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CHECK report for OrganismDbi on tokay1

This page was generated on 2018-04-12 13:22:04 -0400 (Thu, 12 Apr 2018).

Package 985/1472HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
OrganismDbi 1.20.0
Biocore Data Team
Snapshot Date: 2018-04-11 16:45:18 -0400 (Wed, 11 Apr 2018)
URL: https://git.bioconductor.org/packages/OrganismDbi
Branch: RELEASE_3_6
Last Commit: d42e06a
Last Changed Date: 2017-10-30 12:39:50 -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: OrganismDbi
Version: 1.20.0
Command: rm -rf OrganismDbi.buildbin-libdir OrganismDbi.Rcheck && mkdir OrganismDbi.buildbin-libdir OrganismDbi.Rcheck && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=OrganismDbi.buildbin-libdir OrganismDbi_1.20.0.tar.gz >OrganismDbi.Rcheck\00install.out 2>&1 && cp OrganismDbi.Rcheck\00install.out OrganismDbi-install.out && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD check --library=OrganismDbi.buildbin-libdir --install="check:OrganismDbi-install.out" --force-multiarch --no-vignettes --timings OrganismDbi_1.20.0.tar.gz
StartedAt: 2018-04-12 01:57:27 -0400 (Thu, 12 Apr 2018)
EndedAt: 2018-04-12 02:14:41 -0400 (Thu, 12 Apr 2018)
EllapsedTime: 1033.3 seconds
RetCode: 0
Status:  WARNINGS  
CheckDir: OrganismDbi.Rcheck
Warnings: 1

