HTSeqGenie 1.1.0
Gregoire Pau
| Snapshot Date: 2013-01-15 17:01:14 -0800 (Tue, 15 Jan 2013) | | URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/HTSeqGenie | | Last Changed Rev: 70052 / Revision: 72575 | | Last Changed Date: 2012-10-01 15:43:56 -0700 (Mon, 01 Oct 2012) |
| george2 | Linux (Ubuntu 12.04.1 LTS) / x86_64 | ERROR | skipped | |
| lamb2 | Linux (openSUSE 11.4) / x86_64 | [ ERROR ] | skipped | |
| moscato2 | Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64 | N O T S U P P O R T E D |
| petty | Mac OS X Leopard (10.5.8) / i386 | N O T S U P P O R T E D |
* checking for file ‘HTSeqGenie/DESCRIPTION’ ... OK
* preparing ‘HTSeqGenie’:
* checking DESCRIPTION meta-information ... OK
* installing the package to re-build vignettes
* creating vignettes ... ERROR
Loading required package: ShortRead
Loading required package: BiocGenerics
Loading required package: parallel
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’:
Filter, Find, Map, Position, Reduce, anyDuplicated, as.data.frame,
cbind, colnames, duplicated, eval, get, intersect, lapply, mapply,
match, mget, order, paste, pmax, pmax.int, pmin, pmin.int, rank,
rbind, rep.int, rownames, sapply, setdiff, sort, table, tapply,
union, unique, unlist
Loading required package: IRanges
Loading required package: GenomicRanges
Loading required package: Biostrings
Loading required package: lattice
Loading required package: Rsamtools
Loading required package: latticeExtra
Loading required package: RColorBrewer
Loading required package: hwriter
Loading required package: Cairo
Loading required package: tools
Loading required package: gmapR
Loading required package: logging
GSNAP version 2011-12-28 called with args: /loc/home/biocbuild/bbs-2.12-bioc/R/library/gmapR/usr/bin/gsnap --db=TP53_demo --dir=/loc/home/biocbuild/.local/share/gmap --indel-penalty=1 --novelsplicing=1 --format=sam --split-output=H1993/chunks/chunk_000001/bams/H1993 H1993/chunks/chunk_000001/bams/processed.aligner_input_1.fastq H1993/chunks/chunk_000001/bams/processed.aligner_input_2.fastq
Novel splicing (-N) turned on => assume reads are RNA-Seq
Note: >1 sequence detected, so index files are being memory mapped.
GSNAP can run slowly at first while the computer starts to accumulate
pages from the hard disk into its cache. To copy index files into RAM
instead of memory mapping, use -B 3, -B 4, or -B 5, if you have enough RAM.
For more speed, also try multiple threads (-t <int>), if you have multiple processors or cores.
Pre-loading compressed genome....done (759,672 bytes, 186 pages, 0.02 sec)
Looking for index files in directory /loc/home/biocbuild/.local/share/gmap/TP53_demo
Gammaptrs file is TP53_demo.ref12153gammaptrs
Offsetscomp file is TP53_demo.ref12153offsetscomp
Positions file is TP53_demo.ref12153positions
Allocating memory for ref gammaptrs, kmer 15, interval 3...done (67,108,868 bytes, 0.98 sec)
Allocating memory for ref offsets, kmer 15, interval 3...done (203,455,804 bytes, 2.76 sec)
Pre-loading ref positions, kmer 15, interval 3.....done (2,701,004 bytes, 660 pages, 0.03 sec)
GMAP modes: pairsearch, terminal, improvement
Starting alignment
Processed 2500 queries in 4.78 seconds (523.01 queries/sec)
GSNAP version 2011-12-28 called with args: /loc/home/biocbuild/bbs-2.12-bioc/R/library/gmapR/usr/bin/gsnap --db= --version
Error: processing vignette ‘HTSeqGenie.Rnw’ failed with diagnostics:
chunk 4 (label = runPipeline)
Error in sclapply(inext = inext, fun = funlog, max.parallel.jobs = nb.parallel.jobs, :
tools.R/sclapply: error in chunkid=1: Error in path(x) :
error in evaluating the argument ‘object’ in selecting a method for function ‘path’: Error: object ‘x’ not found
Execution halted