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BioC 2.13: CHECK report for ChIPpeakAnno on perceval

This page was generated on 2014-04-05 09:52:18 -0700 (Sat, 05 Apr 2014).

Package 131/750HostnameOS / ArchBUILDCHECKBUILD BIN
ChIPpeakAnno 2.10.0
Lihua Julie Zhu
Snapshot Date: 2014-04-04 16:20:29 -0700 (Fri, 04 Apr 2014)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_13/madman/Rpacks/ChIPpeakAnno
Last Changed Rev: 81642 / Revision: 88450
Last Changed Date: 2013-10-14 14:29:21 -0700 (Mon, 14 Oct 2013)
zin1 Linux (Ubuntu 12.04.4 LTS) / x86_64  OK  OK 
moscato1 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  OK  OK  OK 
perceval Mac OS X Snow Leopard (10.6.8) / x86_64  OK [ OK ] OK 

Summary

Package: ChIPpeakAnno
Version: 2.10.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch ChIPpeakAnno_2.10.0.tar.gz
StartedAt: 2014-04-05 00:11:57 -0700 (Sat, 05 Apr 2014)
EndedAt: 2014-04-05 00:18:44 -0700 (Sat, 05 Apr 2014)
EllapsedTime: 407.1 seconds
RetCode: 0
Status:  OK 
CheckDir: ChIPpeakAnno.Rcheck
Warnings: 0

