BioC 3.3: CHECK report for annotate on morelia

Package: annotate

Version: 1.49.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings annotate_1.49.0.tar.gz

StartedAt: 2015-10-22 03:22:59 -0400 (Thu, 22 Oct 2015)

EndedAt: 2015-10-22 03:25:40 -0400 (Thu, 22 Oct 2015)

EllapsedTime: 161.0 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_1.49.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.3-bioc/meat/annotate.Rcheck’
* using R Under development (unstable) (2015-10-08 r69496)
* 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 ‘1.49.0’
* 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’
Undefined global functions or variables:
  GOBPCHILDREN GOBPPARENTS GOCCCHILDREN GOCCPARENTS GOMFCHILDREN
  GOMFPARENTS GOTERM IRanges xmlToDataFrame
* 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 ... [26s/79s] OK
Examples with CPU or elapsed time > 5s
                user system elapsed
chrCats        8.821  0.272   9.528
blastSequences 0.108  0.007  34.779
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘annotate_unit_tests.R’ [5s/5s]
 [5s/5s] 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
  ‘/Users/biocbuild/bbs-3.3-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	1.522	0.019	1.541
GO2heatmap	0.116	0.006	0.121
GOmnplot	0.076	0.003	0.103
HTMLPage-class	0.001	0.000	0.000
LL2homology	0.001	0.000	0.001
PMIDAmat	0.212	0.004	0.386
PWAmat	2.825	0.060	2.885
UniGeneQuery	0.003	0.000	0.003
accessionToUID	0.363	0.015	2.473
annPkgName	0.002	0.000	0.001
aqListGOIDs	0.334	0.038	0.549
blastSequences	0.108	0.007	34.779
buildChromLocation	1.555	0.062	1.616
buildPubMedAbst	0.020	0.001	0.377
chrCats	8.821	0.272	9.528
chromLocation-class	1.436	0.021	1.456
compatibleVersions	0.027	0.001	0.029
dropECode	0.031	0.001	0.032
entrezGeneByID	0.001	0.000	0.001
entrezGeneQuery	0.000	0.001	0.001
filterGOByOntology	0.068	0.008	4.096
findNeighbors	0.016	0.003	0.194
genbank	0.103	0.006	1.156
getAnnMap	0.032	0.009	0.337
getEvidence	0.034	0.001	0.063
getGOTerm	0.136	0.009	1.496
getOntology	0.033	0.001	0.035
getPMInfo	0.376	0.014	0.728
getSYMBOL	0.093	0.010	0.602
getSeq4Acc	0.002	0.000	0.182
hasGOannote	0.022	0.001	0.174
hgByChroms	0.013	0.004	0.017
hgCLengths	0.001	0.001	0.001
hgu95Achroloc	0.050	0.007	0.057
hgu95Achrom	0.042	0.009	0.051
hgu95All	0.047	0.008	0.056
hgu95Asym	0.050	0.009	0.058
homoData-class	0.002	0.000	0.003
htmlpage	0.020	0.001	0.036
isValidkey	0.001	0.000	0.000
makeAnchor	0.000	0.000	0.001
organism	1.505	0.013	1.518
p2LL	0.000	0.000	0.001
pm.abstGrep	0.611	0.010	1.799
pm.getabst	0.626	0.007	1.850
pm.titles	0.625	0.008	2.268
pmAbst2HTML	0.028	0.001	0.772
pmid2MIAME	0	0	0
pmidQuery	0.001	0.000	0.001
pubMedAbst-class	0.019	0.000	0.751
pubmed	0.010	0.001	0.760
readGEOAnn	0	0	0
serializeEnv	0.002	0.000	0.002
setRepository	0.002	0.000	0.002
updateSymbolsToValidKeys	0.000	0.000	0.001
usedChromGenes	0.061	0.006	0.067