Back to "Blame Jeroen" build/check report for BioC 3.11

INSTALL report for GenomeInfoDb on tokay2

This page was generated on 2020-04-15 03:20:09 -0400 (Wed, 15 Apr 2020).

These builds are using Rtools40 and R-testing by Jeroen Ooms (available at https://cran.r-project.org/bin/windows/testing/rtools40.html)
TO THE DEVELOPERS/MAINTAINERS OF THE GenomeInfoDb PACKAGE: Please make sure to use the following settings in order to reproduce any error or warning you see on this page.
Package 40/89HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
GenomeInfoDb 1.23.17
Bioconductor Package Maintainer
Snapshot Date: 2020-04-14 17:00:05 -0400 (Tue, 14 Apr 2020)
URL: https://git.bioconductor.org/packages/GenomeInfoDb
Branch: master
Last Commit: aef7b19
Last Changed Date: 2020-04-13 13:01:30 -0400 (Mon, 13 Apr 2020)
tokay2 Windows Server 2012 R2 Standard / x64 [ OK ] OK  WARNINGS  OK 

Summary

Package: GenomeInfoDb
Version: 1.23.17
Command: C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.11/bioc-testing/src/contrib/GenomeInfoDb_1.23.17.tar.gz && rm -rf GenomeInfoDb.buildbin-libdir && mkdir GenomeInfoDb.buildbin-libdir && C:\Users\bioctesting\bbs-3.11-bioc-testing\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=GenomeInfoDb.buildbin-libdir GenomeInfoDb_1.23.17.tar.gz && C:\Users\bioctesting\bbs-3.11-bioc-testing\R\bin\R.exe CMD INSTALL GenomeInfoDb_1.23.17.zip && rm GenomeInfoDb_1.23.17.tar.gz GenomeInfoDb_1.23.17.zip
StartedAt: 2020-04-14 17:56:41 -0400 (Tue, 14 Apr 2020)
EndedAt: 2020-04-14 17:57:06 -0400 (Tue, 14 Apr 2020)
EllapsedTime: 25.1 seconds
RetCode: 0
Status:  OK  

Command output

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###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.11/bioc-testing/src/contrib/GenomeInfoDb_1.23.17.tar.gz && rm -rf GenomeInfoDb.buildbin-libdir && mkdir GenomeInfoDb.buildbin-libdir && C:\Users\bioctesting\bbs-3.11-bioc-testing\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=GenomeInfoDb.buildbin-libdir GenomeInfoDb_1.23.17.tar.gz && C:\Users\bioctesting\bbs-3.11-bioc-testing\R\bin\R.exe CMD INSTALL GenomeInfoDb_1.23.17.zip && rm GenomeInfoDb_1.23.17.tar.gz GenomeInfoDb_1.23.17.zip
###
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  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed

  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
100 3080k  100 3080k    0     0  41.1M      0 --:--:-- --:--:-- --:--:-- 45.5M

