ensemblVEP 1.10.2
Bioconductor Package Maintainer
| Snapshot Date: 2016-03-23 16:20:31 -0700 (Wed, 23 Mar 2016) | | URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_2/madman/Rpacks/ensemblVEP | | Last Changed Rev: 114944 / Revision: 115201 | | Last Changed Date: 2016-03-17 20:27:05 -0700 (Thu, 17 Mar 2016) |
| zin1 | Linux (Ubuntu 14.04.2 LTS) / x86_64 | NotNeeded | OK | OK | |  |
| moscato1 | Windows Server 2008 R2 Standard (64-bit) / x64 | NotNeeded | [ ERROR ] | skipped | skipped | |
| oaxaca | Mac OS X Mavericks (10.9.5) / x86_64 | NotNeeded | OK | OK | OK | |
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### Running command:
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### chmod a+r ensemblVEP -R && D:\biocbld\bbs-3.2-bioc\R\bin\R.exe CMD build --keep-empty-dirs --no-resave-data ensemblVEP
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* checking for file 'ensemblVEP/DESCRIPTION' ... OK
* preparing 'ensemblVEP':
* checking DESCRIPTION meta-information ... OK
* installing the package to build vignettes
* creating vignettes ...Warning: running command '"D:/biocbld/bbs-3.2-bioc/R/bin/x64/Rscript" --vanilla --default-packages= -e "tools::buildVignettes(dir = '.', tangle = TRUE)"' had status 1
ERROR
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 objects are masked from 'package:stats':
IQR, mad, xtabs
The following objects are masked from 'package:base':
Filter, Find, Map, Position, Reduce, anyDuplicated, append,
as.data.frame, as.vector, cbind, colnames, do.call, duplicated,
eval, evalq, get, grep, grepl, intersect, is.unsorted, lapply,
lengths, mapply, match, mget, order, paste, pmax, pmax.int, pmin,
pmin.int, rank, rbind, rownames, sapply, setdiff, sort, table,
tapply, union, unique, unlist, unsplit
Loading required package: GenomicRanges
Loading required package: S4Vectors
Loading required package: stats4
Loading required package: IRanges
Loading required package: GenomeInfoDb
Loading required package: VariantAnnotation
Loading required package: SummarizedExperiment
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")'.
Loading required package: Rsamtools
Loading required package: XVector
Loading required package: Biostrings
Attaching package: 'VariantAnnotation'
The following object is masked from 'package:base':
tabulate
Attaching package: 'ensemblVEP'
The following object is masked from 'package:Biobase':
cache
-------------------- WARNING ----------------------
MSG: homo_sapiens is not a valid species name (check DB and API version)
FILE: Bio/EnsEMBL/Registry.pm LINE: 1326
CALLED BY: Bio/EnsEMBL/Registry.pm LINE: 1101
Date (localtime) = Wed Mar 23 22:59:22 2016
Ensembl API version = 82
---------------------------------------------------
-------------------- EXCEPTION --------------------
MSG: Can not find internal name for species 'homo_sapiens'
STACK Bio::EnsEMBL::Registry::get_adaptor c:/vep/Bio/EnsEMBL/Registry.pm:1103
STACK main::connect_to_dbs c:\vep\variant_effect_predictor.pl:1220
STACK main::configure c:\vep\variant_effect_predictor.pl:797
STACK toplevel c:\vep\variant_effect_predictor.pl:142
Date (localtime) = Wed Mar 23 22:59:22 2016
Ensembl API version = 82
---------------------------------------------------
Warning: running command '"perl" c:\vep\variant_effect_predictor.pl -i "D:/biocbld/bbs-3.2-bioc/R/library/VariantAnnotation/extdata/structural.vcf" --species homo_sapiens --format vcf --dir $HOME/.vep --dir_cache $HOME/.vep --dir_plugins $HOME/.vep --terms so --host useastdb.ensembl.org --database TRUE --buffer_size 5000 --vcf TRUE --output_file "D:\biocbld\bbs-3.2-bioc\tmpdir\RtmpqEAH7z\file1a441d51637e"' had status 255
Error: processing vignette 'ensemblVEP.Rnw' failed with diagnostics:
chunk 8 (label = rtn_VCF)
Error in .io_check_exists(path(con)) : file(s) do not exist:
'D:\biocbld\bbs-3.2-bioc\tmpdir\RtmpqEAH7z\file1a441d51637e'
Execution halted