property_map/property_map.hpp:844,
                 from ./boost/graph/properties.hpp:19,
                 from ./boost/graph/graph_utility.hpp:30,
                 from PathRanker.cpp:23:
/usr/include/c++/11/bits/unique_ptr.h:57:28: note: declared here
   57 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
In file included from ./boost/shared_ptr.hpp:17,
                 from ./boost/property_map/vector_property_map.hpp:14,
                 from ./boost/property_map/property_map.hpp:844,
                 from ./boost/graph/properties.hpp:19,
                 from ./boost/graph/graph_utility.hpp:30,
                 from PathRanker.cpp:23:
./boost/smart_ptr/shared_ptr.hpp: In function ‘D* boost::detail::basic_get_deleter(const boost::shared_ptr<U>&)’:
./boost/smart_ptr/shared_ptr.hpp:892:71: error: expected primary-expression before ‘)’ token
  892 |     return static_cast<D *>( p._internal_get_deleter(BOOST_SP_TYPEID(D)) );
      |                                                                       ^
./boost/smart_ptr/shared_ptr.hpp:892:54: error: there are no arguments to ‘BOOST_SP_TYPEID’ that depend on a template parameter, so a declaration of ‘BOOST_SP_TYPEID’ must be available [-fpermissive]
  892 |     return static_cast<D *>( p._internal_get_deleter(BOOST_SP_TYPEID(D)) );
      |                                                      ^~~~~~~~~~~~~~~
In file included from ./boost/shared_array.hpp:17,
                 from ./boost/graph/detail/d_ary_heap.hpp:20,
                 from ./boost/graph/named_function_params.hpp:24,
                 from ./boost/graph/depth_first_search.hpp:21,
                 from ./boost/graph/graph_utility.hpp:32,
                 from PathRanker.cpp:23:
./boost/smart_ptr/shared_array.hpp: At global scope:
./boost/smart_ptr/shared_array.hpp:223:50: error: ‘boost::detail::sp_typeinfo’ has not been declared
  223 |     void * _internal_get_deleter( boost::detail::sp_typeinfo const & ti ) const
      |                                                  ^~~~~~~~~~~
./boost/smart_ptr/shared_array.hpp: In function ‘D* boost::get_deleter(const boost::shared_array<T>&)’:
./boost/smart_ptr/shared_array.hpp:283:74: error: expected primary-expression before ‘)’ token
  283 |     return static_cast< D * >( p._internal_get_deleter( BOOST_SP_TYPEID(D) ) );
      |                                                                          ^
./boost/smart_ptr/shared_array.hpp:283:57: error: there are no arguments to ‘BOOST_SP_TYPEID’ that depend on a template parameter, so a declaration of ‘BOOST_SP_TYPEID’ must be available [-fpermissive]
  283 |     return static_cast< D * >( p._internal_get_deleter( BOOST_SP_TYPEID(D) ) );
      |                                                         ^~~~~~~~~~~~~~~
In file included from ./boost/scoped_ptr.hpp:14,
                 from ./boost/graph/adjacency_list.hpp:31,
                 from PathRanker.cpp:24:
./boost/smart_ptr/scoped_ptr.hpp: At global scope:
./boost/smart_ptr/scoped_ptr.hpp:68:31: warning: ‘template<class> class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
   68 |     explicit scoped_ptr( std::auto_ptr<T> p ) BOOST_NOEXCEPT : px( p.release() )
      |                               ^~~~~~~~
In file included from /usr/include/c++/11/memory:76,
                 from ./boost/config/no_tr1/memory.hpp:21,
                 from ./boost/smart_ptr/shared_ptr.hpp:27,
                 from ./boost/shared_ptr.hpp:17,
                 from ./boost/property_map/vector_property_map.hpp:14,
                 from ./boost/property_map/property_map.hpp:844,
                 from ./boost/graph/properties.hpp:19,
                 from ./boost/graph/graph_utility.hpp:30,
                 from PathRanker.cpp:23:
/usr/include/c++/11/bits/unique_ptr.h:57:28: note: declared here
   57 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
In file included from ./boost/graph/adjacency_list.hpp:246,
                 from PathRanker.cpp:24:
./boost/graph/detail/adjacency_list.hpp:278:12: warning: ‘template<class> class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
  278 |       std::auto_ptr<Property> m_property;
      |            ^~~~~~~~
In file included from /usr/include/c++/11/memory:76,
                 from ./boost/config/no_tr1/memory.hpp:21,
                 from ./boost/smart_ptr/shared_ptr.hpp:27,
                 from ./boost/shared_ptr.hpp:17,
                 from ./boost/property_map/vector_property_map.hpp:14,
                 from ./boost/property_map/property_map.hpp:844,
                 from ./boost/graph/properties.hpp:19,
                 from ./boost/graph/graph_utility.hpp:30,
                 from PathRanker.cpp:23:
/usr/include/c++/11/bits/unique_ptr.h:57:28: note: declared here
   57 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
make: *** [/home/biocbuild/bbs-3.17-bioc/R/etc/Makeconf:198: PathRanker.o] Error 1
ERROR: compilation failed for package ‘NetPathMiner’
* removing ‘/home/biocbuild/bbs-3.17-bioc/R/library/NetPathMiner’

bgx.install

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD INSTALL bgx
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.17-bioc/R/library’
* installing *source* package ‘bgx’ ...
** using staged installation
checking for gcc... gcc
checking for C compiler default output file name... a.out
checking whether the C compiler works... yes
checking whether we are cross compiling... no
checking for suffix of executables... 
checking for suffix of object files... o
checking whether we are using the GNU C compiler... yes
checking whether gcc accepts -g... yes
checking for gcc option to accept ISO C89... none needed
checking for C compiler vendor... gnu
checking whether C compiler accepts -ffast-math... yes
checking whether C compiler accepts -O3... yes
checking build system type... ./config.guess: unable to guess system type

This script, last modified 2006-07-02, has failed to recognize
the operating system you are using. It is advised that you
download the most up to date version of the config scripts from

  http://savannah.gnu.org/cgi-bin/viewcvs/*checkout*/config/config/config.guess
and
  http://savannah.gnu.org/cgi-bin/viewcvs/*checkout*/config/config/config.sub

If the version you run (./config.guess) is already up to date, please
send the following data and any information you think might be
pertinent to <[email protected]> in order to provide the needed
information to handle your system.

config.guess timestamp = 2006-07-02

uname -m = aarch64
uname -r = 5.15.0-58-generic
uname -s = Linux
uname -v = #64-Ubuntu SMP Thu Jan 5 12:06:43 UTC 2023

/usr/bin/uname -p = aarch64
/bin/uname -X     = 

hostinfo               = 
/bin/universe          = 
/usr/bin/arch -k       = 
/bin/arch              = aarch64
/usr/bin/oslevel       = 
/usr/convex/getsysinfo = 

UNAME_MACHINE = aarch64
UNAME_RELEASE = 5.15.0-58-generic
UNAME_SYSTEM  = Linux
UNAME_VERSION = #64-Ubuntu SMP Thu Jan 5 12:06:43 UTC 2023
configure: error: cannot guess build type; you must specify one
ERROR: configuration failed for package ‘bgx’
* removing ‘/home/biocbuild/bbs-3.17-bioc/R/library/bgx’

CopywriteR.build

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD build --keep-empty-dirs --no-resave-data CopywriteR
###
##############################################################################
##############################################################################


* checking for file ‘CopywriteR/DESCRIPTION’ ... OK
* preparing ‘CopywriteR’:
* checking DESCRIPTION meta-information ... OK
* installing the package to build vignettes
* creating vignettes ... ERROR
--- re-building ‘CopywriteR.Rnw’ using Sweave
Loading required package: BiocParallel
Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric,  :
  pseudoinverse used at 0.979
Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric,  :
  neighborhood radius 0.001
Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric,  :
  reciprocal condition number  0
Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric,  :
  There are other near singularities as well. 1e-06

Error: processing vignette 'CopywriteR.Rnw' failed with diagnostics:
 chunk 10 (label = CopywriteR) 
Error in value[[3L]](cond) : 
  The GC-content and mappability normalization did not work due to a
  failure to calculate loesses. This can generally be solved by using
  larger bin sizes. Stopping execution of the remaining part of the
  script...

