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BioC 2.14: BUILD report for Rbowtie on petty

This page was generated on 2014-10-08 09:00:39 -0700 (Wed, 08 Oct 2014).

Package 635/824HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
Rbowtie 1.4.5
Michael Stadler
Snapshot Date: 2014-10-07 17:20:37 -0700 (Tue, 07 Oct 2014)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_14/madman/Rpacks/Rbowtie
Last Changed Rev: 91054 / Revision: 95116
Last Changed Date: 2014-06-06 08:34:15 -0700 (Fri, 06 Jun 2014)
zin2 Linux (Ubuntu 12.04.4 LTS) / x86_64  OK  OK  OK 
moscato2 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  OK  OK  OK  OK 
petty Mac OS X Snow Leopard (10.6.8) / x86_64  OK [ ERROR ] skipped  skipped 
morelia Mac OS X Mavericks (10.9.5) / x86_64  OK  OK  OK  OK 

Summary

Package: Rbowtie
Version: 1.4.5
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD build --keep-empty-dirs --no-resave-data Rbowtie
StartedAt: 2014-10-07 19:40:38 -0700 (Tue, 07 Oct 2014)
EndedAt: 2014-10-07 19:42:12 -0700 (Tue, 07 Oct 2014)
EllapsedTime: 94.7 seconds
RetCode: 1
Status:  ERROR 
PackageFile: None
PackageFileSize: NA

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD build --keep-empty-dirs --no-resave-data Rbowtie
###
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* checking for file ‘Rbowtie/DESCRIPTION’ ... OK
* preparing ‘Rbowtie’:
* checking DESCRIPTION meta-information ... OK
* cleaning src
* installing the package to build vignettes
* creating vignettes ... ERROR
[SpliceMap] splitting reads into 25mers...done
[SpliceMap] aligning 25mers...sh: line 1: 64922 Segmentation fault      '/private/tmp/RtmpyN29Az/Rinstf52c4129c9f2/Rbowtie/bowtie' -y -S -k 10 -m 10 -v 2 -r -p 4 --best --strata '/tmp/Rtmpn8u4v5/refsIndex/index' '/tmp/Rtmpn8u4v5/SpliceMapTemp_fd7d7c7bacf9/25mers.map' '/tmp/Rtmpn8u4v5/SpliceMapTemp_fd7d7c7bacf9/25mers.map_unsorted' 2>&1
Warning: running command ''/private/tmp/RtmpyN29Az/Rinstf52c4129c9f2/Rbowtie/bowtie' -y -S -k 10 -m 10 -v 2 -r -p 4 --best --strata '/tmp/Rtmpn8u4v5/refsIndex/index' '/tmp/Rtmpn8u4v5/SpliceMapTemp_fd7d7c7bacf9/25mers.map' '/tmp/Rtmpn8u4v5/SpliceMapTemp_fd7d7c7bacf9/25mers.map_unsorted' 2>&1' had status 139

Error: processing vignette 'Rbowtie-Overview.Rnw' failed with diagnostics:
 chunk 9 (label = SpliceMap) 
Error in SpliceMap(cfg) : failed while aligning 25mers
Execution halted