Michael Lawrence
| Snapshot Date: 2021-05-05 14:51:38 -0400 (Wed, 05 May 2021) |
| URL: https://git.bioconductor.org/packages/VariantTools |
| Branch: RELEASE_3_12 |
| Last Commit: ed6c8be |
| Last Changed Date: 2020-10-27 10:47:52 -0400 (Tue, 27 Oct 2020) |
| Back to Multiple platform build/check report for BioC 3.12 |
|
This page was generated on 2021-05-06 12:34:09 -0400 (Thu, 06 May 2021).
|
To the developers/maintainers of the VariantTools package: Please make sure to use the following settings in order to reproduce any error or warning you see on this page. |
| Package 1933/1974 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| VariantTools 1.32.0 (landing page) Michael Lawrence
| malbec1 | Linux (Ubuntu 18.04.5 LTS) / x86_64 | OK | OK | WARNINGS | | ||||||||
| tokay1 | Windows Server 2012 R2 Standard / x64 | OK | OK | WARNINGS | OK | | ||||||||
| merida1 | macOS 10.14.6 Mojave / x86_64 | OK | OK | WARNINGS | OK | | ||||||||
| Package: VariantTools |
| Version: 1.32.0 |
| Command: C:\cygwin\bin\curl.exe -O http://172.29.0.3/BBS/3.12/bioc/src/contrib/VariantTools_1.32.0.tar.gz && rm -rf VariantTools.buildbin-libdir && mkdir VariantTools.buildbin-libdir && C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=VariantTools.buildbin-libdir VariantTools_1.32.0.tar.gz && C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD INSTALL VariantTools_1.32.0.zip && rm VariantTools_1.32.0.tar.gz VariantTools_1.32.0.zip |
| StartedAt: 2021-05-05 18:04:05 -0400 (Wed, 05 May 2021) |
| EndedAt: 2021-05-05 18:05:51 -0400 (Wed, 05 May 2021) |
| EllapsedTime: 106.0 seconds |
| RetCode: 0 |
| Status: OK |
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### Running command:
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### C:\cygwin\bin\curl.exe -O http://172.29.0.3/BBS/3.12/bioc/src/contrib/VariantTools_1.32.0.tar.gz && rm -rf VariantTools.buildbin-libdir && mkdir VariantTools.buildbin-libdir && C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=VariantTools.buildbin-libdir VariantTools_1.32.0.tar.gz && C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD INSTALL VariantTools_1.32.0.zip && rm VariantTools_1.32.0.tar.gz VariantTools_1.32.0.zip
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install for i386
* installing *source* package 'VariantTools' ...
** using staged installation
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
converting help for package 'VariantTools'
finding HTML links ... done
FilterConstructors html
annnotateWithControlDepth html
callGenotypes html
callSampleSpecificVariants html
callVariants html
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/Rtmp2ZXaq0/R.INSTALL1c1415a87a9a/VariantTools/man/callVariants.Rd:84: file link 'FilterRules' in package 'S4Vectors' does not exist and so has been treated as a topic
callWildtype html
concordance html
extractCoverageForPositions html
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/Rtmp2ZXaq0/R.INSTALL1c1415a87a9a/VariantTools/man/extractCoverageForPositions.Rd:16: file link 'coverage' in package 'IRanges' does not exist and so has been treated as a topic
matchVariants html
pileupVariants html
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/Rtmp2ZXaq0/R.INSTALL1c1415a87a9a/VariantTools/man/pileupVariants.Rd:21: file link 'PileupFiles' in package 'Rsamtools' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/Rtmp2ZXaq0/R.INSTALL1c1415a87a9a/VariantTools/man/pileupVariants.Rd:28: file link 'ApplyPileupsParam' in package 'Rsamtools' does not exist and so has been treated as a topic
postFilterVariants html
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/Rtmp2ZXaq0/R.INSTALL1c1415a87a9a/VariantTools/man/postFilterVariants.Rd:50: file link 'FilterRules' in package 'S4Vectors' does not exist and so has been treated as a topic
qaVariants html
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/Rtmp2ZXaq0/R.INSTALL1c1415a87a9a/VariantTools/man/qaVariants.Rd:51: file link 'FilterRules' in package 'S4Vectors' does not exist and so has been treated as a topic
tallyVariants html
finding level-2 HTML links ... done
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/Rtmp2ZXaq0/R.INSTALL1c1415a87a9a/VariantTools/man/tallyVariants.Rd:60: file link 'stackSamples' in package 'VariantAnnotation' does not exist and so has been treated as a topic
variantGR2Vcf html
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/Rtmp2ZXaq0/R.INSTALL1c1415a87a9a/VariantTools/man/variantGR2Vcf.Rd:8: file link 'VCF' in package 'VariantAnnotation' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/Rtmp2ZXaq0/R.INSTALL1c1415a87a9a/VariantTools/man/variantGR2Vcf.Rd:10: file link 'writeVcf' in package 'VariantAnnotation' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/Rtmp2ZXaq0/R.INSTALL1c1415a87a9a/VariantTools/man/variantGR2Vcf.Rd:19: file link 'VRanges' in package 'VariantAnnotation' does not exist and so has been treated as a topic
vignette html
** building package indices
** installing vignettes
'VariantTools.Rnw'
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
install for x64
* installing *source* package 'VariantTools' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'VariantTools' as VariantTools_1.32.0.zip
* DONE (VariantTools)
* installing to library 'C:/Users/biocbuild/bbs-3.12-bioc/R/library'
package 'VariantTools' successfully unpacked and MD5 sums checked