Hi
I am trying to install DESeq2 on Google Cloud Platform (Ubuntu 18.04.2 LTS; 4 CPUs; 15 GB RAM; sessionInfo()
below) and get the following non-zero exit status
. R appears to be installed correctly, it is started with sudo -i R
, and I was able to install BiocManager
(see below). Non-zero exits are also returned when installing XML
, annotate
, genefilter
, or geneplotter
individually.
I successfully install DESeq2 on macOS 10.14.4 (Mojave). Any suggestions?
Thank you Emilio
BiocManager Installed
BiocManager::valid()
[1] TRUE
DESeq2 Install Command
if (!requireNamespace("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("DESeq2", version = "3.8")
DESeq2 Install Error (returned at the end)
ERROR: dependencies ‘genefilter’, ‘geneplotter’ are not available for package ‘DESeq2’
* removing ‘/usr/local/lib/R/site-library/DESeq2’
The downloaded source packages are in
‘/tmp/Rtmpurxecw/downloaded_packages’
Warning messages:
1: In install.packages(pkgs = doing, lib = lib, repos = repos, ...) :
installation of package ‘XML’ had non-zero exit status
2: In install.packages(pkgs = doing, lib = lib, repos = repos, ...) :
installation of package ‘annotate’ had non-zero exit status
3: In install.packages(pkgs = doing, lib = lib, repos = repos, ...) :
installation of package ‘genefilter’ had non-zero exit status
4: In install.packages(pkgs = doing, lib = lib, repos = repos, ...) :
installation of package ‘geneplotter’ had non-zero exit status
5: In install.packages(pkgs = doing, lib = lib, repos = repos, ...) :
installation of package ‘DESeq2’ had non-zero exit status
Session Information
> sessionInfo()
R version 3.5.3 (2019-03-11)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 18.04.2 LTS
Matrix products: default
BLAS: /usr/lib/x86_64-linux-gnu/blas/libblas.so.3.7.1
LAPACK: /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.7.1
locale:
[1] LC_CTYPE=C.UTF-8 LC_NUMERIC=C LC_TIME=C.UTF-8
[4] LC_COLLATE=C.UTF-8 LC_MONETARY=C.UTF-8 LC_MESSAGES=C.UTF-8
[7] LC_PAPER=C.UTF-8 LC_NAME=C LC_ADDRESS=C
[10] LC_TELEPHONE=C LC_MEASUREMENT=C.UTF-8 LC_IDENTIFICATION=C
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] BiocManager_1.30.4
loaded via a namespace (and not attached):
[1] compiler_3.5.3 tools_3.5.3
This issue with the devel libraries comes up so frequently, it's even a FAQ in the DESeq2 vignette :-)
Thank you for the suggestion! Got DESeq2 installed.