Comments (6)
cziegenhain
commented on June 13, 2024
1
Stringi should be available for R3.4.4! Have you tried just running:
install.packages("stringi")
Sometimes dependencies don't install well automatically although they are available.
from powsimr.
sulgithub
commented on June 13, 2024
Yes - I came to the same conclusion as well.
install.packages("stringi") worked - though I had to fix another error (apparently due to a previous package installation is interrupted / terminated abnormally - found a way to unlink it here: https://support.rstudio.com/hc/en-us/community/posts/203309146-Build-error)
I then tried the install command
devtools::install_github("bvieth/powsimR", build_vignettes = TRUE, dependencies = FALSE)
but ran into a similar SVN issue as someone else posted previously.
So I used Homebrew on my MacOS to install SVN:
brew options subversion
brew install --with-gettext --with-gpg-agent --with-java subversion
However, it still produces an error:
devtools::install_github("bvieth/powsimR", build_vignettes = TRUE, dependencies = FALSE)
Downloading GitHub repo bvieth/powsimR@master
from URL https://api.github.com/repos/bvieth/powsimR/zipball/master
Installing powsimR
svn: E170013: Unable to connect to a repository at URL 'https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/AnnotationDbi'
svn: E230001: Server SSL certificate verification failed: issuer is not trusted
Installation failed: There was a problem retrieving the current SVN revision
Warning message:
running command ''/usr/bin/svn' info --xml --username readonly --password readonly https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/AnnotationDbi' had status 1
Any thoughts?
from powsimr.
cziegenhain
commented on June 13, 2024
There was similar issue related to SVN previously, I think Beate suggested to install all packages manually: (there is a code snippet for that)
from powsimr.
sulgithub
commented on June 13, 2024
Yes I read through the other issue and ran installed all packages manually after installing "stringi" and SVN, but I still received the error message. There were multiple warnings which I assumed that I could ignore, as they were not errors per se, so I will include the entire log here after the manual package installs - in case there is something that I am missing.
library(devtools)
install.packages("stringi")
In Terminal:
$ brew options subversion
$ brew install --with-gettext --with-gpg-agent --with-java subversion
R code snippet
ipak <- function(pkg, repository = c("CRAN", "Bioconductor", "github")) {
-
new.pkg <- pkg[!(pkg %in% installed.packages()[, "Package"])] -
# new.pkg <- pkg -
if (length(new.pkg)) { -
if (repository == "CRAN") { -
install.packages(new.pkg, dependencies = TRUE) -
} -
if (repository == "Bioconductor") { -
source("https://bioconductor.org/biocLite.R") -
biocLite(new.pkg, dependencies = TRUE, ask = FALSE) -
} -
if (repository == "github") { -
devtools::install_github(new.pkg, build_vignettes = FALSE, dependencies = TRUE) -
} -
} - }
cranpackages <- c("bbmle", "broom", "cluster", "cobs", "cowplot", "data.table",
-
"doParallel", "dplyr", "drc", "DrImpute", "fastICA", "fitdistrplus", "foreach", -
"gamlss.dist", "ggExtra", "ggplot2", "ggthemes", "grDevices", "glmnet", -
"grid", "gtools", "Hmisc", "kernlab", "MASS", "matrixStats", "mclust", "methods", -
"minpack.lm", "moments", "msir", "NBPSeq", "nonnest2", "parallel", "penalized", -
"plyr", "pscl", "reshape2", "ROCR", "Rtsne", "scales", "Seurat", "snow", -
"stats", "tibble", "tidyr", "VGAM", "ZIM")
ipak(cranpackages, repository = "CRAN")
biocpackages <- c("AnnotationDbi", "baySeq", "Biobase", "BiocGenerics", "BiocParallel",
-
"DEDS", "DESeq2", "EBSeq", "edgeR", "IHW", "iCOBRA", "limma", "Linnorm", -
"MAST", "monocle", "NOISeq", "qvalue", "ROTS", "RUVSeq", "S4Vectors", "scater", -
"scDD", "scde", "scone", "scran", "SCnorm", "SingleCellExperiment", "SummarizedExperiment", -
"zinbwave")
ipak(biocpackages, repository = "Bioconductor")
githubpackages <- c("nghiavtr/BPSC", "VCCRI/cidr", "cz-ye/DECENT", "mohuangx/SAVER",
-
"statOmics/zingeR")
ipak(githubpackages, repository = "github")
Downloading GitHub repo nghiavtr/BPSC@master
from URL https://api.github.com/repos/nghiavtr/BPSC/zipball/master
Installing BPSC
'/Library/Frameworks/R.framework/Resources/bin/R' --no-site-file --no-environ --no-save --no-restore --quiet CMD INSTALL
'/private/var/folders/7g/0kdlw4h53q7dpmghhbpjvn7h0000gn/T/RtmppKRZ5x/devtoolsf98f4ed82b71/nghiavtr-BPSC-1fe6f32'
--library='/Library/Frameworks/R.framework/Versions/3.4/Resources/library' --install-tests
-
installing source package ‘BPSC’ ...
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
‘BPSC.Rnw’
sh: kpsewhich: command not found
Warning in test_latex_pkg("framed", system.file("misc", "framed.sty", package = "knitr")) :
unable to find LaTeX package 'framed'; will use a copy from knitr
** testing if installed package can be loaded -
DONE (BPSC)
Downloading GitHub repo VCCRI/cidr@master
from URL https://api.github.com/repos/VCCRI/cidr/zipball/master
Installing cidr
'/Library/Frameworks/R.framework/Resources/bin/R' --no-site-file --no-environ --no-save --no-restore --quiet CMD INSTALL
'/private/var/folders/7g/0kdlw4h53q7dpmghhbpjvn7h0000gn/T/RtmppKRZ5x/devtoolsf98f3bc702e4/VCCRI-CIDR-c05ac7d'
--library='/Library/Frameworks/R.framework/Versions/3.4/Resources/library' --install-tests -
installing source package ‘cidr’ ...
