I'm having a lot of trouble trying to install WGCNA, edgeR, and limma. First I tried to just the base bioconductor packges but there was the following error:
conda create -n r_test python=3 --yes
conda activate r_test
conda install -c r r --yes
# This was successful
(r_test) jespinozlt-osx:~ jespinoz$ R
R version 3.4.2 (2017-09-28) -- "Short Summer"
Copyright (C) 2017 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin13.4.0 (64-bit)
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.
Natural language support but running in an English locale
R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.
Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.
[Previously saved workspace restored]
> source("http://bioconductor.org/biocLite.R"
+ )
trying URL 'https://bioconductor.org/packages/3.6/bioc/src/contrib/BiocInstaller_1.28.0.tar.gz'
Content type 'application/x-gzip' length 18624 bytes (18 KB)
==================================================
downloaded 18 KB
* installing *source* package ‘BiocInstaller’ ...
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** testing if installed package can be loaded
Bioconductor version 3.6 (BiocInstaller 1.28.0), ?biocLite for help
* DONE (BiocInstaller)
The downloaded source packages are in
‘/private/var/folders/6z/5vbtz_gmkr76ftgc3149dvtr0003c0/T/RtmpTCr3v4/downloaded_packages’
Updating HTML index of packages in '.Library'
Making 'packages.html' ... done
Bioconductor version 3.6 (BiocInstaller 1.28.0), ?biocLite for help
> bioc
biocases_group biocinstallRepos biocLite biocUpdatePackages biocValid biocVersion
> biocLite()
BioC_mirror: https://bioconductor.org
Using Bioconductor 3.6 (BiocInstaller 1.28.0), R 3.4.2 (2017-09-28).
Installing package(s) ‘Biobase’, ‘IRanges’, ‘AnnotationDbi’
also installing the dependencies ‘assertthat’, ‘utf8’, ‘cli’, ‘crayon’, ‘pillar’, ‘rlang’, ‘bit’, ‘tibble’, ‘digest’, ‘bit64’, ‘blob’, ‘memoise’, ‘pkgconfig’, ‘Rcpp’, ‘BH’, ‘plogr’, ‘BiocGenerics’, ‘S4Vectors’, ‘DBI’, ‘RSQLite’
trying URL 'http://cran.r-project.org/src/contrib/assertthat_0.2.0.tar.gz'
Content type 'application/x-gzip' length 11612 bytes (11 KB)
==================================================
# Downloading packages
* installing *source* package ‘assertthat’ ...
** package ‘assertthat’ successfully unpacked and MD5 sums checked
** R
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** testing if installed package can be loaded
* DONE (assertthat)
* installing *source* package ‘utf8’ ...
** package ‘utf8’ successfully unpacked and MD5 sums checked
** libs
x86_64-apple-darwin13.4.0-clang -I/Users/jespinoz/anaconda/envs/r_test/lib/R/include -DNDEBUG -D_FORTIFY_SOURCE=2 -mmacosx-version-min=10.9 -I/Users/jespinoz/anaconda/envs/r_test/include -Iutf8lite/src -fPIC -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fPIE -fstack-protector-strong -O2 -pipe -I/Users/jespinoz/anaconda/envs/r_test/include -c as_utf8.c -o as_utf8.o
make: x86_64-apple-darwin13.4.0-clang: No such file or directory
make: *** [as_utf8.o] Error 1
ERROR: compilation failed for package ‘utf8’
* removing ‘/Users/jespinoz/anaconda/envs/r_test/lib/R/library/utf8’
* installing *source* package ‘crayon’ ...
** package ‘crayon’ successfully unpacked and MD5 sums checked
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** testing if installed package can be loaded
* DONE (crayon)
* installing *source* package ‘rlang’ ...