install for i386

* installing *source* package 'GenomeInfoDb' ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'GenomeInfoDb'
    finding HTML links ... done
    GenomeDescription-class                 html  
Rd warning: C:/Users/bioctesting/bbs-3.11-bioc-testing/tmpdir/RtmpABIAiU/R.INSTALLcdc7b04899/GenomeInfoDb/man/GenomeDescription-class.Rd:45: file link 'BSgenome' in package 'BSgenome' does not exist and so has been treated as a topic
Rd warning: C:/Users/bioctesting/bbs-3.11-bioc-testing/tmpdir/RtmpABIAiU/R.INSTALLcdc7b04899/GenomeInfoDb/man/GenomeDescription-class.Rd:46: file link 'BSgenome' in package 'BSgenome' does not exist and so has been treated as a topic
Rd warning: C:/Users/bioctesting/bbs-3.11-bioc-testing/tmpdir/RtmpABIAiU/R.INSTALLcdc7b04899/GenomeInfoDb/man/GenomeDescription-class.Rd:126: file link 'BSgenome' in package 'BSgenome' does not exist and so has been treated as a topic
    GenomeInfoDb-internals                  html  
    Seqinfo-class                           html  
    fetchExtendedChromInfoFromUCSC          html  
Rd warning: C:/Users/bioctesting/bbs-3.11-bioc-testing/tmpdir/RtmpABIAiU/R.INSTALLcdc7b04899/GenomeInfoDb/man/fetchExtendedChromInfoFromUCSC.Rd:145: file link 'getBSgenome' in package 'BSgenome' does not exist and so has been treated as a topic
    getChromInfoFromEnsembl                 html  
    getChromInfoFromNCBI                    html  
    getChromInfoFromUCSC                    html  
Rd warning: C:/Users/bioctesting/bbs-3.11-bioc-testing/tmpdir/RtmpABIAiU/R.INSTALLcdc7b04899/GenomeInfoDb/man/getChromInfoFromUCSC.Rd:170: file link 'getBSgenome' in package 'BSgenome' does not exist and so has been treated as a topic
Rd warning: C:/Users/bioctesting/bbs-3.11-bioc-testing/tmpdir/RtmpABIAiU/R.INSTALLcdc7b04899/GenomeInfoDb/man/getChromInfoFromUCSC.Rd:171: file link 'BSgenome' in package 'BSgenome' does not exist and so has been treated as a topic
    loadTaxonomyDb                          html  
    mapGenomeBuilds                         html  
    rankSeqlevels                           html  
    seqinfo                                 html  
Rd warning: C:/Users/bioctesting/bbs-3.11-bioc-testing/tmpdir/RtmpABIAiU/R.INSTALLcdc7b04899/GenomeInfoDb/man/seqinfo.Rd:82: file link 'GRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/bioctesting/bbs-3.11-bioc-testing/tmpdir/RtmpABIAiU/R.INSTALLcdc7b04899/GenomeInfoDb/man/seqinfo.Rd:105: file link 'GRangesList' in package 'GenomicRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/bioctesting/bbs-3.11-bioc-testing/tmpdir/RtmpABIAiU/R.INSTALLcdc7b04899/GenomeInfoDb/man/seqinfo.Rd:106: file link 'GAlignmentPairs' in package 'GenomicAlignments' does not exist and so has been treated as a topic
Rd warning: C:/Users/bioctesting/bbs-3.11-bioc-testing/tmpdir/RtmpABIAiU/R.INSTALLcdc7b04899/GenomeInfoDb/man/seqinfo.Rd:107: file link 'GAlignmentsList' in package 'GenomicAlignments' does not exist and so has been treated as a topic
Rd warning: C:/Users/bioctesting/bbs-3.11-bioc-testing/tmpdir/RtmpABIAiU/R.INSTALLcdc7b04899/GenomeInfoDb/man/seqinfo.Rd:116: file link 'GRangesList' in package 'GenomicRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/bioctesting/bbs-3.11-bioc-testing/tmpdir/RtmpABIAiU/R.INSTALLcdc7b04899/GenomeInfoDb/man/seqinfo.Rd:118: file link 'exonsBy' in package 'GenomicFeatures' does not exist and so has been treated as a topic
Rd warning: C:/Users/bioctesting/bbs-3.11-bioc-testing/tmpdir/RtmpABIAiU/R.INSTALLcdc7b04899/GenomeInfoDb/man/seqinfo.Rd:131: file link 'GRangesList' in package 'GenomicRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/bioctesting/bbs-3.11-bioc-testing/tmpdir/RtmpABIAiU/R.INSTALLcdc7b04899/GenomeInfoDb/man/seqinfo.Rd:136: file link 'GRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/bioctesting/bbs-3.11-bioc-testing/tmpdir/RtmpABIAiU/R.INSTALLcdc7b04899/GenomeInfoDb/man/seqinfo.Rd:137: file link 'GAlignments' in package 'GenomicAlignments' does not exist and so has been treated as a topic
