installation of package ‘DESeq2’ had non-zero exit status
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GA ▴ 10
@293af73d
Last seen 16 days ago
United States

I tried to download DESeq2 in ubuntu 20.04 by:

BiocManager::install("DESeq2")

I got a lot of warning messages of different packages having a "non-zero exit status." I was able to resolve most of them by installing each package individually. However, there is one warning message that remaind and I don't know how to solve:

Warning message:
In install.packages(...) :
  installation of package ‘DESeq2’ had non-zero exit status

What should I do to fix this??

Thank you!!

DESeq2 • 132 views
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ATpoint ★ 1.2k
@atpoint-13662
Last seen 3 days ago
Germany

Please show the full log, this error can mean anything.

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This is the full message I get after entering BiocManager::install("DESeq2"):

'getOption("repos")' replaces Bioconductor standard repositories, see '?repositories' for details

replacement repositories: CRAN: https://cloud.r-project.org

Bioconductor version 3.14 (BiocManager 1.30.17), R 4.1.3 (2022-03-10) Installing package(s) 'DESeq2' trying URL 'https://bioconductor.org/packages/3.14/bioc/src/contrib/DESeq2_1.34.0.tar.gz'

Content type 'application/x-gzip' length 2088431 bytes (2.0 MB)

downloaded 2.0 MB

  • installing source package ‘DESeq2’ ...

** using staged installation

** libs

g++ -std=gnu++14 -I"/usr/share/R/include" -DNDEBUG -I'/home/gimena/R/x86_64-pc-linux-gnu-library/4.1/Rcpp/include' -I'/usr/lib/R/site-library/RcppArmadillo/include' -fpic -g -O2 -fdebug-prefix-map=/build/r-base-lENDSu/r-base-4.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c DESeq2.cpp -o DESeq2.o

g++ -std=gnu++14 -I"/usr/share/R/include" -DNDEBUG -I'/home/gimena/R/x86_64-pc-linux-gnu-library/4.1/Rcpp/include' -I'/usr/lib/R/site-library/RcppArmadillo/include' -fpic -g -O2 -fdebug-prefix-map=/build/r-base-lENDSu/r-base-4.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c RcppExports.cpp -o RcppExports.o

g++ -std=gnu++14 -shared -L/usr/lib/R/lib -Wl,-Bsymbolic-functions -Wl,-z,relro -o DESeq2.so DESeq2.o RcppExports.o -llapack -lblas -lgfortran -lm -lquadmath -L/usr/lib/R/lib -lR

/usr/bin/ld: cannot find -lgfortran

collect2: error: ld returned 1 exit status

make: *** [/usr/share/R/share/make/shlib.mk:10: DESeq2.so] Error 1

ERROR: compilation failed for package ‘DESeq2’

  • removing ‘/home/gimena/R/x86_64-pc-linux-gnu-library/4.1/DESeq2’

The downloaded source packages are in

    ‘/tmp/RtmpeWaBbb/downloaded_packages’

Installation paths not writeable, unable to update packages

path: /usr/lib/R/library

packages:

cluster, MASS, Matrix, mgcv, nlme

Warning message:

In install.packages(...) :

installation of package ‘DESeq2’ had non-zero exit status

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