| Back to Multiple platform build/check report for BioC 3.11 |
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This page was generated on 2020-10-17 11:56:40 -0400 (Sat, 17 Oct 2020).
| TO THE DEVELOPERS/MAINTAINERS OF THE GenomicFiles PACKAGE: Please make sure to use the following settings in order to reproduce any error or warning you see on this page. |
| Package 709/1905 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| GenomicFiles 1.24.0 Bioconductor Package Maintainer
| malbec2 | Linux (Ubuntu 18.04.4 LTS) / x86_64 | OK | OK | OK |  | ||||||
| tokay2 | Windows Server 2012 R2 Standard / x64 | [ OK ] | OK | WARNINGS | OK | | ||||||
| machv2 | macOS 10.14.6 Mojave / x86_64 | OK | OK | OK | OK | |
| Package: GenomicFiles |
| Version: 1.24.0 |
| Command: C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.11/bioc/src/contrib/GenomicFiles_1.24.0.tar.gz && rm -rf GenomicFiles.buildbin-libdir && mkdir GenomicFiles.buildbin-libdir && C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=GenomicFiles.buildbin-libdir GenomicFiles_1.24.0.tar.gz && C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD INSTALL GenomicFiles_1.24.0.zip && rm GenomicFiles_1.24.0.tar.gz GenomicFiles_1.24.0.zip |
| StartedAt: 2020-10-16 19:12:09 -0400 (Fri, 16 Oct 2020) |
| EndedAt: 2020-10-16 19:13:25 -0400 (Fri, 16 Oct 2020) |
| EllapsedTime: 76.3 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/GenomicFiles_1.24.0.tar.gz && rm -rf GenomicFiles.buildbin-libdir && mkdir GenomicFiles.buildbin-libdir && C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=GenomicFiles.buildbin-libdir GenomicFiles_1.24.0.tar.gz && C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD INSTALL GenomicFiles_1.24.0.zip && rm GenomicFiles_1.24.0.tar.gz GenomicFiles_1.24.0.zip
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install for i386
* installing *source* package 'GenomicFiles' ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
converting help for package 'GenomicFiles'
finding HTML links ... done
GenomicFiles-class html
Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/RtmpgZMtU8/R.INSTALL27004bf2624b/GenomicFiles/man/GenomicFiles-class.Rd:111: file link 'SummarizedExperiment' in package 'SummarizedExperiment' does not exist and so has been treated as a topic
GenomicFiles-deprecated html
VcfStack-class html
Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/RtmpgZMtU8/R.INSTALL27004bf2624b/GenomicFiles/man/VcfStack-class.Rd:78: file link 'DataFrame' in package 'S4Vectors' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/RtmpgZMtU8/R.INSTALL27004bf2624b/GenomicFiles/man/VcfStack-class.Rd:98: file link 'GRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/RtmpgZMtU8/R.INSTALL27004bf2624b/GenomicFiles/man/VcfStack-class.Rd:129: file link 'VcfFileList' in package 'VariantAnnotation' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/RtmpgZMtU8/R.INSTALL27004bf2624b/GenomicFiles/man/VcfStack-class.Rd:130: file link 'VcfFileList' in package 'VariantAnnotation' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/RtmpgZMtU8/R.INSTALL27004bf2624b/GenomicFiles/man/VcfStack-class.Rd:133: file link 'seqinfo<-' in package 'GenomeInfoDb' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/RtmpgZMtU8/R.INSTALL27004bf2624b/GenomicFiles/man/VcfStack-class.Rd:139: file link 'seqlevelsStyle<-' in package 'GenomeInfoDb' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/RtmpgZMtU8/R.INSTALL27004bf2624b/GenomicFiles/man/VcfStack-class.Rd:143: file link 'DataFrame' in package 'S4Vectors' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/RtmpgZMtU8/R.INSTALL27004bf2624b/GenomicFiles/man/VcfStack-class.Rd:148: file link 'GRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/RtmpgZMtU8/R.INSTALL27004bf2624b/GenomicFiles/man/VcfStack-class.Rd:155: file link 'GRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/RtmpgZMtU8/R.INSTALL27004bf2624b/GenomicFiles/man/VcfStack-class.Rd:162: file link 'CharacterList' in package 'IRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/RtmpgZMtU8/R.INSTALL27004bf2624b/GenomicFiles/man/VcfStack-class.Rd:170: file link 'genotypeToSnpMatrix' in package 'VariantAnnotation' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/RtmpgZMtU8/R.INSTALL27004bf2624b/GenomicFiles/man/VcfStack-class.Rd:180: file link 'ScanVcfParam' in package 'VariantAnnotation' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/RtmpgZMtU8/R.INSTALL27004bf2624b/GenomicFiles/man/VcfStack-class.Rd:227: file link 'VcfFile' in package 'VariantAnnotation' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/RtmpgZMtU8/R.INSTALL27004bf2624b/GenomicFiles/man/VcfStack-class.Rd:227: file link 'VcfFileList' in package 'VariantAnnotation' does not exist and so has been treated as a topic
pack-methods html
reduceByFile-methods html
reduceByRange-methods html
reduceByYield html
Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/RtmpgZMtU8/R.INSTALL27004bf2624b/GenomicFiles/man/reduceByYield.Rd:12: file link 'BamFile' in package 'Rsamtools' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/RtmpgZMtU8/R.INSTALL27004bf2624b/GenomicFiles/man/reduceByYield.Rd:29: file link 'BamFile' in package 'Rsamtools' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/RtmpgZMtU8/R.INSTALL27004bf2624b/GenomicFiles/man/reduceByYield.Rd:121: file link 'BamFile' in package 'Rsamtools' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/RtmpgZMtU8/R.INSTALL27004bf2624b/GenomicFiles/man/reduceByYield.Rd:122: file link 'TabixFile' in package 'Rsamtools' does not exist and so has been treated as a topic
registry-utils html
unpack-methods html
** 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 'GenomicFiles' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'GenomicFiles' as GenomicFiles_1.24.0.zip
* DONE (GenomicFiles)
* installing to library 'C:/Users/biocbuild/bbs-3.11-bioc/R/library'
package 'GenomicFiles' successfully unpacked and MD5 sums checked