Your message dated Fri, 28 Jul 2023 04:22:35 +0000
with message-id <e1qpezr-00cd8q...@fasolo.debian.org>
and subject line Bug#1025045: fixed in r-bioc-structuralvariantannotation
1.16.0+ds-1
has caused the Debian Bug report #1025045,
regarding r-bioc-structuralvariantannotation: Test failures in autopkgtest
to be marked as done.
This means that you claim that the problem has been dealt with.
If this is not the case it is now your responsibility to reopen the
Bug report if necessary, and/or fix the problem forthwith.
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--
1025045: https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=1025045
Debian Bug Tracking System
Contact ow...@bugs.debian.org with problems
--- Begin Message ---
Source: r-bioc-structuralvariantannotation
Version: 1.13.0+ds-1
Severity: normal
X-Debbugs-Cc: 1023...@bugs.debian.org
Hi,
the package fails its autopkgtest. The errors starts with:
[ FAIL 30 | WARN 4 | SKIP 0 | PASS 85 ]
══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test-extensions-VCF.R:28'): INFO column import ──────────────────────
Error in `h(simpleError(msg, call))`: error in evaluating the argument 'x' in
selecting a method for function 'breakpointRanges': no 'header' line "#CHROM
POS ID..."?
Backtrace:
▆
1.
├─StructuralVariantAnnotation::breakpointRanges(.testrecord(c("chr10\t2991435\tINV\tN\t<INV>\t.\tLowQual\tSVTYPE=INV;CHR2=chr1;END=19357517;CT=3to5")))
at test-extensions-VCF.R:28:8
2.
├─StructuralVariantAnnotation:::.testrecord(c("chr10\t2991435\tINV\tN\t<INV>\t.\tLowQual\tSVTYPE=INV;CHR2=chr1;END=19357517;CT=3to5"))
3. │ ├─VariantAnnotation::readVcf(.testfile(filename), "")
4. │ └─VariantAnnotation::readVcf(.testfile(filename), "")
5. │ └─VariantAnnotation (local) .local(file, genome = genome, param =
param, ...)
6. │ └─VariantAnnotation:::.readVcf(...)
7. │ └─VariantAnnotation:::.scanVcfToVCF(...)
8. │ ├─VariantAnnotation::scanVcfHeader(file)
9. │ └─VariantAnnotation::scanVcfHeader(file)
10. │ ├─Rsamtools::scanBcfHeader(file[[1]], ...)
11. │ └─Rsamtools::scanBcfHeader(file[[1]], ...)
12. │ └─BiocGenerics::Map(...)
13. │ ├─BiocGenerics (local) standardGeneric("Map")
14. │ │ ├─BiocGenerics::eval(mc, env)
15. │ │ └─base::eval(mc, env)
16. │ │ └─base::eval(mc, env)
17. │ └─base::Map(f = f, ...)
18. │ └─base::mapply(FUN = f, ..., SIMPLIFY = FALSE)
19. │ └─Rsamtools (local) `<fn>`(dots[[1L]][[1L]])
20. │ ├─Rsamtools::scanBcfHeader(bf)
21. │ └─Rsamtools::scanBcfHeader(bf)
22. └─base::.handleSimpleError(...)
23. └─base (local) h(simpleError(msg, call))
── Error ('test-extensions-VCF.R:49'): Delly TRA ───────────────────────────────
Error in `h(simpleError(msg, call))`: error in evaluating the argument 'x' in
selecting a method for function 'breakpointRanges': no 'header' line "#CHROM
POS ID..."?
Backtrace:
▆
1.
├─StructuralVariantAnnotation::breakpointRanges(.testrecord(c("chr10\t2991435\tTRA00000001\tN\t<TRA>\t.\tLowQual\tCIEND=0,100;CIPOS=0,50;SVTYPE=TRA;CHR2=chr1;END=19357517;CT=3to5")))
at test-extensions-VCF.R:49:4
2.
├─StructuralVariantAnnotation:::.testrecord(c("chr10\t2991435\tTRA00000001\tN\t<TRA>\t.\tLowQual\tCIEND=0,100;CIPOS=0,50;SVTYPE=TRA;CHR2=chr1;END=19357517;CT=3to5"))
3. │ ├─VariantAnnotation::readVcf(.testfile(filename), "")
4. │ └─VariantAnnotation::readVcf(.testfile(filename), "")
5. │ └─VariantAnnotation (local) .local(file, genome = genome, param =
param, ...)