--- failed re-building ‘CopywriteR.Rnw’

SUMMARY: processing the following file failed:
  ‘CopywriteR.Rnw’

Error: Vignette re-building failed.
Execution halted

ArrayExpressHTS.install

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD INSTALL ArrayExpressHTS
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.17-bioc/R/library’
* installing *source* package ‘ArrayExpressHTS’ ...
** using staged installation
** libs
using C compiler: ‘gcc (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0’
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.17-bioc/R/library/Rhtslib/include' -I/usr/local/include    -fPIC  -g -O2  -Wall -c addXS.c -o addXS.o
addXS.c: In function ‘addXS’:
addXS.c:42:5: warning: implicit declaration of function ‘Rprintf’; did you mean ‘dprintf’? [-Wimplicit-function-declaration]
   42 |     Rprintf("What?\n");
      |     ^~~~~~~
      |     dprintf
In file included from /usr/include/string.h:535,
                 from addXS.c:7:
In function ‘strncpy’,
    inlined from ‘pastefield’ at addXS.c:17:5:
/usr/include/aarch64-linux-gnu/bits/string_fortified.h:95:10: warning: ‘__builtin_strncpy’ output truncated before terminating nul copying as many bytes from a string as its length [-Wstringop-truncation]
   95 |   return __builtin___strncpy_chk (__dest, __src, __len,
      |          ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
   96 |                                   __glibc_objsize (__dest));
      |                                   ~~~~~~~~~~~~~~~~~~~~~~~~~
addXS.c: In function ‘pastefield’:
addXS.c:14:19: note: length computed here
   14 |     int length1 = strlen(text1);
      |                   ^~~~~~~~~~~~~
In file included from /usr/include/string.h:535,
                 from addXS.c:7:
In function ‘strncpy’,
    inlined from ‘pastefield’ at addXS.c:18:5:
/usr/include/aarch64-linux-gnu/bits/string_fortified.h:95:10: warning: ‘__builtin_strncpy’ output truncated before terminating nul copying as many bytes from a string as its length [-Wstringop-truncation]
   95 |   return __builtin___strncpy_chk (__dest, __src, __len,
      |          ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
   96 |                                   __glibc_objsize (__dest));
      |                                   ~~~~~~~~~~~~~~~~~~~~~~~~~
addXS.c: In function ‘pastefield’:
addXS.c:15:19: note: length computed here
   15 |     int length2 = strlen(text2);
      |                   ^~~~~~~~~~~~~
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.17-bioc/R/library/Rhtslib/include' -I/usr/local/include    -fPIC  -g -O2  -Wall -c bam_plbuf.c -o bam_plbuf.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.17-bioc/R/library/Rhtslib/include' -I/usr/local/include    -fPIC  -g -O2  -Wall -c fltbam.c -o fltbam.o
fltbam.c:2:10: fatal error: sam.h: No such file or directory
    2 | #include "sam.h"
      |          ^~~~~~~
compilation terminated.
make: *** [/home/biocbuild/bbs-3.17-bioc/R/etc/Makeconf:191: fltbam.o] Error 1
ERROR: compilation failed for package ‘ArrayExpressHTS’
* removing ‘/home/biocbuild/bbs-3.17-bioc/R/library/ArrayExpressHTS’

tiledb.install

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.17-bioc/R/bin/Rscript -e "source('/home/biocbuild/BBS/utils/installNonTargetPkg.R');installNonTargetPkg('tiledb')"
###
##############################################################################
##############################################################################


trying URL 'https://cran.rstudio.com/src/contrib/tiledb_0.18.0.tar.gz'
Content type 'application/x-gzip' length 433482 bytes (423 KB)
==================================================
downloaded 423 KB

* installing *source* package ‘tiledb’ ...
** package ‘tiledb’ successfully unpacked and MD5 sums checked
** using staged installation
checking whether the C++ compiler works... yes
checking for C++ compiler default output file name... a.out
checking for suffix of executables... 
checking whether we are cross compiling... no
checking for suffix of object files... o
checking whether the compiler supports GNU C++... yes
checking whether g++ -std=gnu++14 accepts -g... yes
checking for g++ -std=gnu++14 option to enable C++11 features... none needed
checking how to run the C++ preprocessor... g++ -std=gnu++14 -E
checking whether the compiler supports GNU C++... (cached) yes
checking whether g++ -std=gnu++14 accepts -g... (cached) yes
checking for g++ -std=gnu++14 option to enable C++11 features... (cached) none needed
checking whether g++ -std=gnu++14 supports C++17 features by default... no
checking whether g++ -std=gnu++14 supports C++17 features with -std=gnu++17... yes
checking for pkg-config... /usr/bin/pkg-config
checking if pkg-config knows TileDB... no
checking for stdio.h... yes
checking for stdlib.h... yes
checking for string.h... yes
checking for inttypes.h... yes
checking for stdint.h... yes
checking for strings.h... yes
checking for sys/stat.h... yes
checking for sys/types.h... yes
checking for unistd.h... yes
checking for tiledb/tiledb... no
configure: error: currently unsupported system Linux on aarch64
ERROR: configuration failed for package ‘tiledb’
* removing ‘/home/biocbuild/bbs-3.17-bioc/R/library/tiledb’

The downloaded source packages are in
	‘/tmp/RtmpSoMxXx/downloaded_packages’
Updating HTML index of packages in '.Library'
Making 'packages.html' ... done
Warning message:
In install.packages(pkg, repos = .NON_TARGET_REPOS, dependencies = FALSE,  :
  installation of package ‘tiledb’ had non-zero exit status

mmuphin.install

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD INSTALL MMUPHin
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.17-bioc/R/library’
ERROR: dependency ‘Maaslin2’ is not available for package ‘MMUPHin’
* removing ‘/home/biocbuild/bbs-3.17-bioc/R/library/MMUPHin’

BSgenome.Hsapiens.UCSC.hg38.masked.install

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.17-bioc/R/bin/Rscript -e "source('/home/biocbuild/BBS/utils/installNonTargetPkg.R');installNonTargetPkg('BSgenome.Hsapiens.UCSC.hg38.masked')"
###
##############################################################################
##############################################################################


trying URL 'https://bioconductor.org/packages/3.17/data/annotation/src/contrib/BSgenome.Hsapiens.UCSC.hg38.masked_1.4.4.tar.gz'
Content type 'application/x-gzip' length 23380513 bytes (22.3 MB)
==================================================
downloaded 22.3 MB