** libs
clang++ -std=gnu++11 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/RcppParallel/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/RcppEigen/include" -I/usr/local/include -fPIC -Wall -g -O2 -c RcppExports.cpp -o RcppExports.o
In file included from RcppExports.cpp:4:
In file included from /Library/Frameworks/R.framework/Versions/3.4/Resources/library/RcppEigen/include/RcppEigen.h:25:
In file included from /Library/Frameworks/R.framework/Versions/3.4/Resources/library/RcppEigen/include/RcppEigenForward.h:30:
In file included from /Library/Frameworks/R.framework/Versions/3.4/Resources/library/RcppEigen/include/Eigen/Dense:1:
In file included from /Library/Frameworks/R.framework/Versions/3.4/Resources/library/RcppEigen/include/Eigen/Core:531:
/Library/Frameworks/R.framework/Versions/3.4/Resources/library/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas]
#pragma clang diagnostic pop
^
In file included from RcppExports.cpp:4:
In file included from /Library/Frameworks/R.framework/Versions/3.4/Resources/library/RcppEigen/include/RcppEigen.h:25:
In file included from /Library/Frameworks/R.framework/Versions/3.4/Resources/library/RcppEigen/include/RcppEigenForward.h:30:
In file included from /Library/Frameworks/R.framework/Versions/3.4/Resources/library/RcppEigen/include/Eigen/Dense:2:
In file included from /Library/Frameworks/R.framework/Versions/3.4/Resources/library/RcppEigen/include/Eigen/LU:47:
/Library/Frameworks/R.framework/Versions/3.4/Resources/library/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas]
#pragma clang diagnostic pop
^
In file included from RcppExports.cpp:4:
In file included from /Library/Frameworks/R.framework/Versions/3.4/Resources/library/RcppEigen/include/RcppEigen.h:25:
In file included from /Library/Frameworks/R.framework/Versions/3.4/Resources/library/RcppEigen/include/RcppEigenForward.h:30:
In file included from /Library/Frameworks/R.framework/Versions/3.4/Resources/library/RcppEigen/include/Eigen/Dense:3:
In file included from /Library/Frameworks/R.framework/Versions/3.4/Resources/library/RcppEigen/include/Eigen/Cholesky:12:
In file included from /Library/Frameworks/R.framework/Versions/3.4/Resources/library/RcppEigen/include/Eigen/Jacobi:29:
/Library/Frameworks/R.framework/Versions/3.4/Resources/library/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas]
#pragma clang diagnostic pop
^
In file included from RcppExports.cpp:4:
In file included from /Library/Frameworks/R.framework/Versions/3.4/Resources/library/RcppEigen/include/RcppEigen.h:25:
In file included from /Library/Frameworks/R.framework/Versions/3.4/Resources/library/RcppEigen/include/RcppEigenForward.h:30:
In file included from /Library/Frameworks/R.framework/Versions/3.4/Resources/library/RcppEigen/include/Eigen/Dense:3:
In file included from /Library/Frameworks/R.framework/Versions/3.4/Resources/library/RcppEigen/include/Eigen/Cholesky:43:
/Library/Frameworks/R.framework/Versions/3.4/Resources/library/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas]
#pragma clang diagnostic pop
^
In file included from RcppExports.cpp:4:
In file included from /Library/Frameworks/R.framework/Versions/3.4/Resources/library/RcppEigen/include/RcppEigen.h:25:
In file included from /Library/Frameworks/R.framework/Versions/3.4/Resources/library/RcppEigen/include/RcppEigenForward.h:30:
In file included from /Library/Frameworks/R.framework/Versions/3.4/Resources/library/RcppEigen/include/Eigen/Dense:4:
In file included from /Library/Frameworks/R.framework/Versions/3.4/Resources/library/RcppEigen/include/Eigen/QR:17:
In file included from /Library/Frameworks/R.framework/Versions/3.4/Resources/library/RcppEigen/include/Eigen/Householder:27:
/Library/Frameworks/R.framework/Versions/3.4/Resources/library/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas]
#pragma clang diagnostic pop
^
In file included from RcppExports.cpp:4:
In file included from /Library/Frameworks/R.framework/Versions/3.4/Resources/library/RcppEigen/include/RcppEigen.h:25:
In file included from /Library/Frameworks/R.framework/Versions/3.4/Resources/library/RcppEigen/include/RcppEigenForward.h:30:
In file included from /Library/Frameworks/R.framework/Versions/3.4/Resources/library/RcppEigen/include/Eigen/Dense:5:
In file included from /Library/Frameworks/R.framework/Versions/3.4/Resources/library/RcppEigen/include/Eigen/SVD:48:
/Library/Frameworks/R.framework/Versions/3.4/Resources/library/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas]
#pragma clang diagnostic pop
^
In file included from RcppExports.cpp:4:
In file included from /Library/Frameworks/R.framework/Versions/3.4/Resources/library/RcppEigen/include/RcppEigen.h:25:
In file included from /Library/Frameworks/R.framework/Versions/3.4/Resources/library/RcppEigen/include/RcppEigenForward.h:30:
In file included from /Library/Frameworks/R.framework/Versions/3.4/Resources/library/RcppEigen/include/Eigen/Dense:6:
In file included from /Library/Frameworks/R.framework/Versions/3.4/Resources/library/RcppEigen/include/Eigen/Geometry:58:
/Library/Frameworks/R.framework/Versions/3.4/Resources/library/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas]
#pragma clang diagnostic pop
^
In file included from RcppExports.cpp:4:
In file included from /Library/Frameworks/R.framework/Versions/3.4/Resources/library/RcppEigen/include/RcppEigen.h:25:
In file included from /Library/Frameworks/R.framework/Versions/3.4/Resources/library/RcppEigen/include/RcppEigenForward.h:30:
In file included from /Library/Frameworks/R.framework/Versions/3.4/Resources/library/RcppEigen/include/Eigen/Dense:7:
In file included from /Library/Frameworks/R.framework/Versions/3.4/Resources/library/RcppEigen/include/Eigen/Eigenvalues:58:
/Library/Frameworks/R.framework/Versions/3.4/Resources/library/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas]
#pragma clang diagnostic pop
^
In file included from RcppExports.cpp:4:
In file included from /Library/Frameworks/R.framework/Versions/3.4/Resources/library/RcppEigen/include/RcppEigen.h:25:
In file included from /Library/Frameworks/R.framework/Versions/3.4/Resources/library/RcppEigen/include/RcppEigenForward.h:31:
In file included from /Library/Frameworks/R.framework/Versions/3.4/Resources/library/RcppEigen/include/Eigen/Sparse:26:
In file included from /Library/Frameworks/R.framework/Versions/3.4/Resources/library/RcppEigen/include/Eigen/SparseCore:66:
/Library/Frameworks/R.framework/Versions/3.4/Resources/library/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas]
#pragma clang diagnostic pop
^
In file included from RcppExports.cpp:4:
In file included from /Library/Frameworks/R.framework/Versions/3.4/Resources/library/RcppEigen/include/RcppEigen.h:25:
In file included from /Library/Frameworks/R.framework/Versions/3.4/Resources/library/RcppEigen/include/RcppEigenForward.h:31:
In file included from /Library/Frameworks/R.framework/Versions/3.4/Resources/library/RcppEigen/include/Eigen/Sparse:27:
In file included from /Library/Frameworks/R.framework/Versions/3.4/Resources/library/RcppEigen/include/Eigen/OrderingMethods:71:
/Library/Frameworks/R.framework/Versions/3.4/Resources/library/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas]
#pragma clang diagnostic pop
^
In file included from RcppExports.cpp:4:
In file included from /Library/Frameworks/R.framework/Versions/3.4/Resources/library/RcppEigen/include/RcppEigen.h:25:
In file included from /Library/Frameworks/R.framework/Versions/3.4/Resources/library/RcppEigen/include/RcppEigenForward.h:31:
In file included from /Library/Frameworks/R.framework/Versions/3.4/Resources/library/RcppEigen/include/Eigen/Sparse:29:
In file included from /Library/Frameworks/R.framework/Versions/3.4/Resources/library/RcppEigen/include/Eigen/SparseCholesky:43:
/Library/Frameworks/R.framework/Versions/3.4/Resources/library/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas]
#pragma clang diagnostic pop
^
In file included from RcppExports.cpp:4:
In file included from /Library/Frameworks/R.framework/Versions/3.4/Resources/library/RcppEigen/include/RcppEigen.h:25:
In file included from /Library/Frameworks/R.framework/Versions/3.4/Resources/library/RcppEigen/include/RcppEigenForward.h:31:
In file included from /Library/Frameworks/R.framework/Versions/3.4/Resources/library/RcppEigen/include/Eigen/Sparse:32:
In file included from /Library/Frameworks/R.framework/Versions/3.4/Resources/library/RcppEigen/include/Eigen/SparseQR:35:
/Library/Frameworks/R.framework/Versions/3.4/Resources/library/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas]
#pragma clang diagnostic pop
^
In file included from RcppExports.cpp:4:
In file included from /Library/Frameworks/R.framework/Versions/3.4/Resources/library/RcppEigen/include/RcppEigen.h:25:
In file included from /Library/Frameworks/R.framework/Versions/3.4/Resources/library/RcppEigen/include/RcppEigenForward.h:31:
In file included from /Library/Frameworks/R.framework/Versions/3.4/Resources/library/RcppEigen/include/Eigen/Sparse:33:
In file included from /Library/Frameworks/R.framework/Versions/3.4/Resources/library/RcppEigen/include/Eigen/IterativeLinearSolvers:46:
/Library/Frameworks/R.framework/Versions/3.4/Resources/library/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas]
#pragma clang diagnostic pop
^
In file included from RcppExports.cpp:4:
In file included from /Library/Frameworks/R.framework/Versions/3.4/Resources/library/RcppEigen/include/RcppEigen.h:25:
In file included from /Library/Frameworks/R.framework/Versions/3.4/Resources/library/RcppEigen/include/RcppEigenForward.h:32:
In file included from /Library/Frameworks/R.framework/Versions/3.4/Resources/library/RcppEigen/include/Eigen/CholmodSupport:45:
/Library/Frameworks/R.framework/Versions/3.4/Resources/library/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas]
#pragma clang diagnostic pop
^
In file included from RcppExports.cpp:4:
In file included from /Library/Frameworks/R.framework/Versions/3.4/Resources/library/RcppEigen/include/RcppEigen.h:25:
In file included from /Library/Frameworks/R.framework/Versions/3.4/Resources/library/RcppEigen/include/RcppEigenForward.h:35:
In file included from /Library/Frameworks/R.framework/Versions/3.4/Resources/library/RcppEigen/include/unsupported/Eigen/KroneckerProduct:34:
/Library/Frameworks/R.framework/Versions/3.4/Resources/library/RcppEigen/include/unsupported/Eigen/../../Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas]
#pragma clang diagnostic pop
^
In file included from RcppExports.cpp:4:
In file included from /Library/Frameworks/R.framework/Versions/3.4/Resources/library/RcppEigen/include/RcppEigen.h:25:
In file included from /Library/Frameworks/R.framework/Versions/3.4/Resources/library/RcppEigen/include/RcppEigenForward.h:39:
In file included from /Library/Frameworks/R.framework/Versions/3.4/Resources/library/RcppEigen/include/unsupported/Eigen/Polynomials:135:
/Library/Frameworks/R.framework/Versions/3.4/Resources/library/RcppEigen/include/unsupported/Eigen/../../Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas]
#pragma clang diagnostic pop
^
In file included from RcppExports.cpp:4:
In file included from /Library/Frameworks/R.framework/Versions/3.4/Resources/library/RcppEigen/include/RcppEigen.h:25:
In file included from /Library/Frameworks/R.framework/Versions/3.4/Resources/library/RcppEigen/include/RcppEigenForward.h:40:
In file included from /Library/Frameworks/R.framework/Versions/3.4/Resources/library/RcppEigen/include/unsupported/Eigen/SparseExtra:51:
/Library/Frameworks/R.framework/Versions/3.4/Resources/library/RcppEigen/include/unsupported/Eigen/../../Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas]
#pragma clang diagnostic pop
^
17 warnings generated.