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   rm -rf OrganismDbi.buildbin-libdir OrganismDbi.Rcheck && mkdir OrganismDbi.buildbin-libdir OrganismDbi.Rcheck && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=OrganismDbi.buildbin-libdir OrganismDbi_1.20.0.tar.gz >OrganismDbi.Rcheck\00install.out 2>&1 && cp OrganismDbi.Rcheck\00install.out OrganismDbi-install.out  &&  C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD check --library=OrganismDbi.buildbin-libdir --install="check:OrganismDbi-install.out" --force-multiarch --no-vignettes --timings OrganismDbi_1.20.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.6-bioc/meat/OrganismDbi.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 'OrganismDbi/DESCRIPTION' ... OK
* this is package 'OrganismDbi' version '1.20.0'
* 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 'OrganismDbi' can be installed ... WARNING
Found the following significant warnings:
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpUTVGLw/R.INSTALL14e05d914242/OrganismDbi/man/OrganismDb.Rd:191: missing file link 'seqlevels'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpUTVGLw/R.INSTALL14e05d914242/OrganismDbi/man/OrganismDb.Rd:192: missing file link 'seqlengths'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpUTVGLw/R.INSTALL14e05d914242/OrganismDbi/man/OrganismDb.Rd:193: missing file link 'isCircular'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpUTVGLw/R.INSTALL14e05d914242/OrganismDbi/man/OrganismDb.Rd:194: missing file link 'genome'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpUTVGLw/R.INSTALL14e05d914242/OrganismDbi/man/coordinate-mapping-method.Rd:11: missing file link 'mapToAlignments'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpUTVGLw/R.INSTALL14e05d914242/OrganismDbi/man/coordinate-mapping-method.Rd:101: missing file link 'mapToTranscripts'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpUTVGLw/R.INSTALL14e05d914242/OrganismDbi/man/rangeBasedAccessors.Rd:93: missing file link 'BSgenome'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpUTVGLw/R.INSTALL14e05d914242/OrganismDbi/man/rangeBasedAccessors.Rd:120: missing file link 'GRangesList'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpUTVGLw/R.INSTALL14e05d914242/OrganismDbi/man/rangeBasedAccessors.Rd:123: missing file link 'GRangesList'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpUTVGLw/R.INSTALL14e05d914242/OrganismDbi/man/rangeBasedAccessors.Rd:125: missing file link 'GRangesList'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpUTVGLw/R.INSTALL14e05d914242/OrganismDbi/man/rangeBasedAccessors.Rd:195: missing file link 'GRangesList'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpUTVGLw/R.INSTALL14e05d914242/OrganismDbi/man/rangeBasedAccessors.Rd:196: missing file link 'BSgenome'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpUTVGLw/R.INSTALL14e05d914242/OrganismDbi/man/rangeBasedAccessors.Rd:197: missing file link 'GRangesList'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpUTVGLw/R.INSTALL14e05d914242/OrganismDbi/man/rangeBasedAccessors.Rd:201: missing file link 'DNAString'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpUTVGLw/R.INSTALL14e05d914242/OrganismDbi/man/rangeBasedAccessors.Rd:203: missing file link 'Rle'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpUTVGLw/R.INSTALL14e05d914242/OrganismDbi/man/rangeBasedAccessors.Rd:206: missing file link 'Rle'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpUTVGLw/R.INSTALL14e05d914242/OrganismDbi/man/rangeBasedAccessors.Rd:209: missing file link 'RangesList'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpUTVGLw/R.INSTALL14e05d914242/OrganismDbi/man/rangeBasedAccessors.Rd:215: missing file link 'RangesList'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpUTVGLw/R.INSTALL14e05d914242/OrganismDbi/man/rangeBasedAccessors.Rd:225: missing file link 'GenomicRanges'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpUTVGLw/R.INSTALL14e05d914242/OrganismDbi/man/rangeBasedAccessors.Rd:253: missing file link 'MultiDb-class'
See 'C:/Users/biocbuild/bbs-3.6-bioc/meat/OrganismDbi.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: 'BiocGenerics:::testPackage'
  See the note in ?`:::` about the use of this operator.
There are ::: calls to the package's namespace in its code. A package
  almost never needs to use ::: for its own objects:
  '.biocAnnPackages' '.extractPkgsAndCols' '.gentlyExtractDbFiles'
  '.lookupDbNameFromKeytype' '.mungeGraphData' '.taxIdToOrgDb'
  '.taxIdToOrgDbName' '.testGraphData' '.testKeys' 'OrganismDb'
* 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 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
makeOrganismDbFromBiomart 16.98   0.71   42.30
OrganismDb                10.67   0.29   11.21
rangeBasedAccessors       10.16   0.07   10.47
makeOrganismDbFromTxDb     6.94   0.24   25.45
makeOrganismDbFromUCSC     6.00   0.19   27.94
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
                           user system elapsed
makeOrganismDbFromBiomart 18.31   0.37   42.83
OrganismDb                10.84   0.22   11.10
rangeBasedAccessors        7.54   0.16    7.68
makeOrganismDbFromTxDb     5.72   0.14   23.34
makeOrganismDbFromUCSC     4.41   0.08   25.02
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
  Running 'OrganismDbi_unit_tests.R'
 OK
** running tests for arch 'x64' ...
  Running 'OrganismDbi_unit_tests.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-3.6-bioc/meat/OrganismDbi.Rcheck/00check.log'
for details.

Installation output

OrganismDbi.Rcheck/00install.out


install for i386

* installing *source* package 'OrganismDbi' ...
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
  converting help for package 'OrganismDbi'
    finding HTML links ... done
    OrganismDb                              html  
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpUTVGLw/R.INSTALL14e05d914242/OrganismDbi/man/OrganismDb.Rd:191: missing file link 'seqlevels'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpUTVGLw/R.INSTALL14e05d914242/OrganismDbi/man/OrganismDb.Rd:192: missing file link 'seqlengths'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpUTVGLw/R.INSTALL14e05d914242/OrganismDbi/man/OrganismDb.Rd:193: missing file link 'isCircular'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpUTVGLw/R.INSTALL14e05d914242/OrganismDbi/man/OrganismDb.Rd:194: missing file link 'genome'
    coordinate-mapping-method               html  
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpUTVGLw/R.INSTALL14e05d914242/OrganismDbi/man/coordinate-mapping-method.Rd:11: missing file link 'mapToAlignments'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpUTVGLw/R.INSTALL14e05d914242/OrganismDbi/man/coordinate-mapping-method.Rd:101: missing file link 'mapToTranscripts'
    makeOrganismDbFromBiomart               html  
    finding level-2 HTML links ... done

