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CHECK report for OrganismDbi on tokay2

This page was generated on 2018-10-17 08:36:32 -0400 (Wed, 17 Oct 2018).

Package 1040/1561HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
OrganismDbi 1.22.0
Biocore Data Team
Snapshot Date: 2018-10-15 16:45:08 -0400 (Mon, 15 Oct 2018)
URL: https://git.bioconductor.org/packages/OrganismDbi
Branch: RELEASE_3_7
Last Commit: 24e953e
Last Changed Date: 2018-04-30 10:35:26 -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: OrganismDbi
Version: 1.22.0
Command: C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:OrganismDbi.install-out.txt --library=C:\Users\biocbuild\bbs-3.7-bioc\R\library --no-vignettes --timings OrganismDbi_1.22.0.tar.gz
StartedAt: 2018-10-17 03:47:42 -0400 (Wed, 17 Oct 2018)
EndedAt: 2018-10-17 04:03:44 -0400 (Wed, 17 Oct 2018)
EllapsedTime: 962.0 seconds
RetCode: 0
Status:  WARNINGS  
CheckDir: OrganismDbi.Rcheck
Warnings: 1

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:OrganismDbi.install-out.txt --library=C:\Users\biocbuild\bbs-3.7-bioc\R\library --no-vignettes --timings OrganismDbi_1.22.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.7-bioc/meat/OrganismDbi.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 'OrganismDbi/DESCRIPTION' ... OK
* this is package 'OrganismDbi' version '1.22.0'
* 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 'OrganismDbi' can be installed ... WARNING
Found the following significant warnings:
  Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpKuFDN2/R.INSTALL204045036eac/OrganismDbi/man/OrganismDb.Rd:191: file link 'seqlevels' in package 'GenomeInfoDb' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpKuFDN2/R.INSTALL204045036eac/OrganismDbi/man/OrganismDb.Rd:192: file link 'seqlengths' in package 'GenomeInfoDb' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpKuFDN2/R.INSTALL204045036eac/OrganismDbi/man/OrganismDb.Rd:193: file link 'isCircular' in package 'GenomeInfoDb' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpKuFDN2/R.INSTALL204045036eac/OrganismDbi/man/OrganismDb.Rd:194: file link 'genome' in package 'GenomeInfoDb' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpKuFDN2/R.INSTALL204045036eac/OrganismDbi/man/coordinate-mapping-method.Rd:11: file link 'mapToAlignments' in package 'GenomicAlignments' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpKuFDN2/R.INSTALL204045036eac/OrganismDbi/man/coordinate-mapping-method.Rd:101: file link 'mapToTranscripts' in package 'GenomicFeatures' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpKuFDN2/R.INSTALL204045036eac/OrganismDbi/man/rangeBasedAccessors.Rd:93: 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/RtmpKuFDN2/R.INSTALL204045036eac/OrganismDbi/man/rangeBasedAccessors.Rd:120: 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/RtmpKuFDN2/R.INSTALL204045036eac/OrganismDbi/man/rangeBasedAccessors.Rd:123: 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/RtmpKuFDN2/R.INSTALL204045036eac/OrganismDbi/man/rangeBasedAccessors.Rd:125: 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/RtmpKuFDN2/R.INSTALL204045036eac/OrganismDbi/man/rangeBasedAccessors.Rd:195: 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/RtmpKuFDN2/R.INSTALL204045036eac/OrganismDbi/man/rangeBasedAccessors.Rd:196: 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/RtmpKuFDN2/R.INSTALL204045036eac/OrganismDbi/man/rangeBasedAccessors.Rd:197: 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/RtmpKuFDN2/R.INSTALL204045036eac/OrganismDbi/man/rangeBasedAccessors.Rd:201: file link 'DNAString' in package 'Biostrings' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpKuFDN2/R.INSTALL204045036eac/OrganismDbi/man/rangeBasedAccessors.Rd:203: file link 'Rle' in package 'S4Vectors' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpKuFDN2/R.INSTALL204045036eac/OrganismDbi/man/rangeBasedAccessors.Rd:206: file link 'Rle' in package 'S4Vectors' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpKuFDN2/R.INSTALL204045036eac/OrganismDbi/man/rangeBasedAccessors.Rd:209: file link 'IntegerRangesList' in package 'IRanges' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpKuFDN2/R.INSTALL204045036eac/OrganismDbi/man/rangeBasedAccessors.Rd:215: file link 'IntegerRangesList' in package 'IRanges' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpKuFDN2/R.INSTALL204045036eac/OrganismDbi/man/rangeBasedAccessors.Rd:225: file link 'GenomicRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpKuFDN2/R.INSTALL204045036eac/OrganismDbi/man/rangeBasedAccessors.Rd:253: file link 'MultiDb-class' in package 'OrganismDbi' does not exist and so has been treated as a topic
See 'C:/Users/biocbuild/bbs-3.7-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 files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
Examples with CPU or elapsed time > 5s
                           user system elapsed
makeOrganismDbFromBiomart 23.05   1.45   50.86
rangeBasedAccessors       12.31   0.81   14.56
OrganismDb                 8.67   0.50    9.23
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
                           user system elapsed
makeOrganismDbFromBiomart 26.82   0.51   52.87
OrganismDb                10.58   0.30   11.42
rangeBasedAccessors        8.89   0.22    9.11
* 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-3.7-bioc/meat/OrganismDbi.Rcheck/00check.log'
for details.

