ensemblVEP 1.12.0
Bioconductor Package Maintainer
| Snapshot Date: 2016-10-12 17:20:15 -0700 (Wed, 12 Oct 2016) | | URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_3/madman/Rpacks/ensemblVEP | | Last Changed Rev: 117079 / Revision: 122332 | | Last Changed Date: 2016-05-03 14:20:18 -0700 (Tue, 03 May 2016) |
| zin2 | Linux (Ubuntu 14.04.2 LTS) / x86_64 | NotNeeded | [ ERROR ] | skipped | | |
| moscato2 | Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64 | ...NOT SUPPORTED...NOT SUPPORTED...NOT SUPPORTED... |
| oaxaca | Mac OS X Mavericks (10.9.5) / x86_64 | NotNeeded | ERROR | skipped | skipped | |
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### Running command:
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### /home/biocbuild/bbs-3.3-bioc/R/bin/R 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 ... 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, 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, unsplit
Loading required package: GenomicRanges
Loading required package: S4Vectors
Loading required package: stats4
Attaching package: ‘S4Vectors’
The following objects are masked from ‘package:base’:
colMeans, colSums, expand.grid, rowMeans, rowSums
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: Biostrings
Loading required package: XVector
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: 1327
CALLED BY: Bio/EnsEMBL/Registry.pm LINE: 1102
Date (localtime) = Wed Oct 12 20:40:05 2016
Ensembl API version = 84
---------------------------------------------------
-------------------- EXCEPTION --------------------
MSG: Can not find internal name for species 'homo_sapiens'
STACK Bio::EnsEMBL::Registry::get_adaptor /usr/local/variant_effect_predictor/Bio/EnsEMBL/Registry.pm:1104
STACK main::connect_to_dbs /usr/local/variant_effect_predictor/variant_effect_predictor.pl:1263
STACK main::configure /usr/local/variant_effect_predictor/variant_effect_predictor.pl:810
STACK toplevel /usr/local/variant_effect_predictor/variant_effect_predictor.pl:145
Date (localtime) = Wed Oct 12 20:40:05 2016
Ensembl API version = 84
---------------------------------------------------
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:
'/tmp/RtmpuNzl6R/file1b061a8c8343'
Execution halted