BioC 3.4: CHECK report for annotate on zin1

Package: annotate

Version: 1.51.1

Command: /home/biocbuild/bbs-3.4-bioc/R/bin/R CMD check --no-vignettes --timings annotate_1.51.1.tar.gz

StartedAt: 2016-09-20 03:09:48 -0700 (Tue, 20 Sep 2016)

EndedAt: 2016-09-20 03:12:23 -0700 (Tue, 20 Sep 2016)

EllapsedTime: 154.9 seconds

RetCode: 0

Status:  OK

CheckDir: annotate.Rcheck

Warnings: 0

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### Running command:
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###   /home/biocbuild/bbs-3.4-bioc/R/bin/R CMD check --no-vignettes --timings annotate_1.51.1.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.4-bioc/meat/annotate.Rcheck’
* using R version 3.3.1 (2016-06-21)
* 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 ‘1.51.1’
* 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 ... 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
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 ... OK
* 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 ... OK
Examples with CPU or elapsed time > 5s
                 user system elapsed
chrCats        10.364  0.008  10.369
blastSequences  0.136  0.004  43.728
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘annotate_unit_tests.R’
 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: 1 NOTE
See
  ‘/home/biocbuild/bbs-3.4-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	1.504	0.016	1.520
GO2heatmap	0.132	0.004	0.136
GOmnplot	0.076	0.000	0.076
HTMLPage-class	0	0	0
LL2homology	0.004	0.000	0.001
PMIDAmat	0.116	0.000	0.208
PWAmat	2.996	0.032	3.026
UniGeneQuery	0.004	0.000	0.002
accessionToUID	0.432	0.008	3.293
annPkgName	0.000	0.000	0.001
aqListGOIDs	0.288	0.000	0.288
blastSequences	0.136	0.004	43.728
buildChromLocation	1.088	0.020	1.109
buildPubMedAbst	0.036	0.000	0.665
chrCats	10.364	0.008	10.369
chromLocation-class	0.984	0.000	0.985
compatibleVersions	0.036	0.000	0.036
dropECode	0.040	0.000	0.038
entrezGeneByID	0.004	0.000	0.001
entrezGeneQuery	0.000	0.000	0.001
filterGOByOntology	0.064	0.004	0.066
findNeighbors	0.020	0.000	0.063
genbank	0.140	0.004	1.083
getAnnMap	0.032	0.000	0.138
getEvidence	0.028	0.000	0.028
getGOTerm	0.148	0.004	0.152
getOntology	0.028	0.000	0.030
getPMInfo	0.436	0.012	1.198
getSYMBOL	0.100	0.004	0.170
getSeq4Acc	0.016	0.000	0.499
hasGOannote	0.02	0.00	0.02
hgByChroms	0.016	0.000	0.014
hgCLengths	0.000	0.000	0.002
hgu95Achroloc	0.056	0.000	0.060
hgu95Achrom	0.048	0.004	0.052
hgu95All	0.056	0.000	0.056
hgu95Asym	0.056	0.004	0.058
homoData-class	0.004	0.000	0.002
htmlpage	0.020	0.000	0.021
isValidkey	0.000	0.000	0.001
makeAnchor	0	0	0
organism	1.060	0.000	1.061
p2LL	0	0	0
pm.abstGrep	0.712	0.012	2.094
pm.getabst	0.716	0.008	2.182
pm.titles	0.776	0.000	2.170
pmAbst2HTML	0.044	0.000	1.043
pmid2MIAME	0	0	0
pmidQuery	0.000	0.000	0.001
pubMedAbst-class	0.032	0.000	0.923
pubmed	0.016	0.004	0.686
readGEOAnn	0	0	0
serializeEnv	0.000	0.000	0.002
setRepository	0.000	0.000	0.002
updateSymbolsToValidKeys	0.004	0.000	0.000
usedChromGenes	0.072	0.000	0.073