6. │ └─VariantAnnotation:::.readVcf(...)
7. │ └─VariantAnnotation:::.scanVcfToVCF(...)
8. │ ├─VariantAnnotation::scanVcfHeader(file)
9. │ └─VariantAnnotation::scanVcfHeader(file)
10. │ ├─Rsamtools::scanBcfHeader(file[[1]], ...)
11. │ └─Rsamtools::scanBcfHeader(file[[1]], ...)
12. │ └─BiocGenerics::Map(...)
13. │ ├─BiocGenerics (local) standardGeneric("Map")
14. │ │ ├─BiocGenerics::eval(mc, env)
15. │ │ └─base::eval(mc, env)
16. │ │ └─base::eval(mc, env)
17. │ └─base::Map(f = f, ...)
18. │ └─base::mapply(FUN = f, ..., SIMPLIFY = FALSE)
19. │ └─Rsamtools (local) `<fn>`(dots[[1L]][[1L]])
20. │ ├─Rsamtools::scanBcfHeader(bf)
21. │ └─Rsamtools::scanBcfHeader(bf)
22. └─base::.handleSimpleError(...)
23. └─base (local) h(simpleError(msg, call))
── Error ('test-extensions-VCF.R:71'): empty VCF ───────────────────────────────
Error in `h(simpleError(msg, call))`: error in evaluating the argument 'x' in
selecting a method for function 'breakpointRanges': no 'header' line "#CHROM
POS ID..."?
You can find a full build log here
https://ci.debian.net/data/autopkgtest/testing/amd64/r/r-bioc-structuralvariantannotation/28747149/log.gz
Kind regards
Andreas.
-- System Information:
Debian Release: bookworm/sid
APT prefers testing
APT policy: (501, 'testing'), (50, 'buildd-unstable'), (50, 'unstable'), (5,
'experimental'), (1, 'buildd-experimental')
Architecture: amd64 (x86_64)
Kernel: Linux 6.0.0-2-amd64 (SMP w/4 CPU threads; PREEMPT)
Locale: LANG=de_DE.UTF-8, LC_CTYPE=de_DE.UTF-8 (charmap=UTF-8),
LANGUAGE=de_DE:de
Shell: /bin/sh linked to /usr/bin/dash
Init: systemd (via /run/systemd/system)
LSM: AppArmor: enabled
--- End Message ---
--- Begin Message ---
Source: r-bioc-structuralvariantannotation
Source-Version: 1.16.0+ds-1
Done: Andreas Tille <ti...@debian.org>
We believe that the bug you reported is fixed in the latest version of
r-bioc-structuralvariantannotation, which is due to be installed in the Debian
FTP archive.
A summary of the changes between this version and the previous one is
attached.
Thank you for reporting the bug, which will now be closed. If you
have further comments please address them to 1025...@bugs.debian.org,
and the maintainer will reopen the bug report if appropriate.
Debian distribution maintenance software
pp.
Andreas Tille <ti...@debian.org> (supplier of updated
r-bioc-structuralvariantannotation package)
(This message was generated automatically at their request; if you
believe that there is a problem with it please contact the archive
administrators by mailing ftpmas...@ftp-master.debian.org)
-----BEGIN PGP SIGNED MESSAGE-----
Hash: SHA256
Format: 1.8
Date: Fri, 28 Jul 2023 05:54:35 +0200
Source: r-bioc-structuralvariantannotation
Architecture: source
Version: 1.16.0+ds-1
Distribution: unstable
Urgency: medium
Maintainer: Debian R Packages Maintainers <r-pkg-t...@alioth-lists.debian.net>
Changed-By: Andreas Tille <ti...@debian.org>
Closes: 1025045
Changes:
r-bioc-structuralvariantannotation (1.16.0+ds-1) unstable; urgency=medium
.
* Team upload.
* Rebuild against latest r-base
Closes: #1025045
* Standards-Version: 4.6.2 (routine-update)
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