When BioC 2.14 was released, it did work on OS X 10.6.8, but not on 10.9 and neither on some flavours of 32-bit Linux.
The bowtie developers have released version 1.0.1 which addresses some of these issues. For the remaining one that still made it fail on OS X 10.9, I have been in contact with them and they provided a patch (see http://sourceforge.net/p/bowtie-bio/bugs/312/) which seems to fix it on the OS X machines that I have access to, but apparently not for petty. Going back to the version at release is not an option, since I rate support for OS X 10.9 more important, especially in the long run. Michael On 13.06.2014 15:19, Kasper Daniel Hansen wrote: > That is pretty weird. Since this is a segmentation fault in Bowtie, > perhaps there are resource demands which are only satisfied on perceval > (tmp space, #cores). > > Presumably this worked when Bioc was released, so what have you changed > in between? > > Best, > Kasper > > > On Fri, Jun 13, 2014 at 3:32 AM, Michael Stadler <michael.stad...@fmi.ch > <mailto:michael.stad...@fmi.ch>> wrote: > > Hi Dan, > > I'm cc'ing the list; maybe somebody else has experienced differences > between petty and perceval. > > Rbowtie release (1.4.5) is not building under OS X 10.6.8 (petty). > > Rbowtie release (1.4.5) and development (1.5.5) are virtually identical > (only DESCRIPTION and NEWS differ). > > The development version builds without problems on perceval, but the > release version fails on petty: > > http://bioconductor.org/checkResults/devel/bioc-LATEST/Rbowtie/perceval-buildsrc.html > > http://bioconductor.org/checkResults/release/bioc-LATEST/Rbowtie/petty-buildsrc.html > > The only difference I can make out from the node info pages is that > perceval has an additional section on "C++11 compiler" that is lacking > from petty's NodeInfo page. > > Unfortunately, I cannot reproduce the issue, both Rbowtie 1.4.5 and > 1.5.5 build successfully under OS X 10.6.8 and 10.7.5 using > llvm-gcc-4.2. > > Do you have any idea what else could be different between petty and > perceval? > > Thank you, > Michael > > _______________________________________________ > Bioc-devel@r-project.org <mailto:Bioc-devel@r-project.org> mailing list > https://stat.ethz.ch/mailman/listinfo/bioc-devel > > -- -------------------------------------------- Michael Stadler, PhD Head of Computational Biology Friedrich Miescher Institute Basel (Switzerland) Phone : +41 61 697 6492 Fax : +41 61 697 3976 Mail : michael.stad...@fmi.ch _______________________________________________ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel