Back to "Blame Jeroen" build/check report for BioC 3.11

BUILD report for VariantAnnotation on tokay2

This page was generated on 2020-04-15 03:20:11 -0400 (Wed, 15 Apr 2020).

These builds are using Rtools40 and R-testing by Jeroen Ooms (available at https://cran.r-project.org/bin/windows/testing/rtools40.html)
TO THE DEVELOPERS/MAINTAINERS OF THE VariantAnnotation PACKAGE: Please make sure to use the following settings in order to reproduce any error or warning you see on this page.
Package 85/89HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
VariantAnnotation 1.33.4
Bioconductor Package Maintainer
Snapshot Date: 2020-04-14 17:00:05 -0400 (Tue, 14 Apr 2020)
URL: https://git.bioconductor.org/packages/VariantAnnotation
Branch: master
Last Commit: 5f14082
Last Changed Date: 2020-04-08 18:20:28 -0400 (Wed, 08 Apr 2020)
tokay2 Windows Server 2012 R2 Standard / x64  OK [ ERROR ] skipped  skipped 

Summary

Package: VariantAnnotation
Version: 1.33.4
Command: chmod a+r VariantAnnotation -R && C:\Users\bioctesting\bbs-3.11-bioc-testing\R\bin\R.exe CMD build --keep-empty-dirs --no-resave-data VariantAnnotation
StartedAt: 2020-04-14 19:07:21 -0400 (Tue, 14 Apr 2020)
EndedAt: 2020-04-14 19:15:49 -0400 (Tue, 14 Apr 2020)
EllapsedTime: 507.9 seconds
RetCode: 1
Status:  ERROR  
PackageFile: None
PackageFileSize: NA

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   chmod a+r VariantAnnotation -R && C:\Users\bioctesting\bbs-3.11-bioc-testing\R\bin\R.exe CMD build --keep-empty-dirs --no-resave-data VariantAnnotation
###
##############################################################################
##############################################################################


* checking for file 'VariantAnnotation/DESCRIPTION' ... OK
* preparing 'VariantAnnotation':
* checking DESCRIPTION meta-information ... OK
* cleaning src
* installing the package to build vignettes
* creating vignettes ... ERROR
--- re-building 'VariantAnnotation.Rnw' using Sweave
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, 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, which.max, which.min

Loading required package: GenomeInfoDb
Loading required package: S4Vectors
Loading required package: stats4

Attaching package: 'S4Vectors'

The following object is masked from 'package:base':

    expand.grid

Loading required package: IRanges

Attaching package: 'IRanges'

The following object is masked from 'package:grDevices':

    windows

Loading required package: GenomicRanges
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


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:base':

    strsplit


Attaching package: 'VariantAnnotation'

The following object is masked from 'package:base':

    tabulate

  Please note that the SNPlocs.Hsapiens.dbSNP.20101109 package
  contains outdated dbSNP data and will be deprecated in the near
  future. We highly recommend that you use a SNPlocs package
  based on a more recent dbSNP build for your analyses instead.
  See available.SNPs() for the list of SNPlocs packages currently
  available and make sure to pick up the most recent one.
Loading required package: GenomicFeatures
Loading required package: AnnotationDbi
Warning in valid.GenomicRanges.seqinfo(x, suggest.trim = TRUE) :
  GRanges object contains 2405 out-of-bound ranges located on
  sequences 75253, 74357, 74359, 74360, 74361, 74362, 74363,
  74358, 74364, 74365, 75254, 75259, 74368, 74369, 74366, 74367,
  74370, 74372, 74373, 74374, 74375, 74378, 74377, 74380, 74381,
  75262, 75263, 75265, 75266, 75268, 75269, 75271, 75273, 75276,
  75281, 75282, 75283, 74389, 74383, 74384, 74385, 74386, 74387,
  75287, 75288, 75286, 75289, 74390, 74391, 74392, 74393, 74394,
  75291, 74395, 74396, 74397, 74398, 75302, 75304, 75305, and
  75306. Note that ranges located on a sequence whose length is
  unknown (NA) or on a circular sequence are not considered
  out-of-bound (use seqlengths() and isCircular() to get the
  lengths and circularity flags of the underlying sequences). You
  can use trim() to trim these ranges. See
  ?`trim,GenomicRanges-method` for more information.
'select()' returned many:1 mapping between keys and columns
Loading required package: BSgenome
Loading required package: rtracklayer
Warning in valid.GenomicRanges.seqinfo(x, suggest.trim = TRUE) :
  GRanges object contains 2405 out-of-bound ranges located on
  sequences 75253, 74357, 74359, 74360, 74361, 74362, 74363,
  74358, 74364, 74365, 75254, 75259, 74368, 74369, 74366, 74367,
  74370, 74372, 74373, 74374, 74375, 74378, 74377, 74380, 74381,
  75262, 75263, 75265, 75266, 75268, 75269, 75271, 75273, 75276,
  75281, 75282, 75283, 74389, 74383, 74384, 74385, 74386, 74387,
  75287, 75288, 75286, 75289, 74390, 74391, 74392, 74393, 74394,
  75291, 74395, 74396, 74397, 74398, 75302, 75304, 75305, and
  75306. Note that ranges located on a sequence whose length is
  unknown (NA) or on a circular sequence are not considered
  out-of-bound (use seqlengths() and isCircular() to get the
  lengths and circularity flags of the underlying sequences). You
  can use trim() to trim these ranges. See
  ?`trim,GenomicRanges-method` for more information.
Loading required package: RSQLite
Warning: 228 keys not found in PolyPhen database: rs114264124 rs149209714 ... rs146628983 rs138319189

