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CHECK report for GenomeInfoDb on tokay2

This page was generated on 2018-10-17 08:38:08 -0400 (Wed, 17 Oct 2018).

Package 589/1561HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
GenomeInfoDb 1.16.0
Bioconductor Package Maintainer
Snapshot Date: 2018-10-15 16:45:08 -0400 (Mon, 15 Oct 2018)
URL: https://git.bioconductor.org/packages/GenomeInfoDb
Branch: RELEASE_3_7
Last Commit: 6543dad
Last Changed Date: 2018-04-30 10:35:32 -0400 (Mon, 30 Apr 2018)
malbec2 Linux (Ubuntu 16.04.1 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  OK  OK [ WARNINGS ] OK UNNEEDED, same version exists in internal repository
merida2 OS X 10.11.6 El Capitan / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: GenomeInfoDb
Version: 1.16.0
Command: C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:GenomeInfoDb.install-out.txt --library=C:\Users\biocbuild\bbs-3.7-bioc\R\library --no-vignettes --timings GenomeInfoDb_1.16.0.tar.gz
StartedAt: 2018-10-17 02:14:53 -0400 (Wed, 17 Oct 2018)
EndedAt: 2018-10-17 02:18:38 -0400 (Wed, 17 Oct 2018)
EllapsedTime: 224.5 seconds
RetCode: 0
Status:  WARNINGS  
CheckDir: GenomeInfoDb.Rcheck
Warnings: 1

Command output

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###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:GenomeInfoDb.install-out.txt --library=C:\Users\biocbuild\bbs-3.7-bioc\R\library --no-vignettes --timings GenomeInfoDb_1.16.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.7-bioc/meat/GenomeInfoDb.Rcheck'
* using R version 3.5.1 Patched (2018-07-24 r75005)
* 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 '1.16.0'
* 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/biocbuild/bbs-3.7-bioc/tmpdir/RtmpUx8pHI/R.INSTALLf481b097867/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/biocbuild/bbs-3.7-bioc/tmpdir/RtmpUx8pHI/R.INSTALLf481b097867/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/biocbuild/bbs-3.7-bioc/tmpdir/RtmpUx8pHI/R.INSTALLf481b097867/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/biocbuild/bbs-3.7-bioc/tmpdir/RtmpUx8pHI/R.INSTALLf481b097867/GenomeInfoDb/man/fetchExtendedChromInfoFromUCSC.Rd:130: file link 'getBSgenome' in package 'BSgenome' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpUx8pHI/R.INSTALLf481b097867/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/biocbuild/bbs-3.7-bioc/tmpdir/RtmpUx8pHI/R.INSTALLf481b097867/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/biocbuild/bbs-3.7-bioc/tmpdir/RtmpUx8pHI/R.INSTALLf481b097867/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/biocbuild/bbs-3.7-bioc/tmpdir/RtmpUx8pHI/R.INSTALLf481b097867/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/biocbuild/bbs-3.7-bioc/tmpdir/RtmpUx8pHI/R.INSTALLf481b097867/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/biocbuild/bbs-3.7-bioc/tmpdir/RtmpUx8pHI/R.INSTALLf481b097867/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/biocbuild/bbs-3.7-bioc/tmpdir/RtmpUx8pHI/R.INSTALLf481b097867/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/biocbuild/bbs-3.7-bioc/tmpdir/RtmpUx8pHI/R.INSTALLf481b097867/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/biocbuild/bbs-3.7-bioc/tmpdir/RtmpUx8pHI/R.INSTALLf481b097867/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/biocbuild/bbs-3.7-bioc/tmpdir/RtmpUx8pHI/R.INSTALLf481b097867/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/biocbuild/bbs-3.7-bioc/tmpdir/RtmpUx8pHI/R.INSTALLf481b097867/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/biocbuild/bbs-3.7-bioc/tmpdir/RtmpUx8pHI/R.INSTALLf481b097867/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/biocbuild/bbs-3.7-bioc/tmpdir/RtmpUx8pHI/R.INSTALLf481b097867/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/biocbuild/bbs-3.7-bioc/tmpdir/RtmpUx8pHI/R.INSTALLf481b097867/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/biocbuild/bbs-3.7-bioc/tmpdir/RtmpUx8pHI/R.INSTALLf481b097867/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/biocbuild/bbs-3.7-bioc/tmpdir/RtmpUx8pHI/R.INSTALLf481b097867/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/biocbuild/bbs-3.7-bioc/tmpdir/RtmpUx8pHI/R.INSTALLf481b097867/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/biocbuild/bbs-3.7-bioc/tmpdir/RtmpUx8pHI/R.INSTALLf481b097867/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/biocbuild/bbs-3.7-bioc/tmpdir/RtmpUx8pHI/R.INSTALLf481b097867/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/biocbuild/bbs-3.7-bioc/tmpdir/RtmpUx8pHI/R.INSTALLf481b097867/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/biocbuild/bbs-3.7-bioc/tmpdir/RtmpUx8pHI/R.INSTALLf481b097867/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/biocbuild/bbs-3.7-bioc/tmpdir/RtmpUx8pHI/R.INSTALLf481b097867/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/biocbuild/bbs-3.7-bioc/tmpdir/RtmpUx8pHI/R.INSTALLf481b097867/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/biocbuild/bbs-3.7-bioc/tmpdir/RtmpUx8pHI/R.INSTALLf481b097867/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/biocbuild/bbs-3.7-bioc/tmpdir/RtmpUx8pHI/R.INSTALLf481b097867/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/biocbuild/bbs-3.7-bioc/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 or elapsed time > 5s
                         user system elapsed
seqlevels-wrappers      21.90   0.14   22.05
seqinfo                 18.64   0.98   19.63
loadTaxonomyDb           6.34   0.75    7.12
GenomeDescription-class  5.14   0.47    5.61
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
                                user system elapsed
seqinfo                        23.00   0.33   23.33
seqlevels-wrappers             22.30   0.19   22.48
GenomeDescription-class         7.47   0.32    7.78
loadTaxonomyDb                  6.93   0.13    7.07
fetchExtendedChromInfoFromUCSC  2.39   1.01    5.46
* 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/biocbuild/bbs-3.7-bioc/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/3.7/bioc/src/contrib/GenomeInfoDb_1.16.0.tar.gz && rm -rf GenomeInfoDb.buildbin-libdir && mkdir GenomeInfoDb.buildbin-libdir && C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=GenomeInfoDb.buildbin-libdir GenomeInfoDb_1.16.0.tar.gz && C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD INSTALL GenomeInfoDb_1.16.0.zip && rm GenomeInfoDb_1.16.0.tar.gz GenomeInfoDb_1.16.0.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 3030k  100 3030k    0     0  36.6M      0 --:--:-- --:--:-- --:--:-- 40.5M

