BioC 3.3: CHECK report for annotate on morelia

Package: annotate

Version: 1.49.2

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings annotate_1.49.2.tar.gz

StartedAt: 2016-04-20 23:14:58 -0700 (Wed, 20 Apr 2016)

EndedAt: 2016-04-20 23:17:41 -0700 (Wed, 20 Apr 2016)

EllapsedTime: 162.7 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_1.49.2.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.3-bioc/meat/annotate.Rcheck’
* using R version 3.3.0 beta (2016-04-06 r70435)
* 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 ‘1.49.2’
* 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’
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 ... [34s/67s] OK
Examples with CPU or elapsed time > 5s
                 user system elapsed
chrCats        11.963  0.143  12.639
blastSequences  0.177  0.006  17.211
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘annotate_unit_tests.R’ [7s/7s]
 [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
  ‘/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	1.978	0.021	2.002
GO2heatmap	0.157	0.006	0.163
GOmnplot	0.101	0.006	0.187
HTMLPage-class	0.001	0.000	0.001
LL2homology	0.000	0.001	0.001
PMIDAmat	0.256	0.004	0.453
PWAmat	3.212	0.072	3.287
UniGeneQuery	0.001	0.000	0.002
accessionToUID	0.268	0.015	3.088
annPkgName	0.001	0.000	0.001
aqListGOIDs	0.476	0.029	0.508
blastSequences	0.177	0.006	17.211
buildChromLocation	2.567	0.072	2.658
buildPubMedAbst	0.031	0.001	0.366
chrCats	11.963	0.143	12.639
chromLocation-class	2.239	0.016	2.259
compatibleVersions	0.039	0.001	0.041
dropECode	0.041	0.000	0.042
entrezGeneByID	0.001	0.000	0.002
entrezGeneQuery	0.001	0.000	0.001
filterGOByOntology	0.101	0.004	0.105
findNeighbors	0.025	0.003	0.084
genbank	0.153	0.008	1.526
getAnnMap	0.044	0.011	0.216
getEvidence	0.043	0.001	0.044
getGOTerm	0.188	0.008	0.413
getOntology	0.046	0.002	0.048
getPMInfo	0.583	0.006	1.006
getSYMBOL	0.142	0.017	0.337
getSeq4Acc	0.003	0.001	0.213
hasGOannote	0.027	0.001	0.039
hgByChroms	0.015	0.011	0.026
hgCLengths	0.001	0.001	0.002
hgu95Achroloc	0.078	0.023	0.102
hgu95Achrom	0.073	0.020	0.094
hgu95All	0.079	0.020	0.099
hgu95Asym	0.083	0.020	0.104
homoData-class	0.004	0.000	0.004
htmlpage	0.032	0.002	0.034
isValidkey	0.001	0.000	0.001
makeAnchor	0.001	0.001	0.001
organism	2.425	0.011	2.439
p2LL	0.001	0.000	0.001
pm.abstGrep	0.909	0.024	2.839
pm.getabst	1.049	0.039	2.295
pm.titles	0.754	0.015	3.424
pmAbst2HTML	0.037	0.005	0.345
pmid2MIAME	0	0	0
pmidQuery	0.001	0.000	0.001
pubMedAbst-class	0.030	0.001	0.357
pubmed	0.023	0.001	2.362
readGEOAnn	0	0	0
serializeEnv	0.002	0.001	0.002
setRepository	0.002	0.000	0.002
updateSymbolsToValidKeys	0.000	0.000	0.001
usedChromGenes	0.078	0.013	0.090