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BioC 2.13: CHECK report for ChIPpeakAnno on moscato1

This page was generated on 2014-04-05 09:49:55 -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: rm -rf ChIPpeakAnno.buildbin-libdir && mkdir ChIPpeakAnno.buildbin-libdir && D:\biocbld\bbs-2.13-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=ChIPpeakAnno.buildbin-libdir ChIPpeakAnno_2.10.0.tar.gz >ChIPpeakAnno-install.out 2>&1 && D:\biocbld\bbs-2.13-bioc\R\bin\R.exe CMD check --library=ChIPpeakAnno.buildbin-libdir --install="check:ChIPpeakAnno-install.out" --force-multiarch --no-vignettes --timings ChIPpeakAnno_2.10.0.tar.gz && mv ChIPpeakAnno.buildbin-libdir/* ChIPpeakAnno.Rcheck/ && rmdir ChIPpeakAnno.buildbin-libdir
StartedAt: 2014-04-05 02:56:33 -0700 (Sat, 05 Apr 2014)
EndedAt: 2014-04-05 03:03:32 -0700 (Sat, 05 Apr 2014)
EllapsedTime: 419.1 seconds
RetCode: 0
Status:  OK  
CheckDir: ChIPpeakAnno.Rcheck
Warnings: 0

Command output

* using log directory 'D:/biocbld/bbs-2.13-bioc/meat/ChIPpeakAnno.Rcheck'
* using R version 3.0.3 (2014-03-06)
* 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 '2.10.0'
* 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 whether package 'ChIPpeakAnno' can be installed ... 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
* 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
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 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 ...
** running examples for arch 'i386' ... [37s] OK
Examples with CPU or elapsed time > 5s
                         user system elapsed
ExonPlusUtr.human.GRCh37 6.51   0.03    6.55
addGeneIDs               2.41   0.09    6.52
** running examples for arch 'x64' ... [50s] OK
Examples with CPU or elapsed time > 5s
                         user system elapsed
ExonPlusUtr.human.GRCh37 9.20   0.08    9.28
addAncestors             6.23   0.08    6.30
addGeneIDs               4.32   0.14   12.34
* 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
  'D:/biocbld/bbs-2.13-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_2.10.0.zip
* DONE (ChIPpeakAnno)

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

nameusersystemelapsed
BED2RangedData0.100.000.09
ChIPpeakAnno-package0.030.000.04
ExonPlusUtr.human.GRCh376.510.036.55
GFF2RangedData0.050.000.05
Peaks.Ste12.Replicate10.040.000.04
Peaks.Ste12.Replicate20.030.000.03
Peaks.Ste12.Replicate30.050.000.05
TSS.human.GRCh370.220.000.22
TSS.human.NCBI360.210.000.20
TSS.mouse.GRCm380.120.000.12
TSS.mouse.NCBIM370.190.020.20
TSS.rat.RGSC3.40.150.000.16
TSS.rat.Rnor_5.00.080.000.07
TSS.zebrafish.Zv80.140.000.15
TSS.zebrafish.Zv90.120.000.12
addAncestors3.110.033.14
addGeneIDs2.410.096.52
annotatePeakInBatch0.030.000.03
annotatedPeak0.150.000.16
assignChromosomeRegion000
condenseMatrixByColnames0.030.000.03
convert2EntrezID0.320.000.33
countPatternInSeqs0.140.000.14
enrichedGO000
findOverlappingPeaks000
getAllPeakSequence1.060.004.48
getAnnotation000
getEnrichedGO0.010.020.03
getEnrichedPATH000
getGeneSeq0.020.000.02
getUniqueGOidCount0.020.000.02
hyperGtest0.010.000.01
makeVennDiagram000
myPeakList0.030.030.06
peaksNearBDP0.020.000.02
summarizePatternInPeaks0.970.000.97
translatePattern000
write2FASTA0.060.000.07

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

nameusersystemelapsed
BED2RangedData0.140.000.14
ChIPpeakAnno-package0.030.000.03
ExonPlusUtr.human.GRCh379.200.089.28
GFF2RangedData0.050.000.05
Peaks.Ste12.Replicate10.030.020.04
Peaks.Ste12.Replicate20.050.000.05
Peaks.Ste12.Replicate30.050.000.04
TSS.human.GRCh370.330.000.33
TSS.human.NCBI360.330.000.32
TSS.mouse.GRCm380.190.000.19
TSS.mouse.NCBIM370.270.010.28
TSS.rat.RGSC3.40.280.000.28
TSS.rat.Rnor_5.00.160.020.17
TSS.zebrafish.Zv80.250.010.27
TSS.zebrafish.Zv90.180.000.19
addAncestors6.230.086.30
addGeneIDs 4.32 0.1412.34
annotatePeakInBatch0.000.020.01
annotatedPeak0.220.000.21
assignChromosomeRegion0.030.000.03
condenseMatrixByColnames0.050.000.05
convert2EntrezID0.60.00.6
countPatternInSeqs0.200.000.21
enrichedGO0.010.000.01
findOverlappingPeaks000
getAllPeakSequence1.340.021.36
getAnnotation000
getEnrichedGO0.050.020.06
getEnrichedPATH0.000.020.02
getGeneSeq0.020.000.02
getUniqueGOidCount0.030.000.03
hyperGtest0.010.000.02
makeVennDiagram0.020.000.02
myPeakList0.070.000.08
peaksNearBDP000
summarizePatternInPeaks1.410.001.40
translatePattern000
write2FASTA0.120.000.13