* installing *source* package ‘BSgenome.Hsapiens.UCSC.hg38.masked’ ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** testing if installed package can be loaded from temporary location
Error: package or namespace load failed for ‘BSgenome.Hsapiens.UCSC.hg38.masked’:
 .onLoad failed in loadNamespace() for 'BSgenome.Hsapiens.UCSC.hg38.masked', details:
  call: validObject(.Object)
  error: invalid class “RdaCollection” object: 
    files
    '/home/biocbuild/bbs-3.17-bioc/R/library/00LOCK-BSgenome.Hsapiens.UCSC.hg38.masked/00new/BSgenome.Hsapiens.UCSC.hg38.masked/extdata/chr1_MU273333v1_fix.masks.rda',
    '/home/biocbuild/bbs-3.17-bioc/R/library/00LOCK-BSgenome.Hsapiens.UCSC.hg38.masked/00new/BSgenome.Hsapiens.UCSC.hg38.masked/extdata/chr1_MU273334v1_fix.masks.rda',
    '/home/biocbuild/bbs-3.17-bioc/R/library/00LOCK-BSgenome.Hsapiens.UCSC.hg38.masked/00new/BSgenome.Hsapiens.UCSC.hg38.masked/extdata/chr1_MU273335v1_fix.masks.rda',
    '/home/biocbuild/bbs-3.17-bioc/R/library/00LOCK-BSgenome.Hsapiens.UCSC.hg38.masked/00new/BSgenome.Hsapiens.UCSC.hg38.masked/extdata/chr1_MU273336v1_fix.masks.rda',
    '/home/biocbuild/bbs-3.17-bioc/R/library/00LOCK-BSgenome.Hsapiens.UCSC.hg38.masked/00new/BSgenome.Hsapiens.UCSC.hg38.masked/extdata/chr2_MU273341v1_fix.masks.rda',
    '/home/biocbuild/bbs-3.17-bioc/R/library/00LOCK-BSgenome.Hsapiens.UCSC.hg38.masked/00new/BSgenome.Hsapiens.UCSC.hg38.masked/extdata/chr2_MU273342v1_fix.masks.rda',
    '/home/biocbuild/bbs-3.17-bioc/R/library/00LOCK-BSgenome.Hsapiens.UCSC.hg38.masked/00new/BSgenome.Hsapiens.UCSC.hg38.masked/extdata/chr2_MU273343v1_fix.masks.rda',
    '/home/biocbuild/bbs-3.17-bioc/R/library/00LOCK-BSgenome.Hsapiens.UCSC.hg38.masked/00new/BSgenome.Hsapiens.UCSC.hg38.masked/extdata/chr2_MU273344v1_fix.masks.rda',
    '/home/biocbuild/bbs-3.17-bioc/R/library/00LOCK-BSgenome.Hsapiens.UCSC.hg38.masked/00new/BSgenome.Hsapiens.UCSC.hg38.masked/extdata/chr2_MU273345v1_fix.masks.rda',
    '/home/biocbuild/bbs-3.17-bioc/R/library/00LOCK-BSgenome.Hsapiens.UCSC.hg38.masked/00new/BSgenome.Hsapiens.UCSC.hg38.masked/extdata/chr3_MU273346v1_fix.masks.rda',
    '/home/biocbuild/bbs-3.17-bioc/R/library/00LOCK-BSgenome.Hsapiens.UCSC.hg38.masked/00new/BSgenome.Hsapiens.UCSC.hg38.masked/extdata/chr3_MU273347v1_fix.masks.rda',
    '/home/biocbuild/bbs-3.17-bioc/R/library/00LOCK-BSgenome.Hsapiens.UCSC.hg38.masked/00new/BSgenome.Hsapiens.UCSC.hg38.masked/extdata/chr3_MU273348v1_fix.masks.rda',
    '/home/biocbuild/bbs-3.17-bioc/R/library/00LOCK-BSgenome.Hsapiens.UCSC.hg38.masked/00new/BSgenome.Hsapiens.UCSC.hg38.masked/extdata/chr4_MU273350v1_fix.masks.rda',
    '/home/biocbuild/bbs-3.17-bioc/R/library/00LOCK-BSgenome.Hsapiens.UCSC.hg38.masked/00new/BSgenome.Hsapiens.UCSC.hg38.masked/extdata/chr4_MU273351v1_fix.masks.rda',
    '/home/biocbuild/bbs-3.17-bioc/R/library/00LOCK-BSgenome.Hsapiens.UCSC.hg38.masked/00new/BSgenome.Hsapiens.UCSC.hg38.masked/extdata/chr5_MU273352v1_fix.masks.rda',
    '/home/biocbuild/bbs-3.17-bioc/R/library/00LOCK-BSgenome.Hsapiens.UCSC.hg38.masked/00new/BSgenome.Hsapiens.UCSC.hg38.masked/extdata/chr5_MU273353v1_fix.masks.rda',
    '/home/biocbuild/bbs-3.17-bioc/R/library/00LOCK-BSgenome.Hsapiens.UCSC.hg38.masked/00new/BSgenome.Hsapiens.UCSC.hg38.masked/extdata/chr5_MU273354v1_fix.masks.rda',
    '/home/biocbuild/bbs-3.17-bioc/R/library/00LOCK-BSgenome.Hsapiens.UCSC.hg38.masked/00new/BSgenome.Hsapiens.UCSC.hg38.masked/extdata/chr5_MU273355v1_fix.masks.rda',
    '/home/biocbuild/bbs-3.17-bioc/R/library/00LOCK-BSgenome.Hsapiens.UCSC.hg38.masked/00new/BSgenome.Hsapiens.UCSC.hg38.masked/extdata/chr8_MU273359v1_fix.masks.rda',
    '/home/biocbuild/bbs-3.17-bioc/R/library/00LOCK-BSgenome.Hsapiens.UCSC.hg38.masked/00new/BSgenome.Hsapiens.UCSC.hg38.masked/extdata/chr8_MU273360v1_fix.masks.rda',
    '/home/biocbuild/bbs-3.17-bioc/R/library/00LOCK-BSgenome.Hsapiens.UCSC.hg38.masked/00new/BSgenome.Hsapiens.UCSC.hg38.masked/extdata/chr8_MU273361v1_fix.masks.rda',
    '/home/biocbuild/bbs-3.17-bioc/R/library/00LOCK-BSgenome.Hsapiens.UCSC.hg38.masked/00new/BSgenome.Hsapiens.UCSC.hg38.masked/extdata/chr8_MU273362v1_fix.masks.rda',
    '/home/biocbuild/bbs-3.17-bioc/R/library/00LOCK-BSgenome.Hsapiens.UCSC.hg38.masked/00new/BSgenome.Hsapiens.UCSC.hg38.masked/extdata/chr8_MU273363v1_fix.masks.rda',
