[Debian-med-packaging] Test failure in rtracklayer (Was: [devteam-bioc] How to create the precompued results in GenomicAlignments)
Andreas Tille
tille at debian.org
Thu Jul 24 12:33:58 UTC 2014
Hi Martin,
thanks for the quick and helpful response. This helped to get
GenomicAlignments into Debian. Now I have the next problem in updating
rtracklayer to version 1.24.2. The package builds fine. I have
installed the following dependencies:
$ LANG=C apt-cache policy r-bioc-biocgenerics r-bioc-iranges r-bioc-biostrings r-bioc-genomicranges r-bioc-genomicalignments r-bioc-bsgenome r-bioc-rsamtools | grep -e ^r-bioc -e Installed
r-bioc-biocgenerics:
Installed: 0.10.0-1
r-bioc-iranges:
Installed: 1.22.8-1
r-bioc-biostrings:
Installed: 2.32.0-1
r-bioc-genomicranges:
Installed: 1.16.3-1
r-bioc-genomicalignments:
Installed: 1.0.2-1
r-bioc-bsgenome:
Installed: 1.32.0-1
r-bioc-rsamtools:
Installed: 1.16.1-2
When trying to run the test suite I get:
$ LC_ALL=C R --no-save <<EOT
> require("rtracklayer")
> rtracklayer:::.test()
> EOT
R version 3.1.1 (2014-07-10) -- "Sock it to Me"
Copyright (C) 2014 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.
R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.
Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.
> require("rtracklayer")
Loading required package: rtracklayer
Loading required package: GenomicRanges
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 object is masked from 'package:stats':
xtabs
The following objects are masked from 'package:base':
Filter, Find, Map, Position, Reduce, anyDuplicated, append,
as.data.frame, as.vector, cbind, colnames, do.call, duplicated,
eval, evalq, get, intersect, is.unsorted, lapply, mapply, match,
mget, order, paste, pmax, pmax.int, pmin, pmin.int, rank, rbind,
rep.int, rownames, sapply, setdiff, sort, table, tapply, union,
unique, unlist
Loading required package: IRanges
Loading required package: GenomeInfoDb
> rtracklayer:::.test()
Timing stopped at: 0.556 0.02 0.578
Error in seqlevels(seqinfo(x)) :
error in evaluating the argument 'x' in selecting a method for function 'seqlevels': Error in (function (classes, fdef, mtable) :
unable to find an inherited method for function 'seqinfo' for signature '"NULL"'
Calls: seqinfo -> <Anonymous>
Timing stopped at: 0.284 0.004 0.286
Error in seqlevels(seqinfo(x)) :
error in evaluating the argument 'x' in selecting a method for function 'seqlevels': Error in (function (classes, fdef, mtable) :
unable to find an inherited method for function 'seqinfo' for signature '"NULL"'
Calls: seqinfo -> <Anonymous>
Timing stopped at: 0.012 0 0.015
Error in seqlengths(seqinfo(x)) :
error in evaluating the argument 'x' in selecting a method for function 'seqlengths': Error in (function (classes, fdef, mtable) :
unable to find an inherited method for function 'seqinfo' for signature '"NULL"'
Calls: seqinfo -> <Anonymous>
Timing stopped at: 1.792 0.004 1.8
Error in seqlevels(seqinfo(x)) :
error in evaluating the argument 'x' in selecting a method for function 'seqlevels': Error in (function (classes, fdef, mtable) :
unable to find an inherited method for function 'seqinfo' for signature '"NULL"'
Calls: seqinfo -> <Anonymous>
Timing stopped at: 0.5 0 0.497
Error in seqlevels(seqinfo(x)) :
error in evaluating the argument 'x' in selecting a method for function 'seqlevels': Error in (function (classes, fdef, mtable) :
unable to find an inherited method for function 'seqinfo' for signature '"NULL"'
Calls: seqinfo -> <Anonymous>
RUNIT TEST PROTOCOL -- Thu Jul 24 14:38:56 2014
***********************************************
Number of test functions: 7
Number of errors: 5
Number of failures: 0
1 Test Suite :
rtracklayer RUnit Tests - 7 test functions, 5 errors, 0 failures
ERROR in test_bed: Error in seqlevels(seqinfo(x)) :
error in evaluating the argument 'x' in selecting a method for function 'seqlevels': Error in (function (classes, fdef, mtable) :
