BioC 3.0: CHECK report for annotate on perceval

Package: annotate

Version: 1.44.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch annotate_1.44.0.tar.gz

StartedAt: 2015-04-09 22:39:34 -0700 (Thu, 09 Apr 2015)

EndedAt: 2015-04-09 22:44:34 -0700 (Thu, 09 Apr 2015)

EllapsedTime: 300.8 seconds

RetCode: 0

Status:  OK

CheckDir: annotate.Rcheck

Warnings: 0

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch annotate_1.44.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.0-bioc/meat/annotate.Rcheck’
* using R version 3.1.3 (2015-03-09)
* using platform: x86_64-apple-darwin10.8.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘annotate/DESCRIPTION’ ... OK
* this is package ‘annotate’ version ‘1.44.0’
* 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 for sufficient/correct file permissions ... OK
* checking whether package ‘annotate’ can be installed ... [17s/28s] 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
* 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
.blastSequencesToDataFrame: no visible global function definition for
  ‘xpathSApply’
.blastSequencesToDataFrame: no visible global function definition for
  ‘xmlToDataFrame’
.blastSequencesToDataFrame: no visible binding for global variable
  ‘xpathSApply’
.blastSequencesToDNAMultipleAlignment: no visible global function
  definition for ‘xpathSApply’
.blastSequencesToDNAMultipleAlignment: no visible global function
  definition for ‘IRanges’
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’
* 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 sizes of PDF files under ‘inst/doc’ ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [63s/96s] OK
Examples with CPU or elapsed time > 5s
                 user system elapsed
chrCats        17.869  0.108  20.257
PWAmat          8.654  0.164   8.822
probesByLL      6.334  0.019   6.356
blastSequences  0.112  0.028  20.339
* checking for unstated dependencies in tests ... OK
* checking tests ...
  Running ‘annotate_unit_tests.R’ [13s/13s]
 [14s/14s] 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

NOTE: There were 2 notes.
See
  ‘/Users/biocbuild/bbs-3.0-bioc/meat/annotate.Rcheck/00check.log’
for details.

* 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
* DONE (annotate)

name	user	system	elapsed
ACCNUMStats	3.449	0.055	3.506
GO2heatmap	0.334	0.029	0.884
GOmnplot	0.207	0.016	0.249
HTMLPage-class	0.001	0.000	0.001
LL2homology	0.001	0.000	0.001
PMIDAmat	0.281	0.010	0.319
PWAmat	8.654	0.164	8.822
UniGeneQuery	0.004	0.000	0.004
accessionToUID	0.234	0.038	2.611
annPkgName	0.001	0.000	0.002
aqListGOIDs	0.586	0.078	0.666
blastSequences	0.112	0.028	20.339
buildChromLocation	2.374	0.116	2.491
buildPubMedAbst	0.037	0.001	0.399
chrCats	17.869	0.108	20.257
chromLocation-class	2.311	0.009	2.320
compatibleVersions	0.192	0.008	0.200
dropECode	0.179	0.008	0.186
entrezGeneByID	0.001	0.001	0.002
entrezGeneQuery	0.002	0.000	0.003
filterGOByOntology	0.131	0.013	0.143
findNeighbors	0.098	0.012	0.141
genbank	0.234	0.027	1.195
getAnnMap	0.148	0.023	0.172
getEvidence	0.150	0.007	0.162
getGOTerm	0.361	0.018	0.477
getOntology	0.154	0.007	0.162
getPMInfo	0.948	0.005	1.333
getSYMBOL	0.303	0.023	0.411
getSeq4Acc	0.006	0.001	0.181
hasGOannote	0.084	0.005	0.089
hgByChroms	0.017	0.006	0.024
hgCLengths	0.002	0.000	0.003
hgu95Achroloc	0.085	0.014	0.099
hgu95Achrom	0.084	0.015	0.098
hgu95All	0.077	0.013	0.089
hgu95Asym	0.081	0.014	0.095
homoData-class	0.005	0.001	0.006
htmlpage	0.047	0.003	0.063
isValidkey	0.001	0.000	0.001
makeAnchor	0.001	0.000	0.002
organism	2.675	0.014	2.690
p2LL	0.001	0.000	0.001
pm.abstGrep	1.423	0.039	2.629
pm.getabst	1.423	0.046	2.634
pm.titles	1.817	0.061	3.047
pmAbst2HTML	0.056	0.003	0.525
pmid2MIAME	0.001	0.000	0.001
pmidQuery	0.001	0.000	0.001
probesByLL	6.334	0.019	6.356
pubMedAbst-class	0.036	0.001	0.399
pubmed	0.017	0.002	0.748
readGEOAnn	0.001	0.000	0.001
serializeEnv	0.003	0.001	0.004
setRepository	0.004	0.000	0.005
updateSymbolsToValidKeys	0.000	0.000	0.001
usedChromGenes	0.111	0.016	0.127