BioC 3.0: CHECK report for annotate on zin1

Package: annotate

Version: 1.44.0

Command: /home/biocbuild/bbs-3.0-bioc/R/bin/R CMD check --no-vignettes --timings annotate_1.44.0.tar.gz

StartedAt: 2015-04-09 21:31:34 -0700 (Thu, 09 Apr 2015)

EndedAt: 2015-04-09 21:34:40 -0700 (Thu, 09 Apr 2015)

EllapsedTime: 186.5 seconds

RetCode: 0

Status:  OK

CheckDir: annotate.Rcheck

Warnings: 0

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### Running command:
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###   /home/biocbuild/bbs-3.0-bioc/R/bin/R CMD check --no-vignettes --timings annotate_1.44.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.0-bioc/meat/annotate.Rcheck’
* using R version 3.1.3 (2015-03-09)
* using platform: x86_64-unknown-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘annotate/DESCRIPTION’ ... OK
* this is package ‘annotate’ version ‘1.44.0’
* 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 ... [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 ‘xpathSApply’
.blastSequencesToDNAMultipleAlignment: no visible global function
  definition for ‘IRanges’
.blastSequencesToDataFrame: no visible global function definition for
  ‘xpathSApply’
.blastSequencesToDataFrame: no visible global function definition for
  ‘xmlToDataFrame’
.blastSequencesToDataFrame: no visible binding for global variable
  ‘xpathSApply’
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 installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [40s/69s] OK
Examples with CPU or elapsed time > 5s
                 user system elapsed
chrCats        13.693  0.020  13.758
blastSequences  0.076  0.012  19.883
* checking for unstated dependencies in tests ... OK
* checking tests ...
  Running ‘annotate_unit_tests.R’ [8s/8s]
 [8s/8s] 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

NOTE: There were 2 notes.
See
  ‘/home/biocbuild/bbs-3.0-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	2.000	0.036	2.040
GO2heatmap	0.160	0.016	0.176
GOmnplot	0.100	0.012	0.111
HTMLPage-class	0	0	0
LL2homology	0	0	0
PMIDAmat	0.136	0.000	0.168
PWAmat	4.744	0.060	4.810
UniGeneQuery	0.004	0.000	0.003
accessionToUID	0.176	0.004	2.152
annPkgName	0.000	0.000	0.001
aqListGOIDs	0.336	0.020	0.355
blastSequences	0.076	0.012	19.883
buildChromLocation	1.168	0.024	1.224
buildPubMedAbst	0.032	0.000	0.615
chrCats	13.693	0.020	13.758
chromLocation-class	1.032	0.000	1.034
compatibleVersions	0.072	0.004	0.075
dropECode	0.076	0.008	0.086
entrezGeneByID	0.000	0.000	0.001
entrezGeneQuery	0.000	0.000	0.001
filterGOByOntology	0.06	0.00	0.06
findNeighbors	0.036	0.004	0.083
genbank	0.124	0.004	1.067
getAnnMap	0.084	0.000	0.083
getEvidence	0.060	0.008	0.071
getGOTerm	0.192	0.000	0.190
getOntology	0.068	0.004	0.071
getPMInfo	0.660	0.000	1.092
getSYMBOL	0.164	0.000	0.185
getSeq4Acc	0.000	0.000	0.172
hasGOannote	0.040	0.000	0.041
hgByChroms	0.016	0.000	0.015
hgCLengths	0.004	0.000	0.002
hgu95Achroloc	0.064	0.000	0.065
hgu95Achrom	0.060	0.000	0.057
hgu95All	0.068	0.000	0.070
hgu95Asym	0.068	0.000	0.071
homoData-class	0.004	0.000	0.004
htmlpage	0.032	0.000	0.033
isValidkey	0.000	0.000	0.001
makeAnchor	0.000	0.000	0.001
organism	1.108	0.008	1.117
p2LL	0.000	0.000	0.001
pm.abstGrep	0.953	0.000	2.027
pm.getabst	1.144	0.000	2.367
pm.titles	0.880	0.000	2.076
pmAbst2HTML	0.044	0.000	0.400
pmid2MIAME	0.000	0.000	0.001
pmidQuery	0.004	0.000	0.001
probesByLL	4.816	0.000	4.825
pubMedAbst-class	0.028	0.000	0.483
pubmed	0.012	0.000	0.388
readGEOAnn	0	0	0
serializeEnv	0.004	0.000	0.003
setRepository	0.004	0.000	0.003
updateSymbolsToValidKeys	0.000	0.000	0.001
usedChromGenes	0.076	0.004	0.080