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 zin1

This page was generated on 2015-04-10 09:36:21 -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: /home/biocbuild/bbs-3.0-bioc/R/bin/R CMD check --no-vignettes --timings annotate_1.44.0.tar.gz
StartedAt: 2015-04-09 21:31:34 -0700 (Thu, 09 Apr 2015)
EndedAt: 2015-04-09 21:34:40 -0700 (Thu, 09 Apr 2015)
EllapsedTime: 186.5 seconds
RetCode: 0
Status:  OK 
CheckDir: annotate.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.0-bioc/R/bin/R CMD check --no-vignettes --timings annotate_1.44.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.0-bioc/meat/annotate.Rcheck’
* using R version 3.1.3 (2015-03-09)
* using platform: x86_64-unknown-linux-gnu (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 ... [11s/11s] 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 installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [40s/69s] OK
Examples with CPU or elapsed time > 5s
                 user system elapsed
chrCats        13.693  0.020  13.758
blastSequences  0.076  0.012  19.883
* checking for unstated dependencies in tests ... OK
* checking tests ...
  Running ‘annotate_unit_tests.R’ [8s/8s]
 [8s/8s] 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
  ‘/home/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
ACCNUMStats2.0000.0362.040
GO2heatmap0.1600.0160.176
GOmnplot0.1000.0120.111
HTMLPage-class000
LL2homology000
PMIDAmat0.1360.0000.168
PWAmat4.7440.0604.810
UniGeneQuery0.0040.0000.003
accessionToUID0.1760.0042.152
annPkgName0.0000.0000.001
aqListGOIDs0.3360.0200.355
blastSequences 0.076 0.01219.883
buildChromLocation1.1680.0241.224
buildPubMedAbst0.0320.0000.615
chrCats13.693 0.02013.758
chromLocation-class1.0320.0001.034
compatibleVersions0.0720.0040.075
dropECode0.0760.0080.086
entrezGeneByID0.0000.0000.001
entrezGeneQuery0.0000.0000.001
filterGOByOntology0.060.000.06
findNeighbors0.0360.0040.083
genbank0.1240.0041.067
getAnnMap0.0840.0000.083
getEvidence0.0600.0080.071
getGOTerm0.1920.0000.190
getOntology0.0680.0040.071
getPMInfo0.6600.0001.092
getSYMBOL0.1640.0000.185
getSeq4Acc0.0000.0000.172
hasGOannote0.0400.0000.041
hgByChroms0.0160.0000.015
hgCLengths0.0040.0000.002
hgu95Achroloc0.0640.0000.065
hgu95Achrom0.0600.0000.057
hgu95All0.0680.0000.070
hgu95Asym0.0680.0000.071
homoData-class0.0040.0000.004
htmlpage0.0320.0000.033
isValidkey0.0000.0000.001
makeAnchor0.0000.0000.001
organism1.1080.0081.117
p2LL0.0000.0000.001
pm.abstGrep0.9530.0002.027
pm.getabst1.1440.0002.367
pm.titles0.8800.0002.076
pmAbst2HTML0.0440.0000.400
pmid2MIAME0.0000.0000.001
pmidQuery0.0040.0000.001
probesByLL4.8160.0004.825
pubMedAbst-class0.0280.0000.483
pubmed0.0120.0000.388
readGEOAnn000
serializeEnv0.0040.0000.003
setRepository0.0040.0000.003
updateSymbolsToValidKeys0.0000.0000.001
usedChromGenes0.0760.0040.080