Unable to install DeSeq2 and EdgeR in ubuntu 16.04 , this is what happens when I install DeSeq2
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Entering edit mode
@aditya531996-12339
Last seen 4.7 years ago

This is the error I get when installing DESeq2

 

> source("https://bioconductor.org/biocLite.R")
Bioconductor version 3.4 (BiocInstaller 1.24.0), ?biocLite for help
> 
> biocLite("DESeq2")
 //LOTS OF LINES OF COMPILATION I DELETED TO FIT THIS IN
 // I PASTED ONLY THE LAST PART


gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG   -I"/home/aditya/R/x86_64-pc-linux-gnu-library/3.3/S4Vectors/include" -I"/home/aditya/R/x86_64-pc-linux-gnu-library/3.3/IRanges/include"   -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c SharedRaw_class.c -o SharedRaw_class.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG   -I"/home/aditya/R/x86_64-pc-linux-gnu-library/3.3/S4Vectors/include" -I"/home/aditya/R/x86_64-pc-linux-gnu-library/3.3/IRanges/include"   -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c SharedVector_class.c -o SharedVector_class.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG   -I"/home/aditya/R/x86_64-pc-linux-gnu-library/3.3/S4Vectors/include" -I"/home/aditya/R/x86_64-pc-linux-gnu-library/3.3/IRanges/include"   -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c XRawList_comparison.c -o XRawList_comparison.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG   -I"/home/aditya/R/x86_64-pc-linux-gnu-library/3.3/S4Vectors/include" -I"/home/aditya/R/x86_64-pc-linux-gnu-library/3.3/IRanges/include"   -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c XVectorList_class.c -o XVectorList_class.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG   -I"/home/aditya/R/x86_64-pc-linux-gnu-library/3.3/S4Vectors/include" -I"/home/aditya/R/x86_64-pc-linux-gnu-library/3.3/IRanges/include"   -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c XVector_class.c -o XVector_class.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG   -I"/home/aditya/R/x86_64-pc-linux-gnu-library/3.3/S4Vectors/include" -I"/home/aditya/R/x86_64-pc-linux-gnu-library/3.3/IRanges/include"   -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c io_utils.c -o io_utils.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG   -I"/home/aditya/R/x86_64-pc-linux-gnu-library/3.3/S4Vectors/include" -I"/home/aditya/R/x86_64-pc-linux-gnu-library/3.3/IRanges/include"   -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c slice_methods.c -o slice_methods.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG   -I"/home/aditya/R/x86_64-pc-linux-gnu-library/3.3/S4Vectors/include" -I"/home/aditya/R/x86_64-pc-linux-gnu-library/3.3/IRanges/include"   -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c vector_copy.c -o vector_copy.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG   -I"/home/aditya/R/x86_64-pc-linux-gnu-library/3.3/S4Vectors/include" -I"/home/aditya/R/x86_64-pc-linux-gnu-library/3.3/IRanges/include"   -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c view_summarization_methods.c -o view_summarization_methods.o
gcc -std=gnu99 -shared -L/usr/lib/R/lib -Wl,-Bsymbolic-functions -Wl,-z,relro -o XVector.so IRanges_stubs.o Ocopy_byteblocks.o R_init_XVector.o S4Vectors_stubs.o SharedDouble_class.o SharedInteger_class.o SharedRaw_class.o SharedVector_class.o XRawList_comparison.o XVectorList_class.o XVector_class.o io_utils.o slice_methods.o vector_copy.o view_summarization_methods.o -lz -L/usr/lib/R/lib -lR
installing to /home/aditya/R/x86_64-pc-linux-gnu-library/3.3/XVector/libs
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** testing if installed package can be loaded
* DONE (XVector)
* installing *source* package ‘futile.logger’ ...
** package ‘futile.logger’ successfully unpacked and MD5 sums checked
** R
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** testing if installed package can be loaded
* DONE (futile.logger)
* installing *source* package ‘annotate’ ...
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (annotate)
* installing *source* package ‘viridis’ ...
** package ‘viridis’ successfully unpacked and MD5 sums checked
** R
** data
*** moving datasets to lazyload DB
** inst
** preparing package for lazy loading
** help
*** installing help indices
*** copying figures
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (viridis)
* installing *source* package ‘htmlTable’ ...
** package ‘htmlTable’ successfully unpacked and MD5 sums checked
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (htmlTable)
* installing *source* package ‘GenomicRanges’ ...
