[R] Problems installing biocLite on Fedora 23

Morgan, Martin Martin.Morgan at roswellpark.org
Mon Nov 23 12:52:15 CET 2015

This is in reference to Bioconductor, and should be addressed to the Bioconductor support site


The problem is not with biocLite per se, but with installation of Rsamtools.

My guess is that Rsamtools wraps a library 'samtools', and tries to re-map samtool's use of stderr and friends to R. The implementation requires use of -U_FORTIFY_SOURCE (undefine the _FORTIFY_SOURCE symbol when compiling), but unfortunately (or otherwise, depending on your level of paranoia) recent Fedora re-defines the symbol. A rough work-around might be to use the clang compiler, e.g., editing a file ~/.R/Makevars to contain something like the line


When posting to the support site, please provide the full output of


as well as the output from the command line of

  gcc --version

From: R-help [r-help-bounces at r-project.org] on behalf of Knut Hansen [knut.hansen at uit.no]
Sent: Monday, November 23, 2015 6:27 AM
To: r-help at r-project.org
Subject: [R] Problems installing biocLite on Fedora 23

I'm running Fedora 23 with KDE 5.16. I'm trying to install biocLite using the commands


as root.

During installation I get error messages like this:

gcc -m64 -I/usr/include/R -DNDEBUG  -I/usr/local/include -
I"/usr/lib64/R/library/S4Vectors/include" -I"/usr/lib64/R/library/IRanges/include" -
I"/usr/lib64/R/library/XVector/include" -I"/usr/lib64/R/libr
*gcc:* *error: */usr/lib/rpm/redhat/redhat-hardened-cc1: No such file or directory

(Rsamtools is an example here, I get the same error message for all modules).

It did not help to reinstall gcc.

Any suggestions?

Knut Hansen
University of Tromsø

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