Back to Multiple platform build/check report for BioC 3.6
ABCDEF[G]HIJKLMNOPQRSTUVWXYZ

CHECK report for GenomeInfoDb on tokay1

This page was generated on 2018-04-12 13:23:46 -0400 (Thu, 12 Apr 2018).

Package 559/1472HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
GenomeInfoDb 1.14.0
Bioconductor Package Maintainer
Snapshot Date: 2018-04-11 16:45:18 -0400 (Wed, 11 Apr 2018)
URL: https://git.bioconductor.org/packages/GenomeInfoDb
Branch: RELEASE_3_6
Last Commit: 4978308
Last Changed Date: 2017-10-30 12:40:11 -0400 (Mon, 30 Oct 2017)
malbec1 Linux (Ubuntu 16.04.1 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
tokay1 Windows Server 2012 R2 Standard / x64  OK  OK [ WARNINGS ] OK UNNEEDED, same version exists in internal repository
veracruz1 OS X 10.11.6 El Capitan / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: GenomeInfoDb
Version: 1.14.0
Command: rm -rf GenomeInfoDb.buildbin-libdir GenomeInfoDb.Rcheck && mkdir GenomeInfoDb.buildbin-libdir GenomeInfoDb.Rcheck && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=GenomeInfoDb.buildbin-libdir GenomeInfoDb_1.14.0.tar.gz >GenomeInfoDb.Rcheck\00install.out 2>&1 && cp GenomeInfoDb.Rcheck\00install.out GenomeInfoDb-install.out && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD check --library=GenomeInfoDb.buildbin-libdir --install="check:GenomeInfoDb-install.out" --force-multiarch --no-vignettes --timings GenomeInfoDb_1.14.0.tar.gz
StartedAt: 2018-04-12 00:16:53 -0400 (Thu, 12 Apr 2018)
EndedAt: 2018-04-12 00:20:44 -0400 (Thu, 12 Apr 2018)
EllapsedTime: 231.1 seconds
RetCode: 0
Status:  WARNINGS  
CheckDir: GenomeInfoDb.Rcheck
Warnings: 1

