psichomics() Error in xj[i] : invalid subscript type 'list' about psichomics HOT 3 CLOSED

remotes::install_github("nuno-agostinho/psichomics")

Downloading GitHub repo nuno-agostinho/psichomics@HEAD
These packages have more recent versions available.
It is recommended to update all of them.
Which would you like to update?

1: All                                           
2: CRAN packages only                            
3: None                                          
4: RcppArmad... (0.10.7.0.0 -> 0.10.7.3.0) [CRAN]

Enter one or more numbers, or an empty line to skip updates: a
Enter one or more numbers, or an empty line to skip updates: 1
RcppArmad... (0.10.7.0.0 -> 0.10.7.3.0) [CRAN]
Installing 1 packages: RcppArmadillo

  There is a binary version available but the source version is later:
                  binary     source needs_compilation
RcppArmadillo 0.10.7.0.0 0.10.7.3.0              TRUE

Do you want to install from sources the package which needs compilation? (Yes/no/cancel) y
installing the source package ‘RcppArmadillo’

trying URL 'https://cran.rstudio.com/src/contrib/RcppArmadillo_0.10.7.3.0.tar.gz'
Content type 'application/x-gzip' length 1360186 bytes (1.3 MB)
==================================================
downloaded 1.3 MB

* installing *source* package ‘RcppArmadillo’ ...
** package ‘RcppArmadillo’ 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 we are using the GNU C++ compiler... yes
checking whether clang++ -mmacosx-version-min=10.13 -std=gnu++11 accepts -g... yes
checking how to run the C++ preprocessor... clang++ -mmacosx-version-min=10.13 -std=gnu++11 -E
checking whether we are using the GNU C++ compiler... (cached) yes
checking whether clang++ -mmacosx-version-min=10.13 -std=gnu++11 accepts -g... (cached) yes
checking whether we have a suitable tempdir... /var/folders/2_/s4f95b5s2bg0bv464z8gr56h0000gn/T
checking whether R CMD SHLIB can already compile programs using OpenMP... yes
checking LAPACK_LIBS... R-supplied partial LAPACK found
configure: WARNING: Some complex-valued LAPACK functions may not be available
configure: creating ./config.status
config.status: creating inst/include/RcppArmadilloConfigGenerated.h
config.status: creating src/Makevars
** libs
clang++ -mmacosx-version-min=10.13 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rcpp/include' -I/usr/local/include  -I../inst/include  -fPIC  -Wall -g -O2  -c RcppArmadillo.cpp -o RcppArmadillo.o
clang++ -mmacosx-version-min=10.13 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rcpp/include' -I/usr/local/include  -I../inst/include  -fPIC  -Wall -g -O2  -c RcppExports.cpp -o RcppExports.o
clang++ -mmacosx-version-min=10.13 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rcpp/include' -I/usr/local/include  -I../inst/include  -fPIC  -Wall -g -O2  -c fastLm.cpp -o fastLm.o
clang++ -mmacosx-version-min=10.13 -std=gnu++11 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/Library/Frameworks/R.framework/Resources/lib -L/usr/local/lib -o RcppArmadillo.so RcppArmadillo.o RcppExports.o fastLm.o -L/Library/Frameworks/R.framework/Resources/lib -lRlapack -L/Library/Frameworks/R.framework/Resources/lib -lRblas -L/usr/local/gfortran/lib/gcc/x86_64-apple-darwin18/8.2.0 -L/usr/local/gfortran/lib -lgfortran -lquadmath -lm -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
ld: warning: directory not found for option '-L/usr/local/gfortran/lib/gcc/x86_64-apple-darwin18/8.2.0'
ld: warning: directory not found for option '-L/usr/local/gfortran/lib'
ld: library not found for -lgfortran
clang: error: linker command failed with exit code 1 (use -v to see invocation)
make: *** [RcppArmadillo.so] Error 1
ERROR: compilation failed for package ‘RcppArmadillo’
* removing ‘/Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppArmadillo’
* restoring previous ‘/Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppArmadillo’

The downloaded source packages are in
	‘/private/var/folders/2_/s4f95b5s2bg0bv464z8gr56h0000gn/T/RtmpFdIV0Q/downloaded_packages’
✓  checking for file ‘/private/var/folders/2_/s4f95b5s2bg0bv464z8gr56h0000gn/T/RtmpFdIV0Q/remotesa9571931e28/nuno-agostinho-psichomics-ff7d8f2/DESCRIPTION’ ...
─  preparing ‘psichomics’: (389ms)
✓  checking DESCRIPTION meta-information ...
─  cleaning src
─  checking for LF line-endings in source and make files and shell scripts (398ms)
─  checking for empty or unneeded directories
─  building ‘psichomics_1.20.0.tar.gz’
   
* installing *source* package ‘psichomics’ ...
** using staged installation
** libs
clang++ -mmacosx-version-min=10.13 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rcpp/include' -I/usr/local/include   -fPIC  -Wall -g -O2  -c RcppExports.cpp -o RcppExports.o
clang++ -mmacosx-version-min=10.13 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rcpp/include' -I/usr/local/include   -fPIC  -Wall -g -O2  -c progressBar.cpp -o progressBar.o
clang++ -mmacosx-version-min=10.13 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rcpp/include' -I/usr/local/include   -fPIC  -Wall -g -O2  -c psiFastCalc.cpp -o psiFastCalc.o
clang++ -mmacosx-version-min=10.13 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rcpp/include' -I/usr/local/include   -fPIC  -Wall -g -O2  -c vastToolsParser.cpp -o vastToolsParser.o
clang++ -mmacosx-version-min=10.13 -std=gnu++11 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/Library/Frameworks/R.framework/Resources/lib -L/usr/local/lib -o psichomics.so RcppExports.o progressBar.o psiFastCalc.o vastToolsParser.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Library/Frameworks/R.framework/Versions/4.0/Resources/library/00LOCK-psichomics/00new/psichomics/libs
** R
** inst
** byte-compile and prepare package for lazy loading
Creating a generic function for ‘colSums’ from package ‘base’ in package ‘psichomics’
** help
*** installing help indices
*** copying figures
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (psichomics)
Warning message:
In i.p(...) :
  installation of package ‘RcppArmadillo’ had non-zero exit status

library("psichomics")
Loading required package: shiny
Loading required package: shinyBS
Registered S3 method overwritten by 'quantmod':
  method            from
  as.zoo.data.frame zoo 
Setting options('download.file.method.GEOquery'='auto')
Setting options('GEOquery.inmemory.gpl'=FALSE)

psichomics 1.20.0: start the visual interface by running psichomics()
Full documentation and tutorials at https://nuno-agostinho.github.io/psichomics

psichomics()

Listening on http://127.0.0.1:3364

R.version.string
[1] "R version 4.0.4 (2021-02-15)"

packageVersion("psichomics")
[1] ‘1.20.0’