Rd warning: C:/Users/bioctesting/bbs-3.11-bioc-testing/tmpdir/RtmpABIAiU/R.INSTALLcdc7b04899/GenomeInfoDb/man/seqinfo.Rd:182: file link 'GRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/bioctesting/bbs-3.11-bioc-testing/tmpdir/RtmpABIAiU/R.INSTALLcdc7b04899/GenomeInfoDb/man/seqinfo.Rd:182: file link 'GRangesList' in package 'GenomicRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/bioctesting/bbs-3.11-bioc-testing/tmpdir/RtmpABIAiU/R.INSTALLcdc7b04899/GenomeInfoDb/man/seqinfo.Rd:184: file link 'SummarizedExperiment' in package 'SummarizedExperiment' does not exist and so has been treated as a topic
Rd warning: C:/Users/bioctesting/bbs-3.11-bioc-testing/tmpdir/RtmpABIAiU/R.INSTALLcdc7b04899/GenomeInfoDb/man/seqinfo.Rd:186: file link 'GAlignments' in package 'GenomicAlignments' does not exist and so has been treated as a topic
Rd warning: C:/Users/bioctesting/bbs-3.11-bioc-testing/tmpdir/RtmpABIAiU/R.INSTALLcdc7b04899/GenomeInfoDb/man/seqinfo.Rd:187: file link 'GAlignmentPairs' in package 'GenomicAlignments' does not exist and so has been treated as a topic
Rd warning: C:/Users/bioctesting/bbs-3.11-bioc-testing/tmpdir/RtmpABIAiU/R.INSTALLcdc7b04899/GenomeInfoDb/man/seqinfo.Rd:188: file link 'GAlignmentsList' in package 'GenomicAlignments' does not exist and so has been treated as a topic
Rd warning: C:/Users/bioctesting/bbs-3.11-bioc-testing/tmpdir/RtmpABIAiU/R.INSTALLcdc7b04899/GenomeInfoDb/man/seqinfo.Rd:190: file link 'TxDb' in package 'GenomicFeatures' does not exist and so has been treated as a topic
Rd warning: C:/Users/bioctesting/bbs-3.11-bioc-testing/tmpdir/RtmpABIAiU/R.INSTALLcdc7b04899/GenomeInfoDb/man/seqinfo.Rd:192: file link 'BSgenome' in package 'BSgenome' does not exist and so has been treated as a topic
Rd warning: C:/Users/bioctesting/bbs-3.11-bioc-testing/tmpdir/RtmpABIAiU/R.INSTALLcdc7b04899/GenomeInfoDb/man/seqinfo.Rd:226: file link 'GRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/bioctesting/bbs-3.11-bioc-testing/tmpdir/RtmpABIAiU/R.INSTALLcdc7b04899/GenomeInfoDb/man/seqinfo.Rd:226: file link 'GRangesList' in package 'GenomicRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/bioctesting/bbs-3.11-bioc-testing/tmpdir/RtmpABIAiU/R.INSTALLcdc7b04899/GenomeInfoDb/man/seqinfo.Rd:229: file link 'SummarizedExperiment' in package 'SummarizedExperiment' does not exist and so has been treated as a topic
Rd warning: C:/Users/bioctesting/bbs-3.11-bioc-testing/tmpdir/RtmpABIAiU/R.INSTALLcdc7b04899/GenomeInfoDb/man/seqinfo.Rd:232: file link 'GAlignments' in package 'GenomicAlignments' does not exist and so has been treated as a topic
Rd warning: C:/Users/bioctesting/bbs-3.11-bioc-testing/tmpdir/RtmpABIAiU/R.INSTALLcdc7b04899/GenomeInfoDb/man/seqinfo.Rd:233: file link 'GAlignmentPairs' in package 'GenomicAlignments' does not exist and so has been treated as a topic
Rd warning: C:/Users/bioctesting/bbs-3.11-bioc-testing/tmpdir/RtmpABIAiU/R.INSTALLcdc7b04899/GenomeInfoDb/man/seqinfo.Rd:234: file link 'GAlignmentsList' in package 'GenomicAlignments' does not exist and so has been treated as a topic
Rd warning: C:/Users/bioctesting/bbs-3.11-bioc-testing/tmpdir/RtmpABIAiU/R.INSTALLcdc7b04899/GenomeInfoDb/man/seqinfo.Rd:237: file link 'TxDb' in package 'GenomicFeatures' does not exist and so has been treated as a topic
Rd warning: C:/Users/bioctesting/bbs-3.11-bioc-testing/tmpdir/RtmpABIAiU/R.INSTALLcdc7b04899/GenomeInfoDb/man/seqinfo.Rd:240: file link 'BSgenome' in package 'BSgenome' does not exist and so has been treated as a topic
    seqlevels-wrappers                      html  
    seqlevelsStyle                          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 'GenomeInfoDb' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'GenomeInfoDb' as GenomeInfoDb_1.23.17.zip
* DONE (GenomeInfoDb)
* installing to library 'C:/Users/bioctesting/bbs-3.11-bioc-testing/R/library'
package 'GenomeInfoDb' successfully unpacked and MD5 sums checked