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: 2015-10-27 05:23:08 -0400 (Tue, 27 Oct 2015)

EndedAt: 2015-10-27 05:26:58 -0400 (Tue, 27 Oct 2015)

EllapsedTime: 229.6 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 ... [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 ... [49s/96s] OK
Examples with CPU or elapsed time > 5s
                 user system elapsed
chrCats        16.298  0.214  16.849
PWAmat          4.939  0.115   5.055
blastSequences  0.210  0.007  34.943
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘annotate_unit_tests.R’ [9s/10s]
 [9s/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	2.862	0.024	2.893
GO2heatmap	0.271	0.012	0.283
GOmnplot	0.249	0.006	0.256
HTMLPage-class	0.001	0.000	0.001
LL2homology	0.001	0.000	0.001
PMIDAmat	0.482	0.006	0.630
PWAmat	4.939	0.115	5.055
UniGeneQuery	0.005	0.000	0.005
accessionToUID	0.407	0.029	2.454
annPkgName	0.002	0.000	0.002
aqListGOIDs	1.596	0.108	2.540
blastSequences	0.210	0.007	34.943
buildChromLocation	2.897	0.062	2.960
buildPubMedAbst	0.035	0.001	0.408
chrCats	16.298	0.214	16.849
chromLocation-class	2.764	0.012	2.777
compatibleVersions	0.158	0.002	0.160
dropECode	0.125	0.003	0.126
entrezGeneByID	0.001	0.000	0.001
entrezGeneQuery	0.001	0.000	0.002
filterGOByOntology	0.621	0.013	0.930
findNeighbors	0.064	0.005	0.224
genbank	0.180	0.014	1.065
getAnnMap	0.122	0.017	0.367
getEvidence	0.156	0.002	0.158
getGOTerm	0.284	0.012	0.756
getOntology	0.125	0.001	0.127
getPMInfo	0.700	0.002	1.110
getSYMBOL	0.256	0.012	0.425
getSeq4Acc	0.003	0.001	0.181
hasGOannote	0.071	0.002	0.104
hgByChroms	0.017	0.004	0.021
hgCLengths	0.002	0.000	0.002
hgu95Achroloc	0.086	0.010	0.095
hgu95Achrom	0.074	0.008	0.082
hgu95All	0.080	0.008	0.087
hgu95Asym	0.083	0.009	0.092
homoData-class	0.005	0.000	0.006
htmlpage	0.043	0.001	0.051
isValidkey	0.001	0.000	0.002
makeAnchor	0.001	0.000	0.002
organism	2.813	0.010	2.823
p2LL	0.001	0.000	0.001
pm.abstGrep	1.168	0.028	2.546
pm.getabst	1.159	0.021	2.391
pm.titles	1.164	0.019	2.351
pmAbst2HTML	0.048	0.002	0.411
pmid2MIAME	0.001	0.001	0.001
pmidQuery	0.001	0.000	0.001
pubMedAbst-class	0.034	0.001	0.407
pubmed	0.016	0.001	0.567
readGEOAnn	0.001	0.000	0.001
serializeEnv	0.002	0.001	0.003
setRepository	0.004	0.000	0.004
updateSymbolsToValidKeys	0.001	0.000	0.001
usedChromGenes	0.100	0.011	0.112