** package ‘rlang’ successfully unpacked and MD5 sums checked
** libs
x86_64-apple-darwin13.4.0-clang -I/Users/jespinoz/anaconda/envs/r_test/lib/R/include -DNDEBUG -I./lib/ -D_FORTIFY_SOURCE=2 -mmacosx-version-min=10.9 -I/Users/jespinoz/anaconda/envs/r_test/include -fPIC -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fPIE -fstack-protector-strong -O2 -pipe -I/Users/jespinoz/anaconda/envs/r_test/include -c capture.c -o capture.o
make: x86_64-apple-darwin13.4.0-clang: No such file or directory
make: *** [capture.o] Error 1
ERROR: compilation failed for package ‘rlang’
* removing ‘/Users/jespinoz/anaconda/envs/r_test/lib/R/library/rlang’
* installing *source* package ‘bit’ ...
** package ‘bit’ successfully unpacked and MD5 sums checked
** libs
x86_64-apple-darwin13.4.0-clang -I/Users/jespinoz/anaconda/envs/r_test/lib/R/include -DNDEBUG -D_FORTIFY_SOURCE=2 -mmacosx-version-min=10.9 -I/Users/jespinoz/anaconda/envs/r_test/include -fPIC -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fPIE -fstack-protector-strong -O2 -pipe -I/Users/jespinoz/anaconda/envs/r_test/include -c attrutil.c -o attrutil.o
make: x86_64-apple-darwin13.4.0-clang: No such file or directory
make: *** [attrutil.o] Error 1
ERROR: compilation failed for package ‘bit’
* removing ‘/Users/jespinoz/anaconda/envs/r_test/lib/R/library/bit’
* installing *source* package ‘digest’ ...
** package ‘digest’ successfully unpacked and MD5 sums checked
** libs
x86_64-apple-darwin13.4.0-clang -I/Users/jespinoz/anaconda/envs/r_test/lib/R/include -DNDEBUG -D_FORTIFY_SOURCE=2 -mmacosx-version-min=10.9 -I/Users/jespinoz/anaconda/envs/r_test/include -fPIC -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fPIE -fstack-protector-strong -O2 -pipe -I/Users/jespinoz/anaconda/envs/r_test/include -c aes.c -o aes.o
make: x86_64-apple-darwin13.4.0-clang: No such file or directory
make: *** [aes.o] Error 1
ERROR: compilation failed for package ‘digest’
* removing ‘/Users/jespinoz/anaconda/envs/r_test/lib/R/library/digest’
* installing *source* package ‘pkgconfig’ ...
** package ‘pkgconfig’ successfully unpacked and MD5 sums checked
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** testing if installed package can be loaded
* DONE (pkgconfig)
* installing *source* package ‘Rcpp’ ...
** package ‘Rcpp’ successfully unpacked and MD5 sums checked
** libs
x86_64-apple-darwin13.4.0-clang++ -I/Users/jespinoz/anaconda/envs/r_test/lib/R/include -DNDEBUG -I../inst/include/ -D_FORTIFY_SOURCE=2 -mmacosx-version-min=10.9 -I/Users/jespinoz/anaconda/envs/r_test/include -fPIC -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fPIE -fstack-protector-strong -O2 -pipe -stdlib=libc++ -fvisibility-inlines-hidden -fmessage-length=0 -I/Users/jespinoz/anaconda/envs/r_test/include -c Date.cpp -o Date.o
make: x86_64-apple-darwin13.4.0-clang++: No such file or directory
make: *** [Date.o] Error 1
ERROR: compilation failed for package ‘Rcpp’
* removing ‘/Users/jespinoz/anaconda/envs/r_test/lib/R/library/Rcpp’
* installing *source* package ‘BH’ ...
** package ‘BH’ successfully unpacked and MD5 sums checked
** inst
** help
*** installing help indices
** building package indices
** testing if installed package can be loaded
* DONE (BH)
* installing *source* package ‘plogr’ ...
** package ‘plogr’ successfully unpacked and MD5 sums checked
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** testing if installed package can be loaded
* DONE (plogr)
* installing *source* package ‘BiocGenerics’ ...