Attaching package: 'Matrix'

The following object is masked from 'package:VariantAnnotation':

    expand

The following object is masked from 'package:S4Vectors':

    expand

non-single nucleotide variations are set to NA
[W::bcf_hdr_check_sanity] GL should be declared as Number=G
non-single nucleotide variations are set to NA
non-single nucleotide variations are set to NA
Warning in system(paste(shQuote(texi2dvi), if (quiet) "--quiet" else "",  :
  running command '"C:\PROGRA~1\MIKTEX~1.9\miktex\bin\x64\texify.exe" --quiet --pdf "VariantAnnotation.tex" --max-iterations=20 -I "C:/Users/bioctesting/bbs-3.11-bioc-testing/R/share/texmf/tex/latex" -I "C:/Users/bioctesting/bbs-3.11-bioc-testing/R/share/texmf/bibtex/bst"' had status 1
Error: processing vignette 'VariantAnnotation.Rnw' failed with diagnostics:
Failed to locate 'texi2pdf' output file 'VariantAnnotation.pdf' for vignette with name 'VariantAnnotation' and engine 'utils::Sweave'. The following files exist in working directory 'C:\Users\bioctesting\bbs-3.11-bioc-testing\tmpdir\Rtmpo3fBbN\Rbuild128c706f6690\VariantAnnotation\vignettes': 'VariantAnnotation-DS_hist.pdf' (4665 bytes), 'VariantAnnotation-examine_ggplot2.pdf' (11921 bytes), 'VariantAnnotation.Rnw' (21087 bytes), 'VariantAnnotation.tex' (46330 bytes), 'filterVcf.Rnw' (12588 bytes), 'filterVcf.bib' (764 bytes)
--- failed re-building 'VariantAnnotation.Rnw'

--- re-building 'filterVcf.Rnw' using Sweave
starting prefilter
prefiltering 3791 records
prefiltered to C:\Users\bioctesting\bbs-3.11-bioc-testing\tmpdir\Rtmpsb2yGz\filebc8274a203c
prefilter compressing and indexing 'C:\Users\bioctesting\bbs-3.11-bioc-testing\tmpdir\Rtmpsb2yGz\filebc8274a203c'
starting filter
filtering 48 records
completed filtering
Loading required package: BiocFileCache
Loading required package: dbplyr

Attaching package: 'AnnotationHub'

The following object is masked from 'package:Biobase':

    cache

using temporary cache C:\Users\bioctesting\bbs-3.11-bioc-testing\tmpdir\Rtmpsb2yGz/BiocFileCache
snapshotDate(): 2020-03-31
downloading 1 resources
retrieving 1 resource
loading from cache
'select()' returned 1:1 mapping between keys and columns
Warning in system(paste(shQuote(texi2dvi), if (quiet) "--quiet" else "",  :
  running command '"C:\PROGRA~1\MIKTEX~1.9\miktex\bin\x64\texify.exe" --quiet --pdf "filterVcf.tex" --max-iterations=20 -I "C:/Users/bioctesting/bbs-3.11-bioc-testing/R/share/texmf/tex/latex" -I "C:/Users/bioctesting/bbs-3.11-bioc-testing/R/share/texmf/bibtex/bst"' had status 1
Error: processing vignette 'filterVcf.Rnw' failed with diagnostics:
Failed to locate 'texi2pdf' output file 'filterVcf.pdf' for vignette with name 'filterVcf' and engine 'utils::Sweave'. The following files exist in working directory 'C:\Users\bioctesting\bbs-3.11-bioc-testing\tmpdir\Rtmpo3fBbN\Rbuild128c706f6690\VariantAnnotation\vignettes': 'VariantAnnotation-DS_hist.pdf' (4665 bytes), 'VariantAnnotation-examine_ggplot2.pdf' (11921 bytes), 'VariantAnnotation.R' (9686 bytes), 'VariantAnnotation.Rnw' (21087 bytes), 'VariantAnnotation.tex' (46330 bytes), 'filterVcf.Rnw' (12588 bytes), 'filterVcf.bib' (764 bytes), 'filterVcf.tex' (15504 bytes)
--- failed re-building 'filterVcf.Rnw'

SUMMARY: processing the following files failed:
  'VariantAnnotation.Rnw' 'filterVcf.Rnw'

Error: Vignette re-building failed.
Execution halted