    '/home/biocbuild/bbs-3.17-bioc/R/library/00LOCK-BSgenome.Hsapiens.UCSC.hg38.masked/00new/BSgenome.Hsapiens.UCSC.hg38.masked/extdata/chr9_MU273364v1_fix.masks.rda',
    '/home/biocbuild/bbs-3.17-bioc/R/library/00LOCK-BSgenome.Hsapiens.UCSC.hg38.masked/00new/BSgenome.Hsapiens.UCSC.hg38.masked/extdata/chr9_MU273365v1_fix.masks.rda',
    '/home/biocbuild/bbs-3.17-bioc/R/library/00LOCK-BSgenome.Hsapiens.UCSC.hg38.masked/00new/BSgenome.Hsapiens.UCSC.hg38.masked/extdata/chr9_MU273366v1_fix.masks.rda',
    '/home/biocbuild/bbs-3.17-bioc/R/library/00LOCK-BSgenome.Hsapiens.UCSC.hg38.masked/00new/BSgenome.Hsapiens.UCSC.hg38.masked/extdata/chr10_MU273367v1_fix.masks.rda',
    '/home/biocbuild/bbs-3.17-bioc/R/library/00LOCK-BSgenome.Hsapiens.UCSC.hg38.masked/00new/BSgenome.Hsapiens.UCSC.hg38.masked/extdata/chr11_KQ759759v2_fix.masks.rda',
    '/home/biocbuild/bbs-3.17-bioc/R/library/00LOCK-BSgenome.Hsapiens.UCSC.hg38.masked/00new/BSgenome.Hsapiens.UCSC.hg38.masked/extdata/chr11_MU273369v1_fix.masks.rda',
    '/home/biocbuild/bbs-3.17-bioc/R/library/00LOCK-BSgenome.Hsapiens.UCSC.hg38.masked/00new/BSgenome.Hsapiens.UCSC.hg38.masked/extdata/chr11_MU273370v1_fix.masks.rda',
    '/home/biocbuild/bbs-3.17-bioc/R/library/00LOCK-BSgenome.Hsapiens.UCSC.hg38.masked/00new/BSgenome.Hsapiens.UCSC.hg38.masked/extdata/chr11_MU273371v1_fix.masks.rda',
    '/home/biocbuild/bbs-3.17-bioc/R/library/00LOCK-BSgenome.Hsapiens.UCSC.hg38.masked/00new/BSgenome.Hsapiens.UCSC.hg38.masked/extdata/chr12_MU273372v1_fix.masks.rda',
    '/home/biocbuild/bbs-3.17-bioc/R/library/00LOCK-BSgenome.Hsapiens.UCSC.hg38.masked/00new/BSgenome.Hsapiens.UCSC.hg38.masked/extdata/chr14_MU273373v1_fix.masks.rda',
    '/home/biocbuild/bbs-3.17-bioc/R/library/00LOCK-BSgenome.Hsapiens.UCSC.hg38.masked/00new/BSgenome.Hsapiens.UCSC.hg38.masked/extdata/chr15_MU273374v1_fix.masks.rda',
    '/home/biocbuild/bbs-3.17-bioc/R/library/00LOCK-BSgenome.Hsapiens.UCSC.hg38.masked/00new/BSgenome.Hsapiens.UCSC.hg38.masked/extdata/chr16_MU273376v1_fix.masks.rda',
    '/home/biocbuild/bbs-3.17-bioc/R/library/00LOCK-BSgenome.Hsapiens.UCSC.hg38.masked/00new/BSgenome.Hsapiens.UCSC.hg38.masked/extdata/chr16_MU273377v1_fix.masks.rda',
    '/home/biocbuild/bbs-3.17-bioc/R/library/00LOCK-BSgenome.Hsapiens.UCSC.hg38.masked/00new/BSgenome.Hsapiens.UCSC.hg38.masked/extdata/chr17_MU273379v1_fix.masks.rda',
    '/home/biocbuild/bbs-3.17-bioc/R/library/00LOCK-BSgenome.Hsapiens.UCSC.hg38.masked/00new/BSgenome.Hsapiens.UCSC.hg38.masked/extdata/chr17_MU273380v1_fix.masks.rda',
    '/home/biocbuild/bbs-3.17-bioc/R/library/00LOCK-BSgenome.Hsapiens.UCSC.hg38.masked/00new/BSgenome.Hsapiens.UCSC.hg38.masked/extdata/chr17_MU273381v1_fix.masks.rda',
    '/home/biocbuild/bbs-3.17-bioc/R/library/00LOCK-BSgenome.Hsapiens.UCSC.hg38.masked/00new/BSgenome.Hsapiens.UCSC.hg38.masked/extdata/chr17_MU273382v1_fix.masks.rda',
    '/home/biocbuild/bbs-3.17-bioc/R/library/00LOCK-BSgenome.Hsapiens.UCSC.hg38.masked/00new/BSgenome.Hsapiens.UCSC.hg38.masked/extdata/chr17_MU273383v1_fix.masks.rda',
    '/home/biocbuild/bbs-3.17-bioc/R/library/00LOCK-BSgenome.Hsapiens.UCSC.hg38.masked/00new/BSgenome.Hsapiens.UCSC.hg38.masked/extdata/chr19_MU273384v1_fix.masks.rda',
    '/home/biocbuild/bbs-3.17-bioc/R/library/00LOCK-BSgenome.Hsapiens.UCSC.hg38.masked/00new/BSgenome.Hsapiens.UCSC.hg38.masked/extdata/chr19_MU273385v1_fix.masks.rda',
    '/home/biocbuild/bbs-3.17-bioc/R/library/00LOCK-BSgenome.Hsapiens.UCSC.hg38.masked/00new/BSgenome.Hsapiens.UCSC.hg38.masked/extdata/chr19_MU273386v1_fix.masks.rda',
    '/home/biocbuild/bbs-3.17-bioc/R/library/00LOCK-BSgenome.Hsapiens.UCSC.hg38.masked/00new/BSgenome.Hsapiens.UCSC.hg38.masked/extdata/chr20_MU273388v1_fix.masks.rda',
    '/home/biocbuild/bbs-3.17-bioc/R/library/00LOCK-BSgenome.Hsapiens.UCSC.hg38.masked/00new/BSgenome.Hsapiens.UCSC.hg38.masked/extdata/chr20_MU273389v1_fix.masks.rda',
    '/home/biocbuild/bbs-3.17-bioc/R/library/00LOCK-BSgenome.Hsapiens.UCSC.hg38.masked/00new/BSgenome.Hsapiens.UCSC.hg38.masked/extdata/chr21_MU273390v1_fix.masks.rda',
    '/home/biocbuild/bbs-3.17-bioc/R/library/00LOCK-BSgenome.Hsapiens.UCSC.hg38.masked/00new/BSge
Error: loading failed
Execution halted
ERROR: loading failed
* removing ‘/home/biocbuild/bbs-3.17-bioc/R/library/BSgenome.Hsapiens.UCSC.hg38.masked’

