BioC 3.1: CHECK report for annotate on petty

Package: annotate

Version: 1.46.1

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings annotate_1.46.1.tar.gz

StartedAt: 2015-10-08 21:26:01 -0700 (Thu, 08 Oct 2015)

EndedAt: 2015-10-08 21:30:22 -0700 (Thu, 08 Oct 2015)

EllapsedTime: 261.2 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_1.46.1.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.1-bioc/meat/annotate.Rcheck’
* using R version 3.2.2 Patched (2015-08-14 r69078)
* using platform: x86_64-apple-darwin10.8.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘annotate/DESCRIPTION’ ... OK
* this is package ‘annotate’ version ‘1.46.1’
* 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 ... [14s/14s] 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
.blastSequencesToDataFrame: no visible global function definition for
  ‘xpathSApply’
.blastSequencesToDataFrame: no visible global function definition for
  ‘xmlToDataFrame’
.blastSequencesToDataFrame: no visible binding for global variable
  ‘xpathSApply’
.blastSequencesToDNAMultipleAlignment: no visible global function
  definition for ‘xpathSApply’
.blastSequencesToDNAMultipleAlignment: no visible global function
  definition for ‘IRanges’
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 ... [57s/98s] OK
Examples with CPU or elapsed time > 5s
                 user system elapsed
chrCats        19.338  0.113  19.516
PWAmat          5.711  0.109   5.824
blastSequences  0.146  0.007  30.675
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘annotate_unit_tests.R’ [12s/12s]
 [12s/12s] 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-3.1-bioc/meat/annotate.Rcheck/00check.log’
for details.

* installing *source* package ‘annotate’ ...
** R
** data
** inst
** preparing package for lazy loading
Creating a generic function for ‘nchar’ from package ‘base’ in package ‘S4Vectors’
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
Creating a generic function for ‘nchar’ from package ‘base’ in package ‘S4Vectors’
* DONE (annotate)

name	user	system	elapsed
ACCNUMStats	3.471	0.039	3.512
GO2heatmap	0.340	0.017	0.358
GOmnplot	0.265	0.010	0.277
HTMLPage-class	0.000	0.000	0.001
LL2homology	0.001	0.000	0.001
PMIDAmat	0.328	0.008	0.652
PWAmat	5.711	0.109	5.824
UniGeneQuery	0.002	0.000	0.003
accessionToUID	0.425	0.028	2.378
annPkgName	0.002	0.000	0.002
aqListGOIDs	1.154	0.077	1.345
blastSequences	0.146	0.007	30.675
buildChromLocation	3.220	0.102	3.324
buildPubMedAbst	0.053	0.002	0.490
chrCats	19.338	0.113	19.516
chromLocation-class	2.937	0.005	2.944
compatibleVersions	0.170	0.002	0.173
dropECode	0.152	0.003	0.154
entrezGeneByID	0.003	0.000	0.003
entrezGeneQuery	0.002	0.001	0.002
filterGOByOntology	0.118	0.007	0.125
findNeighbors	0.097	0.005	0.212
genbank	0.258	0.013	1.120
getAnnMap	0.183	0.024	0.361
getEvidence	0.122	0.002	0.124
getGOTerm	0.360	0.015	0.680
getOntology	0.148	0.002	0.150
getPMInfo	1.054	0.007	1.410
getSYMBOL	0.319	0.018	0.584
getSeq4Acc	0.005	0.000	0.176
hasGOannote	0.105	0.002	0.113
hgByChroms	0.024	0.003	0.028
hgCLengths	0.003	0.000	0.003
hgu95Achroloc	0.118	0.008	0.126
hgu95Achrom	0.091	0.009	0.101
hgu95All	0.109	0.010	0.118
hgu95Asym	0.118	0.010	0.127
homoData-class	0.005	0.000	0.006
htmlpage	0.050	0.002	0.051
isValidkey	0.001	0.001	0.002
makeAnchor	0.002	0.000	0.002
organism	3.397	0.007	3.407
p2LL	0.001	0.000	0.002
pm.abstGrep	1.695	0.031	2.960
pm.getabst	1.714	0.027	2.902
pm.titles	1.538	0.021	3.083
pmAbst2HTML	0.067	0.002	0.406
pmid2MIAME	0.001	0.000	0.001
pmidQuery	0.002	0.000	0.003
pubMedAbst-class	0.042	0.002	0.382
pubmed	0.016	0.002	0.374
readGEOAnn	0.001	0.000	0.002
serializeEnv	0.003	0.001	0.004
setRepository	0.005	0.001	0.005
updateSymbolsToValidKeys	0.001	0.000	0.001
usedChromGenes	0.12	0.01	0.13