** R
** inst
** preparing package for lazy loading
Creating a new generic function for ‘append’ in package ‘BiocGenerics’
# Followed by a bunch of similar functions
** help
*** installing help indices
** building package indices
** testing if installed package can be loaded
* DONE (BiocGenerics)
* installing *source* package ‘DBI’ ...
** package ‘DBI’ successfully unpacked and MD5 sums checked
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (DBI)
* installing *source* package ‘cli’ ...
** package ‘cli’ successfully unpacked and MD5 sums checked
** R
** preparing package for lazy loading
** help
*** installing help indices
*** copying figures
** building package indices
** testing if installed package can be loaded
* DONE (cli)
ERROR: dependency ‘bit’ is not available for package ‘bit64’
* removing ‘/Users/jespinoz/anaconda/envs/r_test/lib/R/library/bit64’
ERROR: dependency ‘digest’ is not available for package ‘memoise’
* removing ‘/Users/jespinoz/anaconda/envs/r_test/lib/R/library/memoise’
* installing *source* package ‘S4Vectors’ ...
** libs
x86_64-apple-darwin13.4.0-clang -I/Users/jespinoz/anaconda/envs/r_test/lib/R/include -DNDEBUG -D_FORTIFY_SOURCE=2 -mmacosx-version-min=10.9 -I/Users/jespinoz/anaconda/envs/r_test/include -fPIC -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fPIE -fstack-protector-strong -O2 -pipe -I/Users/jespinoz/anaconda/envs/r_test/include -c AEbufs.c -o AEbufs.o
make: x86_64-apple-darwin13.4.0-clang: No such file or directory
make: *** [AEbufs.o] Error 1
ERROR: compilation failed for package ‘S4Vectors’
* removing ‘/Users/jespinoz/anaconda/envs/r_test/lib/R/library/S4Vectors’
* installing *source* package ‘Biobase’ ...
** libs
x86_64-apple-darwin13.4.0-clang -I/Users/jespinoz/anaconda/envs/r_test/lib/R/include -DNDEBUG -D_FORTIFY_SOURCE=2 -mmacosx-version-min=10.9 -I/Users/jespinoz/anaconda/envs/r_test/include -fPIC -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fPIE -fstack-protector-strong -O2 -pipe -I/Users/jespinoz/anaconda/envs/r_test/include -c Rinit.c -o Rinit.o
make: x86_64-apple-darwin13.4.0-clang: No such file or directory
make: *** [Rinit.o] Error 1
ERROR: compilation failed for package ‘Biobase’
* removing ‘/Users/jespinoz/anaconda/envs/r_test/lib/R/library/Biobase’
ERROR: dependencies ‘rlang’, ‘utf8’ are not available for package ‘pillar’
* removing ‘/Users/jespinoz/anaconda/envs/r_test/lib/R/library/pillar’
ERROR: dependency ‘S4Vectors’ is not available for package ‘IRanges’
* removing ‘/Users/jespinoz/anaconda/envs/r_test/lib/R/library/IRanges’
ERROR: dependencies ‘pillar’, ‘rlang’ are not available for package ‘tibble’
* removing ‘/Users/jespinoz/anaconda/envs/r_test/lib/R/library/tibble’
ERROR: dependency ‘tibble’ is not available for package ‘blob’
* removing ‘/Users/jespinoz/anaconda/envs/r_test/lib/R/library/blob’
ERROR: dependencies ‘bit64’, ‘blob’, ‘memoise’, ‘Rcpp’ are not available for package ‘RSQLite’
* removing ‘/Users/jespinoz/anaconda/envs/r_test/lib/R/library/RSQLite’
ERROR: dependencies ‘Biobase’, ‘IRanges’, ‘RSQLite’, ‘S4Vectors’ are not available for package ‘AnnotationDbi’
* removing ‘/Users/jespinoz/anaconda/envs/r_test/lib/R/library/AnnotationDbi’
The downloaded source packages are in
‘/private/var/folders/6z/5vbtz_gmkr76ftgc3149dvtr0003c0/T/RtmpTCr3v4/downloaded_packages’
Updating HTML index of packages in '.Library'
Making 'packages.html' ... done