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

CHECK 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:\Users\bioctesting\bbs-3.11-bioc-testing\R\bin\R.exe CMD check --force-multiarch --install=check:GenomeInfoDb.install-out.txt --library=C:\Users\bioctesting\bbs-3.11-bioc-testing\R\library --no-vignettes --timings GenomeInfoDb_1.23.17.tar.gz
StartedAt: 2020-04-14 20:47:15 -0400 (Tue, 14 Apr 2020)
EndedAt: 2020-04-14 20:54:39 -0400 (Tue, 14 Apr 2020)
EllapsedTime: 444.5 seconds
RetCode: 0
Status:  WARNINGS  
CheckDir: GenomeInfoDb.Rcheck
Warnings: 1

Command output

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###
### Running command:
###
###   C:\Users\bioctesting\bbs-3.11-bioc-testing\R\bin\R.exe CMD check --force-multiarch --install=check:GenomeInfoDb.install-out.txt --library=C:\Users\bioctesting\bbs-3.11-bioc-testing\R\library --no-vignettes --timings GenomeInfoDb_1.23.17.tar.gz
###
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* using log directory 'C:/Users/bioctesting/bbs-3.11-bioc-testing/meat/GenomeInfoDb.Rcheck'
* using R version 4.0.0 alpha (Rtools40) (2020-03-31 r78116)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'GenomeInfoDb/DESCRIPTION' ... OK
* this is package 'GenomeInfoDb' version '1.23.17'
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking whether package 'GenomeInfoDb' can be installed ... WARNING
Found the following significant warnings:
  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
  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
  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
  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
See 'C:/Users/bioctesting/bbs-3.11-bioc-testing/meat/GenomeInfoDb.Rcheck/00install.out' for details.
* checking installed package size ... OK
* checking package directory ... OK
* checking 'build' directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* loading checks for arch 'i386'
** checking whether the package can be loaded ... OK
** checking whether the package can be loaded with stated dependencies ... OK
** checking whether the package can be unloaded cleanly ... OK
** checking whether the namespace can be loaded with stated dependencies ... OK
** checking whether the namespace can be unloaded cleanly ... OK
* loading checks for arch 'x64'
** checking whether the package can be loaded ... OK
** checking whether the package can be loaded with stated dependencies ... OK
** checking whether the package can be unloaded cleanly ... OK
** checking whether the namespace can be loaded with stated dependencies ... OK
** checking whether the namespace can be unloaded cleanly ... OK
* checking dependencies in R code ... NOTE
Unexported object imported by a ':::' call: 'utils:::.roman2numeric'
  See the note in ?`:::` about the use of this operator.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
Examples with CPU (user + system) or elapsed time > 5s
                        user system elapsed
loadTaxonomyDb          9.94   0.34   10.70
GenomeDescription-class 7.42   0.52   14.16
seqinfo                 6.20   0.97   20.89
seqlevels-wrappers      4.53   0.79    5.36
getChromInfoFromUCSC    1.20   0.52    9.75
getChromInfoFromEnsembl 1.05   0.33   27.57
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
                        user system elapsed
loadTaxonomyDb          8.58   0.15    8.80
GenomeDescription-class 6.31   0.14    6.45
seqinfo                 5.63   0.27    5.89
getChromInfoFromEnsembl 1.03   0.16   19.45
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
  Running 'run_unitTests.R'
 OK
** running tests for arch 'x64' ...
  Running 'run_unitTests.R'
 OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in 'inst/doc' ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 1 WARNING, 1 NOTE
See
  'C:/Users/bioctesting/bbs-3.11-bioc-testing/meat/GenomeInfoDb.Rcheck/00check.log'
for details.

Installation output

GenomeInfoDb.Rcheck/00install.out

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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

Tests output

GenomeInfoDb.Rcheck/tests_i386/run_unitTests.Rout


R version 4.0.0 alpha (Rtools40) (2020-03-31 r78116) -- "Blame Jeroen"
Copyright (C) 2020 The R Foundation for Statistical Computing
Platform: i386-w64-mingw32/i386 (32-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> require("GenomeInfoDb") || stop("unable to load GenomeInfoDb package")
Loading required package: GenomeInfoDb
Loading required package: BiocGenerics
Loading required package: parallel

Attaching package: 'BiocGenerics'

The following objects are masked from 'package:parallel':

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
    clusterExport, clusterMap, parApply, parCapply, parLapply,
    parLapplyLB, parRapply, parSapply, parSapplyLB

