BioC 3.2: CHECK report for annotate on perceval

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: 2015-11-10 01:59:52 -0800 (Tue, 10 Nov 2015)

EndedAt: 2015-11-10 02:09:54 -0800 (Tue, 10 Nov 2015)

EllapsedTime: 602.1 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_1.48.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.2-bioc/meat/annotate.Rcheck’
* using R version 3.2.2 Patched (2015-10-08 r69496)
* 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 ‘1.48.0’
* 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/96s] 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 ... [45s/240s] OK
Examples with CPU or elapsed time > 5s
                     user system elapsed
chrCats            15.849  0.111  24.606
ACCNUMStats         2.583  0.040   6.327
aqListGOIDs         1.407  0.265  92.253
filterGOByOntology  0.607  0.025  13.379
getGOTerm           0.257  0.019   6.272
blastSequences      0.201  0.007  26.411
getAnnMap           0.101  0.055  25.228
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘annotate_unit_tests.R’ [9s/53s]
 [9s/53s] 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	2.583	0.040	6.327
GO2heatmap	0.238	0.012	0.250
GOmnplot	0.188	0.006	0.370
HTMLPage-class	0.001	0.000	0.001
LL2homology	0.001	0.000	0.001
PMIDAmat	0.398	0.007	2.227
PWAmat	3.984	0.085	4.069
UniGeneQuery	0.003	0.001	0.003
accessionToUID	0.301	0.027	3.255
annPkgName	0.001	0.000	0.001
aqListGOIDs	1.407	0.265	92.253
blastSequences	0.201	0.007	26.411
buildChromLocation	2.943	0.066	4.034
buildPubMedAbst	0.035	0.001	0.512
chrCats	15.849	0.111	24.606
chromLocation-class	2.584	0.013	2.596
compatibleVersions	0.146	0.002	0.148
dropECode	0.123	0.002	0.125
entrezGeneByID	0.002	0.001	0.002
entrezGeneQuery	0.002	0.000	0.001
filterGOByOntology	0.607	0.025	13.379
findNeighbors	0.062	0.007	1.802
genbank	0.177	0.013	1.056
getAnnMap	0.101	0.055	25.228
getEvidence	0.142	0.002	0.144
getGOTerm	0.257	0.019	6.272
getOntology	0.114	0.002	0.116
getPMInfo	0.659	0.005	1.161
getSYMBOL	0.250	0.017	2.725
getSeq4Acc	0.003	0.001	0.201
hasGOannote	0.068	0.002	0.165
hgByChroms	0.018	0.006	0.024
hgCLengths	0.002	0.000	0.002
hgu95Achroloc	0.080	0.014	0.094
hgu95Achrom	0.070	0.013	0.083
hgu95All	0.074	0.013	0.087
hgu95Asym	0.077	0.014	0.091
homoData-class	0.004	0.000	0.004
htmlpage	0.034	0.002	0.395
isValidkey	0.001	0.000	0.001
makeAnchor	0.001	0.001	0.001
organism	2.610	0.007	2.617
p2LL	0.001	0.000	0.001
pm.abstGrep	1.083	0.022	2.338
pm.getabst	1.082	0.020	2.208
pm.titles	1.089	0.020	2.260
pmAbst2HTML	0.046	0.004	0.646
pmid2MIAME	0.000	0.000	0.001
pmidQuery	0.001	0.000	0.002
pubMedAbst-class	0.033	0.000	0.322
pubmed	0.015	0.001	0.411
readGEOAnn	0.001	0.000	0.001
serializeEnv	0.002	0.000	0.036
setRepository	0.004	0.000	0.004
updateSymbolsToValidKeys	0.001	0.001	0.001
usedChromGenes	0.088	0.008	0.096