clang++ -std=gnu++11 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/RcppParallel/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/RcppEigen/include" -I/usr/local/include -fPIC -Wall -g -O2 -c eigenSpace.cpp -o eigenSpace.o
In file included from eigenSpace.cpp:1:
In file included from /Library/Frameworks/R.framework/Versions/3.4/Resources/library/RcppEigen/include/RcppEigen.h:25:
In file included from /Library/Frameworks/R.framework/Versions/3.4/Resources/library/RcppEigen/include/RcppEigenForward.h:30:
In file included from /Library/Frameworks/R.framework/Versions/3.4/Resources/library/RcppEigen/include/Eigen/Dense:1:
In file included from /Library/Frameworks/R.framework/Versions/3.4/Resources/library/RcppEigen/include/Eigen/Core:531:
/Library/Frameworks/R.framework/Versions/3.4/Resources/library/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas]
#pragma clang diagnostic pop
^
In file included from eigenSpace.cpp:1:
In file included from /Library/Frameworks/R.framework/Versions/3.4/Resources/library/RcppEigen/include/RcppEigen.h:25:
In file included from /Library/Frameworks/R.framework/Versions/3.4/Resources/library/RcppEigen/include/RcppEigenForward.h:30:
In file included from /Library/Frameworks/R.framework/Versions/3.4/Resources/library/RcppEigen/include/Eigen/Dense:2:
In file included from /Library/Frameworks/R.framework/Versions/3.4/Resources/library/RcppEigen/include/Eigen/LU:47:
/Library/Frameworks/R.framework/Versions/3.4/Resources/library/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas]
#pragma clang diagnostic pop
^
In file included from eigenSpace.cpp:1:
In file included from /Library/Frameworks/R.framework/Versions/3.4/Resources/library/RcppEigen/include/RcppEigen.h:25:
In file included from /Library/Frameworks/R.framework/Versions/3.4/Resources/library/RcppEigen/include/RcppEigenForward.h:30:
In file included from /Library/Frameworks/R.framework/Versions/3.4/Resources/library/RcppEigen/include/Eigen/Dense:3:
In file included from /Library/Frameworks/R.framework/Versions/3.4/Resources/library/RcppEigen/include/Eigen/Cholesky:12:
In file included from /Library/Frameworks/R.framework/Versions/3.4/Resources/library/RcppEigen/include/Eigen/Jacobi:29:
/Library/Frameworks/R.framework/Versions/3.4/Resources/library/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas]
#pragma clang diagnostic pop
^
In file included from eigenSpace.cpp:1:
In file included from /Library/Frameworks/R.framework/Versions/3.4/Resources/library/RcppEigen/include/RcppEigen.h:25:
In file included from /Library/Frameworks/R.framework/Versions/3.4/Resources/library/RcppEigen/include/RcppEigenForward.h:30:
In file included from /Library/Frameworks/R.framework/Versions/3.4/Resources/library/RcppEigen/include/Eigen/Dense:3:
In file included from /Library/Frameworks/R.framework/Versions/3.4/Resources/library/RcppEigen/include/Eigen/Cholesky:43:
/Library/Frameworks/R.framework/Versions/3.4/Resources/library/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas]
#pragma clang diagnostic pop
^
In file included from eigenSpace.cpp:1:
In file included from /Library/Frameworks/R.framework/Versions/3.4/Resources/library/RcppEigen/include/RcppEigen.h:25:
In file included from /Library/Frameworks/R.framework/Versions/3.4/Resources/library/RcppEigen/include/RcppEigenForward.h:30:
In file included from /Library/Frameworks/R.framework/Versions/3.4/Resources/library/RcppEigen/include/Eigen/Dense:4:
In file included from /Library/Frameworks/R.framework/Versions/3.4/Resources/library/RcppEigen/include/Eigen/QR:17:
In file included from /Library/Frameworks/R.framework/Versions/3.4/Resources/library/RcppEigen/include/Eigen/Householder:27:
/Library/Frameworks/R.framework/Versions/3.4/Resources/library/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas]
#pragma clang diagnostic pop
^
In file included from eigenSpace.cpp:1:
In file included from /Library/Frameworks/R.framework/Versions/3.4/Resources/library/RcppEigen/include/RcppEigen.h:25:
In file included from /Library/Frameworks/R.framework/Versions/3.4/Resources/library/RcppEigen/include/RcppEigenForward.h:30:
In file included from /Library/Frameworks/R.framework/Versions/3.4/Resources/library/RcppEigen/include/Eigen/Dense:5:
In file included from /Library/Frameworks/R.framework/Versions/3.4/Resources/library/RcppEigen/include/Eigen/SVD:48:
/Library/Frameworks/R.framework/Versions/3.4/Resources/library/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas]
#pragma clang diagnostic pop
^
In file included from eigenSpace.cpp:1:
In file included from /Library/Frameworks/R.framework/Versions/3.4/Resources/library/RcppEigen/include/RcppEigen.h:25:
In file included from /Library/Frameworks/R.framework/Versions/3.4/Resources/library/RcppEigen/include/RcppEigenForward.h:30:
In file included from /Library/Frameworks/R.framework/Versions/3.4/Resources/library/RcppEigen/include/Eigen/Dense:6:
In file included from /Library/Frameworks/R.framework/Versions/3.4/Resources/library/RcppEigen/include/Eigen/Geometry:58:
/Library/Frameworks/R.framework/Versions/3.4/Resources/library/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas]
#pragma clang diagnostic pop
^
In file included from eigenSpace.cpp:1:
In file included from /Library/Frameworks/R.framework/Versions/3.4/Resources/library/RcppEigen/include/RcppEigen.h:25:
In file included from /Library/Frameworks/R.framework/Versions/3.4/Resources/library/RcppEigen/include/RcppEigenForward.h:30:
In file included from /Library/Frameworks/R.framework/Versions/3.4/Resources/library/RcppEigen/include/Eigen/Dense:7:
In file included from /Library/Frameworks/R.framework/Versions/3.4/Resources/library/RcppEigen/include/Eigen/Eigenvalues:58:
/Library/Frameworks/R.framework/Versions/3.4/Resources/library/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas]
#pragma clang diagnostic pop
^
In file included from eigenSpace.cpp:1:
In file included from /Library/Frameworks/R.framework/Versions/3.4/Resources/library/RcppEigen/include/RcppEigen.h:25:
In file included from /Library/Frameworks/R.framework/Versions/3.4/Resources/library/RcppEigen/include/RcppEigenForward.h:31:
In file included from /Library/Frameworks/R.framework/Versions/3.4/Resources/library/RcppEigen/include/Eigen/Sparse:26:
In file included from /Library/Frameworks/R.framework/Versions/3.4/Resources/library/RcppEigen/include/Eigen/SparseCore:66:
