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aditya531996
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@aditya531996-12339
Last seen 7.9 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