The downloaded source packages are in
	‘/tmp/RtmpKbtBH7/downloaded_packages’
Updating HTML index of packages in '.Library'
Making 'packages.html' ... done
Warning message:
In install.packages(pkg, repos = .NON_TARGET_REPOS, dependencies = FALSE,  :
  installation of package ‘BSgenome.Hsapiens.UCSC.hg38.masked’ had non-zero exit status

maanova.install

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD INSTALL maanova
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.17-bioc/R/library’
* installing *source* package ‘maanova’ ...
** using staged installation
** libs
using C compiler: ‘gcc (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0’
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG   -I/usr/local/include    -fPIC  -g -O2  -Wall -c makeratio.c -o makeratio.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG   -I/usr/local/include    -fPIC  -g -O2  -Wall -c masvd.c -o masvd.o
In file included from /home/biocbuild/bbs-3.17-bioc/R/include/R_ext/Lapack.h:40,
                 from masvd.h:1,
                 from masvd.c:17:
masvd.h:14:15: error: conflicting types for ‘dgesvd_’; have ‘void(const char *, const char *, const int *, const int *, double *, const int *, double *, double *, const int *, double *, const int *, double *, const int *, int *)’
   14 | void F77_NAME(dgesvd)(const char *jobu, const char *jobvt,
      |               ^~~~~~
/home/biocbuild/bbs-3.17-bioc/R/include/R_ext/RS.h:77:25: note: in definition of macro ‘F77_CALL’
   77 | # define F77_CALL(x)    x ## _
      |                         ^
masvd.h:14:6: note: in expansion of macro ‘F77_NAME’
   14 | void F77_NAME(dgesvd)(const char *jobu, const char *jobvt,
      |      ^~~~~~~~
/home/biocbuild/bbs-3.17-bioc/R/include/R_ext/Lapack.h:348:10: note: previous declaration of ‘dgesvd_’ with type ‘void(const char *, const char *, const int *, const int *, double *, const int *, double *, double *, const int *, double *, const int *, double *, const int *, int *, size_t,  size_t)’ {aka ‘void(const char *, const char *, const int *, const int *, double *, const int *, double *, double *, const int *, double *, const int *, double *, const int *, int *, long unsigned int,  long unsigned int)’}
  348 | F77_NAME(dgesvd)(const char* jobu, const char* jobvt, const int* m,
      |          ^~~~~~
/home/biocbuild/bbs-3.17-bioc/R/include/R_ext/RS.h:77:25: note: in definition of macro ‘F77_CALL’
   77 | # define F77_CALL(x)    x ## _
      |                         ^
/home/biocbuild/bbs-3.17-bioc/R/include/R_ext/Lapack.h:348:1: note: in expansion of macro ‘F77_NAME’
  348 | F77_NAME(dgesvd)(const char* jobu, const char* jobvt, const int* m,
      | ^~~~~~~~
masvd.c: In function ‘masvd’:
masvd.c:68:18: error: too few arguments to function ‘dgesdd_’
   68 |         F77_CALL(dgesdd)(CHAR(STRING_ELT(jobu, 0)),
      |                  ^~~~~~
/home/biocbuild/bbs-3.17-bioc/R/include/R_ext/RS.h:77:25: note: in definition of macro ‘F77_CALL’
   77 | # define F77_CALL(x)    x ## _
      |                         ^
/home/biocbuild/bbs-3.17-bioc/R/include/R_ext/Lapack.h:2397:10: note: declared here
 2397 | F77_NAME(dgesdd)(const char* jobz,
      |          ^~~~~~
/home/biocbuild/bbs-3.17-bioc/R/include/R_ext/RS.h:77:25: note: in definition of macro ‘F77_CALL’
   77 | # define F77_CALL(x)    x ## _
      |                         ^
/home/biocbuild/bbs-3.17-bioc/R/include/R_ext/Lapack.h:2397:1: note: in expansion of macro ‘F77_NAME’
 2397 | F77_NAME(dgesdd)(const char* jobz,
      | ^~~~~~~~
masvd.c:77:18: error: too few arguments to function ‘dgesdd_’
   77 |         F77_CALL(dgesdd)(CHAR(STRING_ELT(jobu, 0)),
      |                  ^~~~~~
masvd.c:77:9: note: in expansion of macro ‘F77_CALL’
   77 |         F77_CALL(dgesdd)(CHAR(STRING_ELT(jobu, 0)),
      |         ^~~~~~~~
/home/biocbuild/bbs-3.17-bioc/R/include/R_ext/Lapack.h:2397:10: note: declared here
 2397 | F77_NAME(dgesdd)(const char* jobz,
      |          ^~~~~~
/home/biocbuild/bbs-3.17-bioc/R/include/R_ext/RS.h:77:25: note: in definition of macro ‘F77_CALL’
   77 | # define F77_CALL(x)    x ## _
      |                         ^
/home/biocbuild/bbs-3.17-bioc/R/include/R_ext/Lapack.h:2397:1: note: in expansion of macro ‘F77_NAME’
 2397 | F77_NAME(dgesdd)(const char* jobz,
      | ^~~~~~~~
masvd.c: At top level:
masvd.c:114:9: warning: "/*" within comment [-Wcomment]
  114 |         /* work on a copy of x */
      |          
masvd.c:154:1: warning: "/*" within comment [-Wcomment]
  154 | /*#ifndef IEEE_754
      |  
masvd.c:161:5: warning: "/*" within comment [-Wcomment]
  161 |     /* work on a copy of x */
      |      
masvd.c:165:9: warning: "/*" within comment [-Wcomment]
  165 |         /* ask for optimal size of work array */
      |          
masvd.c:189:9: warning: "/*" within comment [-Wcomment]
  189 |         /* ask for optimal size of work array */
      |          
make: *** [/home/biocbuild/bbs-3.17-bioc/R/etc/Makeconf:191: masvd.o] Error 1
ERROR: compilation failed for package ‘maanova’
* removing ‘/home/biocbuild/bbs-3.17-bioc/R/library/maanova’

