BioC 3.2: CHECK report for annotate on zin1

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: 2016-04-22 22:06:31 -0700 (Fri, 22 Apr 2016)

EndedAt: 2016-04-22 22:09:12 -0700 (Fri, 22 Apr 2016)

EllapsedTime: 160.3 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 3.2.4 Revised (2016-03-16 r70336)
* 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 ... [7s/7s] 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 sizes of PDF files under ‘inst/doc’ ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [29s/80s] OK
Examples with CPU or elapsed time > 5s
                 user system elapsed
chrCats        11.914  0.028  12.055
blastSequences  0.294  0.000  40.084
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘annotate_unit_tests.R’ [6s/6s]
 [6s/6s] 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	1.617	0.028	1.647
GO2heatmap	0.181	0.000	0.183
GOmnplot	0.096	0.000	0.096
HTMLPage-class	0.001	0.000	0.001
LL2homology	0.001	0.000	0.001
PMIDAmat	0.262	0.000	0.350
PWAmat	3.572	0.051	3.641
UniGeneQuery	0.002	0.000	0.002
accessionToUID	0.197	0.020	3.189
annPkgName	0.001	0.000	0.001
aqListGOIDs	0.380	0.000	0.392
blastSequences	0.294	0.000	40.084
buildChromLocation	1.037	0.012	1.048
buildPubMedAbst	0.028	0.000	0.350
chrCats	11.914	0.028	12.055
chromLocation-class	1.108	0.004	1.113
compatibleVersions	0.043	0.008	0.051
dropECode	0.052	0.000	0.054
entrezGeneByID	0.001	0.000	0.000
entrezGeneQuery	0.001	0.000	0.001
filterGOByOntology	0.077	0.000	0.078
findNeighbors	0.029	0.000	0.061
genbank	0.117	0.000	1.198
getAnnMap	0.074	0.016	0.180
getEvidence	0.048	0.004	0.052
getGOTerm	0.173	0.004	0.215
getOntology	0.051	0.000	0.050
getPMInfo	0.452	0.004	0.844
getSYMBOL	0.139	0.004	0.188
getSeq4Acc	0.002	0.000	0.174
hasGOannote	0.034	0.000	0.033
hgByChroms	0.015	0.000	0.016
hgCLengths	0.002	0.000	0.002
hgu95Achroloc	0.07	0.00	0.07
hgu95Achrom	0.059	0.000	0.059
hgu95All	0.065	0.000	0.066
hgu95Asym	0.060	0.000	0.061
homoData-class	0.003	0.000	0.003
htmlpage	0.023	0.000	0.022
isValidkey	0.000	0.000	0.001
makeAnchor	0.001	0.000	0.001
organism	1.146	0.004	1.150
p2LL	0.000	0.000	0.001
pm.abstGrep	0.746	0.008	2.264
pm.getabst	0.774	0.004	2.215
pm.titles	0.726	0.000	2.578
pmAbst2HTML	0.028	0.004	0.744
pmid2MIAME	0.001	0.000	0.000
pmidQuery	0.001	0.000	0.001
pubMedAbst-class	0.025	0.000	0.292
pubmed	0.011	0.000	0.376
readGEOAnn	0	0	0
serializeEnv	0.000	0.000	0.002
setRepository	0.002	0.000	0.002
updateSymbolsToValidKeys	0.000	0.000	0.001
usedChromGenes	0.074	0.004	0.078