install for i386

* installing *source* package 'GenomeInfoDb' ...
** 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/biocbuild/bbs-3.7-bioc/tmpdir/RtmpUx8pHI/R.INSTALLf481b097867/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/biocbuild/bbs-3.7-bioc/tmpdir/RtmpUx8pHI/R.INSTALLf481b097867/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/biocbuild/bbs-3.7-bioc/tmpdir/RtmpUx8pHI/R.INSTALLf481b097867/GenomeInfoDb/man/GenomeDescription-class.Rd:126: file link 'BSgenome' in package 'BSgenome' does not exist and so has been treated as a topic
    Seqinfo-class                           html  
    fetchExtendedChromInfoFromUCSC          html  
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpUx8pHI/R.INSTALLf481b097867/GenomeInfoDb/man/fetchExtendedChromInfoFromUCSC.Rd:130: file link 'getBSgenome' 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/biocbuild/bbs-3.7-bioc/tmpdir/RtmpUx8pHI/R.INSTALLf481b097867/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/biocbuild/bbs-3.7-bioc/tmpdir/RtmpUx8pHI/R.INSTALLf481b097867/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/biocbuild/bbs-3.7-bioc/tmpdir/RtmpUx8pHI/R.INSTALLf481b097867/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/biocbuild/bbs-3.7-bioc/tmpdir/RtmpUx8pHI/R.INSTALLf481b097867/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/biocbuild/bbs-3.7-bioc/tmpdir/RtmpUx8pHI/R.INSTALLf481b097867/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/biocbuild/bbs-3.7-bioc/tmpdir/RtmpUx8pHI/R.INSTALLf481b097867/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/biocbuild/bbs-3.7-bioc/tmpdir/RtmpUx8pHI/R.INSTALLf481b097867/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/biocbuild/bbs-3.7-bioc/tmpdir/RtmpUx8pHI/R.INSTALLf481b097867/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/biocbuild/bbs-3.7-bioc/tmpdir/RtmpUx8pHI/R.INSTALLf481b097867/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/biocbuild/bbs-3.7-bioc/tmpdir/RtmpUx8pHI/R.INSTALLf481b097867/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/biocbuild/bbs-3.7-bioc/tmpdir/RtmpUx8pHI/R.INSTALLf481b097867/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/biocbuild/bbs-3.7-bioc/tmpdir/RtmpUx8pHI/R.INSTALLf481b097867/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/biocbuild/bbs-3.7-bioc/tmpdir/RtmpUx8pHI/R.INSTALLf481b097867/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/biocbuild/bbs-3.7-bioc/tmpdir/RtmpUx8pHI/R.INSTALLf481b097867/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/biocbuild/bbs-3.7-bioc/tmpdir/RtmpUx8pHI/R.INSTALLf481b097867/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/biocbuild/bbs-3.7-bioc/tmpdir/RtmpUx8pHI/R.INSTALLf481b097867/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/biocbuild/bbs-3.7-bioc/tmpdir/RtmpUx8pHI/R.INSTALLf481b097867/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/biocbuild/bbs-3.7-bioc/tmpdir/RtmpUx8pHI/R.INSTALLf481b097867/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/biocbuild/bbs-3.7-bioc/tmpdir/RtmpUx8pHI/R.INSTALLf481b097867/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/biocbuild/bbs-3.7-bioc/tmpdir/RtmpUx8pHI/R.INSTALLf481b097867/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/biocbuild/bbs-3.7-bioc/tmpdir/RtmpUx8pHI/R.INSTALLf481b097867/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/biocbuild/bbs-3.7-bioc/tmpdir/RtmpUx8pHI/R.INSTALLf481b097867/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/biocbuild/bbs-3.7-bioc/tmpdir/RtmpUx8pHI/R.INSTALLf481b097867/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/biocbuild/bbs-3.7-bioc/tmpdir/RtmpUx8pHI/R.INSTALLf481b097867/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/biocbuild/bbs-3.7-bioc/tmpdir/RtmpUx8pHI/R.INSTALLf481b097867/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
In R CMD INSTALL

