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@valentinalosardo-16555
Last seen 6.7 years ago
Hello, I'm a very naive user of R and I'm trying to install packages that I need for RNA sequencing analysis. I would like to use the DESeq2 package and I'm trying to install it on my Mac computer. This is the output that I get. Any suggestion to fix the problem?Thanks!
> install.packages("DESeq2") Warning in install.packages : package ‘DESeq2’ is not available (for R version 3.3.3) > source("http://bioconductor.org/biocLite.R") Bioconductor version 3.4 (BiocInstaller 1.24.0), ?biocLite for help A new version of Bioconductor is available after installing the most recent version of R; see http://bioconductor.org/install > ?biocLite > source("https://bioconductor.org/biocLite.R") Bioconductor version 3.4 (BiocInstaller 1.24.0), ?biocLite for help A new version of Bioconductor is available after installing the most recent version of R; see http://bioconductor.org/install > biocLite("DESeq2") BioC_mirror: https://bioconductor.org Using Bioconductor 3.4 (BiocInstaller 1.24.0), R 3.3.3 (2017-03-06). Installing package(s) ‘DESeq2’ also installing the dependency ‘RcppArmadillo’ There is a binary version available but the source version is later: binary source needs_compilation RcppArmadillo 0.8.300.1.0 0.8.600.0.0 TRUE Do you want to install from sources the package which needs compilation? y/n: y
after this it runs for a bit and at the end this is the message
ld: warning: directory not found for option '-L/usr/local/lib/gcc/x86_64-apple-darwin13.0.0/4.8.2' ld: library not found for -lgfortran clang: error: linker command failed with exit code 1 (use -v to see invocation) make: *** [mgcv.so] Error 1 ERROR: compilation failed for package ‘mgcv’ * removing ‘/Library/Frameworks/R.framework/Versions/3.3/Resources/library/mgcv’ * restoring previous ‘/Library/Frameworks/R.framework/Versions/3.3/Resources/library/mgcv’ The downloaded source packages are in ‘/private/var/folders/p3/p1yv73h132gd9w3wfkzq8gfr0000gn/T/RtmpnKaYT6/downloaded_packages’ Warning messages: 1: In install.packages(pkgs = doing, lib = lib, ...) : installation of package ‘RcppArmadillo’ had non-zero exit status 2: In install.packages(update[instlib == l, "Package"], l, repos = repos, : installation of package ‘cluster’ had non-zero exit status 3: In install.packages(update[instlib == l, "Package"], l, repos = repos, : installation of package ‘Matrix’ had non-zero exit status 4: In install.packages(update[instlib == l, "Package"], l, repos = repos, : installation of package ‘mgcv’ had non-zero exit status > sessionInfo("DESeq2") R version 3.3.3 (2017-03-06) Platform: x86_64-apple-darwin13.4.0 (64-bit) Running under: OS X Yosemite 10.10.5 locale: [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8 attached base packages: character(0) other attached packages: [1] DESeq2_1.14.1 loaded via a namespace (and not attached): [1] BiocInstaller_1.24.0 graphics_3.3.3 tools_3.3.3 utils_3.3.3 [5] grDevices_3.3.3 stats_3.3.3 datasets_3.3.3 methods_3.3.3 [9] base_3.3.3
Thanks a lot!!