BioC 3.2: CHECK report for annotate on perceval

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 22:10:01 -0700 (Sun, 23 Aug 2015)

EndedAt: 2015-08-23 22:13:49 -0700 (Sun, 23 Aug 2015)

EllapsedTime: 228.3 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 Patched (2015-08-14 r69078)
* 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 ‘1.47.4’
* 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 ... [12s/12s] 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
  ‘xmlToDataFrame’
.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 ... [46s/98s] OK
Examples with CPU or elapsed time > 5s
                 user system elapsed
chrCats        15.856  0.069  15.979
PWAmat          4.863  0.148   5.011
blastSequences  0.205  0.018  43.122
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘annotate_unit_tests.R’ [10s/10s]
 [10s/10s] 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	2.713	0.034	2.748
GO2heatmap	0.258	0.016	0.275
GOmnplot	0.174	0.006	0.181
HTMLPage-class	0.001	0.001	0.001
LL2homology	0.000	0.000	0.001
PMIDAmat	0.613	0.005	0.621
PWAmat	4.863	0.148	5.011
UniGeneQuery	0.003	0.000	0.003
accessionToUID	0.687	0.040	2.593
annPkgName	0.001	0.000	0.001
aqListGOIDs	1.287	0.064	1.353
blastSequences	0.205	0.018	43.122
buildChromLocation	2.134	0.109	2.243
buildPubMedAbst	0.036	0.002	0.374
chrCats	15.856	0.069	15.979
chromLocation-class	2.120	0.025	2.146
compatibleVersions	0.157	0.003	0.184
dropECode	0.131	0.002	0.134
entrezGeneByID	0.002	0.000	0.001
entrezGeneQuery	0.002	0.000	0.002
filterGOByOntology	0.584	0.011	0.597
findNeighbors	0.070	0.005	0.118
genbank	0.170	0.018	1.034
getAnnMap	0.118	0.023	0.258
getEvidence	0.121	0.002	0.124
getGOTerm	0.317	0.013	0.382
getOntology	0.124	0.001	0.126
getPMInfo	0.667	0.003	1.141
getSYMBOL	0.273	0.017	0.290
getSeq4Acc	0.004	0.001	0.179
hasGOannote	0.076	0.003	0.079
hgByChroms	0.019	0.007	0.026
hgCLengths	0.003	0.001	0.005
hgu95Achroloc	0.077	0.010	0.087
hgu95Achrom	0.093	0.011	0.103
hgu95All	0.072	0.010	0.082
hgu95Asym	0.077	0.011	0.087
homoData-class	0.004	0.000	0.004
htmlpage	0.034	0.002	0.036
isValidkey	0.000	0.000	0.001
makeAnchor	0.001	0.001	0.001
organism	2.149	0.010	2.160
p2LL	0.001	0.001	0.001
pm.abstGrep	1.227	0.031	2.748
pm.getabst	1.163	0.031	2.321
pm.titles	1.121	0.024	2.308
pmAbst2HTML	0.046	0.004	0.408
pmid2MIAME	0.001	0.000	0.000
pmidQuery	0.002	0.000	0.004
pubMedAbst-class	0.036	0.001	0.412
pubmed	0.016	0.002	0.365
readGEOAnn	0.001	0.000	0.001
serializeEnv	0.004	0.001	0.004
setRepository	0.005	0.001	0.005
updateSymbolsToValidKeys	0.001	0.000	0.002
usedChromGenes	0.091	0.016	0.107