ensemblVEP 1.14.0
Bioconductor Package Maintainer
| Snapshot Date: 2017-04-14 17:17:13 -0400 (Fri, 14 Apr 2017) | | URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_4/madman/Rpacks/ensemblVEP | | Last Changed Rev: 122710 / Revision: 128728 | | Last Changed Date: 2016-10-17 14:45:06 -0400 (Mon, 17 Oct 2016) |
| malbec1 | Linux (Ubuntu 16.04.1 LTS) / x86_64 | OK | ERROR | skipped | | |
| tokay1 | Windows Server 2012 R2 Standard / x64 | ...NOT SUPPORTED...NOT SUPPORTED...NOT SUPPORTED... |
| morelia | Mac OS X Mavericks (10.9.5) / x86_64 | OK | [ ERROR ] | skipped | skipped | |
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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 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, which, which.max, which.min
Loading required package: GenomicRanges
Loading required package: stats4
Loading required package: S4Vectors
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: 1332
CALLED BY: Bio/EnsEMBL/Registry.pm LINE: 1107
Date (localtime) = Fri Apr 14 18:07:43 2017
Ensembl API version = 86
---------------------------------------------------
-------------------- 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:1109
STACK main::connect_to_dbs /usr/local/variant_effect_predictor/variant_effect_predictor.pl:1274
STACK main::configure /usr/local/variant_effect_predictor/variant_effect_predictor.pl:813
STACK toplevel /usr/local/variant_effect_predictor/variant_effect_predictor.pl:146
Date (localtime) = Fri Apr 14 18:07:43 2017
Ensembl API version = 86
---------------------------------------------------
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/RtmpY386YO/file1b70433a6222'
Execution halted