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BioC 2.14: CHECK report for ChIPpeakAnno on petty

This page was generated on 2014-10-08 08:58:47 -0700 (Wed, 08 Oct 2014).

Package 141/824HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
ChIPpeakAnno 2.14.1
Lihua Julie Zhu
Snapshot Date: 2014-10-07 17:20:37 -0700 (Tue, 07 Oct 2014)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_14/madman/Rpacks/ChIPpeakAnno
Last Changed Rev: 93700 / Revision: 95116
Last Changed Date: 2014-08-29 13:08:48 -0700 (Fri, 29 Aug 2014)
zin2 Linux (Ubuntu 12.04.4 LTS) / x86_64  OK  OK  OK 
moscato2 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  OK  OK  OK  OK 
petty Mac OS X Snow Leopard (10.6.8) / x86_64  OK  OK [ OK ] OK 
morelia Mac OS X Mavericks (10.9.5) / x86_64  OK  OK  OK  OK 

Summary

Package: ChIPpeakAnno
Version: 2.14.1
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch ChIPpeakAnno_2.14.1.tar.gz
StartedAt: 2014-10-07 21:12:54 -0700 (Tue, 07 Oct 2014)
EndedAt: 2014-10-07 21:21:42 -0700 (Tue, 07 Oct 2014)
EllapsedTime: 528.5 seconds
RetCode: 0
Status:  OK 
CheckDir: ChIPpeakAnno.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch ChIPpeakAnno_2.14.1.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-2.14-bioc/meat/ChIPpeakAnno.Rcheck’
* using R version 3.1.1 (2014-07-10)
* 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 ‘2.14.1’
* 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 ... [45s/49s] OK
* checking installed package size ... NOTE
  installed size is 10.8Mb
  sub-directories of 1Mb or more:
    data   9.8Mb
* 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
':::' 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 ... NOTE
annotatePeakInBatch: no visible binding for global variable ‘peakEnd’
annotatePeakInBatch: no visible binding for global variable
  ‘start_position’
annotatePeakInBatch: no visible binding for global variable ‘peakStart’
annotatePeakInBatch: no visible binding for global variable
  ‘end_position’
* 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:32-33: Dropping empty section \details
prepare_Rd: annotatePeakInBatch.Rd:49-50: 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 files in ‘vignettes’ ... OK
* checking examples ... [50s/58s] OK
Examples with CPU or elapsed time > 5s
                          user system elapsed
ExonPlusUtr.human.GRCh37 9.773  0.256  10.039
addGeneIDs               4.321  0.080  11.779
* checking for unstated dependencies in tests ... OK
* checking tests ...
  Running ‘runTests.R’ [1s/1s]
 [1s/1s] 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

NOTE: There were 4 notes.
See
  ‘/Users/biocbuild/bbs-2.14-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
BED2RangedData0.1750.0010.176
ChIPpeakAnno-package0.0290.0010.029
ExonPlusUtr.human.GRCh37 9.773 0.25610.039
GFF2RangedData0.0690.0010.071
Peaks.Ste12.Replicate10.0580.0030.061
Peaks.Ste12.Replicate20.0480.0030.052
Peaks.Ste12.Replicate30.0480.0040.053
TSS.human.GRCh370.3970.0500.448
TSS.human.NCBI360.9020.0650.969
TSS.mouse.GRCm380.1650.0090.176
TSS.mouse.NCBIM370.2440.0570.301
TSS.rat.RGSC3.40.1980.0560.255
TSS.rat.Rnor_5.00.1210.0070.128
TSS.zebrafish.Zv80.1900.0540.245
TSS.zebrafish.Zv90.1600.0080.169
addAncestors3.5130.2353.754
addGeneIDs 4.321 0.08011.779
annotatePeakInBatch0.0230.0010.023
annotatedPeak0.2440.0260.271
assignChromosomeRegion0.0070.0000.008
condenseMatrixByColnames0.0560.0110.067
convert2EntrezID2.2100.0402.253
countPatternInSeqs0.2480.0020.251
enrichedGO0.0060.0010.007
findOverlappingPeaks0.0060.0000.007
getAllPeakSequence1.9770.0612.312
getAnnotation0.0020.0000.002
getEnrichedGO0.0440.0020.046
getEnrichedPATH0.0030.0000.004
getGeneSeq0.0090.0010.010
getUniqueGOidCount0.0040.0000.005
hyperGtest0.0040.0000.005
makeVennDiagram0.0110.0000.012
myPeakList0.0450.0100.054
peaksNearBDP0.0030.0000.003
summarizePatternInPeaks1.7530.0331.797
translatePattern0.0030.0000.003
write2FASTA0.1700.0020.174