Unable to compile genefilter package
Entering edit mode
Last seen 5.6 years ago

HI everyone,

I have been trying to install genefilter on R version 3.4.3 (2016-05-03). Bioconducter version 3.6


I have used the following commands:

> source("http://www.bioconductor.org/biocLite.R")



I receive the following error:


BioC_mirror: https://bioconductor.org
Using Bioconductor 3.6 (BiocInstaller 1.28.0), R 3.4.3 (2017-11-30).
Installing package(s) ‘genefilter’
trying URL 'https://bioconductor.org/packages/3.6/bioc/src/contrib/genefilter_1.60.0.tar.gz'
Content type 'application/x-gzip' length 1432282 bytes (1.4 MB)
downloaded 1.4 MB

* installing *source* package ‘genefilter’ ...
** libs
g++  -I/usr/share/R/include -DNDEBUG      -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c half_range_mode.cpp -o half_range_mode.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG      -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c init.c -o init.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG      -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c nd.c -o nd.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG      -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c pAUC.c -o pAUC.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG      -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c rowPAUCs.c -o rowPAUCs.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG      -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c rowttests.c -o rowttests.o
gfortran   -fpic  -g -O2 -fstack-protector-strong  -c ttest.f -o ttest.o
/bin/bash: gfortran: command not found
/usr/lib/R/etc/Makeconf:182: recipe for target 'ttest.o' failed
make: *** [ttest.o] Error 127
ERROR: compilation failed for package ‘genefilter’
* removing ‘/home/joanne/R/x86_64-pc-linux-gnu-library/3.4/genefilter’

The downloaded source packages are in
installation path not writeable, unable to update packages: XML, Matrix, nlme
Warning message:
In install.packages(pkgs = doing, lib = lib, ...) :
  installation of package ‘genefilter’ had non-zero exit status


What can I do to allow the package to compile?

bioconductor genefilter compile • 1.3k views
Entering edit mode
Last seen 7 hours ago
United States

The important part of the output is this line

/bin/bash: gfortran: command not found

If you have sudo privileges you could google about gfortran and how to install it on your distro (which you neglect to mention). If you do not have sudo privileges you should ask someone who does to install gfortran for you.


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