/Library/Frameworks/R.framework/Versions/3.4/Resources/library/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas]
#pragma clang diagnostic pop
^
In file included from eigenSpace.cpp:1:
In file included from /Library/Frameworks/R.framework/Versions/3.4/Resources/library/RcppEigen/include/RcppEigen.h:25:
In file included from /Library/Frameworks/R.framework/Versions/3.4/Resources/library/RcppEigen/include/RcppEigenForward.h:31:
In file included from /Library/Frameworks/R.framework/Versions/3.4/Resources/library/RcppEigen/include/Eigen/Sparse:27:
In file included from /Library/Frameworks/R.framework/Versions/3.4/Resources/library/RcppEigen/include/Eigen/OrderingMethods:71:
/Library/Frameworks/R.framework/Versions/3.4/Resources/library/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas]
#pragma clang diagnostic pop
^
In file included from eigenSpace.cpp:1:
In file included from /Library/Frameworks/R.framework/Versions/3.4/Resources/library/RcppEigen/include/RcppEigen.h:25:
In file included from /Library/Frameworks/R.framework/Versions/3.4/Resources/library/RcppEigen/include/RcppEigenForward.h:31:
In file included from /Library/Frameworks/R.framework/Versions/3.4/Resources/library/RcppEigen/include/Eigen/Sparse:29:
In file included from /Library/Frameworks/R.framework/Versions/3.4/Resources/library/RcppEigen/include/Eigen/SparseCholesky:43:
/Library/Frameworks/R.framework/Versions/3.4/Resources/library/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas]
#pragma clang diagnostic pop
^
In file included from eigenSpace.cpp:1:
In file included from /Library/Frameworks/R.framework/Versions/3.4/Resources/library/RcppEigen/include/RcppEigen.h:25:
In file included from /Library/Frameworks/R.framework/Versions/3.4/Resources/library/RcppEigen/include/RcppEigenForward.h:31:
In file included from /Library/Frameworks/R.framework/Versions/3.4/Resources/library/RcppEigen/include/Eigen/Sparse:32:
In file included from /Library/Frameworks/R.framework/Versions/3.4/Resources/library/RcppEigen/include/Eigen/SparseQR:35:
/Library/Frameworks/R.framework/Versions/3.4/Resources/library/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas]
#pragma clang diagnostic pop
^
In file included from eigenSpace.cpp:1:
In file included from /Library/Frameworks/R.framework/Versions/3.4/Resources/library/RcppEigen/include/RcppEigen.h:25:
In file included from /Library/Frameworks/R.framework/Versions/3.4/Resources/library/RcppEigen/include/RcppEigenForward.h:31:
In file included from /Library/Frameworks/R.framework/Versions/3.4/Resources/library/RcppEigen/include/Eigen/Sparse:33:
In file included from /Library/Frameworks/R.framework/Versions/3.4/Resources/library/RcppEigen/include/Eigen/IterativeLinearSolvers:46:
/Library/Frameworks/R.framework/Versions/3.4/Resources/library/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas]
#pragma clang diagnostic pop
^
In file included from eigenSpace.cpp:1:
In file included from /Library/Frameworks/R.framework/Versions/3.4/Resources/library/RcppEigen/include/RcppEigen.h:25:
In file included from /Library/Frameworks/R.framework/Versions/3.4/Resources/library/RcppEigen/include/RcppEigenForward.h:32:
In file included from /Library/Frameworks/R.framework/Versions/3.4/Resources/library/RcppEigen/include/Eigen/CholmodSupport:45:
/Library/Frameworks/R.framework/Versions/3.4/Resources/library/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas]
#pragma clang diagnostic pop
^
In file included from eigenSpace.cpp:1:
In file included from /Library/Frameworks/R.framework/Versions/3.4/Resources/library/RcppEigen/include/RcppEigen.h:25:
In file included from /Library/Frameworks/R.framework/Versions/3.4/Resources/library/RcppEigen/include/RcppEigenForward.h:35:
In file included from /Library/Frameworks/R.framework/Versions/3.4/Resources/library/RcppEigen/include/unsupported/Eigen/KroneckerProduct:34:
/Library/Frameworks/R.framework/Versions/3.4/Resources/library/RcppEigen/include/unsupported/Eigen/../../Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas]
#pragma clang diagnostic pop
^
In file included from eigenSpace.cpp:1:
In file included from /Library/Frameworks/R.framework/Versions/3.4/Resources/library/RcppEigen/include/RcppEigen.h:25:
In file included from /Library/Frameworks/R.framework/Versions/3.4/Resources/library/RcppEigen/include/RcppEigenForward.h:39:
In file included from /Library/Frameworks/R.framework/Versions/3.4/Resources/library/RcppEigen/include/unsupported/Eigen/Polynomials:135:
/Library/Frameworks/R.framework/Versions/3.4/Resources/library/RcppEigen/include/unsupported/Eigen/../../Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas]
#pragma clang diagnostic pop
^
In file included from eigenSpace.cpp:1:
In file included from /Library/Frameworks/R.framework/Versions/3.4/Resources/library/RcppEigen/include/RcppEigen.h:25:
In file included from /Library/Frameworks/R.framework/Versions/3.4/Resources/library/RcppEigen/include/RcppEigenForward.h:40:
In file included from /Library/Frameworks/R.framework/Versions/3.4/Resources/library/RcppEigen/include/unsupported/Eigen/SparseExtra:51:
/Library/Frameworks/R.framework/Versions/3.4/Resources/library/RcppEigen/include/unsupported/Eigen/../../Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas]
#pragma clang diagnostic pop
^
17 warnings generated.
clang++ -std=gnu++11 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/RcppParallel/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/RcppEigen/include" -I/usr/local/include -fPIC -Wall -g -O2 -c scPCA.cpp -o scPCA.o
clang++ -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 cidr.so RcppExports.o eigenSpace.o scPCA.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Library/Frameworks/R.framework/Versions/3.4/Resources/library/cidr/libs
** R
** tests
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** testing if installed package can be loaded -
DONE (cidr)
Downloading GitHub repo cz-ye/DECENT@master
from URL https://api.github.com/repos/cz-ye/DECENT/zipball/master
Installing DECENT
'/Library/Frameworks/R.framework/Resources/bin/R' --no-site-file --no-environ --no-save --no-restore --quiet CMD INSTALL
'/private/var/folders/7g/0kdlw4h53q7dpmghhbpjvn7h0000gn/T/RtmppKRZ5x/devtoolsf98f7167e3cf/cz-ye-DECENT-fb9a045'
--library='/Library/Frameworks/R.framework/Versions/3.4/Resources/library' --install-tests -
installing source package ‘DECENT’ ...