    makeOrganismDbFromTxDb                  html  
    makeOrganismDbFromUCSC                  html  
    makeOrganismPackage                     html  
    rangeBasedAccessors                     html  
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpUTVGLw/R.INSTALL14e05d914242/OrganismDbi/man/rangeBasedAccessors.Rd:93: missing file link 'BSgenome'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpUTVGLw/R.INSTALL14e05d914242/OrganismDbi/man/rangeBasedAccessors.Rd:120: missing file link 'GRangesList'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpUTVGLw/R.INSTALL14e05d914242/OrganismDbi/man/rangeBasedAccessors.Rd:123: missing file link 'GRangesList'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpUTVGLw/R.INSTALL14e05d914242/OrganismDbi/man/rangeBasedAccessors.Rd:125: missing file link 'GRangesList'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpUTVGLw/R.INSTALL14e05d914242/OrganismDbi/man/rangeBasedAccessors.Rd:195: missing file link 'GRangesList'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpUTVGLw/R.INSTALL14e05d914242/OrganismDbi/man/rangeBasedAccessors.Rd:196: missing file link 'BSgenome'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpUTVGLw/R.INSTALL14e05d914242/OrganismDbi/man/rangeBasedAccessors.Rd:197: missing file link 'GRangesList'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpUTVGLw/R.INSTALL14e05d914242/OrganismDbi/man/rangeBasedAccessors.Rd:201: missing file link 'DNAString'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpUTVGLw/R.INSTALL14e05d914242/OrganismDbi/man/rangeBasedAccessors.Rd:203: missing file link 'Rle'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpUTVGLw/R.INSTALL14e05d914242/OrganismDbi/man/rangeBasedAccessors.Rd:206: missing file link 'Rle'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpUTVGLw/R.INSTALL14e05d914242/OrganismDbi/man/rangeBasedAccessors.Rd:209: missing file link 'RangesList'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpUTVGLw/R.INSTALL14e05d914242/OrganismDbi/man/rangeBasedAccessors.Rd:215: missing file link 'RangesList'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpUTVGLw/R.INSTALL14e05d914242/OrganismDbi/man/rangeBasedAccessors.Rd:225: missing file link 'GenomicRanges'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpUTVGLw/R.INSTALL14e05d914242/OrganismDbi/man/rangeBasedAccessors.Rd:253: missing file link 'MultiDb-class'
** building package indices
** installing vignettes
** testing if installed package can be loaded
In R CMD INSTALL

install for x64

* installing *source* package 'OrganismDbi' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'OrganismDbi' as OrganismDbi_1.20.0.zip
* DONE (OrganismDbi)
In R CMD INSTALL
In R CMD INSTALL

Tests output

OrganismDbi.Rcheck/tests_i386/OrganismDbi_unit_tests.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.

> BiocGenerics:::testPackage("OrganismDbi")

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

Welcome to Bioconductor

    Vignettes contain introductory material; view with
    'browseVignettes()'. To cite Bioconductor, see
    'citation("Biobase")', and for packages 'citation("pkgname")'.


