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BioC 3.0: CHECK report for ChIPpeakAnno on moscato1

This page was generated on 2015-04-10 09:45:53 -0700 (Fri, 10 Apr 2015).

Package 147/933HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
ChIPpeakAnno 2.16.4
Lihua Julie Zhu
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/ChIPpeakAnno
Last Changed Rev: 97612 / Revision: 102249
Last Changed Date: 2014-12-12 17:02:49 -0800 (Fri, 12 Dec 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: ChIPpeakAnno
Version: 2.16.4
Command: rm -rf ChIPpeakAnno.buildbin-libdir ChIPpeakAnno.Rcheck && mkdir ChIPpeakAnno.buildbin-libdir ChIPpeakAnno.Rcheck && D:\biocbld\bbs-3.0-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=ChIPpeakAnno.buildbin-libdir ChIPpeakAnno_2.16.4.tar.gz >ChIPpeakAnno.Rcheck\00install.out 2>&1 && cp ChIPpeakAnno.Rcheck\00install.out ChIPpeakAnno-install.out && D:\biocbld\bbs-3.0-bioc\R\bin\R.exe CMD check --library=ChIPpeakAnno.buildbin-libdir --install="check:ChIPpeakAnno-install.out" --force-multiarch --no-vignettes --timings ChIPpeakAnno_2.16.4.tar.gz
StartedAt: 2015-04-09 23:34:04 -0700 (Thu, 09 Apr 2015)
EndedAt: 2015-04-09 23:41:11 -0700 (Thu, 09 Apr 2015)
EllapsedTime: 427.3 seconds
RetCode: 0
Status:  OK  
CheckDir: ChIPpeakAnno.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   rm -rf ChIPpeakAnno.buildbin-libdir ChIPpeakAnno.Rcheck && mkdir ChIPpeakAnno.buildbin-libdir ChIPpeakAnno.Rcheck && D:\biocbld\bbs-3.0-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=ChIPpeakAnno.buildbin-libdir ChIPpeakAnno_2.16.4.tar.gz >ChIPpeakAnno.Rcheck\00install.out 2>&1 && cp ChIPpeakAnno.Rcheck\00install.out ChIPpeakAnno-install.out  && D:\biocbld\bbs-3.0-bioc\R\bin\R.exe CMD check --library=ChIPpeakAnno.buildbin-libdir --install="check:ChIPpeakAnno-install.out" --force-multiarch --no-vignettes --timings ChIPpeakAnno_2.16.4.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'D:/biocbld/bbs-3.0-bioc/meat/ChIPpeakAnno.Rcheck'
* using R version 3.1.3 (2015-03-09)
* using platform: i386-w64-mingw32 (32-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'ChIPpeakAnno/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'ChIPpeakAnno' version '2.16.4'
* 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 whether package 'ChIPpeakAnno' can be installed ... 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
* loading checks for arch 'i386'
** 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
* loading checks for arch 'x64'
** 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.
* 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'
assignChromosomeRegion: no visible global function definition for
  'GRangesList'
* 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 installed files from 'inst/doc' ... OK
* checking files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... [25s] OK
Examples with CPU or elapsed time > 5s
                         user system elapsed
ExonPlusUtr.human.GRCh37 5.47   0.05    5.52
** running examples for arch 'x64' ... [29s] OK
Examples with CPU or elapsed time > 5s
                         user system elapsed
ExonPlusUtr.human.GRCh37 6.69   0.01    6.71
* checking for unstated dependencies in tests ... OK
* checking tests ...
** running tests for arch 'i386' ...
  Running 'runTests.R' [0s]
 [1s] OK
** running tests for arch 'x64' ...
  Running 'runTests.R' [0s]
 [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
* DONE

NOTE: There were 4 notes.
See
  'D:/biocbld/bbs-3.0-bioc/meat/ChIPpeakAnno.Rcheck/00check.log'
for details.

ChIPpeakAnno.Rcheck/00install.out:


install for i386

* 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

install for x64

* installing *source* package 'ChIPpeakAnno' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'ChIPpeakAnno' as ChIPpeakAnno_2.16.4.zip
* DONE (ChIPpeakAnno)

ChIPpeakAnno.Rcheck/examples_i386/ChIPpeakAnno-Ex.timings:

nameusersystemelapsed
BED2RangedData0.040.000.05
ChIPpeakAnno-package0.020.000.01
ExonPlusUtr.human.GRCh375.470.055.52
GFF2RangedData0.020.000.02
Peaks.Ste12.Replicate10.030.000.03
Peaks.Ste12.Replicate20.030.000.03
Peaks.Ste12.Replicate30.020.000.02
TSS.human.GRCh370.220.030.25
TSS.human.NCBI360.480.010.50
TSS.mouse.GRCm380.090.000.09
TSS.mouse.NCBIM370.170.000.17
TSS.rat.RGSC3.40.160.000.16
TSS.rat.Rnor_5.00.130.000.12
TSS.zebrafish.Zv80.170.030.20
TSS.zebrafish.Zv90.120.000.13
addAncestors1.290.101.38
addGeneIDs1.720.001.72
annotatePeakInBatch000
annotatedPeak0.150.000.16
assignChromosomeRegion000
condenseMatrixByColnames0.020.000.01
convert2EntrezID0.300.010.31
countPatternInSeqs0.120.000.13
enrichedGO000
findOverlappingPeaks000
getAllPeakSequence0.840.081.20
getAnnotation000
getEnrichedGO0.010.000.02
getEnrichedPATH0.020.000.02
getGeneSeq000
getUniqueGOidCount000
hyperGtest000
makeVennDiagram0.020.000.01
myPeakList0.030.000.03
peaksNearBDP000
summarizePatternInPeaks0.760.030.80
translatePattern000
write2FASTA0.060.000.06

ChIPpeakAnno.Rcheck/examples_x64/ChIPpeakAnno-Ex.timings:

nameusersystemelapsed
BED2RangedData0.050.000.04
ChIPpeakAnno-package0.010.000.02
ExonPlusUtr.human.GRCh376.690.016.71
GFF2RangedData0.050.000.04
Peaks.Ste12.Replicate10.050.000.05
Peaks.Ste12.Replicate20.030.020.05
Peaks.Ste12.Replicate30.050.000.04
TSS.human.GRCh370.340.000.36
TSS.human.NCBI360.610.000.61
TSS.mouse.GRCm380.110.000.11
TSS.mouse.NCBIM370.150.000.16
TSS.rat.RGSC3.40.130.000.12
TSS.rat.Rnor_5.00.080.000.08
TSS.zebrafish.Zv80.110.000.11
TSS.zebrafish.Zv90.090.000.09
addAncestors1.330.111.43
addGeneIDs2.100.032.14
annotatePeakInBatch0.020.000.01
annotatedPeak0.120.000.13
assignChromosomeRegion000
condenseMatrixByColnames0.010.000.02
convert2EntrezID0.360.000.36
countPatternInSeqs0.120.000.13
enrichedGO000
findOverlappingPeaks000
getAllPeakSequence0.990.001.01
getAnnotation000
getEnrichedGO0.030.000.03
getEnrichedPATH000
getGeneSeq000
getUniqueGOidCount000
hyperGtest0.010.000.02
makeVennDiagram000
myPeakList0.030.000.03
peaksNearBDP000
summarizePatternInPeaks0.850.050.89
translatePattern000
write2FASTA0.060.000.07