[R] Problems installing biocLite on Fedora 23

[Morgan, Martin]

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

  https://support.bioconductor.org

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

   CC=clang

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

  biocLite("Rsamtools")

as well as the output from the command line of

  gcc --version

Martin
________________________________________
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

source("https://bioconductor.org/biocLite.R")
biocLite()

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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