install for x64

* installing *source* package 'GenomeInfoDb' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'GenomeInfoDb' as GenomeInfoDb_1.16.0.zip
* DONE (GenomeInfoDb)
In R CMD INSTALL
In R CMD INSTALL
* installing to library 'C:/Users/biocbuild/bbs-3.7-bioc/R/library'
package 'GenomeInfoDb' successfully unpacked and MD5 sums checked
In R CMD INSTALL

Tests output

GenomeInfoDb.Rcheck/tests_i386/run_unitTests.Rout


R version 3.5.1 Patched (2018-07-24 r75005) -- "Feather Spray"
Copyright (C) 2018 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, colMeans, colSums, colnames,
    dirname, do.call, duplicated, eval, evalq, get, grep, grepl,
    intersect, is.unsorted, lapply, lengths, mapply, match, mget,
    order, paste, pmax, pmax.int, pmin, pmin.int, rank, rbind,
    rowMeans, rowSums, 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 -- Wed Oct 17 02:18:25 2018 
*********************************************** 
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 
Warning messages:
1: In .Seqinfo.mergexy(x, y) :
  Each of the 2 combined objects has sequence levels not in the other:
  - in 'x': chr1, chr2
  - in 'y': chr4
  Make sure to always combine/compare objects based on the same reference
  genome (use suppressWarnings() to suppress this warning).
2: 'organism' not found: nothere 
3: 'organism' not found: nothere 
4: 'genome' not found: nothere 
5: 'genome' not found: nothere 
> 
> proc.time()
   user  system elapsed 
   6.23    0.40    6.67

GenomeInfoDb.Rcheck/tests_x64/run_unitTests.Rout


R version 3.5.1 Patched (2018-07-24 r75005) -- "Feather Spray"
Copyright (C) 2018 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, colMeans, colSums, colnames,
    dirname, do.call, duplicated, eval, evalq, get, grep, grepl,
    intersect, is.unsorted, lapply, lengths, mapply, match, mget,
    order, paste, pmax, pmax.int, pmin, pmin.int, rank, rbind,
    rowMeans, rowSums, 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 -- Wed Oct 17 02:18:32 2018 
*********************************************** 
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 
Warning messages:
1: In .Seqinfo.mergexy(x, y) :
  Each of the 2 combined objects has sequence levels not in the other:
  - in 'x': chr1, chr2
  - in 'y': chr4
  Make sure to always combine/compare objects based on the same reference
  genome (use suppressWarnings() to suppress this warning).
2: 'organism' not found: nothere 
3: 'organism' not found: nothere 
4: 'genome' not found: nothere 
5: 'genome' not found: nothere 
> 
> proc.time()
   user  system elapsed 
   6.12    0.29    6.42

Example timings

GenomeInfoDb.Rcheck/examples_i386/GenomeInfoDb-Ex.timings

nameusersystemelapsed
GenomeDescription-class5.140.475.61
Seqinfo-class0.050.000.04
fetchExtendedChromInfoFromUCSC1.861.224.91
loadTaxonomyDb6.340.757.12
mapGenomeBuilds0.030.000.03
rankSeqlevels0.140.000.14
seqinfo18.64 0.9819.63
seqlevels-wrappers21.90 0.1422.05
seqlevelsStyle0.480.000.49

GenomeInfoDb.Rcheck/examples_x64/GenomeInfoDb-Ex.timings

nameusersystemelapsed
GenomeDescription-class7.470.327.78
Seqinfo-class0.080.000.08
fetchExtendedChromInfoFromUCSC2.391.015.46
loadTaxonomyDb6.930.137.07
mapGenomeBuilds0.130.010.15
rankSeqlevels0.120.000.12
seqinfo23.00 0.3323.33
seqlevels-wrappers22.30 0.1922.48
seqlevelsStyle0.380.080.46