Attaching package: 'S4Vectors'

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

    expand.grid

Loading required package: Homo.sapiens
Loading required package: GO.db

Loading required package: org.Hs.eg.db

Loading required package: TxDb.Hsapiens.UCSC.hg19.knownGene
'select()' returned 1:many mapping between keys and columns
'select()' returned 1:many mapping between keys and columns
'select()' returned 1:many mapping between keys and columns
'select()' returned 1:many mapping between keys and columns
'select()' returned 1:many mapping between keys and columns
Loading required package: RSQLite
Loading required package: Rattus.norvegicus
Loading required package: org.Rn.eg.db

Loading required package: TxDb.Rnorvegicus.UCSC.rn5.refGene
'select()' returned 1:many mapping between keys and columns
'select()' returned 1:many mapping between keys and columns
'select()' returned 1:many mapping between keys and columns
'select()' returned 1:many mapping between keys and columns
'select()' returned 1:many mapping between keys and columns
'select()' returned 1:many mapping between keys and columns
'select()' returned 1:many mapping between keys and columns
'select()' returned 1:many mapping between keys and columns
'select()' returned 1:many mapping between keys and columns
'select()' returned 1:many mapping between keys and columns
'select()' returned 1:many mapping between keys and columns
'select()' returned 1:many mapping between keys and columns
'select()' returned 1:many mapping between keys and columns
'select()' returned 1:many mapping between keys and columns
'select()' returned 1:many mapping between keys and columns
'select()' returned 1:many mapping between keys and columns
'select()' returned 1:1 mapping between keys and columns
'select()' returned 1:1 mapping between keys and columns
'select()' returned 1:1 mapping between keys and columns
'select()' returned 1:many mapping between keys and columns
'select()' returned 1:1 mapping between keys and columns
'select()' returned 1:1 mapping between keys and columns
'select()' returned 1:1 mapping between keys and columns
'select()' returned 1:1 mapping between keys and columns
'select()' returned 1:1 mapping between keys and columns
'select()' returned 1:1 mapping between keys and columns
'select()' returned 1:many mapping between keys and columns
'select()' returned many:many mapping between keys and columns
'select()' returned 1:many mapping between keys and columns
'select()' returned 1:many mapping between keys and columns
'select()' returned 1:many mapping between keys and columns
'select()' returned many:many mapping between keys and columns
'select()' returned 1:many mapping between keys and columns
'select()' returned 1:1 mapping between keys and columns
'select()' returned 1:1 mapping between keys and columns
'select()' returned 1:1 mapping between keys and columns
Loading required package: FDb.UCSC.tRNAs
Loading required package: BSgenome.Hsapiens.UCSC.hg19
Loading required package: BSgenome
Loading required package: Biostrings
Loading required package: XVector

Attaching package: 'Biostrings'

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

    strsplit

Loading required package: rtracklayer


RUNIT TEST PROTOCOL -- Thu Apr 12 02:10:25 2018 
*********************************************** 
Number of test functions: 42 
Number of errors: 0 
Number of failures: 0 

 
1 Test Suite : 
OrganismDbi RUnit Tests - 42 test functions, 0 errors, 0 failures
Number of test functions: 42 
Number of errors: 0 
Number of failures: 0 
Warning messages:
1: call dbDisconnect() when finished working with a connection 
2: In is.na(txdb) : is.na() applied to non-(list or vector) of type 'S4'
3: In is.na(txdb) : is.na() applied to non-(list or vector) of type 'S4'
> 
> proc.time()
   user  system elapsed 
 250.37    9.21  283.57

OrganismDbi.Rcheck/tests_x64/OrganismDbi_unit_tests.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.

> BiocGenerics:::testPackage("OrganismDbi")

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

Welcome to Bioconductor

    Vignettes contain introductory material; view with
    'browseVignettes()'. To cite Bioconductor, see
    'citation("Biobase")', and for packages 'citation("pkgname")'.


