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Package 115/658HostnameOS / ArchBUILDCHECKBUILD BIN
ChIPpeakAnno 2.7.3
Lihua Julie Zhu
Snapshot Date: 2013-03-23 17:02:20 -0700 (Sat, 23 Mar 2013)
URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/ChIPpeakAnno
Last Changed Rev: 74702 / Revision: 74756
Last Changed Date: 2013-03-22 14:10:11 -0700 (Fri, 22 Mar 2013)
george2 Linux (Ubuntu 12.04.1 LTS) / x86_64  OK  OK 
moscato2 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  OK  OK  OK 
petty Mac OS X Leopard (10.5.8) / i386  OK  OK  OK 
pelham Mac OS X Snow Leopard (10.6.8) / x86_64  OK [ OK ] OK 

Summary

Package: ChIPpeakAnno
Version: 2.7.3
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch ChIPpeakAnno_2.7.3.tar.gz
StartedAt: 2013-03-24 03:29:46 -0700 (Sun, 24 Mar 2013)
EndedAt: 2013-03-24 03:36:25 -0700 (Sun, 24 Mar 2013)
EllapsedTime: 398.4 seconds
RetCode: 0
Status:  OK 
CheckDir: ChIPpeakAnno.Rcheck
Warnings: 0

Command output

* using log directory '/Users/biocbuild/bbs-2.12-bioc/meat/ChIPpeakAnno.Rcheck'
* using R version 3.0.0 beta (2013-03-21 r62346)
* using platform: x86_64-apple-darwin10.8.0 (64-bit)
* using session charset: ASCII
* using option '--no-vignettes'
* checking for file 'ChIPpeakAnno/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'ChIPpeakAnno' version '2.7.3'
* 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 ... [35s/36s] OK
* checking installed package size ... NOTE
  installed size is  7.8Mb
  sub-directories of 1Mb or more:
    data   7.4Mb
* checking package 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 for unstated dependencies in R code ... OK
* 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 installed files from 'inst/doc' ... OK
* checking examples ... [45s/50s] OK
Examples with CPU or elapsed time > 5s
                           user system elapsed
ExonPlusUtr.human.GRCh37 11.050  0.286  11.799
addAncestors              6.931  0.340   8.138
addGeneIDs                3.255  0.191   5.645
* 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 vignettes ... SKIPPED
* checking PDF version of manual ... OK

NOTE: There were 2 notes.
See
  '/Users/biocbuild/bbs-2.12-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
   'ChIPpeakAnno.Rnw' 
** testing if installed package can be loaded
* DONE (ChIPpeakAnno)

ChIPpeakAnno.Rcheck/ChIPpeakAnno-Ex.timings:

nameusersystemelapsed
BED2RangedData0.1280.0040.133
ChIPpeakAnno-package0.0450.0110.056
ExonPlusUtr.human.GRCh3711.050 0.28611.799
GFF2RangedData0.0660.0100.075
Peaks.Ste12.Replicate10.0420.0110.099
Peaks.Ste12.Replicate20.0380.0080.048
Peaks.Ste12.Replicate30.0480.0110.059
TSS.human.GRCh370.2760.0240.321
TSS.human.NCBI360.2820.0320.323
TSS.mouse.NCBIM370.3200.0340.360
TSS.rat.RGSC3.40.1790.0210.232
TSS.zebrafish.Zv80.1620.0190.182
addAncestors6.9310.3408.138
addGeneIDs3.2550.1915.645
annotatePeakInBatch0.0350.0220.056
annotatedPeak0.2610.0630.324
assignChromosomeRegion0.0060.0090.015
condenseMatrixByColnames0.0420.0040.047
convert2EntrezID0.5200.0230.543
countPatternInSeqs0.1240.0090.216
enrichedGO0.0070.0060.083
findOverlappingPeaks0.0060.0080.014
getAllPeakSequence0.7690.0280.846
getAnnotation0.0040.0070.010
getEnrichedGO0.0270.0090.036
getEnrichedPATH0.0270.0080.035
getGeneSeq0.0330.0140.046
getUniqueGOidCount0.0060.0060.011
hyperGtest0.0070.0080.015
makeVennDiagram0.0370.0130.049
myPeakList0.0680.0250.488
peaksNearBDP0.0050.0070.012
summarizePatternInPeaks0.7450.0250.770
translatePattern0.0290.0080.040
write2FASTA0.0900.0070.114