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DESeq2 R package - problem with installation

When I am trying install:

if (!requireNamespace("BiocManager", quietly = TRUE))
     install.packages("BiocManager") 
BiocManager::install("DESeq2")

I got error an error:

* installing *source* package ‘DESeq2’ ...
** using staged installation
** libs
g++ -std=gnu++11 -I"/opt/R/4.0.3/lib/R/include" -DNDEBUG  -I'/home/rstudio-user/R/x86_64-pc-linux-gnu-
library/4.0/Rcpp/include' -I'/home/rstudio-user/R/x86_64-pc-linux-gnu-library/4.0/RcppArmadillo/include' -I/usr/local/include   
-fpic  -g -O2  -c DESeq2.cpp -o DESeq2.o
g++: internal compiler error: Killed (program cc1plus)
Please submit a full bug report,
with preprocessed source if appropriate.
See <file:///usr/share/doc/gcc-5/README.Bugs> for instructions
make: *** [DESeq2.o] Error 4
/opt/R/4.0.3/lib/R/etc/Makeconf:181: recipe for target 'DESeq2.o' failed
ERROR: compilation failed for package ‘DESeq2’
* removing ‘/home/rstudio-user/R/x86_64-pc-linux-gnu-library/4.0/DESeq2’
The downloaded source packages are in
    ‘/tmp/Rtmprq6ONF/downloaded_packages’
Installation path not writeable, unable to update packages: boot, class, codetools, foreign, KernSmooth, Matrix, nlme,
  nnet, spatial
Warning message:
In install.packages(...) :
  installation of package ‘DESeq2’ had non-zero exit status

Someone know how to fix it?

deseq2 r
• 238 views • link
updated by ATpoint ATpoint • written by ja4123 • ja4123

1 answer

Please post this over at support.bioconductor.org and try to provide the full log from the compilation, for example using a Gist (so paste the log in there and provide the link in the Bioc post).

• 0 views • link
written by ATpoint ATpoint

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