BioC 3.2: CHECK report for annotate on oaxaca

Package: annotate

Version: 1.47.4

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings annotate_1.47.4.tar.gz

StartedAt: 2015-08-23 21:38:10 -0700 (Sun, 23 Aug 2015)

EndedAt: 2015-08-23 21:41:52 -0700 (Sun, 23 Aug 2015)

EllapsedTime: 222.1 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_1.47.4.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.2-bioc/meat/annotate.Rcheck’
* using R version 3.2.2 (2015-08-14)
* 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 ‘1.47.4’
* 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 ... [11s/11s] 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 ... [42s/97s] OK
Examples with CPU or elapsed time > 5s
                 user system elapsed
chrCats        15.768  0.200  16.297
blastSequences  0.184  0.005  43.359
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘annotate_unit_tests.R’ [9s/9s]
 [9s/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	2.525	0.030	2.559
GO2heatmap	0.217	0.010	0.228
GOmnplot	0.129	0.004	0.134
HTMLPage-class	0.001	0.000	0.001
LL2homology	0.001	0.000	0.001
PMIDAmat	0.168	0.004	0.252
PWAmat	4.156	0.088	4.251
UniGeneQuery	0.002	0.000	0.002
accessionToUID	0.266	0.014	2.098
annPkgName	0.001	0.000	0.002
aqListGOIDs	0.755	0.042	0.801
blastSequences	0.184	0.005	43.359
buildChromLocation	2.236	0.040	2.296
buildPubMedAbst	0.039	0.001	0.370
chrCats	15.768	0.200	16.297
chromLocation-class	2.327	0.011	2.362
compatibleVersions	0.097	0.003	0.102
dropECode	0.081	0.002	0.084
entrezGeneByID	0.001	0.001	0.002
entrezGeneQuery	0.001	0.000	0.002
filterGOByOntology	0.122	0.005	0.127
findNeighbors	0.043	0.003	0.101
genbank	0.170	0.007	1.472
getAnnMap	0.122	0.013	0.273
getEvidence	0.072	0.001	0.074
getGOTerm	0.256	0.007	0.296
getOntology	0.075	0.002	0.076
getPMInfo	0.675	0.003	1.074
getSYMBOL	0.204	0.013	0.295
getSeq4Acc	0.003	0.001	0.608
hasGOannote	0.050	0.002	0.051
hgByChroms	0.018	0.004	0.022
hgCLengths	0.002	0.000	0.003
hgu95Achroloc	0.085	0.010	0.095
hgu95Achrom	0.072	0.009	0.092
hgu95All	0.078	0.009	0.092
hgu95Asym	0.076	0.009	0.086
homoData-class	0.004	0.000	0.005
htmlpage	0.036	0.002	0.039
isValidkey	0.001	0.000	0.001
makeAnchor	0.001	0.000	0.001
organism	2.445	0.018	2.471
p2LL	0.000	0.000	0.001
pm.abstGrep	1.079	0.017	2.687
pm.getabst	0.985	0.014	2.586
pm.titles	1.047	0.012	2.977
pmAbst2HTML	0.057	0.002	0.942
pmid2MIAME	0	0	0
pmidQuery	0.001	0.000	0.001
pubMedAbst-class	0.033	0.001	0.386
pubmed	0.015	0.001	0.354
readGEOAnn	0.001	0.000	0.001
serializeEnv	0.002	0.000	0.002
setRepository	0.003	0.000	0.004
updateSymbolsToValidKeys	0.000	0.001	0.001
usedChromGenes	0.093	0.010	0.103