Entering edit mode
Hi,
I m having error in installing DESeq2 on my mac.
library(DESeq2)
Error: package ‘RcppArmadillo’ required by ‘DESeq2’ could not be found
sessionInfo()
R version 3.2.0 (2015-04-16)
Platform: x86_64-apple-darwin13.4.0 (64-bit)
Running under: OS X 10.10.5 (Yosemite)
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:
[1] parallel stats4 stats graphics grDevices utils datasets methods base
other attached packages:
[1] Rcpp_0.11.6 GenomicRanges_1.20.5 GenomeInfoDb_1.4.2 IRanges_2.2.7
[5] S4Vectors_0.6.3 BiocGenerics_0.14.0 BiocInstaller_1.18.4
loaded via a namespace (and not attached):
[1] XVector_0.8.0 tools_3.2.0
HI Andrew,
I selected a different CRAN mirror. Now when im trying install, its showing this message. Do you want to install from sources the packages which need compilation? Should i choose yes or No?
The downloaded binary packages are in
/var/folders/yf/ylf3ln2508x5_54hmg8m_01m0000gp/T//Rtmppp1FZf/downloaded_packages
Old packages: 'nlme', 'RcppArmadillo'
Update all/some/none? [a/s/n]:
a
There are binary versions available but the source versions are later:
binary source needs_compilation
nlme 3.1-121 3.1-122 TRUE
RcppArmadillo 0.5.300.4 0.5.400.2.0 TRUE
Do you want to install from sources the packages which need compilation?
I'd compile from source if you can, if you can't it'll generally pull down pre-compiled binaries
HI,
Im not able to install. Yesterday my mac os updated, may be because of that the issue comes.
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 -lquadmath
clang: error: linker command failed with exit code 1 (use -v to see invocation)
make: *** [RcppArmadillo.so] Error 1
ERROR: compilation failed for package ‘RcppArmadillo’
* removing ‘/Library/Frameworks/R.framework/Versions/3.2/Resources/library/RcppArmadillo’
* restoring previous ‘/Library/Frameworks/R.framework/Versions/3.2/Resources/library/RcppArmadillo’
The downloaded source packages are in
‘/private/var/folders/yf/ylf3ln2508x5_54hmg8m_01m0000gp/T/Rtmppp1FZf/downloaded_packages’
Warning messages:
1: In install.packages(update[instlib == l, "Package"], l, repos = repos, :
installation of package ‘nlme’ had non-zero exit status
2: In install.packages(update[instlib == l, "Package"], l, repos = repos, :
installation of package ‘RcppArmadillo’ had non-zero exit status
Do you have Xcode installed?
I really don't think this is a good suggestion for this user -- install the slightly older, binary version and do not try to compile from source.
Hi Andrew,
Just now i installed Xcode and i tried .
Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) :
there is no package called ‘xtable’
Error: package or namespace load failed for ‘DESeq2
You'd need to do
install.packages("xtable")too. I do agree with Martin, that was probably slightly bad advice on my part, installing from binaries may have been easier, but Xcode should be able to handle the compilation now.Now it worked.
Compiling from source requires additional software. Also, since the system responsible for creating the binary is having trouble creating the binary from the most recent source, this implies there is some extra level of knowledge required to compile from source. if you're struggling with installation, then it is probably much easier to say 'no' you do not want to install from source, and to use the slightly older pre-compiled versions.
Also, be sure to choose a 'main stream' CRAN mirror, e.g., '0-cloud'