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   rm -rf GenomeInfoDb.buildbin-libdir GenomeInfoDb.Rcheck && mkdir GenomeInfoDb.buildbin-libdir GenomeInfoDb.Rcheck && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=GenomeInfoDb.buildbin-libdir GenomeInfoDb_1.14.0.tar.gz >GenomeInfoDb.Rcheck\00install.out 2>&1 && cp GenomeInfoDb.Rcheck\00install.out GenomeInfoDb-install.out  &&  C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD check --library=GenomeInfoDb.buildbin-libdir --install="check:GenomeInfoDb-install.out" --force-multiarch --no-vignettes --timings GenomeInfoDb_1.14.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.6-bioc/meat/GenomeInfoDb.Rcheck'
* using R version 3.4.4 (2018-03-15)
* 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 '1.14.0'
* 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-3.6-bioc/tmpdir/Rtmp2pUE1A/R.INSTALL18b013376054/GenomeInfoDb/man/GenomeDescription-class.Rd:45: missing file link 'BSgenome'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmp2pUE1A/R.INSTALL18b013376054/GenomeInfoDb/man/GenomeDescription-class.Rd:46: missing file link 'BSgenome'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmp2pUE1A/R.INSTALL18b013376054/GenomeInfoDb/man/GenomeDescription-class.Rd:126: missing file link 'BSgenome'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmp2pUE1A/R.INSTALL18b013376054/GenomeInfoDb/man/fetchExtendedChromInfoFromUCSC.Rd:130: missing file link 'getBSgenome'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmp2pUE1A/R.INSTALL18b013376054/GenomeInfoDb/man/seqinfo.Rd:82: missing file link 'GRanges'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmp2pUE1A/R.INSTALL18b013376054/GenomeInfoDb/man/seqinfo.Rd:105: missing file link 'GRangesList'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmp2pUE1A/R.INSTALL18b013376054/GenomeInfoDb/man/seqinfo.Rd:106: missing file link 'GAlignmentPairs'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmp2pUE1A/R.INSTALL18b013376054/GenomeInfoDb/man/seqinfo.Rd:107: missing file link 'GAlignmentsList'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmp2pUE1A/R.INSTALL18b013376054/GenomeInfoDb/man/seqinfo.Rd:116: missing file link 'GRangesList'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmp2pUE1A/R.INSTALL18b013376054/GenomeInfoDb/man/seqinfo.Rd:118: missing file link 'exonsBy'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmp2pUE1A/R.INSTALL18b013376054/GenomeInfoDb/man/seqinfo.Rd:131: missing file link 'GRangesList'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmp2pUE1A/R.INSTALL18b013376054/GenomeInfoDb/man/seqinfo.Rd:136: missing file link 'GRanges'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmp2pUE1A/R.INSTALL18b013376054/GenomeInfoDb/man/seqinfo.Rd:137: missing file link 'GAlignments'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmp2pUE1A/R.INSTALL18b013376054/GenomeInfoDb/man/seqinfo.Rd:182: missing file link 'GRanges'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmp2pUE1A/R.INSTALL18b013376054/GenomeInfoDb/man/seqinfo.Rd:182: missing file link 'GRangesList'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmp2pUE1A/R.INSTALL18b013376054/GenomeInfoDb/man/seqinfo.Rd:184: missing file link 'SummarizedExperiment'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmp2pUE1A/R.INSTALL18b013376054/GenomeInfoDb/man/seqinfo.Rd:186: missing file link 'GAlignments'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmp2pUE1A/R.INSTALL18b013376054/GenomeInfoDb/man/seqinfo.Rd:187: missing file link 'GAlignmentPairs'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmp2pUE1A/R.INSTALL18b013376054/GenomeInfoDb/man/seqinfo.Rd:188: missing file link 'GAlignmentsList'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmp2pUE1A/R.INSTALL18b013376054/GenomeInfoDb/man/seqinfo.Rd:190: missing file link 'TxDb'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmp2pUE1A/R.INSTALL18b013376054/GenomeInfoDb/man/seqinfo.Rd:192: missing file link 'BSgenome'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmp2pUE1A/R.INSTALL18b013376054/GenomeInfoDb/man/seqinfo.Rd:227: missing file link 'GRanges'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmp2pUE1A/R.INSTALL18b013376054/GenomeInfoDb/man/seqinfo.Rd:227: missing file link 'GRangesList'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmp2pUE1A/R.INSTALL18b013376054/GenomeInfoDb/man/seqinfo.Rd:230: missing file link 'SummarizedExperiment'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmp2pUE1A/R.INSTALL18b013376054/GenomeInfoDb/man/seqinfo.Rd:233: missing file link 'GAlignments'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmp2pUE1A/R.INSTALL18b013376054/GenomeInfoDb/man/seqinfo.Rd:234: missing file link 'GAlignmentPairs'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmp2pUE1A/R.INSTALL18b013376054/GenomeInfoDb/man/seqinfo.Rd:235: missing file link 'GAlignmentsList'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmp2pUE1A/R.INSTALL18b013376054/GenomeInfoDb/man/seqinfo.Rd:238: missing file link 'TxDb'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmp2pUE1A/R.INSTALL18b013376054/GenomeInfoDb/man/seqinfo.Rd:241: missing file link 'BSgenome'
See 'C:/Users/biocbuild/bbs-3.6-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 ... NOTE
.getTaxonomyId: no visible binding for global variable 'speciesMap'
.lookupSpeciesFromTaxId: no visible binding for global variable
  'specData'
available.species: no visible binding for global variable 'speciesMap'
Undefined global functions or variables:
  specData speciesMap
* 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 installed files from 'inst/doc' ... OK
* checking files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
Examples with CPU or elapsed time > 5s
                         user system elapsed
seqinfo                 14.74   0.14   22.31
seqlevels-wrappers      13.91   0.11   14.02
available.species       10.64   0.46   11.09
GenomeDescription-class  5.06   0.27    5.33
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
                         user system elapsed
seqlevels-wrappers      18.60   0.14   18.73
seqinfo                 17.55   0.03   17.59
available.species        8.83   0.08    8.91
GenomeDescription-class  5.86   0.15    6.01
* 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, 2 NOTEs
See
  'C:/Users/biocbuild/bbs-3.6-bioc/meat/GenomeInfoDb.Rcheck/00check.log'
for details.

