[Bioc-devel] differences between petty and perceval (OS X 10.6.8 build machines for release/devel)

[Michael Stadler]

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.stadler at fmi.ch
> <mailto:michael.stadler at 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 at r-project.org <mailto:Bioc-devel at 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.stadler at fmi.ch