unable to find an inherited method for function 'seqinfo' for signature '"NULL"'
Calls: seqinfo -> <Anonymous>
ERROR in test_bedGraph: Error in seqlevels(seqinfo(x)) :
error in evaluating the argument 'x' in selecting a method for function 'seqlevels': Error in (function (classes, fdef, mtable) :
unable to find an inherited method for function 'seqinfo' for signature '"NULL"'
Calls: seqinfo -> <Anonymous>
ERROR in test_bw: Error in seqlengths(seqinfo(x)) :
error in evaluating the argument 'x' in selecting a method for function 'seqlengths': Error in (function (classes, fdef, mtable) :
unable to find an inherited method for function 'seqinfo' for signature '"NULL"'
Calls: seqinfo -> <Anonymous>
ERROR in test_gff: Error in seqlevels(seqinfo(x)) :
error in evaluating the argument 'x' in selecting a method for function 'seqlevels': Error in (function (classes, fdef, mtable) :
unable to find an inherited method for function 'seqinfo' for signature '"NULL"'
Calls: seqinfo -> <Anonymous>
ERROR in test_wig: Error in seqlevels(seqinfo(x)) :
error in evaluating the argument 'x' in selecting a method for function 'seqlevels': Error in (function (classes, fdef, mtable) :
unable to find an inherited method for function 'seqinfo' for signature '"NULL"'
Calls: seqinfo -> <Anonymous>
Test files with failing tests
test_bed.R
test_bed
test_bedGraph.R
test_bedGraph
test_bw.R
test_bw
test_gff.R
test_gff
test_wig.R
test_wig
Error in BiocGenerics:::testPackage("rtracklayer") :
unit tests failed for package rtracklayer
Calls: <Anonymous> -> <Anonymous>
Execution halted
Any hint what might be wrong here?
Thanks for your kind cooperation
Andreas.
On Tue, Jul 22, 2014 at 12:03:04PM -0700, Martin Morgan wrote:
> On 07/21/2014 01:36 PM, Maintainer wrote:
> >Hi,
> >
> >I need to package GenomicAlignments for Debian to be able to upgrade
> >several BioConductor modules in Debian to the latest version.
> >Unfortunately there are some binary files in it which are not accepted
> >by our ftpmaster since they come with no visible source. Could you
> >please give a short explanation how
> >
> > vignettes/precomputed_results/*.rda
>
> This is generated by code in the
> GenomicAlignments/vignettes/OverlapEncodings.Rnw file
>
> > vignettes/summarizeOverlaps-modes.pdf
>
> a figure, created by hand, reproduced from the source in the figure.
>
> >
> >were created?
> >
> >Thanks a lot for your support
> >
> > Andreas.
> >
> >
> >----- Forwarded message from Thorsten Alteholz <ftpmaster at ftp-master.debian.org> -----
> >
> >Date: Mon, 21 Jul 2014 17:00:05 +0000
> >From: Thorsten Alteholz <ftpmaster at ftp-master.debian.org>
> >To: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>, Andreas Tille <tille at debian.org>
> >Subject: r-bioc-genomicalignments_1.0.2-1_amd64.changes REJECTED
> >
> >
> >Hi Andreas,
> >
> >unfortunately I have to reject your package.
> >
> >As I like your explanation of rda-files in README.source, I now dearly
> >miss them in this package.
> >
> >Can you please also explain where these two bam-files come from?
> >
> >>From other R packages I learned that each pdf-file is accompanied by an Rnw-file.
> >This does not seem to be the case for ./vignettes/summarizeOverlaps-modes.pdf.
> >So where does this pdf-file come from?
> >
> >Thanks!
> > Thorsten
> >
> >===
> >
> >Please feel free to respond to this email if you don't understand why
> >your files were rejected, or if you upload new files which address our
> >concerns.
> >
> >
> >_______________________________________________
> >Debian-med-packaging mailing list
> >Debian-med-packaging at lists.alioth.debian.org
> >http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-packaging
> >
> >
> >----- End forwarded message -----
> >
>
>
> --
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