Robert Castelo
| Snapshot Date: 2020-10-16 14:40:19 -0400 (Fri, 16 Oct 2020) |
| URL: https://git.bioconductor.org/packages/VariantFiltering |
| Branch: RELEASE_3_11 |
| Last Commit: 4a6c072 |
| Last Changed Date: 2020-04-27 14:39:54 -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 VariantFiltering PACKAGE: Please make sure to use the following settings in order to reproduce any error or warning you see on this page. |
| Package 1866/1905 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| VariantFiltering 1.24.0 Robert Castelo
| malbec2 | Linux (Ubuntu 18.04.4 LTS) / x86_64 | OK | OK | OK | | ||||||
| tokay2 | Windows Server 2012 R2 Standard / x64 | [ OK ] | OK | WARNINGS | NA | |||||||
| machv2 | macOS 10.14.6 Mojave / x86_64 | OK | OK | OK | OK | |
| Package: VariantFiltering |
| Version: 1.24.0 |
| Command: C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.11/bioc/src/contrib/VariantFiltering_1.24.0.tar.gz && rm -rf VariantFiltering.buildbin-libdir && mkdir VariantFiltering.buildbin-libdir && C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=VariantFiltering.buildbin-libdir VariantFiltering_1.24.0.tar.gz && C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD INSTALL VariantFiltering_1.24.0.zip && rm VariantFiltering_1.24.0.tar.gz VariantFiltering_1.24.0.zip |
| StartedAt: 2020-10-16 19:33:36 -0400 (Fri, 16 Oct 2020) |
| EndedAt: 2020-10-16 19:36:16 -0400 (Fri, 16 Oct 2020) |
| EllapsedTime: 160.6 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/VariantFiltering_1.24.0.tar.gz && rm -rf VariantFiltering.buildbin-libdir && mkdir VariantFiltering.buildbin-libdir && C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=VariantFiltering.buildbin-libdir VariantFiltering_1.24.0.tar.gz && C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD INSTALL VariantFiltering_1.24.0.zip && rm VariantFiltering_1.24.0.tar.gz VariantFiltering_1.24.0.zip
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install for i386
* installing *source* package 'VariantFiltering' ...
** using staged installation
** libs
"C:/rtools40/mingw32/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/XVector/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/Biostrings/include' -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c Biostrings_stubs.c -o Biostrings_stubs.o
"C:/rtools40/mingw32/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/XVector/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/Biostrings/include' -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c R_init_VariantFiltering.c -o R_init_VariantFiltering.o
"C:/rtools40/mingw32/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/XVector/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/Biostrings/include' -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c methods-WeightMatrix.c -o methods-WeightMatrix.o
C:/rtools40/mingw32/bin/gcc -shared -s -static-libgcc -o VariantFiltering.dll tmp.def Biostrings_stubs.o R_init_VariantFiltering.o methods-WeightMatrix.o -LC:/extsoft/lib/i386 -LC:/extsoft/lib -LC:/Users/BIOCBU~1/BBS-3~1.11-/R/bin/i386 -lR
installing to C:/Users/biocbuild/bbs-3.11-bioc/meat/VariantFiltering.buildbin-libdir/00LOCK-VariantFiltering/00new/VariantFiltering/libs/i386
** R
** inst
** byte-compile and prepare package for lazy loading
in method for 'annotateVariants' with signature 'annObj="MafDb"': no definition for class "MafDb"
** help
*** installing help indices
converting help for package 'VariantFiltering'
finding HTML links ... done
GenePhylostrataDb-class html
Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/RtmpO4oJt6/R.INSTALL2448c896c47/VariantFiltering/man/GenePhylostrataDb-class.Rd:47: file link 'phastCons100way.UCSC.hg19' in package 'phastCons100way.UCSC.hg19' does not exist and so has been treated as a topic
VariantFiltering-defunct html
VariantFiltering-deprecated html
finding level-2 HTML links ... done
VariantFiltering-package html
VariantFilteringParam-class html
Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/RtmpO4oJt6/R.INSTALL2448c896c47/VariantFiltering/man/VariantFilteringParam-class.Rd:105: file link 'getGeneticCode' in package 'Biostrings' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/RtmpO4oJt6/R.INSTALL2448c896c47/VariantFiltering/man/VariantFilteringParam-class.Rd:123: file link 'TabixFile' in package 'Rsamtools' does not exist and so has been treated as a topic
VariantFilteringResults-class html
Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/RtmpO4oJt6/R.INSTALL2448c896c47/VariantFiltering/man/VariantFilteringResults-class.Rd:81: file link 'VRanges' in package 'VariantAnnotation' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/RtmpO4oJt6/R.INSTALL2448c896c47/VariantFiltering/man/VariantFilteringResults-class.Rd:84: file link 'locateVariants' in package 'VariantAnnotation' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/RtmpO4oJt6/R.INSTALL2448c896c47/VariantFiltering/man/VariantFilteringResults-class.Rd:101: file link 'isSNV' in package 'VariantAnnotation' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/RtmpO4oJt6/R.INSTALL2448c896c47/VariantFiltering/man/VariantFilteringResults-class.Rd:102: file link 'isInsertion' in package 'VariantAnnotation' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/RtmpO4oJt6/R.INSTALL2448c896c47/VariantFiltering/man/VariantFilteringResults-class.Rd:103: file link 'isDeletion' in package 'VariantAnnotation' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/RtmpO4oJt6/R.INSTALL2448c896c47/VariantFiltering/man/VariantFilteringResults-class.Rd:104: file link 'isSubstitution' in package 'VariantAnnotation' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/RtmpO4oJt6/R.INSTALL2448c896c47/VariantFiltering/man/VariantFilteringResults-class.Rd:105: file link 'isDelins' in package 'VariantAnnotation' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/RtmpO4oJt6/R.INSTALL2448c896c47/VariantFiltering/man/VariantFilteringResults-class.Rd:120: file link 'predictCoding' in package 'VariantAnnotation' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/RtmpO4oJt6/R.INSTALL2448c896c47/VariantFiltering/man/VariantFilteringResults-class.Rd:198: file link 'graphNEL' in package 'graph' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/RtmpO4oJt6/R.INSTALL2448c896c47/VariantFiltering/man/VariantFilteringResults-class.Rd:201: file link 'nodeData' in package 'graph' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/RtmpO4oJt6/R.INSTALL2448c896c47/VariantFiltering/man/VariantFilteringResults-class.Rd:207: file link 'BamViews' in package 'Rsamtools' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/RtmpO4oJt6/R.INSTALL2448c896c47/VariantFiltering/man/VariantFilteringResults-class.Rd:211: file link 'VRangesList' in package 'VariantAnnotation' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/RtmpO4oJt6/R.INSTALL2448c896c47/VariantFiltering/man/VariantFilteringResults-class.Rd:215: file link 'VRanges' in package 'VariantAnnotation' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/RtmpO4oJt6/R.INSTALL2448c896c47/VariantFiltering/man/VariantFilteringResults-class.Rd:228: file link 'FilterRules' in package 'S4Vectors' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/RtmpO4oJt6/R.INSTALL2448c896c47/VariantFiltering/man/VariantFilteringResults-class.Rd:235: file link 'FilterRules' in package 'S4Vectors' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/RtmpO4oJt6/R.INSTALL2448c896c47/VariantFiltering/man/VariantFilteringResults-class.Rd:254: file link 'softFilterMatrix' in package 'VariantAnnotation' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/RtmpO4oJt6/R.INSTALL2448c896c47/VariantFiltering/man/VariantFilteringResults-class.Rd:316: file link 'locateVariants' in package 'VariantAnnotation' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/RtmpO4oJt6/R.INSTALL2448c896c47/VariantFiltering/man/VariantFilteringResults-class.Rd:317: file link 'predictCoding' in package 'VariantAnnotation' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/RtmpO4oJt6/R.INSTALL2448c896c47/VariantFiltering/man/VariantFilteringResults-class.Rd:332: file link 'AlignmentsTrack' in package 'Gviz' does not exist and so has been treated as a topic
VariantType-class html
Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/RtmpO4oJt6/R.INSTALL2448c896c47/VariantFiltering/man/VariantType-class.Rd:40: file link 'locateVariants' in package 'VariantAnnotation' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/RtmpO4oJt6/R.INSTALL2448c896c47/VariantFiltering/man/VariantType-class.Rd:56: file link 'locateVariants' in package 'VariantAnnotation' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/RtmpO4oJt6/R.INSTALL2448c896c47/VariantFiltering/man/VariantType-class.Rd:60: file link 'locateVariants' in package 'VariantAnnotation' does not exist and so has been treated as a topic
WeightMatrix-class html
autosomalDominant html
Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/RtmpO4oJt6/R.INSTALL2448c896c47/VariantFiltering/man/autosomalDominant.Rd:23: file link 'readVcf' in package 'VariantAnnotation' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/RtmpO4oJt6/R.INSTALL2448c896c47/VariantFiltering/man/autosomalDominant.Rd:29: file link 'BiocParallelParam' in package 'BiocParallel' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/RtmpO4oJt6/R.INSTALL2448c896c47/VariantFiltering/man/autosomalDominant.Rd:31: file link 'bpparam' in package 'BiocParallel' does not exist and so has been treated as a topic