** libs
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/RcppEigen/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/RcppNumerical/include" -I/usr/local/include -fPIC -Wall -g -O2 -c LRT_logl.cpp -o LRT_logl.o
In file included from LRT_logl.cpp:7:
In file included from /Library/Frameworks/R.framework/Versions/3.4/Resources/library/RcppNumerical/include/RcppNumerical.h:10:
In file included from /Library/Frameworks/R.framework/Versions/3.4/Resources/library/RcppEigen/include/RcppEigen.h:25:
In file included from /Library/Frameworks/R.framework/Versions/3.4/Resources/library/RcppEigen/include/RcppEigenForward.h:30:
In file included from /Library/Frameworks/R.framework/Versions/3.4/Resources/library/RcppEigen/include/Eigen/Dense:1:
In file included from /Library/Frameworks/R.framework/Versions/3.4/Resources/library/RcppEigen/include/Eigen/Core:531:
/Library/Frameworks/R.framework/Versions/3.4/Resources/library/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas]
#pragma clang diagnostic pop
^
In file included from LRT_logl.cpp:7:
In file included from /Library/Frameworks/R.framework/Versions/3.4/Resources/library/RcppNumerical/include/RcppNumerical.h:10:
In file included from /Library/Frameworks/R.framework/Versions/3.4/Resources/library/RcppEigen/include/RcppEigen.h:25:
In file included from /Library/Frameworks/R.framework/Versions/3.4/Resources/library/RcppEigen/include/RcppEigenForward.h:30:
In file included from /Library/Frameworks/R.framework/Versions/3.4/Resources/library/RcppEigen/include/Eigen/Dense:2:
In file included from /Library/Frameworks/R.framework/Versions/3.4/Resources/library/RcppEigen/include/Eigen/LU:47:
/Library/Frameworks/R.framework/Versions/3.4/Resources/library/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas]
#pragma clang diagnostic pop
^
In file included from LRT_logl.cpp:7:
In file included from /Library/Frameworks/R.framework/Versions/3.4/Resources/library/RcppNumerical/include/RcppNumerical.h:10:
In file included from /Library/Frameworks/R.framework/Versions/3.4/Resources/library/RcppEigen/include/RcppEigen.h:25:
In file included from /Library/Frameworks/R.framework/Versions/3.4/Resources/library/RcppEigen/include/RcppEigenForward.h:30:
In file included from /Library/Frameworks/R.framework/Versions/3.4/Resources/library/RcppEigen/include/Eigen/Dense:3:
In file included from /Library/Frameworks/R.framework/Versions/3.4/Resources/library/RcppEigen/include/Eigen/Cholesky:12:
In file included from /Library/Frameworks/R.framework/Versions/3.4/Resources/library/RcppEigen/include/Eigen/Jacobi:29:
/Library/Frameworks/R.framework/Versions/3.4/Resources/library/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas]
#pragma clang diagnostic pop
^
In file included from LRT_logl.cpp:7:
In file included from /Library/Frameworks/R.framework/Versions/3.4/Resources/library/RcppNumerical/include/RcppNumerical.h:10:
In file included from /Library/Frameworks/R.framework/Versions/3.4/Resources/library/RcppEigen/include/RcppEigen.h:25:
In file included from /Library/Frameworks/R.framework/Versions/3.4/Resources/library/RcppEigen/include/RcppEigenForward.h:30:
In file included from /Library/Frameworks/R.framework/Versions/3.4/Resources/library/RcppEigen/include/Eigen/Dense:3:
In file included from /Library/Frameworks/R.framework/Versions/3.4/Resources/library/RcppEigen/include/Eigen/Cholesky:43:
/Library/Frameworks/R.framework/Versions/3.4/Resources/library/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas]
#pragma clang diagnostic pop
^
In file included from LRT_logl.cpp:7:
In file included from /Library/Frameworks/R.framework/Versions/3.4/Resources/library/RcppNumerical/include/RcppNumerical.h:10:
In file included from /Library/Frameworks/R.framework/Versions/3.4/Resources/library/RcppEigen/include/RcppEigen.h:25:
In file included from /Library/Frameworks/R.framework/Versions/3.4/Resources/library/RcppEigen/include/RcppEigenForward.h:30:
In file included from /Library/Frameworks/R.framework/Versions/3.4/Resources/library/RcppEigen/include/Eigen/Dense:4:
In file included from /Library/Frameworks/R.framework/Versions/3.4/Resources/library/RcppEigen/include/Eigen/QR:17:
In file included from /Library/Frameworks/R.framework/Versions/3.4/Resources/library/RcppEigen/include/Eigen/Householder:27:
/Library/Frameworks/R.framework/Versions/3.4/Resources/library/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas]
#pragma clang diagnostic pop
^
In file included from LRT_logl.cpp:7:
In file included from /Library/Frameworks/R.framework/Versions/3.4/Resources/library/RcppNumerical/include/RcppNumerical.h:10:
In file included from /Library/Frameworks/R.framework/Versions/3.4/Resources/library/RcppEigen/include/RcppEigen.h:25:
In file included from /Library/Frameworks/R.framework/Versions/3.4/Resources/library/RcppEigen/include/RcppEigenForward.h:30:
In file included from /Library/Frameworks/R.framework/Versions/3.4/Resources/library/RcppEigen/include/Eigen/Dense:5:
In file included from /Library/Frameworks/R.framework/Versions/3.4/Resources/library/RcppEigen/include/Eigen/SVD:48:
/Library/Frameworks/R.framework/Versions/3.4/Resources/library/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas]
#pragma clang diagnostic pop
^
In file included from LRT_logl.cpp:7:
In file included from /Library/Frameworks/R.framework/Versions/3.4/Resources/library/RcppNumerical/include/RcppNumerical.h:10:
In file included from /Library/Frameworks/R.framework/Versions/3.4/Resources/library/RcppEigen/include/RcppEigen.h:25:
In file included from /Library/Frameworks/R.framework/Versions/3.4/Resources/library/RcppEigen/include/RcppEigenForward.h:30:
In file included from /Library/Frameworks/R.framework/Versions/3.4/Resources/library/RcppEigen/include/Eigen/Dense:6:
In file included from /Library/Frameworks/R.framework/Versions/3.4/Resources/library/RcppEigen/include/Eigen/Geometry:58:
/Library/Frameworks/R.framework/Versions/3.4/Resources/library/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas]
#pragma clang diagnostic pop
^
In file included from LRT_logl.cpp:7:
In file included from /Library/Frameworks/R.framework/Versions/3.4/Resources/library/RcppNumerical/include/RcppNumerical.h:10:
In file included from /Library/Frameworks/R.framework/Versions/3.4/Resources/library/RcppEigen/include/RcppEigen.h:25:
In file included from /Library/Frameworks/R.framework/Versions/3.4/Resources/library/RcppEigen/include/RcppEigenForward.h:30:
In file included from /Library/Frameworks/R.framework/Versions/3.4/Resources/library/RcppEigen/include/Eigen/Dense:7:
In file included from /Library/Frameworks/R.framework/Versions/3.4/Resources/library/RcppEigen/include/Eigen/Eigenvalues:58:
/Library/Frameworks/R.framework/Versions/3.4/Resources/library/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas]
#pragma clang diagnostic pop
^
In file included from LRT_logl.cpp:7:
