BioC 3.3: CHECK report for annotate on windows2.bioconductor.org

Package: annotate

Version: 1.49.0

Command: rm -rf annotate.buildbin-libdir annotate.Rcheck && mkdir annotate.buildbin-libdir annotate.Rcheck && c:\biocbld\bbs-3.3-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=annotate.buildbin-libdir annotate_1.49.0.tar.gz >annotate.Rcheck\00install.out 2>&1 && cp annotate.Rcheck\00install.out annotate-install.out && c:\biocbld\bbs-3.3-bioc\R\bin\R.exe CMD check --library=annotate.buildbin-libdir --install="check:annotate-install.out" --force-multiarch --no-vignettes --timings annotate_1.49.0.tar.gz

StartedAt: 2015-10-27 00:34:55 -0400 (Tue, 27 Oct 2015)

EndedAt: 2015-10-27 00:39:30 -0400 (Tue, 27 Oct 2015)

EllapsedTime: 274.4 seconds

RetCode: 0

Status:  OK

CheckDir: annotate.Rcheck

Warnings: 0

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### Running command:
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###   rm -rf annotate.buildbin-libdir annotate.Rcheck && mkdir annotate.buildbin-libdir annotate.Rcheck && c:\biocbld\bbs-3.3-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=annotate.buildbin-libdir annotate_1.49.0.tar.gz >annotate.Rcheck\00install.out 2>&1 && cp annotate.Rcheck\00install.out annotate-install.out  && c:\biocbld\bbs-3.3-bioc\R\bin\R.exe CMD check --library=annotate.buildbin-libdir --install="check:annotate-install.out" --force-multiarch --no-vignettes --timings annotate_1.49.0.tar.gz
###
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* using log directory 'c:/biocbld/bbs-3.3-bioc/meat/annotate.Rcheck'
* using R Under development (unstable) (2015-09-22 r69418)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'annotate/DESCRIPTION' ... OK
* this is package 'annotate' version '1.49.0'
* 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 'annotate' 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 ... NOTE
'library' or 'require' call to 'Biostrings' in package code.
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
Unexported object imported by a ':::' call: 'AnnotationDbi:::makeFlatBimapUsingSelect'
  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
.blastSequencesToDNAMultipleAlignment: no visible global function
  definition for 'IRanges'
.blastSequencesToDataFrame: no visible global function definition for
  'xmlToDataFrame'
getGOChildren: no visible binding for global variable 'GOMFCHILDREN'
getGOChildren: no visible binding for global variable 'GOBPCHILDREN'
getGOChildren: no visible binding for global variable 'GOCCCHILDREN'
getGOOntology: no visible binding for global variable 'GOTERM'
getGOParents: no visible binding for global variable 'GOMFPARENTS'
getGOParents: no visible binding for global variable 'GOBPPARENTS'
getGOParents: no visible binding for global variable 'GOCCPARENTS'
getGOTerm: no visible binding for global variable 'GOTERM'
Undefined global functions or variables:
  GOBPCHILDREN GOBPPARENTS GOCCCHILDREN GOCCPARENTS GOMFCHILDREN
  GOMFPARENTS GOTERM IRanges xmlToDataFrame
* 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 contents of 'data' directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking installed files from 'inst/doc' ... OK
* checking files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... [90s] OK
Examples with CPU or elapsed time > 5s
               user system elapsed
chrCats        8.97   0.03    9.92
accessionToUID 4.84   2.23    7.66
genbank        3.57   1.45    5.17
pm.getabst     3.30   1.44    5.26
pm.titles      3.64   0.94    5.14
blastSequences 0.06   0.00   31.30
** running examples for arch 'x64' ... [81s] OK
Examples with CPU or elapsed time > 5s
                user system elapsed
chrCats        11.75   0.02   11.77
accessionToUID  2.82   2.17   18.23
blastSequences  0.05   0.00   18.10
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
  Running 'annotate_unit_tests.R' [5s]
 [5s] OK
** running tests for arch 'x64' ...
  Running 'annotate_unit_tests.R' [6s]
 [6s] 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: 2 NOTEs
See
  'c:/biocbld/bbs-3.3-bioc/meat/annotate.Rcheck/00check.log'
for details.

