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BioC 3.2: CHECK report for OrganismDbi on moscato1

This page was generated on 2016-04-23 10:18:46 -0700 (Sat, 23 Apr 2016).

Package 735/1103HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
OrganismDbi 1.12.1
Biocore Data Team
Snapshot Date: 2016-04-22 16:20:12 -0700 (Fri, 22 Apr 2016)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_2/madman/Rpacks/OrganismDbi
Last Changed Rev: 111836 / Revision: 116712
Last Changed Date: 2015-12-22 09:04:48 -0800 (Tue, 22 Dec 2015)
zin1 Linux (Ubuntu 14.04.2 LTS) / x86_64  OK  OK  WARNINGS UNNEEDED, same version exists in internal repository
moscato1 Windows Server 2008 R2 Standard (64-bit) / x64  OK  OK [ WARNINGS ] OK UNNEEDED, same version exists in internal repository
oaxaca Mac OS X Mavericks (10.9.5) / x86_64  OK  OK  WARNINGS  OK UNNEEDED, same version exists in internal repository

Summary

Package: OrganismDbi
Version: 1.12.1
Command: rm -rf OrganismDbi.buildbin-libdir OrganismDbi.Rcheck && mkdir OrganismDbi.buildbin-libdir OrganismDbi.Rcheck && D:\biocbld\bbs-3.2-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=OrganismDbi.buildbin-libdir OrganismDbi_1.12.1.tar.gz >OrganismDbi.Rcheck\00install.out 2>&1 && cp OrganismDbi.Rcheck\00install.out OrganismDbi-install.out && D:\biocbld\bbs-3.2-bioc\R\bin\R.exe CMD check --library=OrganismDbi.buildbin-libdir --install="check:OrganismDbi-install.out" --force-multiarch --no-vignettes --timings OrganismDbi_1.12.1.tar.gz
StartedAt: 2016-04-23 05:39:15 -0700 (Sat, 23 Apr 2016)
EndedAt: 2016-04-23 06:09:37 -0700 (Sat, 23 Apr 2016)
EllapsedTime: 1822.3 seconds
RetCode: 0
Status:  WARNINGS  
CheckDir: OrganismDbi.Rcheck
Warnings: 1

Command output

##############################################################################
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###
### Running command:
###
###   rm -rf OrganismDbi.buildbin-libdir OrganismDbi.Rcheck && mkdir OrganismDbi.buildbin-libdir OrganismDbi.Rcheck && D:\biocbld\bbs-3.2-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=OrganismDbi.buildbin-libdir OrganismDbi_1.12.1.tar.gz >OrganismDbi.Rcheck\00install.out 2>&1 && cp OrganismDbi.Rcheck\00install.out OrganismDbi-install.out  && D:\biocbld\bbs-3.2-bioc\R\bin\R.exe CMD check --library=OrganismDbi.buildbin-libdir --install="check:OrganismDbi-install.out" --force-multiarch --no-vignettes --timings OrganismDbi_1.12.1.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'D:/biocbld/bbs-3.2-bioc/meat/OrganismDbi.Rcheck'
* using R version 3.2.4 (2016-03-10)
* 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 '1.12.1'
* 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 ... OK
* 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 ... WARNING
'library' or 'require' call not declared from: 'AnnotationHub'
'library' or 'require' call to 'GenomicFeatures' which was already attached by Depends.
  Please remove these calls from your code.
'library' or 'require' call to 'AnnotationHub' in package code.
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
Unexported objects imported by ':::' calls:
  'AnnotationDbi:::.chooseCentralOrgPkgSymbol'
  'AnnotationDbi:::.mapIds' 'AnnotationDbi:::.resort'
  'AnnotationDbi:::.testForValidKeytype'
  'AnnotationDbi:::.testSelectArgs' 'BiocGenerics:::testPackage'
  'GenomicFeatures:::.makePackageName'
  'GenomicFeatures:::.set.group.names'
  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 ... NOTE
.selectByRanges: no visible global function definition for
  'findOverlaps'
.selectByRanges: no visible global function definition for 'queryHits'
.selectByRanges: no visible global function definition for
  'subjectHits'
.taxIdToOrgDb: no visible global function definition for
  'AnnotationHub'
.taxIdToOrgDbName: no visible global function definition for
  'AnnotationHub'
available.GTFsForTxDbs: no visible global function definition for
  'AnnotationHub'
makeHubGTFIntoTxDb: no visible global function definition for
  'makeTxDbFromGRanges'
makeOrganismDbFromBiomart: no visible binding for global variable
  'DEFAULT_CIRC_SEQS'
makeOrganismDbFromBiomart: no visible global function definition for
  'makeTxDbFromBiomart'
makeOrganismDbFromTxDb: no visible global function definition for
  'isSingleStringOrNA'
makeOrganismDbFromUCSC: no visible binding for global variable
  'DEFAULT_CIRC_SEQS'
makeOrganismDbFromUCSC: no visible global function definition for
  'makeTxDbFromUCSC'
makeOuterMcolFromInnerMcol: no visible global function definition for
  'elementLengths'
* 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' ... [341s] OK
Examples with CPU or elapsed time > 5s
                           user system elapsed
makeOrganismDbFromBiomart 19.50   0.47  134.47
rangeBasedAccessors       16.92   0.22   20.70
makeOrganismDbFromTxDb    12.76   0.06   81.35
makeOrganismDbFromUCSC    10.46   0.13   80.76
OrganismDb                10.00   0.20   10.34
** running examples for arch 'x64' ... [329s] OK
Examples with CPU or elapsed time > 5s
                           user system elapsed
makeOrganismDbFromBiomart 23.60   0.71  130.10
rangeBasedAccessors       15.08   0.25   15.92
OrganismDb                14.92   0.21   15.34
makeOrganismDbFromTxDb    10.06   0.22   76.26
makeOrganismDbFromUCSC     7.89   0.17   74.40
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
  Running 'OrganismDbi_unit_tests.R' [493s]
 [494s] OK
** running tests for arch 'x64' ...
  Running 'OrganismDbi_unit_tests.R' [363s]
 [364s] 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
  'D:/biocbld/bbs-3.2-bioc/meat/OrganismDbi.Rcheck/00check.log'
for details.


OrganismDbi.Rcheck/00install.out:


install for i386

* installing *source* package 'OrganismDbi' ...
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded

install for x64

* installing *source* package 'OrganismDbi' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'OrganismDbi' as OrganismDbi_1.12.1.zip
* DONE (OrganismDbi)

OrganismDbi.Rcheck/examples_i386/OrganismDbi-Ex.timings:

nameusersystemelapsed
OrganismDb10.00 0.2010.34
coordinate-mapping-method1.790.001.79
makeOrganismDbFromBiomart 19.50 0.47134.47
makeOrganismDbFromTxDb12.76 0.0681.35
makeOrganismDbFromUCSC10.46 0.1380.76
makeOrganismPackage000
rangeBasedAccessors16.92 0.2220.70

OrganismDbi.Rcheck/examples_x64/OrganismDbi-Ex.timings:

nameusersystemelapsed
OrganismDb14.92 0.2115.34
coordinate-mapping-method1.680.031.71
makeOrganismDbFromBiomart 23.60 0.71130.10
makeOrganismDbFromTxDb10.06 0.2276.26
makeOrganismDbFromUCSC 7.89 0.1774.40
makeOrganismPackage000
rangeBasedAccessors15.08 0.2515.92