Command output

* using log directory ‘/Users/biocbuild/bbs-2.13-bioc/meat/ChIPpeakAnno.Rcheck’
* using R version 3.0.3 (2014-03-06)
* using platform: x86_64-apple-darwin10.8.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘ChIPpeakAnno/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘ChIPpeakAnno’ version ‘2.10.0’
* 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 ‘ChIPpeakAnno’ can be installed ... [33s/33s] OK
* checking installed package size ... NOTE
  installed size is 10.3Mb
  sub-directories of 1Mb or more:
    data   9.8Mb
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Packages listed in more than one of Depends, Imports, Suggests, Enhances:
  ‘BiocGenerics’ ‘biomaRt’ ‘multtest’ ‘IRanges’ ‘Biostrings’ ‘BSgenome’ ‘GO.db’ ‘limma’ ‘GenomicFeatures’
A package should be listed in only one of these fields.
* 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
Namespace in Imports field not imported from: ‘gplots’
  All declared Imports should be used.
Packages in Depends field not imported from:
  ‘BSgenome.Ecoli.NCBI.20080805’ ‘org.Hs.eg.db’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
‘:::’ call which should be ‘::’: ‘IRanges:::space’
  See the note in ?`:::` about the use of this operator.
See the information on DESCRIPTION files in the chapter ‘Creating R
packages’ of the ‘Writing R Extensions’ manual.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... NOTE
prepare_Rd: ExonPlusUtr.human.GRCh37.Rd:28-30: Dropping empty section \source
prepare_Rd: ExonPlusUtr.human.GRCh37.Rd:31-32: Dropping empty section \references
prepare_Rd: GFF2RangedData.Rd:16-18: Dropping empty section \details
prepare_Rd: GFF2RangedData.Rd:23: Dropping empty section \references
prepare_Rd: GFF2RangedData.Rd:28: Dropping empty section \seealso
prepare_Rd: Peaks.Ste12.Replicate1.Rd:14-16: Dropping empty section \details
prepare_Rd: Peaks.Ste12.Replicate1.Rd:17-18: Dropping empty section \source
prepare_Rd: Peaks.Ste12.Replicate2.Rd:14-16: Dropping empty section \details
prepare_Rd: Peaks.Ste12.Replicate3.Rd:14-16: Dropping empty section \details
prepare_Rd: TSS.human.GRCh37.Rd:25-27: Dropping empty section \source
prepare_Rd: TSS.human.GRCh37.Rd:28-29: Dropping empty section \references
prepare_Rd: TSS.human.NCBI36.Rd:26-28: Dropping empty section \source
prepare_Rd: TSS.human.NCBI36.Rd:29-30: Dropping empty section \references
prepare_Rd: TSS.mouse.NCBIM37.Rd:26-28: Dropping empty section \source
prepare_Rd: TSS.mouse.NCBIM37.Rd:29-30: Dropping empty section \references
prepare_Rd: TSS.rat.RGSC3.4.Rd:25-27: Dropping empty section \source
prepare_Rd: TSS.rat.RGSC3.4.Rd:28-29: Dropping empty section \references
prepare_Rd: TSS.zebrafish.Zv8.Rd:26-28: Dropping empty section \source
prepare_Rd: TSS.zebrafish.Zv8.Rd:29-31: Dropping empty section \references
prepare_Rd: addAncestors.Rd:23-25: Dropping empty section \details
prepare_Rd: addAncestors.Rd:34-36: Dropping empty section \note
prepare_Rd: addAncestors.Rd:29-30: Dropping empty section \references
prepare_Rd: addAncestors.Rd:38-40: Dropping empty section \seealso
prepare_Rd: annotatePeakInBatch.Rd:31-32: Dropping empty section \details
prepare_Rd: annotatePeakInBatch.Rd:48-49: Dropping empty section \note
prepare_Rd: annotatedPeak.Rd:26-28: Dropping empty section \source
prepare_Rd: annotatedPeak.Rd:29-31: Dropping empty section \references
prepare_Rd: assignChromosomeRegion.Rd:45-47: Dropping empty section \details
prepare_Rd: assignChromosomeRegion.Rd:61-62: Dropping empty section \note
prepare_Rd: condenseMatrixByColnames.Rd:19-21: Dropping empty section \details
prepare_Rd: condenseMatrixByColnames.Rd:30-31: Dropping empty section \note
prepare_Rd: condenseMatrixByColnames.Rd:25-26: Dropping empty section \references
prepare_Rd: condenseMatrixByColnames.Rd:33-35: Dropping empty section \seealso
prepare_Rd: convert2EntrezID.Rd:20-22: Dropping empty section \details
prepare_Rd: convert2EntrezID.Rd:31-32: Dropping empty section \note
prepare_Rd: convert2EntrezID.Rd:26-27: Dropping empty section \references
prepare_Rd: convert2EntrezID.Rd:34-36: Dropping empty section \seealso
prepare_Rd: countPatternInSeqs.Rd:22-24: Dropping empty section \details
prepare_Rd: countPatternInSeqs.Rd:34-36: Dropping empty section \note
prepare_Rd: countPatternInSeqs.Rd:28-30: Dropping empty section \references
prepare_Rd: enrichedGO.Rd:79-81: Dropping empty section \details
prepare_Rd: enrichedGO.Rd:88-90: Dropping empty section \note
prepare_Rd: enrichedGO.Rd:82-83: Dropping empty section \source
prepare_Rd: enrichedGO.Rd:84-86: Dropping empty section \references
prepare_Rd: findOverlappingPeaks.Rd:59-61: Dropping empty section \note
prepare_Rd: findVennCounts.Rd:31-33: Dropping empty section \details
prepare_Rd: findVennCounts.Rd:39-41: Dropping empty section \references
prepare_Rd: findVennCounts.Rd:60-61: Dropping empty section \examples
prepare_Rd: getAllPeakSequence.Rd:20-22: Dropping empty section \details
prepare_Rd: getAllPeakSequence.Rd:31-34: Dropping empty section \note
prepare_Rd: getAllPeakSequence.Rd:35: Dropping empty section \seealso
prepare_Rd: getAnnotation.Rd:17-19: Dropping empty section \details
prepare_Rd: getAnnotation.Rd:31: Dropping empty section \seealso
prepare_Rd: getEnrichedGO.Rd:22-23: Dropping empty section \details
prepare_Rd: getEnrichedGO.Rd:92-95: Dropping empty section \note
prepare_Rd: getGeneSeq.Rd:15-17: Dropping empty section \details
prepare_Rd: getGeneSeq.Rd:26: Dropping empty section \references
prepare_Rd: getGeneSeq.Rd:31: Dropping empty section \seealso
prepare_Rd: getUniqueGOidCount.Rd:15-17: Dropping empty section \details
prepare_Rd: getUniqueGOidCount.Rd:23: Dropping empty section \references
prepare_Rd: makeVennDiagram.Rd:44-46: Dropping empty section \note
prepare_Rd: makeVennDiagram.Rd:39-40: Dropping empty section \references
prepare_Rd: myPeakList.Rd:14-15: Dropping empty section \details
prepare_Rd: myPeakList.Rd:19-20: Dropping empty section \references
prepare_Rd: peaksNearBDP.Rd:21-22: Dropping empty section \details
prepare_Rd: peaksNearBDP.Rd:52-53: Dropping empty section \note
prepare_Rd: summarizePatternInPeaks.Rd:36-38: Dropping empty section \details
prepare_Rd: summarizePatternInPeaks.Rd:48-50: Dropping empty section \note
prepare_Rd: summarizePatternInPeaks.Rd:42-44: Dropping empty section \references
prepare_Rd: summarizePatternInPeaks.Rd:54-56: Dropping empty section \seealso
prepare_Rd: translatePattern.Rd:21-23: Dropping empty section \details
prepare_Rd: translatePattern.Rd:33-35: Dropping empty section \note
prepare_Rd: translatePattern.Rd:27-29: Dropping empty section \references
prepare_Rd: write2FASTA.Rd:17-18: Dropping empty section \details
prepare_Rd: write2FASTA.Rd:24-26: Dropping empty section \note
prepare_Rd: write2FASTA.Rd:22: Dropping empty section \references
prepare_Rd: write2FASTA.Rd:27: Dropping empty section \seealso
* 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 for old-style vignette sources ... NOTE
Vignette sources only in ‘inst/doc’:
  ‘ChIPpeakAnno.Rnw’
A ‘vignettes’ directory will be required as from R 3.1.0
* checking examples ... [50s/57s] OK
Examples with CPU or elapsed time > 5s
                           user system elapsed
ExonPlusUtr.human.GRCh37 11.847  0.301  12.162
addAncestors              8.283  0.304   8.595
addGeneIDs                3.696  0.203  10.160
* 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

