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BioC 3.3: CHECK report for annotate on oaxaca

This page was generated on 2016-10-13 12:55:21 -0700 (Thu, 13 Oct 2016).

Package 44/1210HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
annotate 1.50.1
Bioconductor Package Maintainer
Snapshot Date: 2016-10-12 17:20:15 -0700 (Wed, 12 Oct 2016)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_3/madman/Rpacks/annotate
Last Changed Rev: 122080 / Revision: 122332
Last Changed Date: 2016-10-07 16:23:16 -0700 (Fri, 07 Oct 2016)
zin2 Linux (Ubuntu 14.04.2 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
moscato2 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository
oaxaca Mac OS X Mavericks (10.9.5) / x86_64  OK  OK [ OK ] OK UNNEEDED, same version exists in internal repository

Summary

Package: annotate
Version: 1.50.1
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings annotate_1.50.1.tar.gz
StartedAt: 2016-10-12 23:13:50 -0700 (Wed, 12 Oct 2016)
EndedAt: 2016-10-12 23:16:52 -0700 (Wed, 12 Oct 2016)
EllapsedTime: 181.3 seconds
RetCode: 0
Status:  OK 
CheckDir: annotate.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings annotate_1.50.1.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.3-bioc/meat/annotate.Rcheck’
* using R version 3.3.1 (2016-06-21)
* 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 ‘1.50.1’
* 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
'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 ... OK
Examples with CPU or elapsed time > 5s
                 user system elapsed
chrCats        12.657  0.667  13.424
blastSequences  0.314  0.011  21.115
* 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: 2 NOTEs
See
  ‘/Users/biocbuild/bbs-3.3-bioc/meat/annotate.Rcheck/00check.log’
for details.


annotate.Rcheck/00install.out:

* 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)

annotate.Rcheck/annotate-Ex.timings:

nameusersystemelapsed
ACCNUMStats2.3650.0282.398
GO2heatmap0.1770.0120.190
GOmnplot0.1150.0080.124
HTMLPage-class0.0010.0000.001
LL2homology0.0000.0000.001
PMIDAmat0.1370.0030.200
PWAmat3.6830.0653.753
UniGeneQuery0.0030.0000.003
accessionToUID0.6600.0364.024
annPkgName0.0010.0000.001
aqListGOIDs0.4300.0330.463
blastSequences 0.314 0.01121.115
buildChromLocation2.5470.0762.626
buildPubMedAbst0.0440.0020.706
chrCats12.657 0.66713.424
chromLocation-class2.4020.0152.420
compatibleVersions0.0430.0010.043
dropECode0.0530.0010.055
entrezGeneByID0.0020.0000.002
entrezGeneQuery0.0020.0000.002
filterGOByOntology0.0870.0040.092
findNeighbors0.0270.0030.279
genbank0.1680.0141.336
getAnnMap0.0470.0120.197
getEvidence0.0490.0020.052
getGOTerm0.2370.0090.304
getOntology0.0530.0020.054
getPMInfo0.6310.0051.401
getSYMBOL0.1540.0121.126
getSeq4Acc0.0110.0010.530
hasGOannote0.0290.0010.030
hgByChroms0.0130.0050.017
hgCLengths0.0010.0000.002
hgu95Achroloc0.0790.0100.089
hgu95Achrom0.0650.0080.074
hgu95All0.0680.0100.077
hgu95Asym0.0690.0100.080
homoData-class0.0020.0000.002
htmlpage0.0310.0020.044
isValidkey0.0010.0000.001
makeAnchor0.0010.0000.001
organism2.3290.0152.349
p2LL0.0000.0000.001
pm.abstGrep0.9180.0222.792
pm.getabst0.9290.0212.569
pm.titles1.0530.0222.600
pmAbst2HTML0.0420.0030.650
pmid2MIAME0.0000.0000.001
pmidQuery0.0010.0010.002
pubMedAbst-class0.0420.0020.769
pubmed0.0240.0020.897
readGEOAnn0.0000.0000.001
serializeEnv0.0020.0000.002
setRepository0.0040.0000.004
updateSymbolsToValidKeys0.0000.0000.001
usedChromGenes0.0990.0120.111