Attaching package: 'S4Vectors'

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

    expand.grid

Loading required package: Homo.sapiens
Loading required package: GO.db

Loading required package: org.Hs.eg.db

Loading required package: TxDb.Hsapiens.UCSC.hg19.knownGene
'select()' returned 1:many mapping between keys and columns
'select()' returned 1:many mapping between keys and columns
'select()' returned 1:many mapping between keys and columns
'select()' returned 1:many mapping between keys and columns
'select()' returned 1:many mapping between keys and columns
Loading required package: RSQLite
Loading required package: Rattus.norvegicus
Loading required package: org.Rn.eg.db

Loading required package: TxDb.Rnorvegicus.UCSC.rn5.refGene
'select()' returned 1:many mapping between keys and columns
'select()' returned 1:many mapping between keys and columns
'select()' returned 1:many mapping between keys and columns
'select()' returned 1:many mapping between keys and columns
'select()' returned 1:many mapping between keys and columns
'select()' returned 1:many mapping between keys and columns
'select()' returned 1:many mapping between keys and columns
'select()' returned 1:many mapping between keys and columns
'select()' returned 1:many mapping between keys and columns
'select()' returned 1:many mapping between keys and columns
'select()' returned 1:many mapping between keys and columns
'select()' returned 1:many mapping between keys and columns
'select()' returned 1:many mapping between keys and columns
'select()' returned 1:many mapping between keys and columns
'select()' returned 1:many mapping between keys and columns
'select()' returned 1:many mapping between keys and columns
'select()' returned 1:1 mapping between keys and columns
'select()' returned 1:1 mapping between keys and columns
'select()' returned 1:1 mapping between keys and columns
'select()' returned 1:many mapping between keys and columns
'select()' returned 1:1 mapping between keys and columns
'select()' returned 1:1 mapping between keys and columns
'select()' returned 1:1 mapping between keys and columns
'select()' returned 1:1 mapping between keys and columns
'select()' returned 1:1 mapping between keys and columns
'select()' returned 1:1 mapping between keys and columns
'select()' returned 1:many mapping between keys and columns
'select()' returned many:many mapping between keys and columns
'select()' returned 1:many mapping between keys and columns
'select()' returned 1:many mapping between keys and columns
'select()' returned 1:many mapping between keys and columns
'select()' returned many:many mapping between keys and columns
'select()' returned 1:many mapping between keys and columns
'select()' returned 1:1 mapping between keys and columns
'select()' returned 1:1 mapping between keys and columns
'select()' returned 1:1 mapping between keys and columns
Loading required package: FDb.UCSC.tRNAs
Loading required package: BSgenome.Hsapiens.UCSC.hg19
Loading required package: BSgenome
Loading required package: Biostrings
Loading required package: XVector

Attaching package: 'Biostrings'

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

    strsplit

Loading required package: rtracklayer


RUNIT TEST PROTOCOL -- Thu Apr 12 02:14:36 2018 
*********************************************** 
Number of test functions: 42 
Number of errors: 0 
Number of failures: 0 

 
1 Test Suite : 
OrganismDbi RUnit Tests - 42 test functions, 0 errors, 0 failures
Number of test functions: 42 
Number of errors: 0 
Number of failures: 0 
Warning messages:
1: call dbDisconnect() when finished working with a connection 
2: In is.na(txdb) : is.na() applied to non-(list or vector) of type 'S4'
3: In is.na(txdb) : is.na() applied to non-(list or vector) of type 'S4'
> 
> proc.time()
   user  system elapsed 
 243.81    6.00  250.01

Example timings

OrganismDbi.Rcheck/examples_i386/OrganismDbi-Ex.timings

nameusersystemelapsed
OrganismDb10.67 0.2911.21
coordinate-mapping-method1.330.041.35
makeOrganismDbFromBiomart16.98 0.7142.30
makeOrganismDbFromTxDb 6.94 0.2425.45
makeOrganismDbFromUCSC 6.00 0.1927.94
makeOrganismPackage000
rangeBasedAccessors10.16 0.0710.47

OrganismDbi.Rcheck/examples_x64/OrganismDbi-Ex.timings

nameusersystemelapsed
OrganismDb10.84 0.2211.10
coordinate-mapping-method1.190.051.24
makeOrganismDbFromBiomart18.31 0.3742.83
makeOrganismDbFromTxDb 5.72 0.1423.34
makeOrganismDbFromUCSC 4.41 0.0825.02
makeOrganismPackage000
rangeBasedAccessors7.540.167.68