Hello, Trying to upgrade bioconductor hit a problem with vsn.

gcc: error: unrecognized command line option -fstack-protector-strong

It seems that "fstack-protector-strong" is a new feature in gcc 4.9 which is not part of Debian Jessie (testing) which I am running. Perhaps I could (should?) fix this by installing gcc 4.9, but that seems a bit unnatural ... so here is the question... Is gcc 4.9 really required for the latest bioconductor? Please see gory details below. Many thanks, regcl

> source("http://bioconductor.org/biocLite.R")
biocLite("vsn")
Bioconductor version 3.0 (BiocInstaller 1.16.1), ?biocLite for help
> 
BioC_mirror: http://bioconductor.org
Using Bioconductor version 3.0 (BiocInstaller 1.16.1), R version 3.1.1.
Installing package(s) 'vsn'
trying URL 'http://bioconductor.org/packages/3.0/bioc/src/contrib/vsn_3.34.0.tar.gz'
Content type 'application/x-gzip' length 1450884 bytes (1.4 Mb)
opened URL
==================================================
downloaded 1.4 Mb

* installing *source* package ‘vsn’ ...
** libs
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG      -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g  -c init.c -o init.o
gcc: error: unrecognized command line option ‘-fstack-protector-strong’
/usr/lib/R/etc/Makeconf:128: recipe for target 'init.o' failed
make: *** [init.o] Error 1
ERROR: compilation failed for package ‘vsn’
* removing ‘/home/regcl/R/x86_64-pc-linux-gnu-library/3.1/vsn’
* restoring previous ‘/home/regcl/R/x86_64-pc-linux-gnu-library/3.1/vsn’


$ uname -av
Linux e3 3.11-2-amd64 #1 SMP Debian 3.11.8-1 (2013-11-13) x86_64 GNU/Linux

$ gcc --version
gcc (Debian 4.8.3-13) 4.8.3

I think the compiler flag is being picked up from your R installation; you could interrogate R for the configure flags it's decided on with R CMD config and R CMD config CFLAGS & friends. Perhaps you installed R under a different version of gcc than the one you are using to install the package with? The solution is to use the same compiler for R installation and for package installation.

Thank you. You are oh so right. I didn't change CFLAGS myself. So maybe my recent apt-get update <Rstuff> as root did.