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INSTALL report for GenomicFiles on tokay1

This page was generated on 2021-05-05 12:11:59 -0400 (Wed, 05 May 2021).

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 717/1974HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
GenomicFiles 1.26.0  (landing page)
Bioconductor Package Maintainer
Snapshot Date: 2021-05-04 14:50:13 -0400 (Tue, 04 May 2021)
URL: https://git.bioconductor.org/packages/GenomicFiles
Branch: RELEASE_3_12
Last Commit: 8c9e00d
Last Changed Date: 2020-10-27 10:56:29 -0400 (Tue, 27 Oct 2020)
malbec1Linux (Ubuntu 18.04.5 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version exists in internal repository
tokay1Windows Server 2012 R2 Standard / x64  OK    OK    WARNINGS    OK  UNNEEDED, same version exists in internal repository
merida1macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version exists in internal repository

Summary

Package: GenomicFiles
Version: 1.26.0
Command: C:\cygwin\bin\curl.exe -O http://172.29.0.3/BBS/3.12/bioc/src/contrib/GenomicFiles_1.26.0.tar.gz && rm -rf GenomicFiles.buildbin-libdir && mkdir GenomicFiles.buildbin-libdir && C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=GenomicFiles.buildbin-libdir GenomicFiles_1.26.0.tar.gz && C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD INSTALL GenomicFiles_1.26.0.zip && rm GenomicFiles_1.26.0.tar.gz GenomicFiles_1.26.0.zip
StartedAt: 2021-05-04 18:06:15 -0400 (Tue, 04 May 2021)
EndedAt: 2021-05-04 18:07:32 -0400 (Tue, 04 May 2021)
EllapsedTime: 77.2 seconds
RetCode: 0
Status:   OK   

Command output

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###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O http://172.29.0.3/BBS/3.12/bioc/src/contrib/GenomicFiles_1.26.0.tar.gz && rm -rf GenomicFiles.buildbin-libdir && mkdir GenomicFiles.buildbin-libdir && C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=GenomicFiles.buildbin-libdir GenomicFiles_1.26.0.tar.gz && C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD INSTALL GenomicFiles_1.26.0.zip && rm GenomicFiles_1.26.0.tar.gz GenomicFiles_1.26.0.zip
###
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  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
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  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
100  289k  100  289k    0     0  8283k      0 --:--:-- --:--:-- --:--:-- 8523k

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-3.12-bioc/tmpdir/RtmpAtdIvA/R.INSTALL140ae15e9e/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-3.12-bioc/tmpdir/RtmpAtdIvA/R.INSTALL140ae15e9e/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-3.12-bioc/tmpdir/RtmpAtdIvA/R.INSTALL140ae15e9e/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-3.12-bioc/tmpdir/RtmpAtdIvA/R.INSTALL140ae15e9e/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-3.12-bioc/tmpdir/RtmpAtdIvA/R.INSTALL140ae15e9e/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-3.12-bioc/tmpdir/RtmpAtdIvA/R.INSTALL140ae15e9e/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-3.12-bioc/tmpdir/RtmpAtdIvA/R.INSTALL140ae15e9e/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-3.12-bioc/tmpdir/RtmpAtdIvA/R.INSTALL140ae15e9e/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-3.12-bioc/tmpdir/RtmpAtdIvA/R.INSTALL140ae15e9e/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-3.12-bioc/tmpdir/RtmpAtdIvA/R.INSTALL140ae15e9e/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-3.12-bioc/tmpdir/RtmpAtdIvA/R.INSTALL140ae15e9e/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-3.12-bioc/tmpdir/RtmpAtdIvA/R.INSTALL140ae15e9e/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-3.12-bioc/tmpdir/RtmpAtdIvA/R.INSTALL140ae15e9e/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-3.12-bioc/tmpdir/RtmpAtdIvA/R.INSTALL140ae15e9e/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-3.12-bioc/tmpdir/RtmpAtdIvA/R.INSTALL140ae15e9e/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-3.12-bioc/tmpdir/RtmpAtdIvA/R.INSTALL140ae15e9e/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-3.12-bioc/tmpdir/RtmpAtdIvA/R.INSTALL140ae15e9e/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-3.12-bioc/tmpdir/RtmpAtdIvA/R.INSTALL140ae15e9e/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-3.12-bioc/tmpdir/RtmpAtdIvA/R.INSTALL140ae15e9e/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_1.26.0.zip
* DONE (GenomicFiles)
* installing to library 'C:/Users/biocbuild/bbs-3.12-bioc/R/library'
package 'GenomicFiles' successfully unpacked and MD5 sums checked