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Question: Cannot use Bioconductor with new conda R installation?
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gravatar for jol.espinoz
3 months ago by
jol.espinoz10
jol.espinoz10 wrote:

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

ADD COMMENTlink modified 3 months ago • written 3 months ago by jol.espinoz10
1
gravatar for jol.espinoz
3 months ago by
jol.espinoz10
jol.espinoz10 wrote:
These solved my problem.  Definitely the second one and possibly the commented out one too. 

​
#conda install gfortran_osx-64 --yes
conda install -c anaconda clangxx_osx-64 --yes
ADD COMMENTlink written 3 months ago by jol.espinoz10
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