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")
>biocLite("genefilter")
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
‘/tmp/RtmpGwh5qF/downloaded_packages’
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?