Travel.install

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD INSTALL Travel
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.17-bioc/R/library’
* installing *source* package ‘Travel’ ...
** using staged installation
** libs
using C++ compiler: ‘g++ (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0’
using C++11
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG `pkg-config fuse --cflags` -I'/home/biocbuild/bbs-3.17-bioc/R/library/Rcpp/include' -I/usr/local/include    -fPIC  -g -O2  -Wall -c Cpp_interface.cpp -o Cpp_interface.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG `pkg-config fuse --cflags` -I'/home/biocbuild/bbs-3.17-bioc/R/library/Rcpp/include' -I/usr/local/include    -fPIC  -g -O2  -Wall -c RcppExports.cpp -o RcppExports.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG `pkg-config fuse --cflags` -I'/home/biocbuild/bbs-3.17-bioc/R/library/Rcpp/include' -I/usr/local/include    -fPIC  -g -O2  -Wall -c altfile_operations.cpp -o altfile_operations.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG `pkg-config fuse --cflags` -I'/home/biocbuild/bbs-3.17-bioc/R/library/Rcpp/include' -I/usr/local/include    -fPIC  -g -O2  -Wall -c altmmap_operations.cpp -o altmmap_operations.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG `pkg-config fuse --cflags` -I'/home/biocbuild/bbs-3.17-bioc/R/library/Rcpp/include' -I/usr/local/include    -fPIC  -g -O2  -Wall -c altrep_manager.cpp -o altrep_manager.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG `pkg-config fuse --cflags` -I'/home/biocbuild/bbs-3.17-bioc/R/library/Rcpp/include' -I/usr/local/include    -fPIC  -g -O2  -Wall -c class_Cache_block.cpp -o class_Cache_block.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG `pkg-config fuse --cflags` -I'/home/biocbuild/bbs-3.17-bioc/R/library/Rcpp/include' -I/usr/local/include    -fPIC  -g -O2  -Wall -c class_Filesystem_cache_copier.cpp -o class_Filesystem_cache_copier.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG `pkg-config fuse --cflags` -I'/home/biocbuild/bbs-3.17-bioc/R/library/Rcpp/include' -I/usr/local/include    -fPIC  -g -O2  -Wall -c class_Filesystem_file_data.cpp -o class_Filesystem_file_data.o
In file included from class_Filesystem_file_data.h:5,
                 from class_Filesystem_file_data.cpp:1:
class_Cache_block.h:10:5: error: ‘size_t’ does not name a type
   10 |     size_t size;
      |     ^~~~~~
class_Cache_block.h:1:1: note: ‘size_t’ is defined in header ‘<cstddef>’; did you forget to ‘#include <cstddef>’?
  +++ |+#include <cstddef>
    1 | #ifndef HEADER_CACHE_BLOCK
class_Cache_block.h:11:5: error: ‘size_t’ does not name a type
   11 |     size_t *counter = nullptr;
      |     ^~~~~~
class_Cache_block.h:11:5: note: ‘size_t’ is defined in header ‘<cstddef>’; did you forget to ‘#include <cstddef>’?
class_Cache_block.h:14:23: error: expected ‘)’ before ‘size’
   14 |     Cache_block(size_t size);
      |                ~      ^~~~~
      |                       )
class_Cache_block.h:21:5: error: ‘size_t’ does not name a type
   21 |     size_t use_count() const;
      |     ^~~~~~
class_Cache_block.h:21:5: note: ‘size_t’ is defined in header ‘<cstddef>’; did you forget to ‘#include <cstddef>’?
class_Cache_block.h:23:5: error: ‘size_t’ does not name a type
   23 |     size_t get_size() const;
      |     ^~~~~~
class_Cache_block.h:23:5: note: ‘size_t’ is defined in header ‘<cstddef>’; did you forget to ‘#include <cstddef>’?
class_Cache_block.h:27:5: error: ‘size_t’ does not name a type
   27 |     size_t get_serialize_size() const;
      |     ^~~~~~
class_Cache_block.h:27:5: note: ‘size_t’ is defined in header ‘<cstddef>’; did you forget to ‘#include <cstddef>’?
class_Filesystem_file_data.cpp: In member function ‘size_t Filesystem_file_data::get_serialize_size()’:
class_Filesystem_file_data.cpp:70:26: error: ‘const class Cache_block’ has no member named ‘get_serialize_size’
   70 |         size += i.second.get_serialize_size();
      |                          ^~~~~~~~~~~~~~~~~~
class_Filesystem_file_data.cpp: In member function ‘void Filesystem_file_data::serialize(void*)’:
class_Filesystem_file_data.cpp:92:39: error: ‘const class Cache_block’ has no member named ‘get_serialize_size’
   92 |         size_t buffer_size = i.second.get_serialize_size();
      |                                       ^~~~~~~~~~~~~~~~~~
class_Filesystem_file_data.cpp: In member function ‘void Filesystem_cache_index_iterator::compute_block_info()’:
class_Filesystem_file_data.cpp:177:39: error: ‘class Cache_block’ has no member named ‘get_size’
  177 |     block_length = block_iter->second.get_size() / type_size;
      |                                       ^~~~~~~~
make: *** [/home/biocbuild/bbs-3.17-bioc/R/etc/Makeconf:198: class_Filesystem_file_data.o] Error 1
ERROR: compilation failed for package ‘Travel’
* removing ‘/home/biocbuild/bbs-3.17-bioc/R/library/Travel’

qrqc.install

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD INSTALL qrqc
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.17-bioc/R/library’
* installing *source* package ‘qrqc’ ...
** using staged installation
** libs
using C compiler: ‘gcc (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0’
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.17-bioc/R/library/Rhtslib/include' -I/usr/local/include    -fPIC  -g -O2  -Wall -c R_init_io.c -o R_init_io.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.17-bioc/R/library/Rhtslib/include' -I/usr/local/include    -fPIC  -g -O2  -Wall -c io.c -o io.o
In file included from /home/biocbuild/bbs-3.17-bioc/R/include/R.h:78,
                 from io.c:7:
io.c: In function ‘hash_seq_kmers’:
io.c:222:39: error: ‘SINT_MAX’ undeclared (first use in this function); did you mean ‘WINT_MAX’?
  222 |   char *a_kmer = Calloc(k + 2 + log10(SINT_MAX), char), *start_ptr;
      |                                       ^~~~~~~~
/home/biocbuild/bbs-3.17-bioc/R/include/R_ext/RS.h:53:56: note: in definition of macro ‘Calloc’
   53 | #define Calloc(n, t)   (t *) R_chk_calloc( (R_SIZE_T) (n), sizeof(t) )
      |                                                        ^
io.c:222:39: note: each undeclared identifier is reported only once for each function it appears in
  222 |   char *a_kmer = Calloc(k + 2 + log10(SINT_MAX), char), *start_ptr;
      |                                       ^~~~~~~~
/home/biocbuild/bbs-3.17-bioc/R/include/R_ext/RS.h:53:56: note: in definition of macro ‘Calloc’
   53 | #define Calloc(n, t)   (t *) R_chk_calloc( (R_SIZE_T) (n), sizeof(t) )
      |                                                        ^
io.c: In function ‘summarize_file’:
io.c:33:25: warning: initialization of ‘struct gzFile_s **’ from incompatible pointer type ‘gzFile’ {aka ‘struct gzFile_s *’} [-Wincompatible-pointer-types]
   33 | #define FILE_OPEN(x, m) (gzopen(x, m))
      |                         ^
io.c:348:19: note: in expansion of macro ‘FILE_OPEN’
  348 |   FILE_TYPE *fp = FILE_OPEN(CHAR(STRING_ELT(filename, 0)), "r");
      |                   ^~~~~~~~~
io.c:351:21: warning: passing argument 1 of ‘kseq_init’ from incompatible pointer type [-Wincompatible-pointer-types]
  351 |   block = kseq_init(fp);
      |                     ^~
      |                     |
      |                     struct gzFile_s **
In file included from io.c:12:
/home/biocbuild/bbs-3.17-bioc/R/library/Rhtslib/include/htslib/kseq.h:165:40: note: expected ‘gzFile’ {aka ‘struct gzFile_s *’} but argument is of type ‘struct gzFile_s **’
  165 |         SCOPE kseq_t *kseq_init(type_t fd)                                                                      \
/home/biocbuild/bbs-3.17-bioc/R/library/Rhtslib/include/htslib/kseq.h:237:9: note: in expansion of macro ‘__KSEQ_BASIC’
  237 |         __KSEQ_BASIC(SCOPE, type_t)                                     \
      |         ^~~~~~~~~~~~
/home/biocbuild/bbs-3.17-bioc/R/library/Rhtslib/include/htslib/kseq.h:240:35: note: in expansion of macro ‘KSEQ_INIT2’
  240 | #define KSEQ_INIT(type_t, __read) KSEQ_INIT2(static, type_t, __read)
      |                                   ^~~~~~~~~~
io.c:35:1: note: in expansion of macro ‘KSEQ_INIT’
   35 | KSEQ_INIT(gzFile, gzread)
      | ^~~~~~~~~
io.c:453:21: warning: passing argument 1 of ‘kseq_init’ from incompatible pointer type [-Wincompatible-pointer-types]
  453 |   block = kseq_init(fp);
      |                     ^~
      |                     |
      |                     struct gzFile_s **
In file included from io.c:12:
/home/biocbuild/bbs-3.17-bioc/R/library/Rhtslib/include/htslib/kseq.h:165:40: note: expected ‘gzFile’ {aka ‘struct gzFile_s *’} but argument is of type ‘struct gzFile_s **’
  165 |         SCOPE kseq_t *kseq_init(type_t fd)                                                                      \
/home/biocbuild/bbs-3.17-bioc/R/library/Rhtslib/include/htslib/kseq.h:237:9: note: in expansion of macro ‘__KSEQ_BASIC’
  237 |         __KSEQ_BASIC(SCOPE, type_t)                                     \
      |         ^~~~~~~~~~~~
/home/biocbuild/bbs-3.17-bioc/R/library/Rhtslib/include/htslib/kseq.h:240:35: note: in expansion of macro ‘KSEQ_INIT2’
  240 | #define KSEQ_INIT(type_t, __read) KSEQ_INIT2(static, type_t, __read)
      |                                   ^~~~~~~~~~
io.c:35:1: note: in expansion of macro ‘KSEQ_INIT’
   35 | KSEQ_INIT(gzFile, gzread)
      | ^~~~~~~~~
io.c:454:14: warning: passing argument 1 of ‘gzclose’ from incompatible pointer type [-Wincompatible-pointer-types]
  454 |   FILE_CLOSE(fp);
      |              ^~
      |              |
      |              struct gzFile_s **
io.c:34:32: note: in definition of macro ‘FILE_CLOSE’
   34 | #define FILE_CLOSE(x) (gzclose(x))
      |                                ^
In file included from /usr/include/zlib.h:34,
                 from io.c:31:
/usr/include/zlib.h:1631:32: note: expected ‘gzFile’ {aka ‘struct gzFile_s *’} but argument is of type ‘struct gzFile_s **’
 1631 | ZEXTERN int ZEXPORT    gzclose OF((gzFile file));
      |                                ^~
In file included from io.c:12:
At top level:
/home/biocbuild/bbs-3.17-bioc/R/library/Rhtslib/include/htslib/kseq.h:171:20: warning: ‘kseq_destroy’ defined but not used [-Wunused-function]
  171 |         SCOPE void kseq_destroy(kseq_t *ks)                                                                     \
      |                    ^~~~~~~~~~~~
/home/biocbuild/bbs-3.17-bioc/R/library/Rhtslib/include/htslib/kseq.h:237:9: note: in expansion of macro ‘__KSEQ_BASIC’
  237 |         __KSEQ_BASIC(SCOPE, type_t)                                     \
      |         ^~~~~~~~~~~~
/home/biocbuild/bbs-3.17-bioc/R/library/Rhtslib/include/htslib/kseq.h:240:35: note: in expansion of macro ‘KSEQ_INIT2’
  240 | #define KSEQ_INIT(type_t, __read) KSEQ_INIT2(static, type_t, __read)
      |                                   ^~~~~~~~~~
io.c:35:1: note: in expansion of macro ‘KSEQ_INIT’
   35 | KSEQ_INIT(gzFile, gzread)
      | ^~~~~~~~~
make: *** [/home/biocbuild/bbs-3.17-bioc/R/etc/Makeconf:191: io.o] Error 1
ERROR: compilation failed for package ‘qrqc’
* removing ‘/home/biocbuild/bbs-3.17-bioc/R/library/qrqc’

