ensemblVEP 1.25.0
Bioconductor Package Maintainer
| Snapshot Date: 2019-04-08 17:01:18 -0400 (Mon, 08 Apr 2019) |
| URL: https://git.bioconductor.org/packages/ensemblVEP |
| Branch: master |
| Last Commit: 8a0adea |
| Last Changed Date: 2018-10-30 11:54:31 -0400 (Tue, 30 Oct 2018) |
| malbec2 | Linux (Ubuntu 18.04.2 LTS) / x86_64 | OK | ERROR | skipped | | |
| tokay2 | Windows Server 2012 R2 Standard / x64 | ...NOT SUPPORTED... |
| celaya2 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | OK | OK |  |
| merida2 | OS X 10.11.6 El Capitan / 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, sd, var, xtabs
The following objects are masked from ‘package:base’:
Filter, Find, Map, Position, Reduce, anyDuplicated, append,
as.data.frame, basename, cbind, colMeans, colSums, colnames,
dirname, do.call, duplicated, eval, evalq, get, grep, grepl,
intersect, is.unsorted, lapply, mapply, match, mget, order, paste,
pmax, pmax.int, pmin, pmin.int, rank, rbind, rowMeans, rowSums,
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 object is masked from ‘package:base’:
expand.grid
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: DelayedArray
Loading required package: matrixStats
Attaching package: ‘matrixStats’
The following objects are masked from ‘package:Biobase’:
anyMissing, rowMedians
Loading required package: BiocParallel
Attaching package: ‘DelayedArray’
The following objects are masked from ‘package:matrixStats’:
colMaxs, colMins, colRanges, rowMaxs, rowMins, rowRanges
The following objects are masked from ‘package:base’:
aperm, apply, rowsum
Loading required package: Rsamtools
Loading required package: Biostrings
Loading required package: XVector
Attaching package: ‘Biostrings’
The following object is masked from ‘package:DelayedArray’:
type
The following object is masked from ‘package:base’:
strsplit
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: VCF line on line 1 looks incomplete, skipping:
1 13220 . T <DEL> 6 PASS IMPRECISE;SVTYPE=DEL;END=13221;SVLEN=-105;CIPOS=-56,20;CIEND=-10,62 GT:GQ 0/1:12
-------------------- WARNING ----------------------
MSG: homo_sapiens is not a valid species name (check DB and API version)
FILE: Bio/EnsEMBL/Registry.pm LINE: 1334
CALLED BY: Bio/EnsEMBL/Registry.pm LINE: 1109
Date (localtime) = Mon Apr 8 20:31:20 2019
Ensembl API version = 94
---------------------------------------------------
-------------------- EXCEPTION --------------------
MSG: Can not find internal name for species 'homo_sapiens'
STACK Bio::EnsEMBL::Registry::get_adaptor /usr/local/ensembl-vep/Bio/EnsEMBL/Registry.pm:1111
STACK Bio::EnsEMBL::VEP::BaseVEP::get_adaptor /usr/local/ensembl-vep/modules/Bio/EnsEMBL/VEP/BaseVEP.pm:307
STACK Bio::EnsEMBL::VEP::BaseVEP::get_database_assembly /usr/local/ensembl-vep/modules/Bio/EnsEMBL/VEP/BaseVEP.pm:419
STACK Bio::EnsEMBL::VEP::BaseRunner::setup_db_connection /usr/local/ensembl-vep/modules/Bio/EnsEMBL/VEP/BaseRunner.pm:123
STACK Bio::EnsEMBL::VEP::Runner::init /usr/local/ensembl-vep/modules/Bio/EnsEMBL/VEP/Runner.pm:118
STACK Bio::EnsEMBL::VEP::Runner::run /usr/local/ensembl-vep/modules/Bio/EnsEMBL/VEP/Runner.pm:194
STACK toplevel /usr/local/ensembl-vep/vep:224
Date (localtime) = Mon Apr 8 20:31:20 2019
Ensembl API version = 94
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Error: processing vignette 'ensemblVEP.Rnw' failed with diagnostics:
chunk 5 (label = rtn_GRanges)
Error in .io_check_exists(path(con)) : file(s) do not exist:
'/tmp/Rtmpkzi395/file2a7c46695b5d'
Execution halted