BioC 3.2: CHECK report for annotate on linux1.bioconductor.org

Package: annotate

Version: 1.48.0

Command: /home/biocbuild/bbs-3.2-bioc/R/bin/R CMD check --no-vignettes --timings annotate_1.48.0.tar.gz

StartedAt: 2015-10-27 01:00:35 -0400 (Tue, 27 Oct 2015)

EndedAt: 2015-10-27 01:03:10 -0400 (Tue, 27 Oct 2015)

EllapsedTime: 154.8 seconds

RetCode: 0

Status:  OK

CheckDir: annotate.Rcheck

Warnings: 0

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### Running command:
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###   /home/biocbuild/bbs-3.2-bioc/R/bin/R CMD check --no-vignettes --timings annotate_1.48.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.2-bioc/meat/annotate.Rcheck’
* using R version 3.2.2 (2015-08-14)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘annotate/DESCRIPTION’ ... OK
* this is package ‘annotate’ version ‘1.48.0’
* 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 ... [8s/8s] 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 installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [30s/72s] OK
Examples with CPU or elapsed time > 5s
                 user system elapsed
chrCats        10.657  0.020  10.689
blastSequences  0.119  0.008  36.896
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘annotate_unit_tests.R’ [6s/6s]
 [7s/7s] 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
  ‘/home/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	2.270	0.024	2.308
GO2heatmap	0.173	0.004	0.177
GOmnplot	0.078	0.000	0.079
HTMLPage-class	0.000	0.000	0.001
LL2homology	0	0	0
PMIDAmat	0.229	0.008	0.243
PWAmat	3.408	0.044	3.453
UniGeneQuery	0.002	0.000	0.002
accessionToUID	0.293	0.016	1.593
annPkgName	0.001	0.000	0.001
aqListGOIDs	0.474	0.020	0.495
blastSequences	0.119	0.008	36.896
buildChromLocation	1.539	0.028	1.572
buildPubMedAbst	0.035	0.000	0.469
chrCats	10.657	0.020	10.689
chromLocation-class	0.843	0.000	0.843
compatibleVersions	0.033	0.004	0.037
dropECode	0.039	0.000	0.039
entrezGeneByID	0.001	0.000	0.001
entrezGeneQuery	0.001	0.000	0.001
filterGOByOntology	0.063	0.000	0.063
findNeighbors	0.023	0.000	0.033
genbank	0.098	0.000	0.404
getAnnMap	0.063	0.000	0.126
getEvidence	0.057	0.000	0.057
getGOTerm	0.148	0.000	0.147
getOntology	0.038	0.000	0.038
getPMInfo	0.665	0.004	1.151
getSYMBOL	0.176	0.000	0.179
getSeq4Acc	0.003	0.000	0.058
hasGOannote	0.04	0.00	0.04
hgByChroms	0.019	0.000	0.019
hgCLengths	0.002	0.000	0.002
hgu95Achroloc	0.088	0.000	0.088
hgu95Achrom	0.076	0.000	0.076
hgu95All	0.079	0.004	0.084
hgu95Asym	0.081	0.004	0.085
homoData-class	0.003	0.000	0.004
htmlpage	0.031	0.000	0.031
isValidkey	0.001	0.000	0.001
makeAnchor	0.001	0.000	0.001
organism	1.526	0.012	1.545
p2LL	0.000	0.000	0.001
pm.abstGrep	1.040	0.012	1.598
pm.getabst	0.612	0.004	1.178
pm.titles	0.871	0.000	1.589
pmAbst2HTML	0.047	0.000	0.242
pmid2MIAME	0.001	0.000	0.001
pmidQuery	0.002	0.000	0.001
pubMedAbst-class	0.032	0.000	0.121
pubmed	0.009	0.000	0.257
readGEOAnn	0	0	0
serializeEnv	0.001	0.000	0.001
setRepository	0.002	0.000	0.002
updateSymbolsToValidKeys	0	0	0
usedChromGenes	0.060	0.008	0.066