autosomalRecessiveHeterozygous html
Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/RtmpO4oJt6/R.INSTALL2448c896c47/VariantFiltering/man/autosomalRecessiveHeterozygous.Rd:22: file link 'readVcf' in package 'VariantAnnotation' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/RtmpO4oJt6/R.INSTALL2448c896c47/VariantFiltering/man/autosomalRecessiveHeterozygous.Rd:26: file link 'BiocParallelParam' in package 'BiocParallel' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/RtmpO4oJt6/R.INSTALL2448c896c47/VariantFiltering/man/autosomalRecessiveHeterozygous.Rd:28: file link 'bpparam' in package 'BiocParallel' does not exist and so has been treated as a topic
autosomalRecessiveHomozygous html
Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/RtmpO4oJt6/R.INSTALL2448c896c47/VariantFiltering/man/autosomalRecessiveHomozygous.Rd:26: file link 'readVcf' in package 'VariantAnnotation' does not exist and so has been treated as a topic
deNovo html
Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/RtmpO4oJt6/R.INSTALL2448c896c47/VariantFiltering/man/deNovo.Rd:23: file link 'readVcf' in package 'VariantAnnotation' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/RtmpO4oJt6/R.INSTALL2448c896c47/VariantFiltering/man/deNovo.Rd:29: file link 'BiocParallelParam' in package 'BiocParallel' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/RtmpO4oJt6/R.INSTALL2448c896c47/VariantFiltering/man/deNovo.Rd:31: file link 'bpparam' in package 'BiocParallel' does not exist and so has been treated as a topic
readAAradicalChangeMatrix html
unrelatedIndividuals html
Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/RtmpO4oJt6/R.INSTALL2448c896c47/VariantFiltering/man/unrelatedIndividuals.Rd:23: file link 'readVcf' in package 'VariantAnnotation' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/RtmpO4oJt6/R.INSTALL2448c896c47/VariantFiltering/man/unrelatedIndividuals.Rd:27: file link 'BiocParallelParam' in package 'BiocParallel' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/RtmpO4oJt6/R.INSTALL2448c896c47/VariantFiltering/man/unrelatedIndividuals.Rd:29: file link 'bpparam' in package 'BiocParallel' does not exist and so has been treated as a topic
xLinked html
Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/RtmpO4oJt6/R.INSTALL2448c896c47/VariantFiltering/man/xLinked.Rd:24: file link 'readVcf' in package 'VariantAnnotation' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/RtmpO4oJt6/R.INSTALL2448c896c47/VariantFiltering/man/xLinked.Rd:30: file link 'BiocParallelParam' in package 'BiocParallel' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/RtmpO4oJt6/R.INSTALL2448c896c47/VariantFiltering/man/xLinked.Rd:32: file link 'bpparam' in package 'BiocParallel' does not exist and so has been treated as a topic
** building package indices
** installing vignettes
** 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 'VariantFiltering' ...
** libs
"C:/rtools40/mingw64/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/XVector/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/Biostrings/include' -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c Biostrings_stubs.c -o Biostrings_stubs.o
"C:/rtools40/mingw64/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/XVector/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/Biostrings/include' -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c R_init_VariantFiltering.c -o R_init_VariantFiltering.o
"C:/rtools40/mingw64/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/XVector/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/Biostrings/include' -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c methods-WeightMatrix.c -o methods-WeightMatrix.o
C:/rtools40/mingw64/bin/gcc -shared -s -static-libgcc -o VariantFiltering.dll tmp.def Biostrings_stubs.o R_init_VariantFiltering.o methods-WeightMatrix.o -LC:/extsoft/lib/x64 -LC:/extsoft/lib -LC:/Users/BIOCBU~1/BBS-3~1.11-/R/bin/x64 -lR
installing to C:/Users/biocbuild/bbs-3.11-bioc/meat/VariantFiltering.buildbin-libdir/VariantFiltering/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'VariantFiltering' as VariantFiltering_1.24.0.zip
* DONE (VariantFiltering)
* installing to library 'C:/Users/biocbuild/bbs-3.11-bioc/R/library'
package 'VariantFiltering' successfully unpacked and MD5 sums checked