bioconcotk.build

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD build --keep-empty-dirs --no-resave-data BiocOncoTK
###
##############################################################################
##############################################################################


* checking for file ‘BiocOncoTK/DESCRIPTION’ ... OK
* preparing ‘BiocOncoTK’:
* checking DESCRIPTION meta-information ... OK
* installing the package to build vignettes
* creating vignettes ... ERROR
--- re-building ‘BiocOncoTK.Rmd’ using rmarkdown
Quitting from lines 690-695 (BiocOncoTK.Rmd) 
Error: processing vignette 'BiocOncoTK.Rmd' failed with diagnostics:
'dimnames' applied to non-array
--- failed re-building ‘BiocOncoTK.Rmd’

--- re-building ‘curatedMSIData.Rmd’ using rmarkdown
--- finished re-building ‘curatedMSIData.Rmd’

--- re-building ‘maptcga.Rmd’ using rmarkdown
--- finished re-building ‘maptcga.Rmd’

SUMMARY: processing the following file failed:
  ‘BiocOncoTK.Rmd’

Error: Vignette re-building failed.
Execution halted

STAN.install

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD INSTALL STAN
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.17-bioc/R/library’
* installing *source* package ‘STAN’ ...
** using staged installation
** libs
using C++ compiler: ‘g++ (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0’
g++ -std=gnu++14  -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG   -I/usr/local/include   -D_RDLL_ -fopenmp  -fPIC  -g -O2  -Wall  -c Bernoulli.cpp -o Bernoulli.o
g++ -std=gnu++14  -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG   -I/usr/local/include   -D_RDLL_ -fopenmp  -fPIC  -g -O2  -Wall  -c EmissionFactory.cpp -o EmissionFactory.o
g++ -std=gnu++14  -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG   -I/usr/local/include   -D_RDLL_ -fopenmp  -fPIC  -g -O2  -Wall  -c EmissionFunction.cpp -o EmissionFunction.o
g++ -std=gnu++14  -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG   -I/usr/local/include   -D_RDLL_ -fopenmp  -fPIC  -g -O2  -Wall  -c HMM.cpp -o HMM.o
g++ -std=gnu++14  -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG   -I/usr/local/include   -D_RDLL_ -fopenmp  -fPIC  -g -O2  -Wall  -c InitialProbability.cpp -o InitialProbability.o
g++ -std=gnu++14  -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG   -I/usr/local/include   -D_RDLL_ -fopenmp  -fPIC  -g -O2  -Wall  -c JointlyIndependent.cpp -o JointlyIndependent.o
g++ -std=gnu++14  -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG   -I/usr/local/include   -D_RDLL_ -fopenmp  -fPIC  -g -O2  -Wall  -c MemoryAllocation.cpp -o MemoryAllocation.o
g++ -std=gnu++14  -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG   -I/usr/local/include   -D_RDLL_ -fopenmp  -fPIC  -g -O2  -Wall  -c Multinomial.cpp -o Multinomial.o
g++ -std=gnu++14  -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG   -I/usr/local/include   -D_RDLL_ -fopenmp  -fPIC  -g -O2  -Wall  -c MultivariateGaussian.cpp -o MultivariateGaussian.o
g++ -std=gnu++14  -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG   -I/usr/local/include   -D_RDLL_ -fopenmp  -fPIC  -g -O2  -Wall  -c NegativeBinomial.cpp -o NegativeBinomial.o
g++ -std=gnu++14  -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG   -I/usr/local/include   -D_RDLL_ -fopenmp  -fPIC  -g -O2  -Wall  -c ParamContainerEmissions.cpp -o ParamContainerEmissions.o
g++ -std=gnu++14  -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG   -I/usr/local/include   -D_RDLL_ -fopenmp  -fPIC  -g -O2  -Wall  -c Poisson.cpp -o Poisson.o
g++ -std=gnu++14  -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG   -I/usr/local/include   -D_RDLL_ -fopenmp  -fPIC  -g -O2  -Wall  -c PoissonLogNormal.cpp -o PoissonLogNormal.o
g++ -std=gnu++14  -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG   -I/usr/local/include   -D_RDLL_ -fopenmp  -fPIC  -g -O2  -Wall  -c RAccessUtils.cpp -o RAccessUtils.o
g++ -std=gnu++14  -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG   -I/usr/local/include   -D_RDLL_ -fopenmp  -fPIC  -g -O2  -Wall  -c RWrapper.cpp -o RWrapper.o
RWrapper.cpp: In function ‘EmissionFunction** RGETEMISSION(SEXP, int, SEXP, int*, const char*, double***, int*, int, SEXP, int*, int*, int*)’:
RWrapper.cpp:350:16: warning: ‘HMMEmissionFunctions’ may be used uninitialized in this function [-Wmaybe-uninitialized]
  350 |         return HMMEmissionFunctions;
      |                ^~~~~~~~~~~~~~~~~~~~
RWrapper.cpp: In function ‘SEXPREC* prepareEmission(const char*, SEXP, SEXP, EmissionFunction**, int)’:
RWrapper.cpp:1157:16: warning: ‘sexpemissionParam’ may be used uninitialized in this function [-Wmaybe-uninitialized]
 1157 |         return sexpemissionParam;
      |                ^~~~~~~~~~~~~~~~~
g++ -std=gnu++14  -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG   -I/usr/local/include   -D_RDLL_ -fopenmp  -fPIC  -g -O2  -Wall  -c TransitionMatrix.cpp -o TransitionMatrix.o
g++ -std=gnu++14  -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG   -I/usr/local/include   -D_RDLL_ -fopenmp  -fPIC  -g -O2  -Wall  -c matUtils.cpp -o matUtils.o
matUtils.cpp: In function ‘double matrixDet(double**, int)’:
matUtils.cpp:118:20: error: too few arguments to function ‘void dspev_(const char*, const char*, const int*, double*, double*, double*, const int*, double*, int*, size_t, size_t)’
  118 |     F77_NAME(dspev)("V", "U", &myN, myAP, myW, myZ, &myldz, myWork, &myInfo) ;
      |                    ^
In file included from /home/biocbuild/bbs-3.17-bioc/R/include/R.h:78,
                 from matUtils.h:6,
                 from matUtils.cpp:2:
/home/biocbuild/bbs-3.17-bioc/R/include/R_ext/Lapack.h:1050:10: note: declared here
 1050 | F77_NAME(dspev)(const char* jobz, const char* uplo, const int* n,
      |          ^~~~~
/home/biocbuild/bbs-3.17-bioc/R/include/R_ext/RS.h:77:25: note: in definition of macro ‘F77_CALL’
   77 | # define F77_CALL(x)    x ## _
      |                         ^
/home/biocbuild/bbs-3.17-bioc/R/include/R_ext/Lapack.h:1050:1: note: in expansion of macro ‘F77_NAME’
 1050 | F77_NAME(dspev)(const char* jobz, const char* uplo, const int* n,
      | ^~~~~~~~
make: *** [/home/biocbuild/bbs-3.17-bioc/R/etc/Makeconf:198: matUtils.o] Error 1
ERROR: compilation failed for package ‘STAN’
* removing ‘/home/biocbuild/bbs-3.17-bioc/R/library/STAN’

