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### Running command:
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###   /Library/Frameworks/R.framework/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
--- re-building ‘PreV90EnsemblVEP.Rnw’ using Sweave
Loading required package: BiocGenerics

Attaching package: ‘BiocGenerics’

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, aperm, append,
    as.data.frame, basename, cbind, 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, rownames, sapply, setdiff, sort, table,
    tapply, union, unique, unsplit, 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’:

    I, expand.grid, unname

Loading required package: IRanges
Loading required package: GenomeInfoDb
Loading required package: VariantAnnotation
Loading required package: MatrixGenerics
Loading required package: matrixStats

Attaching package: ‘MatrixGenerics’

The following objects are masked from ‘package:matrixStats’:

    colAlls, colAnyNAs, colAnys, colAvgsPerRowSet, colCollapse,
    colCounts, colCummaxs, colCummins, colCumprods, colCumsums,
    colDiffs, colIQRDiffs, colIQRs, colLogSumExps, colMadDiffs,
    colMads, colMaxs, colMeans2, colMedians, colMins, colOrderStats,
    colProds, colQuantiles, colRanges, colRanks, colSdDiffs, colSds,
    colSums2, colTabulates, colVarDiffs, colVars, colWeightedMads,
    colWeightedMeans, colWeightedMedians, colWeightedSds,
    colWeightedVars, rowAlls, rowAnyNAs, rowAnys, rowAvgsPerColSet,
    rowCollapse, rowCounts, rowCummaxs, rowCummins, rowCumprods,
    rowCumsums, rowDiffs, rowIQRDiffs, rowIQRs, rowLogSumExps,
    rowMadDiffs, rowMads, rowMaxs, rowMeans2, rowMedians, rowMins,
    rowOrderStats, rowProds, rowQuantiles, rowRanges, rowRanks,
    rowSdDiffs, rowSds, rowSums2, rowTabulates, rowVarDiffs, rowVars,
    rowWeightedMads, rowWeightedMeans, rowWeightedMedians,
    rowWeightedSds, rowWeightedVars

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")'.


Attaching package: ‘Biobase’

The following object is masked from ‘package:MatrixGenerics’:

    rowMedians

The following objects are masked from ‘package:matrixStats’:

    anyMissing, rowMedians

Loading required package: Rsamtools
Loading required package: Biostrings
Loading required package: XVector

Attaching package: ‘Biostrings’

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 in .local(x, VCFRowID, ...) :
  rownames not found in 'x' : 1:13220_T/<DEL>
--- finished re-building ‘PreV90EnsemblVEP.Rnw’

--- re-building ‘ensemblVEP.Rnw’ using Sweave

-------------------- 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 17 05:32:33 2023
Ensembl API version = 107
---------------------------------------------------

-------------------- 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:308
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:123
STACK Bio::EnsEMBL::VEP::Runner::run /usr/local/ensembl-vep/modules/Bio/EnsEMBL/VEP/Runner.pm:199
STACK toplevel /usr/local/ensembl-vep/vep:238
Date (localtime)    = Mon Apr 17 05:32:33 2023
Ensembl API version = 107
---------------------------------------------------

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/RtmpbYL1jH/filec8204fe509b7'

--- failed re-building ‘ensemblVEP.Rnw’

SUMMARY: processing the following file failed:
  ‘ensemblVEP.Rnw’

Error: Vignette re-building failed.
Execution halted