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-boun...@r-project.org] on behalf of Knut Hansen [knut.han...@uit.no] Sent: Monday, November 23, 2015 6:27 AM To: r-help@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 [[alternative HTML version deleted]] ______________________________________________ R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. This email message may contain legally privileged and/or confidential information. If you are not the intended recipient(s), or the employee or agent responsible for the delivery of this message to the intended recipient(s), you are hereby notified that any disclosure, copying, distribution, or use of this email message is prohibited. If you have received this message in error, please notify the sender immediately by e-mail and delete this email message from your computer. Thank you. ______________________________________________ R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
