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BioC 3.5: CHECK report for ChIPpeakAnno on tokay2

This page was generated on 2017-10-18 14:20:27 -0400 (Wed, 18 Oct 2017).

Package 208/1381HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
ChIPpeakAnno 3.10.2
Lihua Julie Zhu
Snapshot Date: 2017-10-17 17:00:52 -0400 (Tue, 17 Oct 2017)
URL: https://git.bioconductor.org/packages/ChIPpeakAnno
Branch: RELEASE_3_5
Last Commit: 9c5f113
Last Changed Date: 2017-10-04 12:33:58 -0400 (Wed, 04 Oct 2017)
malbec2 Linux (Ubuntu 16.04.1 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  OK  OK [ OK ] OK UNNEEDED, same version exists in internal repository
veracruz2 OS X 10.11.6 El Capitan / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: ChIPpeakAnno
Version: 3.10.2
Command: rm -rf ChIPpeakAnno.buildbin-libdir ChIPpeakAnno.Rcheck && mkdir ChIPpeakAnno.buildbin-libdir ChIPpeakAnno.Rcheck && C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=ChIPpeakAnno.buildbin-libdir ChIPpeakAnno_3.10.2.tar.gz >ChIPpeakAnno.Rcheck\00install.out 2>&1 && cp ChIPpeakAnno.Rcheck\00install.out ChIPpeakAnno-install.out && C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD check --library=ChIPpeakAnno.buildbin-libdir --install="check:ChIPpeakAnno-install.out" --force-multiarch --no-vignettes --timings ChIPpeakAnno_3.10.2.tar.gz
StartedAt: 2017-10-17 22:41:19 -0400 (Tue, 17 Oct 2017)
EndedAt: 2017-10-17 22:53:03 -0400 (Tue, 17 Oct 2017)
EllapsedTime: 704.1 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 && C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=ChIPpeakAnno.buildbin-libdir ChIPpeakAnno_3.10.2.tar.gz >ChIPpeakAnno.Rcheck\00install.out 2>&1 && cp ChIPpeakAnno.Rcheck\00install.out ChIPpeakAnno-install.out  &&  C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD check --library=ChIPpeakAnno.buildbin-libdir --install="check:ChIPpeakAnno-install.out" --force-multiarch --no-vignettes --timings ChIPpeakAnno_3.10.2.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.5-bioc/meat/ChIPpeakAnno.Rcheck'
* using R version 3.4.2 Patched (2017-10-07 r73498)
* using platform: x86_64-w64-mingw32 (64-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 '3.10.2'
* checking package namespace information ... OK
* checking package dependencies ... NOTE
Depends: includes the non-default packages:
  'grid' 'IRanges' 'Biostrings' 'GenomicRanges' 'S4Vectors'
  'VennDiagram'
Adding so many packages to the search path is excessive and importing
selectively is preferable.
* 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 19.2Mb
  sub-directories of 1Mb or more:
    data     12.7Mb
    extdata   5.2Mb
* checking package directory ... OK
* checking 'build' directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Package listed in more than one of Depends, Imports, Suggests, Enhances:
  'BiocStyle'
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 ... 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 ... OK
* 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' ... OK
Examples with CPU or elapsed time > 5s
                         user system elapsed
findEnhancers           14.97   0.17   15.14
annoPeaks                3.32   0.15   12.11
summarizeOverlapsByBins  0.56   0.00   15.20
tileCount                0.50   0.01   15.08
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
                          user system elapsed
findEnhancers            18.95   0.17   19.12
ExonPlusUtr.human.GRCh37  5.66   0.11    5.76
tileCount                 0.51   0.00   15.01
summarizeOverlapsByBins   0.50   0.00   16.30
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
  Running 'runTests.R'
 OK
** running tests for arch 'x64' ...
  Running 'runTests.R'
 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

Status: 3 NOTEs
See
  'C:/Users/biocbuild/bbs-3.5-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_3.10.2.zip
* DONE (ChIPpeakAnno)