The following objects are masked from 'package:stats':

    IQR, mad, sd, var, xtabs

The following objects are masked from 'package:base':

    Filter, Find, Map, Position, Reduce, anyDuplicated, append,
    as.data.frame, basename, cbind, colnames, dirname, do.call,
    duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
    lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin,
    pmin.int, rank, rbind, rownames, sapply, setdiff, sort, table,
    tapply, union, unique, unsplit, which, which.max, which.min

Loading required package: S4Vectors
Loading required package: stats4

Attaching package: 'S4Vectors'

The following object is masked from 'package:base':

    expand.grid

Loading required package: IRanges

Attaching package: 'IRanges'

The following object is masked from 'package:grDevices':

    windows

[1] TRUE
> GenomeInfoDb:::.test()


RUNIT TEST PROTOCOL -- Tue Apr 14 20:54:30 2020 
*********************************************** 
Number of test functions: 20 
Number of errors: 0 
Number of failures: 0 

 
1 Test Suite : 
GenomeInfoDb RUnit Tests - 20 test functions, 0 errors, 0 failures
Number of test functions: 20 
Number of errors: 0 
Number of failures: 0 
> 
> proc.time()
   user  system elapsed 
   6.01    0.34    6.48

GenomeInfoDb.Rcheck/tests_x64/run_unitTests.Rout


R version 4.0.0 alpha (Rtools40) (2020-03-31 r78116) -- "Blame Jeroen"
Copyright (C) 2020 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64 (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> require("GenomeInfoDb") || stop("unable to load GenomeInfoDb package")
Loading required package: GenomeInfoDb
Loading required package: BiocGenerics
Loading required package: parallel

Attaching package: 'BiocGenerics'

The following objects are masked from 'package:parallel':

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
    clusterExport, clusterMap, parApply, parCapply, parLapply,
    parLapplyLB, parRapply, parSapply, parSapplyLB

The following objects are masked from 'package:stats':

    IQR, mad, sd, var, xtabs

The following objects are masked from 'package:base':

    Filter, Find, Map, Position, Reduce, anyDuplicated, append,
    as.data.frame, basename, cbind, colnames, dirname, do.call,
    duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
    lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin,
    pmin.int, rank, rbind, rownames, sapply, setdiff, sort, table,
    tapply, union, unique, unsplit, which, which.max, which.min

Loading required package: S4Vectors
Loading required package: stats4

Attaching package: 'S4Vectors'

The following object is masked from 'package:base':

    expand.grid

Loading required package: IRanges

Attaching package: 'IRanges'

The following object is masked from 'package:grDevices':

    windows

[1] TRUE
> GenomeInfoDb:::.test()


RUNIT TEST PROTOCOL -- Tue Apr 14 20:54:37 2020 
*********************************************** 
Number of test functions: 20 
Number of errors: 0 
Number of failures: 0 

 
1 Test Suite : 
GenomeInfoDb RUnit Tests - 20 test functions, 0 errors, 0 failures
Number of test functions: 20 
Number of errors: 0 
Number of failures: 0 
> 
> proc.time()
   user  system elapsed 
   6.50    0.28    6.76

Example timings

GenomeInfoDb.Rcheck/examples_i386/GenomeInfoDb-Ex.timings

nameusersystemelapsed
GenomeDescription-class 7.42 0.5214.16
Seqinfo-class0.340.090.48
fetchExtendedChromInfoFromUCSC000
getChromInfoFromEnsembl 1.05 0.3327.57
getChromInfoFromNCBI0.750.504.32
getChromInfoFromUCSC1.200.529.75
loadTaxonomyDb 9.94 0.3410.70
mapGenomeBuilds0.030.020.08
rankSeqlevels0.080.060.61
seqinfo 6.20 0.9720.89
seqlevels-wrappers4.530.795.36
seqlevelsStyle0.500.120.63

GenomeInfoDb.Rcheck/examples_x64/GenomeInfoDb-Ex.timings

nameusersystemelapsed
GenomeDescription-class6.310.146.45
Seqinfo-class0.190.020.22
fetchExtendedChromInfoFromUCSC000
getChromInfoFromEnsembl 1.03 0.1619.45
getChromInfoFromNCBI1.610.394.40
getChromInfoFromUCSC1.130.173.16
loadTaxonomyDb8.580.158.80
mapGenomeBuilds0.040.020.06
rankSeqlevels0.100.030.13
seqinfo5.630.275.89
seqlevels-wrappers4.030.234.26
seqlevelsStyle0.440.050.49