Installation output

GenomeInfoDb.Rcheck/00install.out


install for i386

* installing *source* package 'GenomeInfoDb' ...
** R
** inst
** preparing 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-3.6-bioc/tmpdir/Rtmp2pUE1A/R.INSTALL18b013376054/GenomeInfoDb/man/GenomeDescription-class.Rd:45: missing file link 'BSgenome'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmp2pUE1A/R.INSTALL18b013376054/GenomeInfoDb/man/GenomeDescription-class.Rd:46: missing file link 'BSgenome'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmp2pUE1A/R.INSTALL18b013376054/GenomeInfoDb/man/GenomeDescription-class.Rd:126: missing file link 'BSgenome'
    Seqinfo-class                           html  
    available.species                       html  
    fetchExtendedChromInfoFromUCSC          html  
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmp2pUE1A/R.INSTALL18b013376054/GenomeInfoDb/man/fetchExtendedChromInfoFromUCSC.Rd:130: missing file link 'getBSgenome'
    mapGenomeBuilds                         html  
    rankSeqlevels                           html  
    seqinfo                                 html  
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmp2pUE1A/R.INSTALL18b013376054/GenomeInfoDb/man/seqinfo.Rd:82: missing file link 'GRanges'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmp2pUE1A/R.INSTALL18b013376054/GenomeInfoDb/man/seqinfo.Rd:105: missing file link 'GRangesList'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmp2pUE1A/R.INSTALL18b013376054/GenomeInfoDb/man/seqinfo.Rd:106: missing file link 'GAlignmentPairs'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmp2pUE1A/R.INSTALL18b013376054/GenomeInfoDb/man/seqinfo.Rd:107: missing file link 'GAlignmentsList'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmp2pUE1A/R.INSTALL18b013376054/GenomeInfoDb/man/seqinfo.Rd:116: missing file link 'GRangesList'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmp2pUE1A/R.INSTALL18b013376054/GenomeInfoDb/man/seqinfo.Rd:118: missing file link 'exonsBy'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmp2pUE1A/R.INSTALL18b013376054/GenomeInfoDb/man/seqinfo.Rd:131: missing file link 'GRangesList'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmp2pUE1A/R.INSTALL18b013376054/GenomeInfoDb/man/seqinfo.Rd:136: missing file link 'GRanges'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmp2pUE1A/R.INSTALL18b013376054/GenomeInfoDb/man/seqinfo.Rd:137: missing file link 'GAlignments'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmp2pUE1A/R.INSTALL18b013376054/GenomeInfoDb/man/seqinfo.Rd:182: missing file link 'GRanges'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmp2pUE1A/R.INSTALL18b013376054/GenomeInfoDb/man/seqinfo.Rd:182: missing file link 'GRangesList'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmp2pUE1A/R.INSTALL18b013376054/GenomeInfoDb/man/seqinfo.Rd:184: missing file link 'SummarizedExperiment'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmp2pUE1A/R.INSTALL18b013376054/GenomeInfoDb/man/seqinfo.Rd:186: missing file link 'GAlignments'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmp2pUE1A/R.INSTALL18b013376054/GenomeInfoDb/man/seqinfo.Rd:187: missing file link 'GAlignmentPairs'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmp2pUE1A/R.INSTALL18b013376054/GenomeInfoDb/man/seqinfo.Rd:188: missing file link 'GAlignmentsList'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmp2pUE1A/R.INSTALL18b013376054/GenomeInfoDb/man/seqinfo.Rd:190: missing file link 'TxDb'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmp2pUE1A/R.INSTALL18b013376054/GenomeInfoDb/man/seqinfo.Rd:192: missing file link 'BSgenome'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmp2pUE1A/R.INSTALL18b013376054/GenomeInfoDb/man/seqinfo.Rd:227: missing file link 'GRanges'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmp2pUE1A/R.INSTALL18b013376054/GenomeInfoDb/man/seqinfo.Rd:227: missing file link 'GRangesList'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmp2pUE1A/R.INSTALL18b013376054/GenomeInfoDb/man/seqinfo.Rd:230: missing file link 'SummarizedExperiment'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmp2pUE1A/R.INSTALL18b013376054/GenomeInfoDb/man/seqinfo.Rd:233: missing file link 'GAlignments'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmp2pUE1A/R.INSTALL18b013376054/GenomeInfoDb/man/seqinfo.Rd:234: missing file link 'GAlignmentPairs'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmp2pUE1A/R.INSTALL18b013376054/GenomeInfoDb/man/seqinfo.Rd:235: missing file link 'GAlignmentsList'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmp2pUE1A/R.INSTALL18b013376054/GenomeInfoDb/man/seqinfo.Rd:238: missing file link 'TxDb'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmp2pUE1A/R.INSTALL18b013376054/GenomeInfoDb/man/seqinfo.Rd:241: missing file link 'BSgenome'
    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_1.14.0.zip
* DONE (GenomeInfoDb)
In R CMD INSTALL
In R CMD INSTALL

Tests output

GenomeInfoDb.Rcheck/tests_i386/run_unitTests.Rout


R version 3.4.4 (2018-03-15) -- "Someone to Lean On"
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, cbind, colMeans, colSums, colnames, 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
[1] TRUE
> GenomeInfoDb:::.test()


RUNIT TEST PROTOCOL -- Thu Apr 12 00:20:22 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 
  12.06    0.37   12.45

GenomeInfoDb.Rcheck/tests_x64/run_unitTests.Rout


R version 3.4.4 (2018-03-15) -- "Someone to Lean On"
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, cbind, colMeans, colSums, colnames, 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
[1] TRUE
> GenomeInfoDb:::.test()


RUNIT TEST PROTOCOL -- Thu Apr 12 00:20:38 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 
  14.57    0.35   14.96

Example timings

GenomeInfoDb.Rcheck/examples_i386/GenomeInfoDb-Ex.timings

nameusersystemelapsed
GenomeDescription-class5.060.275.33
Seqinfo-class0.230.010.26
available.species10.64 0.4611.09
fetchExtendedChromInfoFromUCSC2.050.754.69
mapGenomeBuilds0.090.000.09
rankSeqlevels0.110.000.79
seqinfo14.74 0.1422.31
seqlevels-wrappers13.91 0.1114.02
seqlevelsStyle0.360.060.43

GenomeInfoDb.Rcheck/examples_x64/GenomeInfoDb-Ex.timings

nameusersystemelapsed
GenomeDescription-class5.860.156.01
Seqinfo-class0.160.001.71
available.species8.830.088.91
fetchExtendedChromInfoFromUCSC1.740.413.97
mapGenomeBuilds0.110.000.11
rankSeqlevels0.110.000.11
seqinfo17.55 0.0317.59
seqlevels-wrappers18.60 0.1418.73
seqlevelsStyle0.460.020.47