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 perceval

This page was generated on 2015-04-10 09:51:46 -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 22:39:34 -0700 (Thu, 09 Apr 2015)
EndedAt: 2015-04-09 22:44:34 -0700 (Thu, 09 Apr 2015)
EllapsedTime: 300.8 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-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 ‘1.44.0’
* 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 ... [17s/28s] 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 ... [63s/96s] OK
Examples with CPU or elapsed time > 5s
                 user system elapsed
chrCats        17.869  0.108  20.257
PWAmat          8.654  0.164   8.822
probesByLL      6.334  0.019   6.356
blastSequences  0.112  0.028  20.339
* checking for unstated dependencies in tests ... OK
* checking tests ...
  Running ‘annotate_unit_tests.R’ [13s/13s]
 [14s/14s] 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
ACCNUMStats3.4490.0553.506
GO2heatmap0.3340.0290.884
GOmnplot0.2070.0160.249
HTMLPage-class0.0010.0000.001
LL2homology0.0010.0000.001
PMIDAmat0.2810.0100.319
PWAmat8.6540.1648.822
UniGeneQuery0.0040.0000.004
accessionToUID0.2340.0382.611
annPkgName0.0010.0000.002
aqListGOIDs0.5860.0780.666
blastSequences 0.112 0.02820.339
buildChromLocation2.3740.1162.491
buildPubMedAbst0.0370.0010.399
chrCats17.869 0.10820.257
chromLocation-class2.3110.0092.320
compatibleVersions0.1920.0080.200
dropECode0.1790.0080.186
entrezGeneByID0.0010.0010.002
entrezGeneQuery0.0020.0000.003
filterGOByOntology0.1310.0130.143
findNeighbors0.0980.0120.141
genbank0.2340.0271.195
getAnnMap0.1480.0230.172
getEvidence0.1500.0070.162
getGOTerm0.3610.0180.477
getOntology0.1540.0070.162
getPMInfo0.9480.0051.333
getSYMBOL0.3030.0230.411
getSeq4Acc0.0060.0010.181
hasGOannote0.0840.0050.089
hgByChroms0.0170.0060.024
hgCLengths0.0020.0000.003
hgu95Achroloc0.0850.0140.099
hgu95Achrom0.0840.0150.098
hgu95All0.0770.0130.089
hgu95Asym0.0810.0140.095
homoData-class0.0050.0010.006
htmlpage0.0470.0030.063
isValidkey0.0010.0000.001
makeAnchor0.0010.0000.002
organism2.6750.0142.690
p2LL0.0010.0000.001
pm.abstGrep1.4230.0392.629
pm.getabst1.4230.0462.634
pm.titles1.8170.0613.047
pmAbst2HTML0.0560.0030.525
pmid2MIAME0.0010.0000.001
pmidQuery0.0010.0000.001
probesByLL6.3340.0196.356
pubMedAbst-class0.0360.0010.399
pubmed0.0170.0020.748
readGEOAnn0.0010.0000.001
serializeEnv0.0030.0010.004
setRepository0.0040.0000.005
updateSymbolsToValidKeys0.0000.0000.001
usedChromGenes0.1110.0160.127