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BioC 3.5: CHECK report for ChIPpeakAnno on veracruz2

This page was generated on 2017-10-18 14:28:49 -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: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings ChIPpeakAnno_3.10.2.tar.gz
StartedAt: 2017-10-18 01:33:04 -0400 (Wed, 18 Oct 2017)
EndedAt: 2017-10-18 01:40:13 -0400 (Wed, 18 Oct 2017)
EllapsedTime: 429.6 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 ChIPpeakAnno_3.10.2.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.5-bioc/meat/ChIPpeakAnno.Rcheck’
* using R version 3.4.2 (2017-09-28)
* using platform: x86_64-apple-darwin15.6.0 (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 ‘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 for sufficient/correct file permissions ... OK
* checking whether package ‘ChIPpeakAnno’ can be installed ... OK
* checking installed package size ... NOTE
  installed size is 20.2Mb
  sub-directories of 1Mb or more:
    data     12.7Mb
    doc       1.7Mb
    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
* 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 ... OK
Examples with CPU or elapsed time > 5s
                user system elapsed
findEnhancers 21.137  0.212  21.922
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  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
  ‘/Users/biocbuild/bbs-3.5-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
BED2RangedData0.1820.0010.187
ChIPpeakAnno-package0.0010.0000.001
ExonPlusUtr.human.GRCh374.5150.1224.778
GFF2RangedData0.1620.0030.169
HOT.spots0.1410.0320.174
IDRfilter0.0020.0000.002
Peaks.Ste12.Replicate10.0320.0030.035
Peaks.Ste12.Replicate20.0270.0030.030
Peaks.Ste12.Replicate30.0270.0030.030
TSS.human.GRCh370.1460.0300.179
TSS.human.GRCh380.7370.0150.775
TSS.human.NCBI360.1480.0300.183
TSS.mouse.GRCm380.1470.0340.184
TSS.mouse.NCBIM370.2300.0290.266
TSS.rat.RGSC3.40.1040.0280.133
TSS.rat.Rnor_5.00.0970.0280.127
TSS.zebrafish.Zv80.1040.0300.134
TSS.zebrafish.Zv90.7260.0350.782
addAncestors1.9050.1122.080
addGeneIDs1.5460.1231.703
addMetadata2.5620.0892.712
annoGR0.0010.0000.004
annoPeaks2.6480.2042.954
annotatePeakInBatch2.8900.1313.105
annotatedPeak0.1130.0050.124
assignChromosomeRegion0.0040.0010.005
bdp0.0020.0000.001
binOverFeature0.5560.0210.592
condenseMatrixByColnames0.0680.0010.070
convert2EntrezID0.4550.0090.470
countPatternInSeqs0.3150.0020.325
cumulativePercentage0.0000.0000.001
egOrgMap0.0210.0000.021
enrichedGO0.0030.0020.004
estFragmentLength0.0020.0000.002
estLibSize0.0020.0000.002
featureAlignedDistribution0.6220.0050.638
featureAlignedExtentSignal0.0070.0000.007
featureAlignedHeatmap0.8440.0050.864
featureAlignedSignal0.3700.0290.411
findEnhancers21.137 0.21221.922
findOverlappingPeaks0.0040.0010.004
findOverlapsOfPeaks1.2390.0081.274
getAllPeakSequence0.7150.0210.756
getAnnotation0.0000.0000.001
getEnrichedGO0.0190.0020.021
getEnrichedPATH0.0020.0000.001
getGeneSeq0.0040.0000.005
getUniqueGOidCount0.0020.0000.002
getVennCounts0.0030.0010.003
hyperGtest0.0180.0000.019
makeVennDiagram0.0050.0000.006
mergePlusMinusPeaks0.0030.0000.003
myPeakList0.0220.0040.026
oligoFrequency0.0280.0030.031
oligoSummary0.0010.0000.002
peakPermTest0.0030.0000.003
peaksNearBDP0.0020.0000.003
pie10.0130.0010.014
preparePool0.0030.0000.002
reCenterPeaks0.0190.0000.024
summarizeOverlapsByBins0.4360.1594.427
summarizePatternInPeaks0.9540.0881.065
tileCount0.5740.2194.663
tileGRanges0.0420.0160.058
toGRanges0.0920.0130.108
translatePattern0.0020.0000.002
wgEncodeTfbsV30.2250.0150.244
write2FASTA0.0410.0050.047
xget0.1680.0070.178