Entering edit mode
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!!
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
** 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’
The downloaded source packages are in
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
https://askubuntu.com/questions/276892/cannot-find-lgfortran