BioC 3.2: CHECK report for annotate on oaxaca

Package: annotate

Version: 1.48.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings annotate_1.48.0.tar.gz

StartedAt: 2016-04-22 21:47:21 -0700 (Fri, 22 Apr 2016)

EndedAt: 2016-04-22 21:50:50 -0700 (Fri, 22 Apr 2016)

EllapsedTime: 208.8 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 annotate_1.48.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.2-bioc/meat/annotate.Rcheck’
* using R version 3.2.4 (2016-03-10)
* using platform: x86_64-apple-darwin13.4.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘annotate/DESCRIPTION’ ... OK
* this is package ‘annotate’ version ‘1.48.0’
* 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 ... [10s/10s] 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
.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’
* 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 ... [40s/100s] OK
Examples with CPU or elapsed time > 5s
                 user system elapsed
chrCats        14.412  0.234  14.658
blastSequences  0.197  0.010  47.910
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘annotate_unit_tests.R’ [8s/8s]
 [8s/9s] 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
  ‘/Users/biocbuild/bbs-3.2-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	2.328	0.026	2.355
GO2heatmap	0.194	0.009	0.203
GOmnplot	0.133	0.007	0.140
HTMLPage-class	0.001	0.000	0.000
LL2homology	0.000	0.000	0.001
PMIDAmat	0.328	0.004	0.447
PWAmat	3.873	0.084	3.960
UniGeneQuery	0.003	0.000	0.003
accessionToUID	0.497	0.029	3.961
annPkgName	0.001	0.000	0.001
aqListGOIDs	0.517	0.048	1.523
blastSequences	0.197	0.010	47.910
buildChromLocation	2.531	0.070	2.603
buildPubMedAbst	0.036	0.001	0.359
chrCats	14.412	0.234	14.658
chromLocation-class	1.971	0.020	1.992
compatibleVersions	0.070	0.001	0.072
dropECode	0.061	0.002	0.062
entrezGeneByID	0.001	0.000	0.001
entrezGeneQuery	0.002	0.000	0.001
filterGOByOntology	0.093	0.007	0.100
findNeighbors	0.057	0.012	0.149
genbank	0.147	0.008	1.086
getAnnMap	0.112	0.011	0.399
getEvidence	0.072	0.001	0.073
getGOTerm	0.229	0.006	0.338
getOntology	0.070	0.002	0.072
getPMInfo	0.601	0.003	0.970
getSYMBOL	0.205	0.015	0.278
getSeq4Acc	0.003	0.001	0.182
hasGOannote	0.048	0.001	0.050
hgByChroms	0.016	0.004	0.019
hgCLengths	0.001	0.001	0.002
hgu95Achroloc	0.077	0.008	0.086
hgu95Achrom	0.069	0.009	0.078
hgu95All	0.079	0.010	0.088
hgu95Asym	0.072	0.009	0.082
homoData-class	0.005	0.001	0.005
htmlpage	0.035	0.002	0.036
isValidkey	0.001	0.000	0.001
makeAnchor	0.002	0.000	0.001
organism	2.552	0.021	2.574
p2LL	0.000	0.000	0.001
pm.abstGrep	1.069	0.023	2.254
pm.getabst	1.104	0.021	2.262
pm.titles	1.099	0.019	2.247
pmAbst2HTML	0.057	0.002	0.363
pmid2MIAME	0.001	0.001	0.001
pmidQuery	0.001	0.000	0.002
pubMedAbst-class	0.261	0.026	1.218
pubmed	0.010	0.001	0.389
readGEOAnn	0.001	0.000	0.001
serializeEnv	0.003	0.000	0.002
setRepository	0.004	0.000	0.004
updateSymbolsToValidKeys	0.001	0.000	0.001
usedChromGenes	0.092	0.006	0.099