Michael Lawrence
| Snapshot Date: 2020-10-16 14:40:19 -0400 (Fri, 16 Oct 2020) |
| URL: https://git.bioconductor.org/packages/VariantTools |
| Branch: RELEASE_3_11 |
| Last Commit: 845c555 |
| Last Changed Date: 2020-04-27 14:31:52 -0400 (Mon, 27 Apr 2020) |
| Back to Multiple platform build/check report for BioC 3.11 |
|
This page was generated on 2020-10-17 11:57:59 -0400 (Sat, 17 Oct 2020).
| 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 1867/1905 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| VariantTools 1.30.0 Michael Lawrence
| malbec2 | Linux (Ubuntu 18.04.4 LTS) / x86_64 | OK | OK | WARNINGS | | ||||||
| tokay2 | Windows Server 2012 R2 Standard / x64 | [ OK ] | OK | WARNINGS | NA | |||||||
| machv2 | macOS 10.14.6 Mojave / x86_64 | OK | OK | WARNINGS | OK | |
| Package: VariantTools |
| Version: 1.30.0 |
| Command: C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.11/bioc/src/contrib/VariantTools_1.30.0.tar.gz && rm -rf VariantTools.buildbin-libdir && mkdir VariantTools.buildbin-libdir && C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=VariantTools.buildbin-libdir VariantTools_1.30.0.tar.gz && C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD INSTALL VariantTools_1.30.0.zip && rm VariantTools_1.30.0.tar.gz VariantTools_1.30.0.zip |
| StartedAt: 2020-10-16 19:14:48 -0400 (Fri, 16 Oct 2020) |
| EndedAt: 2020-10-16 19:17:03 -0400 (Fri, 16 Oct 2020) |
| EllapsedTime: 135.0 seconds |
| RetCode: 0 |
| Status: OK |
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### Running command:
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### C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.11/bioc/src/contrib/VariantTools_1.30.0.tar.gz && rm -rf VariantTools.buildbin-libdir && mkdir VariantTools.buildbin-libdir && C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=VariantTools.buildbin-libdir VariantTools_1.30.0.tar.gz && C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD INSTALL VariantTools_1.30.0.zip && rm VariantTools_1.30.0.tar.gz VariantTools_1.30.0.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-3.11-bioc/tmpdir/RtmpKIROqT/R.INSTALL2c2c2608501e/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-3.11-bioc/tmpdir/RtmpKIROqT/R.INSTALL2c2c2608501e/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-3.11-bioc/tmpdir/RtmpKIROqT/R.INSTALL2c2c2608501e/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-3.11-bioc/tmpdir/RtmpKIROqT/R.INSTALL2c2c2608501e/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-3.11-bioc/tmpdir/RtmpKIROqT/R.INSTALL2c2c2608501e/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-3.11-bioc/tmpdir/RtmpKIROqT/R.INSTALL2c2c2608501e/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-3.11-bioc/tmpdir/RtmpKIROqT/R.INSTALL2c2c2608501e/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-3.11-bioc/tmpdir/RtmpKIROqT/R.INSTALL2c2c2608501e/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-3.11-bioc/tmpdir/RtmpKIROqT/R.INSTALL2c2c2608501e/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-3.11-bioc/tmpdir/RtmpKIROqT/R.INSTALL2c2c2608501e/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_1.30.0.zip
* DONE (VariantTools)
* installing to library 'C:/Users/biocbuild/bbs-3.11-bioc/R/library'
package 'VariantTools' successfully unpacked and MD5 sums checked