Installation output

OrganismDbi.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/OrganismDbi_1.22.0.tar.gz && rm -rf OrganismDbi.buildbin-libdir && mkdir OrganismDbi.buildbin-libdir && C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=OrganismDbi.buildbin-libdir OrganismDbi_1.22.0.tar.gz && C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD INSTALL OrganismDbi_1.22.0.zip && rm OrganismDbi_1.22.0.tar.gz OrganismDbi_1.22.0.zip
###
##############################################################################
##############################################################################


  % 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 58828  100 58828    0     0   925k      0 --:--:-- --:--:-- --:--:-- 1044k

install for i386

* installing *source* package 'OrganismDbi' ...
** R
** inst
** byte-compile and prepare 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-3.7-bioc/tmpdir/RtmpKuFDN2/R.INSTALL204045036eac/OrganismDbi/man/OrganismDb.Rd:191: file link 'seqlevels' in package 'GenomeInfoDb' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpKuFDN2/R.INSTALL204045036eac/OrganismDbi/man/OrganismDb.Rd:192: file link 'seqlengths' in package 'GenomeInfoDb' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpKuFDN2/R.INSTALL204045036eac/OrganismDbi/man/OrganismDb.Rd:193: file link 'isCircular' in package 'GenomeInfoDb' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpKuFDN2/R.INSTALL204045036eac/OrganismDbi/man/OrganismDb.Rd:194: file link 'genome' in package 'GenomeInfoDb' does not exist and so has been treated as a topic
    coordinate-mapping-method               html  
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpKuFDN2/R.INSTALL204045036eac/OrganismDbi/man/coordinate-mapping-method.Rd:11: file link 'mapToAlignments' in package 'GenomicAlignments' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpKuFDN2/R.INSTALL204045036eac/OrganismDbi/man/coordinate-mapping-method.Rd:101: file link 'mapToTranscripts' in package 'GenomicFeatures' does not exist and so has been treated as a topic
    makeOrganismDbFromBiomart               html  
    finding level-2 HTML links ... done

    makeOrganismDbFromTxDb                  html  
    makeOrganismDbFromUCSC                  html  
    makeOrganismPackage                     html  
    rangeBasedAccessors                     html  
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpKuFDN2/R.INSTALL204045036eac/OrganismDbi/man/rangeBasedAccessors.Rd:93: 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/RtmpKuFDN2/R.INSTALL204045036eac/OrganismDbi/man/rangeBasedAccessors.Rd:120: 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/RtmpKuFDN2/R.INSTALL204045036eac/OrganismDbi/man/rangeBasedAccessors.Rd:123: 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/RtmpKuFDN2/R.INSTALL204045036eac/OrganismDbi/man/rangeBasedAccessors.Rd:125: 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/RtmpKuFDN2/R.INSTALL204045036eac/OrganismDbi/man/rangeBasedAccessors.Rd:195: 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/RtmpKuFDN2/R.INSTALL204045036eac/OrganismDbi/man/rangeBasedAccessors.Rd:196: 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/RtmpKuFDN2/R.INSTALL204045036eac/OrganismDbi/man/rangeBasedAccessors.Rd:197: 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/RtmpKuFDN2/R.INSTALL204045036eac/OrganismDbi/man/rangeBasedAccessors.Rd:201: file link 'DNAString' in package 'Biostrings' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpKuFDN2/R.INSTALL204045036eac/OrganismDbi/man/rangeBasedAccessors.Rd:203: file link 'Rle' in package 'S4Vectors' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpKuFDN2/R.INSTALL204045036eac/OrganismDbi/man/rangeBasedAccessors.Rd:206: file link 'Rle' in package 'S4Vectors' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpKuFDN2/R.INSTALL204045036eac/OrganismDbi/man/rangeBasedAccessors.Rd:209: file link 'IntegerRangesList' in package 'IRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpKuFDN2/R.INSTALL204045036eac/OrganismDbi/man/rangeBasedAccessors.Rd:215: file link 'IntegerRangesList' in package 'IRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpKuFDN2/R.INSTALL204045036eac/OrganismDbi/man/rangeBasedAccessors.Rd:225: file link 'GenomicRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpKuFDN2/R.INSTALL204045036eac/OrganismDbi/man/rangeBasedAccessors.Rd:253: file link 'MultiDb-class' in package 'OrganismDbi' does not exist and so has been treated as a topic
** 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_1.22.0.zip
* DONE (OrganismDbi)
In R CMD INSTALL
In R CMD INSTALL
* installing to library 'C:/Users/biocbuild/bbs-3.7-bioc/R/library'
package 'OrganismDbi' successfully unpacked and MD5 sums checked
In R CMD INSTALL

Tests output

OrganismDbi.Rcheck/tests_i386/OrganismDbi_unit_tests.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.

> 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, 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

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


Attaching package: 'IRanges'

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

    windows

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 -- Wed Oct 17 03:59:42 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 
 256.60   21.73  284.36

OrganismDbi.Rcheck/tests_x64/OrganismDbi_unit_tests.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.

> 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, 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

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


Attaching package: 'IRanges'

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

    windows

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 -- Wed Oct 17 04:03:38 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 
 228.21    6.62  235.07

Example timings

OrganismDbi.Rcheck/examples_i386/OrganismDbi-Ex.timings

nameusersystemelapsed
OrganismDb8.670.509.23
coordinate-mapping-method0.970.081.05
makeOrganismDbFromBiomart23.05 1.4550.86
makeOrganismDbFromTxDb000
makeOrganismDbFromUCSC000
makeOrganismPackage000
rangeBasedAccessors12.31 0.8114.56

OrganismDbi.Rcheck/examples_x64/OrganismDbi-Ex.timings

nameusersystemelapsed
OrganismDb10.58 0.3011.42
coordinate-mapping-method1.340.001.34
makeOrganismDbFromBiomart26.82 0.5152.87
makeOrganismDbFromTxDb000
makeOrganismDbFromUCSC000
makeOrganismPackage000
rangeBasedAccessors8.890.229.11