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: 2015-10-27 01:17:45 -0400 (Tue, 27 Oct 2015)

EndedAt: 2015-10-27 01:21:05 -0400 (Tue, 27 Oct 2015)

EllapsedTime: 200.0 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 3.2.2 (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 ‘1.48.0’
* 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 ... [36s/77s] OK
Examples with CPU or elapsed time > 5s
                 user system elapsed
chrCats        13.098  0.196  13.353
blastSequences  0.174  0.006  20.882
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘annotate_unit_tests.R’ [6s/9s]
 [6s/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	2.303	0.025	2.334
GO2heatmap	0.225	0.009	0.235
GOmnplot	0.120	0.005	0.125
HTMLPage-class	0.001	0.000	0.001
LL2homology	0.000	0.000	0.001
PMIDAmat	0.298	0.004	0.475
PWAmat	3.968	0.081	4.074
UniGeneQuery	0.001	0.000	0.002
accessionToUID	0.269	0.016	3.541
annPkgName	0.001	0.000	0.045
aqListGOIDs	0.548	0.054	0.871
blastSequences	0.174	0.006	20.882
buildChromLocation	2.702	0.047	2.751
buildPubMedAbst	0.024	0.001	0.386
chrCats	13.098	0.196	13.353
chromLocation-class	2.203	0.017	2.221
compatibleVersions	0.073	0.002	0.075
dropECode	0.068	0.002	0.070
entrezGeneByID	0.001	0.000	0.002
entrezGeneQuery	0.001	0.000	0.001
filterGOByOntology	0.093	0.010	3.348
findNeighbors	0.030	0.003	0.912
genbank	0.103	0.005	1.054
getAnnMap	0.076	0.011	1.119
getEvidence	0.046	0.001	0.046
getGOTerm	0.165	0.008	1.786
getOntology	0.043	0.001	0.044
getPMInfo	0.348	0.002	0.744
getSYMBOL	0.111	0.008	0.552
getSeq4Acc	0.002	0.000	0.176
hasGOannote	0.033	0.002	0.169
hgByChroms	0.013	0.002	0.015
hgCLengths	0.001	0.001	0.001
hgu95Achroloc	0.055	0.005	0.060
hgu95Achrom	0.047	0.004	0.052
hgu95All	0.050	0.005	0.287
hgu95Asym	0.050	0.004	0.055
homoData-class	0.003	0.000	0.003
htmlpage	0.023	0.002	0.024
isValidkey	0	0	0
makeAnchor	0.001	0.000	0.001
organism	1.574	0.030	1.603
p2LL	0.001	0.000	0.001
pm.abstGrep	0.748	0.014	2.126
pm.getabst	0.612	0.007	1.712
pm.titles	0.645	0.012	1.936
pmAbst2HTML	0.029	0.001	0.359
pmid2MIAME	0.001	0.001	0.001
pmidQuery	0.001	0.000	0.001
pubMedAbst-class	0.021	0.000	0.382
pubmed	0.009	0.001	0.389
readGEOAnn	0	0	0
serializeEnv	0.001	0.000	0.002
setRepository	0.002	0.000	0.002
updateSymbolsToValidKeys	0.000	0.000	0.001
usedChromGenes	0.063	0.005	0.108