In file included from /Library/Frameworks/R.framework/Versions/3.4/Resources/library/RcppNumerical/include/RcppNumerical.h:10:
In file included from /Library/Frameworks/R.framework/Versions/3.4/Resources/library/RcppEigen/include/RcppEigen.h:25:
In file included from /Library/Frameworks/R.framework/Versions/3.4/Resources/library/RcppEigen/include/RcppEigenForward.h:31:
In file included from /Library/Frameworks/R.framework/Versions/3.4/Resources/library/RcppEigen/include/Eigen/Sparse:26:
In file included from /Library/Frameworks/R.framework/Versions/3.4/Resources/library/RcppEigen/include/Eigen/SparseCore:66:
/Library/Frameworks/R.framework/Versions/3.4/Resources/library/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas]
#pragma clang diagnostic pop
^
In file included from LRT_logl.cpp:7:
In file included from /Library/Frameworks/R.framework/Versions/3.4/Resources/library/RcppNumerical/include/RcppNumerical.h:10:
In file included from /Library/Frameworks/R.framework/Versions/3.4/Resources/library/RcppEigen/include/RcppEigen.h:25:
In file included from /Library/Frameworks/R.framework/Versions/3.4/Resources/library/RcppEigen/include/RcppEigenForward.h:31:
In file included from /Library/Frameworks/R.framework/Versions/3.4/Resources/library/RcppEigen/include/Eigen/Sparse:27:
In file included from /Library/Frameworks/R.framework/Versions/3.4/Resources/library/RcppEigen/include/Eigen/OrderingMethods:71:
/Library/Frameworks/R.framework/Versions/3.4/Resources/library/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas]
#pragma clang diagnostic pop
^
In file included from LRT_logl.cpp:7:
In file included from /Library/Frameworks/R.framework/Versions/3.4/Resources/library/RcppNumerical/include/RcppNumerical.h:10:
In file included from /Library/Frameworks/R.framework/Versions/3.4/Resources/library/RcppEigen/include/RcppEigen.h:25:
In file included from /Library/Frameworks/R.framework/Versions/3.4/Resources/library/RcppEigen/include/RcppEigenForward.h:31:
In file included from /Library/Frameworks/R.framework/Versions/3.4/Resources/library/RcppEigen/include/Eigen/Sparse:29:
In file included from /Library/Frameworks/R.framework/Versions/3.4/Resources/library/RcppEigen/include/Eigen/SparseCholesky:43:
/Library/Frameworks/R.framework/Versions/3.4/Resources/library/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas]
#pragma clang diagnostic pop
^
In file included from LRT_logl.cpp:7:
In file included from /Library/Frameworks/R.framework/Versions/3.4/Resources/library/RcppNumerical/include/RcppNumerical.h:10:
In file included from /Library/Frameworks/R.framework/Versions/3.4/Resources/library/RcppEigen/include/RcppEigen.h:25:
In file included from /Library/Frameworks/R.framework/Versions/3.4/Resources/library/RcppEigen/include/RcppEigenForward.h:31:
In file included from /Library/Frameworks/R.framework/Versions/3.4/Resources/library/RcppEigen/include/Eigen/Sparse:32:
In file included from /Library/Frameworks/R.framework/Versions/3.4/Resources/library/RcppEigen/include/Eigen/SparseQR:35:
/Library/Frameworks/R.framework/Versions/3.4/Resources/library/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas]
#pragma clang diagnostic pop
^
In file included from LRT_logl.cpp:7:
In file included from /Library/Frameworks/R.framework/Versions/3.4/Resources/library/RcppNumerical/include/RcppNumerical.h:10:
In file included from /Library/Frameworks/R.framework/Versions/3.4/Resources/library/RcppEigen/include/RcppEigen.h:25:
In file included from /Library/Frameworks/R.framework/Versions/3.4/Resources/library/RcppEigen/include/RcppEigenForward.h:31:
In file included from /Library/Frameworks/R.framework/Versions/3.4/Resources/library/RcppEigen/include/Eigen/Sparse:33:
In file included from /Library/Frameworks/R.framework/Versions/3.4/Resources/library/RcppEigen/include/Eigen/IterativeLinearSolvers:46:
/Library/Frameworks/R.framework/Versions/3.4/Resources/library/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas]
#pragma clang diagnostic pop
^
In file included from LRT_logl.cpp:7:
In file included from /Library/Frameworks/R.framework/Versions/3.4/Resources/library/RcppNumerical/include/RcppNumerical.h:10:
In file included from /Library/Frameworks/R.framework/Versions/3.4/Resources/library/RcppEigen/include/RcppEigen.h:25:
In file included from /Library/Frameworks/R.framework/Versions/3.4/Resources/library/RcppEigen/include/RcppEigenForward.h:32:
In file included from /Library/Frameworks/R.framework/Versions/3.4/Resources/library/RcppEigen/include/Eigen/CholmodSupport:45:
/Library/Frameworks/R.framework/Versions/3.4/Resources/library/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas]
#pragma clang diagnostic pop
^
In file included from LRT_logl.cpp:7:
In file included from /Library/Frameworks/R.framework/Versions/3.4/Resources/library/RcppNumerical/include/RcppNumerical.h:10:
In file included from /Library/Frameworks/R.framework/Versions/3.4/Resources/library/RcppEigen/include/RcppEigen.h:25:
In file included from /Library/Frameworks/R.framework/Versions/3.4/Resources/library/RcppEigen/include/RcppEigenForward.h:35:
In file included from /Library/Frameworks/R.framework/Versions/3.4/Resources/library/RcppEigen/include/unsupported/Eigen/KroneckerProduct:34:
/Library/Frameworks/R.framework/Versions/3.4/Resources/library/RcppEigen/include/unsupported/Eigen/../../Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas]
#pragma clang diagnostic pop
^
In file included from LRT_logl.cpp:7:
In file included from /Library/Frameworks/R.framework/Versions/3.4/Resources/library/RcppNumerical/include/RcppNumerical.h:10:
In file included from /Library/Frameworks/R.framework/Versions/3.4/Resources/library/RcppEigen/include/RcppEigen.h:25:
In file included from /Library/Frameworks/R.framework/Versions/3.4/Resources/library/RcppEigen/include/RcppEigenForward.h:39:
In file included from /Library/Frameworks/R.framework/Versions/3.4/Resources/library/RcppEigen/include/unsupported/Eigen/Polynomials:135:
/Library/Frameworks/R.framework/Versions/3.4/Resources/library/RcppEigen/include/unsupported/Eigen/../../Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas]
#pragma clang diagnostic pop
^
In file included from LRT_logl.cpp:7:
In file included from /Library/Frameworks/R.framework/Versions/3.4/Resources/library/RcppNumerical/include/RcppNumerical.h:10:
In file included from /Library/Frameworks/R.framework/Versions/3.4/Resources/library/RcppEigen/include/RcppEigen.h:25:
In file included from /Library/Frameworks/R.framework/Versions/3.4/Resources/library/RcppEigen/include/RcppEigenForward.h:40:
In file included from /Library/Frameworks/R.framework/Versions/3.4/Resources/library/RcppEigen/include/unsupported/Eigen/SparseExtra:51:
/Library/Frameworks/R.framework/Versions/3.4/Resources/library/RcppEigen/include/unsupported/Eigen/../../Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas]
#pragma clang diagnostic pop
^
17 warnings generated.