magick.install

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.17-bioc/R/bin/Rscript -e "source('/home/biocbuild/BBS/utils/installNonTargetPkg.R');installNonTargetPkg('magick')"
###
##############################################################################
##############################################################################


trying URL 'https://cran.rstudio.com/src/contrib/magick_2.7.3.tar.gz'
Content type 'application/x-gzip' length 4813163 bytes (4.6 MB)
==================================================
downloaded 4.6 MB

* installing *source* package ‘magick’ ...
** package ‘magick’ successfully unpacked and MD5 sums checked
** using staged installation
Package Magick++ was not found in the pkg-config search path.
Perhaps you should add the directory containing `Magick++.pc'
to the PKG_CONFIG_PATH environment variable
No package 'Magick++' found
Warning: found GraphicsMagick++ instead of ImageMagick++. GraphicsMagick is not supported.
Using PKG_CFLAGS=
Using PKG_LIBS=-lMagick++-6.Q16
** libs
using C++ compiler: ‘g++ (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0’
using C++11
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.17-bioc/R/library/Rcpp/include' -I/usr/local/include   -fvisibility=hidden -fPIC  -g -O2  -Wall -c RcppExports.cpp -o RcppExports.o
In file included from RcppExports.cpp:4:
magick_types.h:36:9: error: ‘Point’ in namespace ‘Magick’ does not name a type
   36 | Magick::Point Point(const char * str);
      |         ^~~~~
magick_types.h:44:22: error: ‘FilterType’ in namespace ‘Magick’ does not name a type; did you mean ‘FilterTypes’?
   44 | #define myFilterType FilterType
      |                      ^~~~~~~~~~
magick_types.h:44:22: note: in definition of macro ‘myFilterType’
   44 | #define myFilterType FilterType
      |                      ^~~~~~~~~~
make: *** [/home/biocbuild/bbs-3.17-bioc/R/etc/Makeconf:198: RcppExports.o] Error 1
ERROR: compilation failed for package ‘magick’
* removing ‘/home/biocbuild/bbs-3.17-bioc/R/library/magick’

The downloaded source packages are in
	‘/tmp/RtmpLK6WBV/downloaded_packages’
Updating HTML index of packages in '.Library'
Making 'packages.html' ... done
Warning messages:
1: In install.packages(pkg, repos = .NON_TARGET_REPOS, dependencies = FALSE,  :
  installation of package ‘magick’ had non-zero exit status
2: In packageDescription(i, lib.loc = lib, fields = "Title", encoding = "UTF-8") :
  DESCRIPTION file of package 'RedeR' is missing or broken

biomvRCNS.install

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD INSTALL biomvRCNS
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.17-bioc/R/library’
* installing *source* package ‘biomvRCNS’ ...
** using staged installation
** libs
using C compiler: ‘gcc (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0’
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG   -I/usr/local/include    -fPIC  -g -O2  -Wall -c biomvRCNS.c -o biomvRCNS.o
biomvRCNS.c: In function ‘forward’:
biomvRCNS.c:153:43: error: ‘DOUBLE_XMIN’ undeclared (first use in this function); did you mean ‘DBL_MIN’?
  153 |                         m_e(F, t, j, T)+= DOUBLE_XMIN;
      |                                           ^~~~~~~~~~~
      |                                           DBL_MIN
biomvRCNS.c:153:43: note: each undeclared identifier is reported only once for each function it appears in
biomvRCNS.c: In function ‘viterbi’:
biomvRCNS.c:294:36: error: ‘DOUBLE_XMAX’ undeclared (first use in this function); did you mean ‘DBL_MAX’?
  294 |         double obs, prod, maxprod=-DOUBLE_XMAX;
      |                                    ^~~~~~~~~~~
      |                                    DBL_MAX
biomvRCNS.c: In function ‘logviterbi’:
biomvRCNS.c:401:36: error: ‘DOUBLE_XMAX’ undeclared (first use in this function); did you mean ‘DBL_MAX’?
  401 |         double obs, prod, maxprod=-DOUBLE_XMAX;
      |                                    ^~~~~~~~~~~
      |                                    DBL_MAX
make: *** [/home/biocbuild/bbs-3.17-bioc/R/etc/Makeconf:191: biomvRCNS.o] Error 1
ERROR: compilation failed for package ‘biomvRCNS’
* removing ‘/home/biocbuild/bbs-3.17-bioc/R/library/biomvRCNS’

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