** libs
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG   -I"/home/aditya/R/x86_64-pc-linux-gnu-library/3.3/S4Vectors/include" -I"/home/aditya/R/x86_64-pc-linux-gnu-library/3.3/IRanges/include"   -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c IRanges_stubs.c -o IRanges_stubs.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG   -I"/home/aditya/R/x86_64-pc-linux-gnu-library/3.3/S4Vectors/include" -I"/home/aditya/R/x86_64-pc-linux-gnu-library/3.3/IRanges/include"   -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c R_init_GenomicRanges.c -o R_init_GenomicRanges.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG   -I"/home/aditya/R/x86_64-pc-linux-gnu-library/3.3/S4Vectors/include" -I"/home/aditya/R/x86_64-pc-linux-gnu-library/3.3/IRanges/include"   -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c S4Vectors_stubs.c -o S4Vectors_stubs.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG   -I"/home/aditya/R/x86_64-pc-linux-gnu-library/3.3/S4Vectors/include" -I"/home/aditya/R/x86_64-pc-linux-gnu-library/3.3/IRanges/include"   -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c transcript_utils.c -o transcript_utils.o
gcc -std=gnu99 -shared -L/usr/lib/R/lib -Wl,-Bsymbolic-functions -Wl,-z,relro -o GenomicRanges.so IRanges_stubs.o R_init_GenomicRanges.o S4Vectors_stubs.o transcript_utils.o -L/usr/lib/R/lib -lR
installing to /home/aditya/R/x86_64-pc-linux-gnu-library/3.3/GenomicRanges/libs
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (GenomicRanges)
* installing *source* package ‘BiocParallel’ ...
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (BiocParallel)
* installing *source* package ‘genefilter’ ...
** libs
g++ -I/usr/share/R/include -DNDEBUG      -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c half_range_mode.cpp -o half_range_mode.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG      -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c init.c -o init.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG      -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c nd.c -o nd.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG      -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c pAUC.c -o pAUC.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG      -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c rowPAUCs.c -o rowPAUCs.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG      -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c rowttests.c -o rowttests.o
gfortran   -fpic  -g -O2 -fstack-protector-strong  -c ttest.f -o ttest.o
g++ -shared -L/usr/lib/R/lib -Wl,-Bsymbolic-functions -Wl,-z,relro -o genefilter.so half_range_mode.o init.o nd.o pAUC.o rowPAUCs.o rowttests.o ttest.o -lgfortran -lm -lquadmath -L/usr/lib/R/lib -lR
/usr/bin/ld: cannot find -lgfortran
collect2: error: ld returned 1 exit status
/usr/share/R/share/make/shlib.mk:6: recipe for target 'genefilter.so' failed
make: *** [genefilter.so] Error 1
ERROR: compilation failed for package ‘genefilter’
* removing ‘/home/aditya/R/x86_64-pc-linux-gnu-library/3.3/genefilter’
* installing *source* package ‘geneplotter’ ...
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (geneplotter)
* installing *source* package ‘SummarizedExperiment’ ...
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (SummarizedExperiment)
ERROR: dependency ‘acepack’ is not available for package ‘Hmisc’
* removing ‘/home/aditya/R/x86_64-pc-linux-gnu-library/3.3/Hmisc’
ERROR: dependencies ‘genefilter’, ‘Hmisc’, ‘RcppArmadillo’ are not available for package ‘DESeq2’
* removing ‘/home/aditya/R/x86_64-pc-linux-gnu-library/3.3/DESeq2’

The downloaded source packages are in
	‘/tmp/RtmpAOLyfm/downloaded_packages’
installation path not writeable, unable to update packages: Matrix, mgcv, nlme
Warning messages:
1: In install.packages(pkgs = doing, lib = lib, ...) :
  installation of package ‘acepack’ had non-zero exit status
2: In install.packages(pkgs = doing, lib = lib, ...) :
  installation of package ‘RcppArmadillo’ had non-zero exit status
3: In install.packages(pkgs = doing, lib = lib, ...) :
  installation of package ‘genefilter’ had non-zero exit status
4: In install.packages(pkgs = doing, lib = lib, ...) :
  installation of package ‘Hmisc’ had non-zero exit status
5: In install.packages(pkgs = doing, lib = lib, ...) :
  installation of package ‘DESeq2’ had non-zero exit status
deseq2 ubuntu edger dependencies • 1.4k views
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Entering edit mode
@wolfgang-huber-3550
Last seen 11 weeks ago
EMBL European Molecular Biology Laborat…

Have a look at the error message

/usr/bin/ld: cannot find -lgfortran

and try again after installing a fortran compiler.

 

 

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0
Entering edit mode
@aditya531996-12339
Last seen 4.7 years ago

Thanks mate

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