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/RcppEigen/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/RcppNumerical/include" -I/usr/local/include -fPIC -Wall -g -O2 -c RcppExports.cpp -o RcppExports.o
In file included from RcppExports.cpp:4:
In file included from /Library/Frameworks/R.framework/Versions/3.4/Resources/library/RcppEigen/include/RcppEigen.h:25:
In file included from /Library/Frameworks/R.framework/Versions/3.4/Resources/library/RcppEigen/include/RcppEigenForward.h:30:
In file included from /Library/Frameworks/R.framework/Versions/3.4/Resources/library/RcppEigen/include/Eigen/Dense:1:
In file included from /Library/Frameworks/R.framework/Versions/3.4/Resources/library/RcppEigen/include/Eigen/Core:531:
/Library/Frameworks/R.framework/Versions/3.4/Resources/library/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas]
#pragma clang diagnostic pop
^
In file included from RcppExports.cpp:4:
In file included from /Library/Frameworks/R.framework/Versions/3.4/Resources/library/RcppEigen/include/RcppEigen.h:25:
In file included from /Library/Frameworks/R.framework/Versions/3.4/Resources/library/RcppEigen/include/RcppEigenForward.h:30:
In file included from /Library/Frameworks/R.framework/Versions/3.4/Resources/library/RcppEigen/include/Eigen/Dense:2:
In file included from /Library/Frameworks/R.framework/Versions/3.4/Resources/library/RcppEigen/include/Eigen/LU:47:
/Library/Frameworks/R.framework/Versions/3.4/Resources/library/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas]
#pragma clang diagnostic pop
^
In file included from RcppExports.cpp:4:
In file included from /Library/Frameworks/R.framework/Versions/3.4/Resources/library/RcppEigen/include/RcppEigen.h:25:
In file included from /Library/Frameworks/R.framework/Versions/3.4/Resources/library/RcppEigen/include/RcppEigenForward.h:30:
In file included from /Library/Frameworks/R.framework/Versions/3.4/Resources/library/RcppEigen/include/Eigen/Dense:3:
In file included from /Library/Frameworks/R.framework/Versions/3.4/Resources/library/RcppEigen/include/Eigen/Cholesky:12:
In file included from /Library/Frameworks/R.framework/Versions/3.4/Resources/library/RcppEigen/include/Eigen/Jacobi:29:
/Library/Frameworks/R.framework/Versions/3.4/Resources/library/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas]
#pragma clang diagnostic pop
^
In file included from RcppExports.cpp:4:
In file included from /Library/Frameworks/R.framework/Versions/3.4/Resources/library/RcppEigen/include/RcppEigen.h:25:
In file included from /Library/Frameworks/R.framework/Versions/3.4/Resources/library/RcppEigen/include/RcppEigenForward.h:30:
In file included from /Library/Frameworks/R.framework/Versions/3.4/Resources/library/RcppEigen/include/Eigen/Dense:3:
In file included from /Library/Frameworks/R.framework/Versions/3.4/Resources/library/RcppEigen/include/Eigen/Cholesky:43:
/Library/Frameworks/R.framework/Versions/3.4/Resources/library/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas]
#pragma clang diagnostic pop
^
In file included from RcppExports.cpp:4:
In file included from /Library/Frameworks/R.framework/Versions/3.4/Resources/library/RcppEigen/include/RcppEigen.h:25:
In file included from /Library/Frameworks/R.framework/Versions/3.4/Resources/library/RcppEigen/include/RcppEigenForward.h:30:
In file included from /Library/Frameworks/R.framework/Versions/3.4/Resources/library/RcppEigen/include/Eigen/Dense:4:
In file included from /Library/Frameworks/R.framework/Versions/3.4/Resources/library/RcppEigen/include/Eigen/QR:17:
In file included from /Library/Frameworks/R.framework/Versions/3.4/Resources/library/RcppEigen/include/Eigen/Householder:27:
/Library/Frameworks/R.framework/Versions/3.4/Resources/library/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas]
#pragma clang diagnostic pop
^
In file included from RcppExports.cpp:4:
In file included from /Library/Frameworks/R.framework/Versions/3.4/Resources/library/RcppEigen/include/RcppEigen.h:25:
In file included from /Library/Frameworks/R.framework/Versions/3.4/Resources/library/RcppEigen/include/RcppEigenForward.h:30:
In file included from /Library/Frameworks/R.framework/Versions/3.4/Resources/library/RcppEigen/include/Eigen/Dense:5:
In file included from /Library/Frameworks/R.framework/Versions/3.4/Resources/library/RcppEigen/include/Eigen/SVD:48:
/Library/Frameworks/R.framework/Versions/3.4/Resources/library/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas]
#pragma clang diagnostic pop
^
In file included from RcppExports.cpp:4:
In file included from /Library/Frameworks/R.framework/Versions/3.4/Resources/library/RcppEigen/include/RcppEigen.h:25:
In file included from /Library/Frameworks/R.framework/Versions/3.4/Resources/library/RcppEigen/include/RcppEigenForward.h:30:
In file included from /Library/Frameworks/R.framework/Versions/3.4/Resources/library/RcppEigen/include/Eigen/Dense:6:
In file included from /Library/Frameworks/R.framework/Versions/3.4/Resources/library/RcppEigen/include/Eigen/Geometry:58:
/Library/Frameworks/R.framework/Versions/3.4/Resources/library/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas]
#pragma clang diagnostic pop
^
In file included from RcppExports.cpp:4:
In file included from /Library/Frameworks/R.framework/Versions/3.4/Resources/library/RcppEigen/include/RcppEigen.h:25:
In file included from /Library/Frameworks/R.framework/Versions/3.4/Resources/library/RcppEigen/include/RcppEigenForward.h:30:
In file included from /Library/Frameworks/R.framework/Versions/3.4/Resources/library/RcppEigen/include/Eigen/Dense:7:
In file included from /Library/Frameworks/R.framework/Versions/3.4/Resources/library/RcppEigen/include/Eigen/Eigenvalues:58:
/Library/Frameworks/R.framework/Versions/3.4/Resources/library/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas]
#pragma clang diagnostic pop
^
In file included from RcppExports.cpp:4:
In file included from /Library/Frameworks/R.framework/Versions/3.4/Resources/library/RcppEigen/include/RcppEigen.h:25:
In file included from /Library/Frameworks/R.framework/Versions/3.4/Resources/library/RcppEigen/include/RcppEigenForward.h:31:
In file included from /Library/Frameworks/R.framework/Versions/3.4/Resources/library/RcppEigen/include/Eigen/Sparse:26:
In file included from /Library/Frameworks/R.framework/Versions/3.4/Resources/library/RcppEigen/include/Eigen/SparseCore:66:
/Library/Frameworks/R.framework/Versions/3.4/Resources/library/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas]
#pragma clang diagnostic pop
^
In file included from RcppExports.cpp:4:
In file included from /Library/Frameworks/R.framework/Versions/3.4/Resources/library/RcppEigen/include/RcppEigen.h:25:
In file included from /Library/Frameworks/R.framework/Versions/3.4/Resources/library/RcppEigen/include/RcppEigenForward.h:31:
In file included from /Library/Frameworks/R.framework/Versions/3.4/Resources/library/RcppEigen/include/Eigen/Sparse:27:
In file included from /Library/Frameworks/R.framework/Versions/3.4/Resources/library/RcppEigen/include/Eigen/OrderingMethods:71:
/Library/Frameworks/R.framework/Versions/3.4/Resources/library/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas]
#pragma clang diagnostic pop
^
In file included from RcppExports.cpp:4:
In file included from /Library/Frameworks/R.framework/Versions/3.4/Resources/library/RcppEigen/include/RcppEigen.h:25:
In file included from /Library/Frameworks/R.framework/Versions/3.4/Resources/library/RcppEigen/include/RcppEigenForward.h:31:
In file included from /Library/Frameworks/R.framework/Versions/3.4/Resources/library/RcppEigen/include/Eigen/Sparse:29:
In file included from /Library/Frameworks/R.framework/Versions/3.4/Resources/library/RcppEigen/include/Eigen/SparseCholesky:43:
/Library/Frameworks/R.framework/Versions/3.4/Resources/library/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas]
#pragma clang diagnostic pop
^
In file included from RcppExports.cpp:4:
In file included from /Library/Frameworks/R.framework/Versions/3.4/Resources/library/RcppEigen/include/RcppEigen.h:25:
In file included from /Library/Frameworks/R.framework/Versions/3.4/Resources/library/RcppEigen/include/RcppEigenForward.h:31:
In file included from /Library/Frameworks/R.framework/Versions/3.4/Resources/library/RcppEigen/include/Eigen/Sparse:32:
In file included from /Library/Frameworks/R.framework/Versions/3.4/Resources/library/RcppEigen/include/Eigen/SparseQR:35:
/Library/Frameworks/R.framework/Versions/3.4/Resources/library/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas]
#pragma clang diagnostic pop
^
In file included from RcppExports.cpp:4:
In file included from /Library/Frameworks/R.framework/Versions/3.4/Resources/library/RcppEigen/include/RcppEigen.h:25:
In file included from /Library/Frameworks/R.framework/Versions/3.4/Resources/library/RcppEigen/include/RcppEigenForward.h:31:
In file included from /Library/Frameworks/R.framework/Versions/3.4/Resources/library/RcppEigen/include/Eigen/Sparse:33:
In file included from /Library/Frameworks/R.framework/Versions/3.4/Resources/library/RcppEigen/include/Eigen/IterativeLinearSolvers:46:
/Library/Frameworks/R.framework/Versions/3.4/Resources/library/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas]
#pragma clang diagnostic pop
^
In file included from RcppExports.cpp:4:
In file included from /Library/Frameworks/R.framework/Versions/3.4/Resources/library/RcppEigen/include/RcppEigen.h:25:
In file included from /Library/Frameworks/R.framework/Versions/3.4/Resources/library/RcppEigen/include/RcppEigenForward.h:32:
In file included from /Library/Frameworks/R.framework/Versions/3.4/Resources/library/RcppEigen/include/Eigen/CholmodSupport:45:
/Library/Frameworks/R.framework/Versions/3.4/Resources/library/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas]
#pragma clang diagnostic pop
^
In file included from RcppExports.cpp:4:
In file included from /Library/Frameworks/R.framework/Versions/3.4/Resources/library/RcppEigen/include/RcppEigen.h:25:
In file included from /Library/Frameworks/R.framework/Versions/3.4/Resources/library/RcppEigen/include/RcppEigenForward.h:35:
In file included from /Library/Frameworks/R.framework/Versions/3.4/Resources/library/RcppEigen/include/unsupported/Eigen/KroneckerProduct:34:
/Library/Frameworks/R.framework/Versions/3.4/Resources/library/RcppEigen/include/unsupported/Eigen/../../Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas]
#pragma clang diagnostic pop
^
In file included from RcppExports.cpp:4:
In file included from /Library/Frameworks/R.framework/Versions/3.4/Resources/library/RcppEigen/include/RcppEigen.h:25:
In file included from /Library/Frameworks/R.framework/Versions/3.4/Resources/library/RcppEigen/include/RcppEigenForward.h:39:
In file included from /Library/Frameworks/R.framework/Versions/3.4/Resources/library/RcppEigen/include/unsupported/Eigen/Polynomials:135:
/Library/Frameworks/R.framework/Versions/3.4/Resources/library/RcppEigen/include/unsupported/Eigen/../../Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas]
#pragma clang diagnostic pop
^
In file included from RcppExports.cpp:4:
In file included from /Library/Frameworks/R.framework/Versions/3.4/Resources/library/RcppEigen/include/RcppEigen.h:25:
In file included from /Library/Frameworks/R.framework/Versions/3.4/Resources/library/RcppEigen/include/RcppEigenForward.h:40:
In file included from /Library/Frameworks/R.framework/Versions/3.4/Resources/library/RcppEigen/include/unsupported/Eigen/SparseExtra:51:
/Library/Frameworks/R.framework/Versions/3.4/Resources/library/RcppEigen/include/unsupported/Eigen/../../Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas]
#pragma clang diagnostic pop
^
17 warnings generated.