NOTE: There were 5 notes.
See
  ‘/Users/biocbuild/bbs-2.13-bioc/meat/ChIPpeakAnno.Rcheck/00check.log’
for details.

ChIPpeakAnno.Rcheck/00install.out:

* installing *source* package ‘ChIPpeakAnno’ ...
** 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 (ChIPpeakAnno)

ChIPpeakAnno.Rcheck/ChIPpeakAnno-Ex.timings:

nameusersystemelapsed
BED2RangedData0.6560.0080.664
ChIPpeakAnno-package0.5670.0100.580
ExonPlusUtr.human.GRCh3711.847 0.30112.162
GFF2RangedData0.0470.0080.054
Peaks.Ste12.Replicate10.0410.0100.051
Peaks.Ste12.Replicate20.0330.0070.040
Peaks.Ste12.Replicate30.0370.0080.045
TSS.human.GRCh370.2380.0290.267
TSS.human.NCBI360.2490.0250.274
TSS.mouse.GRCm380.1240.0190.143
TSS.mouse.NCBIM370.1740.0300.204
TSS.rat.RGSC3.40.1330.0270.160
TSS.rat.Rnor_5.00.160.010.17
TSS.zebrafish.Zv80.1300.0260.156
TSS.zebrafish.Zv90.1130.0060.120
addAncestors8.2830.3048.595
addGeneIDs 3.696 0.20310.160
annotatePeakInBatch0.0180.0150.034
annotatedPeak0.1600.0210.181
assignChromosomeRegion0.0070.0120.019
condenseMatrixByColnames0.0430.0070.052
convert2EntrezID1.2730.0321.308
countPatternInSeqs0.1690.0100.179
enrichedGO0.0640.0120.076
findOverlappingPeaks0.0070.0090.017
getAllPeakSequence1.3540.0591.415
getAnnotation0.0030.0070.010
getEnrichedGO0.1320.0250.156
getEnrichedPATH0.0050.0080.012
getGeneSeq0.0410.0150.056
getUniqueGOidCount0.0060.0050.010
hyperGtest0.0380.0120.051
makeVennDiagram0.0110.0100.020
myPeakList0.070.020.09
peaksNearBDP0.0050.0060.011
summarizePatternInPeaks1.1390.0391.180
translatePattern0.0040.0040.007
write2FASTA0.1170.0090.127