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

nameusersystemelapsed
BED2RangedData0.130.000.13
ChIPpeakAnno-package000
ExonPlusUtr.human.GRCh374.190.084.26
GFF2RangedData0.110.000.11
HOT.spots0.150.000.15
IDRfilter000
Peaks.Ste12.Replicate10.050.000.05
Peaks.Ste12.Replicate20.010.000.01
Peaks.Ste12.Replicate30.030.000.03
TSS.human.GRCh370.160.000.16
TSS.human.GRCh380.750.030.78
TSS.human.NCBI360.20.00.2
TSS.mouse.GRCm380.200.010.22
TSS.mouse.NCBIM370.160.000.16
TSS.rat.RGSC3.40.610.000.61
TSS.rat.Rnor_5.00.110.000.11
TSS.zebrafish.Zv80.090.000.09
TSS.zebrafish.Zv90.110.020.12
addAncestors1.330.111.44
addGeneIDs1.480.474.50
addMetadata1.610.111.72
annoGR000
annoPeaks 3.32 0.1512.11
annotatePeakInBatch2.490.082.64
annotatedPeak0.180.020.20
assignChromosomeRegion0.020.000.02
bdp000
binOverFeature0.530.000.53
condenseMatrixByColnames0.040.000.05
convert2EntrezID0.420.000.42
countPatternInSeqs0.240.000.24
cumulativePercentage000
egOrgMap0.010.000.01
enrichedGO0.020.000.02
estFragmentLength000
estLibSize000
featureAlignedDistribution0.550.000.54
featureAlignedExtentSignal0.010.000.02
featureAlignedHeatmap0.600.000.59
featureAlignedSignal0.320.000.33
findEnhancers14.97 0.1715.14
findOverlappingPeaks000
findOverlapsOfPeaks0.940.020.95
getAllPeakSequence0.670.000.68
getAnnotation000
getEnrichedGO0.000.010.01
getEnrichedPATH0.020.000.02
getGeneSeq000
getUniqueGOidCount000
getVennCounts000
hyperGtest0.010.000.01
makeVennDiagram000
mergePlusMinusPeaks0.020.000.02
myPeakList0.030.000.03
oligoFrequency0.020.000.02
oligoSummary000
peakPermTest000
peaksNearBDP000
pie10.010.000.01
preparePool000
reCenterPeaks0.020.000.02
summarizeOverlapsByBins 0.56 0.0015.20
summarizePatternInPeaks0.940.020.95
tileCount 0.50 0.0115.08
tileGRanges0.040.000.05
toGRanges0.100.000.09
translatePattern000
wgEncodeTfbsV30.340.020.36
write2FASTA0.030.000.03
xget0.160.000.16

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

nameusersystemelapsed
BED2RangedData0.260.000.26
ChIPpeakAnno-package000
ExonPlusUtr.human.GRCh375.660.115.76
GFF2RangedData0.180.000.19
HOT.spots0.210.000.20
IDRfilter000
Peaks.Ste12.Replicate10.070.020.10
Peaks.Ste12.Replicate20.040.000.03
Peaks.Ste12.Replicate30.030.010.04
TSS.human.GRCh370.180.000.19
TSS.human.GRCh381.190.021.20
TSS.human.NCBI360.140.000.15
TSS.mouse.GRCm380.130.000.12
TSS.mouse.NCBIM370.120.000.13
TSS.rat.RGSC3.40.100.010.10
TSS.rat.Rnor_5.00.070.020.10
TSS.zebrafish.Zv80.080.030.11
TSS.zebrafish.Zv90.110.000.11
addAncestors1.600.081.67
addGeneIDs1.620.341.97
addMetadata2.480.082.57
annoGR000
annoPeaks2.270.232.50
annotatePeakInBatch2.690.112.79
annotatedPeak0.110.020.13
assignChromosomeRegion000
bdp000
binOverFeature0.480.010.50
condenseMatrixByColnames0.060.000.06
convert2EntrezID0.350.000.34
countPatternInSeqs0.250.000.25
cumulativePercentage000
egOrgMap0.010.000.02
enrichedGO000
estFragmentLength000
estLibSize0.020.000.02
featureAlignedDistribution0.420.000.42
featureAlignedExtentSignal0.020.000.01
featureAlignedHeatmap0.620.000.64
featureAlignedSignal0.350.030.38
findEnhancers18.95 0.1719.12
findOverlappingPeaks000
findOverlapsOfPeaks1.140.001.14
getAllPeakSequence0.750.000.75
getAnnotation000
getEnrichedGO0.020.000.02
getEnrichedPATH000
getGeneSeq000
getUniqueGOidCount000
getVennCounts0.020.000.01
hyperGtest0.010.000.02
makeVennDiagram000
mergePlusMinusPeaks000
myPeakList0.020.020.03
oligoFrequency0.010.000.01
oligoSummary000
peakPermTest000
peaksNearBDP000
pie10.010.000.01
preparePool000
reCenterPeaks0.040.000.03
summarizeOverlapsByBins 0.5 0.016.3
summarizePatternInPeaks0.870.000.87
tileCount 0.51 0.0015.01
tileGRanges0.050.000.05
toGRanges0.110.000.11
translatePattern000
wgEncodeTfbsV30.310.040.36
write2FASTA0.050.000.05
xget0.180.020.20