clang++ -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 DECENT.so LRT_logl.o RcppExports.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Library/Frameworks/R.framework/Versions/3.4/Resources/library/DECENT/libs
** R
** data
*** moving datasets to lazyload DB
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** testing if installed package can be loaded -
DONE (DECENT)
Downloading GitHub repo mohuangx/SAVER@master
from URL https://api.github.com/repos/mohuangx/SAVER/zipball/master
Installing SAVER
'/Library/Frameworks/R.framework/Resources/bin/R' --no-site-file --no-environ --no-save --no-restore --quiet CMD INSTALL
'/private/var/folders/7g/0kdlw4h53q7dpmghhbpjvn7h0000gn/T/RtmppKRZ5x/devtoolsf98f25178edf/mohuangx-SAVER-cc00536'
--library='/Library/Frameworks/R.framework/Versions/3.4/Resources/library' --install-tests -
installing source package ‘SAVER’ ...
** R
** data
*** moving datasets to lazyload DB
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** testing if installed package can be loaded -
DONE (SAVER)
Downloading GitHub repo statOmics/zingeR@master
from URL https://api.github.com/repos/statOmics/zingeR/zipball/master
Installing zingeR
'/Library/Frameworks/R.framework/Resources/bin/R' --no-site-file --no-environ --no-save --no-restore --quiet CMD INSTALL
'/private/var/folders/7g/0kdlw4h53q7dpmghhbpjvn7h0000gn/T/RtmppKRZ5x/devtoolsf98f2265d3f3/statOmics-zingeR-c789ae5'
--library='/Library/Frameworks/R.framework/Versions/3.4/Resources/library' --install-tests -
installing source package ‘zingeR’ ...
** R
** data
*** moving datasets to lazyload DB
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded -
DONE (zingeR)
devtools::install_github("bvieth/powsimR", build_vignettes = TRUE, dependencies = FALSE)
Downloading GitHub repo bvieth/powsimR@master
from URL https://api.github.com/repos/bvieth/powsimR/zipball/master
Installing powsimR
svn: E170013: Unable to connect to a repository at URL 'https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/AnnotationDbi'
svn: E230001: Server SSL certificate verification failed: issuer is not trusted
Installation failed: There was a problem retrieving the current SVN revision
Warning message:
running command ''/usr/bin/svn' info --xml --username readonly --password readonly https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/AnnotationDbi' had status 1
library(powsimR)
Error in library(powsimR) : there is no package called ‘powsimR’
from powsimr.
bvieth
commented on June 13, 2024
Hello,
thank you for trying out powsimR! I am sorry for the inconviences that you encountered.
Considering the last part of the error messages, I would say that there are still hiccups with the svn. Either the svn is not set up yet correctly, or the URL did really not exist ('https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/AnnotationDbi') which happened to me once when Bioconductor was updating its repositories.
Just to be sure, I would also try to install powsimR without building the vignette and check that all dependencies are properly installed:
cranpackages <- c("bbmle", "broom", "cluster", "cobs", "cowplot", "data.table",
"doParallel", "dplyr", "drc", "DrImpute", "fastICA", "fitdistrplus", "foreach",
"gamlss.dist", "ggExtra", "ggplot2", "ggthemes", "grDevices", "glmnet",
"grid", "gtools", "Hmisc", "kernlab", "MASS", "matrixStats", "mclust", "methods",
"minpack.lm", "moments", "msir", "NBPSeq", "nonnest2", "parallel", "penalized",
"plyr", "pscl", "reshape2", "ROCR", "Rtsne", "scales", "Seurat", "snow",
"stats", "tibble", "tidyr", "VGAM", "ZIM")
# BIOCONDUCTOR
biocpackages <- c("AnnotationDbi", "baySeq", "Biobase", "BiocGenerics", "BiocParallel",
"DEDS", "DESeq2", "EBSeq", "edgeR", "IHW", "iCOBRA", "limma", "Linnorm",
"MAST", "monocle", "NOISeq", "qvalue", "ROTS", "RUVSeq", "S4Vectors", "scater",
"scDD", "scde", "scone", "scran", "SCnorm", "SingleCellExperiment", "SummarizedExperiment",
"zinbwave")
# GITHUB
githubpackages <- c("BPSC", "cidr", "DECENT", "SAVER",
"zingeR")
powsimRdeps <- data.frame(Package = c(cranpackages, biocpackages, githubpackages), stringsAsFactors = F)
ip <- as.data.frame(installed.packages()[,c(1,3:4)], stringsAsFactors = F)
rownames(ip) <- NULL
head(ip, row.names=FALSE)
library(dplyr)
ipcheck <- powsimRdeps %>%
dplyr::left_join(ip, by="Package")
table(is.na(ipcheck$Version)) # all should be FALSE
devtools::install_github("bvieth/powsimR", build_vignettes = FALSE, dependencies = FALSE)
I hope this helps and please contact me again if you need any further assistance.
Kind regards
Beate
from powsimr.
bvieth
commented on June 13, 2024
Hello,
I will close the issue. Feel free to reopen if my suggestions did not solve the issue for you.
Kind regards
Beate
from powsimr.
Related Issues (20)
- Installation Issue HOT 7
- Dependency Issue HOT 6
- RNA Bulk pipeline HOT 1
- Issue with PowerSimR installation HOT 1
- Can't install in R v4.01 HOT 1
- error building vignette HOT 1
- pLFC input question HOT 1
- installation issue HOT 1
- FDR HOT 1
- Package installation failed HOT 1
- Installation Failed R v. 4.1.0 HOT 1
- simulateDE() error
- installation failed HOT 1
- Unable to install
- The gene number simulated by powsimR is not equal to the custom setting HOT 1
- plotEvalROC bug and statistical question on conditional to the mean TPR
- vector size HOT 2
- Installation error HOT 4
- installation failed: SummarizedExperiment HOT 1
- Error when running simulateDE
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