Back to the "Multiple platform build/check report"[A] B  C  D  E  F  G  H  I  J  K  L  M  N  O  P  Q  R  S  T  U  V  W  X  Y  Z 

BioC 3.0: CHECK report for annotate on oaxaca

This page was generated on 2015-04-10 10:00:50 -0700 (Fri, 10 Apr 2015).

Package 39/933HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
annotate 1.44.0
Bioconductor Package Maintainer
Snapshot Date: 2015-04-09 16:20:12 -0700 (Thu, 09 Apr 2015)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_0/madman/Rpacks/annotate
Last Changed Rev: 95439 / Revision: 102249
Last Changed Date: 2014-10-13 14:38:33 -0700 (Mon, 13 Oct 2014)
zin1 Linux (Ubuntu 12.04.4 LTS) / x86_64  OK  OK  OK 
moscato1 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  OK  OK  OK  OK 
perceval Mac OS X Snow Leopard (10.6.8) / x86_64  OK  OK  OK  OK 
oaxaca Mac OS X Mavericks (10.9.5) / x86_64  OK  OK [ OK ] OK 

Summary

Package: annotate
Version: 1.44.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch annotate_1.44.0.tar.gz
StartedAt: 2015-04-09 21:20:53 -0700 (Thu, 09 Apr 2015)
EndedAt: 2015-04-09 21:25:18 -0700 (Thu, 09 Apr 2015)
EllapsedTime: 265.2 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 --no-multiarch annotate_1.44.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.0-bioc/meat/annotate.Rcheck’
* using R version 3.1.3 (2015-03-09)
* 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 ‘1.44.0’
* 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 ... [13s/15s] 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 ‘xpathSApply’
.blastSequencesToDNAMultipleAlignment: no visible global function
  definition for ‘IRanges’
.blastSequencesToDataFrame: no visible global function definition for
  ‘xpathSApply’
.blastSequencesToDataFrame: no visible global function definition for
  ‘xmlToDataFrame’
.blastSequencesToDataFrame: no visible binding for global variable
  ‘xpathSApply’
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 ... [51s/104s] OK
Examples with CPU or elapsed time > 5s
                 user system elapsed
chrCats        15.026  0.132  15.876
PWAmat          5.754  0.083   5.854
probesByLL      5.535  0.013   5.662
blastSequences  0.104  0.014  42.036
* checking for unstated dependencies in tests ... OK
* checking tests ...
  Running ‘annotate_unit_tests.R’ [10s/10s]
 [11s/11s] 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

NOTE: There were 2 notes.
See
  ‘/Users/biocbuild/bbs-3.0-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
ACCNUMStats2.8330.0332.871
GO2heatmap0.2350.0170.253
GOmnplot0.1450.0110.157
HTMLPage-class0.0010.0000.001
LL2homology0.0000.0000.001
PMIDAmat0.1950.0090.341
PWAmat5.7540.0835.854
UniGeneQuery0.0030.0000.003
accessionToUID0.2200.0142.262
annPkgName0.0010.0000.002
aqListGOIDs0.5140.0430.558
blastSequences 0.104 0.01442.036
buildChromLocation1.8680.0641.933
buildPubMedAbst0.0390.0010.401
chrCats15.026 0.13215.876
chromLocation-class2.2150.0112.233
compatibleVersions0.0810.0060.088
dropECode0.0830.0040.088
entrezGeneByID0.0010.0010.001
entrezGeneQuery0.0010.0000.001
filterGOByOntology0.0830.0050.090
findNeighbors0.0460.0040.172
genbank0.1860.0091.052
getAnnMap0.1150.0140.321
getEvidence0.0860.0040.092
getGOTerm0.2610.0080.363
getOntology0.0830.0050.088
getPMInfo0.8430.0031.236
getSYMBOL0.2130.0170.369
getSeq4Acc0.0030.0000.176
hasGOannote0.0520.0030.055
hgByChroms0.0180.0040.021
hgCLengths0.0020.0000.002
hgu95Achroloc0.0850.0080.093
hgu95Achrom0.0730.0090.081
hgu95All0.0820.0080.091
hgu95Asym0.0830.0090.092
homoData-class0.0040.0010.004
htmlpage0.0350.0020.125
isValidkey0.0000.0000.001
makeAnchor0.0010.0000.001
organism2.5500.0212.579
p2LL000
pm.abstGrep1.3000.0222.382
pm.getabst1.2020.0192.829
pm.titles1.3850.0343.032
pmAbst2HTML0.0490.0020.894
pmid2MIAME000
pmidQuery0.0010.0000.002
probesByLL5.5350.0135.662
pubMedAbst-class0.0380.0010.403
pubmed0.0150.0010.393
readGEOAnn0.0000.0000.001
serializeEnv0.0030.0000.003
setRepository0.0040.0010.005
updateSymbolsToValidKeys0.0010.0000.001
usedChromGenes0.1080.0090.118