BioC 3.4: CHECK report for annotate on morelia

Package: annotate

Version: 1.52.1

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings annotate_1.52.1.tar.gz

StartedAt: 2017-04-14 22:36:17 -0700 (Fri, 14 Apr 2017)

EndedAt: 2017-04-14 22:45:36 -0700 (Fri, 14 Apr 2017)

EllapsedTime: 559.4 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_1.52.1.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.4-bioc/meat/annotate.Rcheck’
* using R version 3.3.3 (2017-03-06)
* using platform: x86_64-apple-darwin13.4.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘annotate/DESCRIPTION’ ... OK
* this is package ‘annotate’ version ‘1.52.1’
* 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 ... OK
* 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        10.454  0.120  11.080
blastSequences  4.618  0.101 408.513
* 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: OK

* 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	2.343	0.029	2.373
GO2heatmap	0.134	0.008	0.141
GOmnplot	0.056	0.004	0.069
HTMLPage-class	0.001	0.000	0.001
LL2homology	0.001	0.000	0.000
PMIDAmat	0.152	0.005	0.379
PWAmat	3.664	0.064	3.731
UniGeneQuery	0.003	0.000	0.003
accessionToUID	0.591	0.033	4.824
annPkgName	0.001	0.000	0.002
aqListGOIDs	0.407	0.028	0.490
blastSequences	4.618	0.101	408.513
buildChromLocation	2.439	0.065	2.504
buildPubMedAbst	0.045	0.002	0.663
chrCats	10.454	0.120	11.080
chromLocation-class	2.211	0.019	2.231
compatibleVersions	0.040	0.001	0.041
dropECode	0.047	0.001	0.048
entrezGeneByID	0.001	0.000	0.001
entrezGeneQuery	0.001	0.000	0.001
filterGOByOntology	0.095	0.004	0.100
findNeighbors	0.020	0.002	0.088
genbank	0.134	0.010	1.195
getAnnMap	0.042	0.010	0.270
getEvidence	0.043	0.001	0.044
getGOTerm	0.208	0.008	0.327
getOntology	0.040	0.001	0.041
getPMInfo	0.436	0.003	1.110
getSYMBOL	0.136	0.012	0.241
getSeq4Acc	0.014	0.001	0.494
hasGOannote	0.025	0.000	0.026
hgByChroms	0.015	0.004	0.019
hgCLengths	0.002	0.000	0.002
hgu95Achroloc	0.064	0.007	0.072
hgu95Achrom	0.043	0.006	0.050
hgu95All	0.051	0.008	0.057
hgu95Asym	0.049	0.007	0.056
homoData-class	0.002	0.000	0.002
htmlpage	0.020	0.006	0.026
isValidkey	0.000	0.000	0.001
makeAnchor	0.001	0.000	0.001
organism	2.105	0.015	2.120
p2LL	0.001	0.000	0.000
pm.abstGrep	0.772	0.024	2.383
pm.getabst	0.928	0.020	2.386
pm.titles	0.971	0.030	2.448
pmAbst2HTML	0.052	0.003	0.649
pmid2MIAME	0.001	0.000	0.001
pmidQuery	0.001	0.001	0.001
pubMedAbst-class	0.051	0.001	0.704
pubmed	0.024	0.001	0.717
readGEOAnn	0.001	0.001	0.000
serializeEnv	0.002	0.000	0.002
setRepository	0.002	0.000	0.003
updateSymbolsToValidKeys	0.001	0.000	0.001
usedChromGenes	0.073	0.007	0.079