I was having compatibility issues with R and bioconductor, so I upgraded to the latest version of R (3.2.0) and am still having trouble. I am trying to install and use DESeq2. Please see the below output and errors. Any help would be greatly appreciated!
R version 3.2.0 (2015-04-16) -- "Full of Ingredients"
Copyright (C) 2015 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin13.4.0 (64-bit)
#error upon installing DESeq2
Using Bioconductor version 3.1 (BiocInstaller 1.18.1), R version 3.2.0.
Installing package(s) ‘DESeq2’
also installing the dependency ‘Hmisc’
There is a binary version available but the source version is later:
binary source needs_compilation
Hmisc 3.15-0 3.16-0 TRUE
Do you want to install from sources the package which needs compilation?
trying URL 'http://bioconductor.org/packages/3.1/bioc/bin/macosx/mavericks/contrib/3.2/DESeq2_1.8.0.tgz'
Content type 'application/x-gzip' length 1422008 bytes (1.4 MB)
downloaded 1.4 MB
The downloaded binary packages are in
installing the source package ‘Hmisc’
trying URL 'http://cran.rstudio.com/src/contrib/Hmisc_3.16-0.tar.gz'
Content type 'application/x-gzip' length 629536 bytes (614 KB)
downloaded 614 KB
* installing *source* package ‘Hmisc’ ...
** package ‘Hmisc’ successfully unpacked and MD5 sums checked
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -fPIC -Wall -mtune=core2 -g -O2 -c Hmisc.c -o Hmisc.o
gfortran-4.8 -fPIC -g -O2 -c cidxcn.f -o cidxcn.o
make: gfortran-4.8: No such file or directory
make: *** [cidxcn.o] Error 1
ERROR: compilation failed for package ‘Hmisc’
* removing ‘/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Hmisc’
The downloaded source packages are in
In install.packages(pkgs = doing, lib = lib, ...) :
installation of package ‘Hmisc’ had non-zero exit status
#error in running DESeq2
> dds <- DESeqDataSetFromMatrix(countData = countData, colData = colData, design= ~trmt)
Error: could not find function "DESeqDataSetFromMatrix"