QuasR 1.4.2
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/QuasR | | Last Changed Rev: 90027 / Revision: 95116 | | Last Changed Date: 2014-05-07 01:24:15 -0700 (Wed, 07 May 2014) |
| zin2 | Linux (Ubuntu 12.04.4 LTS) / x86_64 | NotNeeded | OK | OK | |
| moscato2 | Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64 | NotNeeded | OK | OK | OK |
| petty | Mac OS X Snow Leopard (10.6.8) / x86_64 | NotNeeded | [ ERROR ] | skipped | skipped |
| morelia | Mac OS X Mavericks (10.9.5) / x86_64 | NotNeeded | OK | OK | OK |
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### Running command:
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### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD build --keep-empty-dirs --no-resave-data QuasR
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* checking for file ‘QuasR/DESCRIPTION’ ... OK
* preparing ‘QuasR’:
* checking DESCRIPTION meta-information ... OK
* cleaning src
* installing the package to build vignettes
* creating vignettes ... ERROR
Loading required package: parallel
Loading required package: GenomicRanges
Loading required package: BiocGenerics
Attaching package: 'BiocGenerics'
The following objects are masked from 'package:parallel':
clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
clusterExport, clusterMap, parApply, parCapply, parLapply,
parLapplyLB, parRapply, parSapply, parSapplyLB
The following object is masked from 'package:stats':
xtabs
The following objects are masked from 'package:base':
anyDuplicated, append, as.data.frame, as.vector, cbind, colnames,
do.call, duplicated, eval, evalq, Filter, Find, get, intersect,
is.unsorted, lapply, Map, mapply, match, mget, order, paste, pmax,
pmax.int, pmin, pmin.int, Position, rank, rbind, Reduce, rep.int,
rownames, sapply, setdiff, sort, table, tapply, union, unique,
unlist
Loading required package: IRanges
Loading required package: GenomeInfoDb
Loading required package: Rbowtie
Loading required package: Biostrings
Loading required package: XVector
Loading required package: AnnotationDbi
Loading required package: Biobase
Welcome to Bioconductor
Vignettes contain introductory material; view with
'browseVignettes()'. To cite Bioconductor, see
'citation("Biobase")', and for packages 'citation("pkgname")'.
Attaching package: 'AnnotationDbi'
The following object is masked from 'package:BSgenome':
species
Loading required package: grid
Creating .fai file for: /private/tmp/RtmpyghKbs/Rbuildf5715d51d55e/QuasR/vignettes/extdata/hg19sub.fa
alignment files missing - need to:
create alignment index for the genome
create 2 genomic alignment(s)
Creating an Rbowtie index for /private/tmp/RtmpyghKbs/Rbuildf5715d51d55e/QuasR/vignettes/extdata/hg19sub.fa
Finished creating index
Testing the compute nodes...OK
Loading QuasR on the compute nodes...OK
Available cores:
Performing genomic alignments for 2 samples. See progress in the log file:
/private/tmp/RtmpyghKbs/Rbuildf5715d51d55e/QuasR/vignettes/QuasR_log_f9b150103afa.txt
sh: line 1: 64962 Segmentation fault '/Library/Frameworks/R.framework/Versions/3.1/Resources/library/Rbowtie/bowtie' '/private/tmp/RtmpyghKbs/Rbuildf5715d51d55e/QuasR/vignettes/extdata/hg19sub.fa.Rbowtie/bowtieIndex' '/tmp/RtmpXIOMaj/chip_1_1.fq.bz2fd5451008d82.fastq' -m 1 --best --strata --phred33-quals -S -p 1 '/tmp/RtmpXIOMaj/chip_1_1.fq.bz2fd5451008d82.fastqfd547b4a7b59.sam' 2>&1
Error: processing vignette 'QuasR.Rnw' failed with diagnostics:
chunk 14 (label = SampleSession2)
Error in checkForRemoteErrors(val) :
one node produced an error: Error on petty.local processing sample /tmp/RtmpXIOMaj/chip_1_1.fq.bz2fd5451008d82.fastq : argument is of length zero
Execution halted