install for i386

* installing *source* package 'annotate' ...
** R
** data
** 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 'annotate' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'annotate' as annotate_1.49.0.zip
* DONE (annotate)

name	user	system	elapsed
ACCNUMStats	1.38	0.04	1.42
GO2heatmap	0.11	0.02	0.12
GOmnplot	0.06	0.00	0.06
HTMLPage-class	0	0	0
LL2homology	0	0	0
PMIDAmat	0.18	0.00	0.21
PWAmat	3.88	0.08	3.95
UniGeneQuery	0	0	0
accessionToUID	4.84	2.23	7.66
annPkgName	0	0	0
aqListGOIDs	0.46	0.02	4.43
blastSequences	0.06	0.00	31.30
buildChromLocation	0.89	0.03	0.92
buildPubMedAbst	0.11	0.01	0.24
chrCats	8.97	0.03	9.92
chromLocation-class	0.98	0.02	1.00
compatibleVersions	0.02	0.02	0.03
dropECode	0.01	0.01	0.03
entrezGeneByID	0	0	0
entrezGeneQuery	0	0	0
filterGOByOntology	0.06	0.00	0.06
findNeighbors	0.02	0.00	0.13
genbank	3.57	1.45	5.17
getAnnMap	0.02	0.00	0.31
getEvidence	0.03	0.00	0.03
getGOTerm	0.16	0.02	1.86
getOntology	0.03	0.02	0.05
getPMInfo	0.48	0.06	0.65
getSYMBOL	0.08	0.00	0.39
getSeq4Acc	0.00	0.00	0.06
hasGOannote	0.01	0.00	0.06
hgByChroms	0.00	0.01	0.02
hgCLengths	0.02	0.00	0.02
hgu95Achroloc	0.06	0.00	0.06
hgu95Achrom	0.06	0.00	0.06
hgu95All	0.07	0.00	0.06
hgu95Asym	0.06	0.00	0.07
homoData-class	0.01	0.00	0.01
htmlpage	0.00	0.00	0.03
isValidkey	0	0	0
makeAnchor	0	0	0
organism	0.92	0.02	0.94
p2LL	0	0	0
pm.abstGrep	3.11	1.23	4.89
pm.getabst	3.30	1.44	5.26
pm.titles	3.64	0.94	5.14
pmAbst2HTML	0.11	0.03	0.33
pmid2MIAME	0	0	0
pmidQuery	0	0	0
pubMedAbst-class	0.12	0.02	0.50
pubmed	0.13	0.09	0.34
readGEOAnn	0	0	0
serializeEnv	0.01	0.00	0.02
setRepository	0	0	0
updateSymbolsToValidKeys	0	0	0
usedChromGenes	0.08	0.00	0.08

name	user	system	elapsed
ACCNUMStats	1.47	0.03	1.58
GO2heatmap	0.14	0.00	0.14
GOmnplot	0.08	0.00	0.08
HTMLPage-class	0	0	0
LL2homology	0	0	0
PMIDAmat	0.23	0.01	0.25
PWAmat	3.11	0.07	3.17
UniGeneQuery	0.02	0.00	0.02
accessionToUID	2.82	2.17	18.23
annPkgName	0	0	0
aqListGOIDs	0.30	0.03	0.33
blastSequences	0.05	0.00	18.10
buildChromLocation	1.11	0.03	1.14
buildPubMedAbst	0.08	0.03	0.17
chrCats	11.75	0.02	11.77
chromLocation-class	1.08	0.00	1.08
compatibleVersions	0.03	0.00	0.03
dropECode	0.05	0.00	0.05
entrezGeneByID	0	0	0
entrezGeneQuery	0	0	0
filterGOByOntology	0.08	0.00	0.08
findNeighbors	0.02	0.00	0.02
genbank	2.14	1.64	3.89
getAnnMap	0.03	0.00	0.03
getEvidence	0.05	0.00	0.05
getGOTerm	0.15	0.01	0.17
getOntology	0.03	0.00	0.03
getPMInfo	0.61	0.08	0.78
getSYMBOL	0.13	0.00	0.12
getSeq4Acc	0.00	0.00	0.05
hasGOannote	0.03	0.00	0.03
hgByChroms	0.02	0.00	0.02
hgCLengths	0	0	0
hgu95Achroloc	0.06	0.00	0.06
hgu95Achrom	0.05	0.00	0.05
hgu95All	0.06	0.00	0.06
hgu95Asym	0.04	0.00	0.05
homoData-class	0	0	0
htmlpage	0.05	0.00	0.04
isValidkey	0	0	0
makeAnchor	0	0	0
organism	1.08	0.00	1.08
p2LL	0	0	0
pm.abstGrep	2.78	1.53	4.91
pm.getabst	2.90	1.17	4.71
pm.titles	2.62	1.04	4.21
pmAbst2HTML	0.10	0.01	0.61
pmid2MIAME	0	0	0
pmidQuery	0	0	0
pubMedAbst-class	0.08	0.03	0.20
pubmed	0.18	0.03	0.30
readGEOAnn	0	0	0
serializeEnv	0	0	0
setRepository	0.02	0.00	0.01
updateSymbolsToValidKeys	0	0	0
usedChromGenes	0.06	0.00	0.06