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BioC 3.6: CHECK report for ChIPpeakAnno on malbec1

This page was generated on 2017-08-16 13:18:39 -0400 (Wed, 16 Aug 2017).

Package 210/1410HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
ChIPpeakAnno 3.11.4
Lihua Julie Zhu
Snapshot Date: 2017-08-15 17:18:21 -0400 (Tue, 15 Aug 2017)
URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/ChIPpeakAnno
Last Changed Rev: 129558 / Revision: 131943
Last Changed Date: 2017-05-12 12:27:11 -0400 (Fri, 12 May 2017)
malbec1 Linux (Ubuntu 16.04.1 LTS) / x86_64  OK  OK [ OK ]UNNEEDED, same version exists in internal repository
tokay1 Windows Server 2012 R2 Standard / x64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository
veracruz1 OS X 10.11.6 El Capitan / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: ChIPpeakAnno
Version: 3.11.4
Command: /home/biocbuild/bbs-3.6-bioc/R/bin/R CMD check --no-vignettes --timings ChIPpeakAnno_3.11.4.tar.gz
StartedAt: 2017-08-15 21:54:01 -0400 (Tue, 15 Aug 2017)
EndedAt: 2017-08-15 22:00:06 -0400 (Tue, 15 Aug 2017)
EllapsedTime: 364.9 seconds
RetCode: 0
Status:  OK 
CheckDir: ChIPpeakAnno.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.6-bioc/R/bin/R CMD check --no-vignettes --timings ChIPpeakAnno_3.11.4.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.6-bioc/meat/ChIPpeakAnno.Rcheck’
* using R version 3.4.1 (2017-06-30)
* using platform: x86_64-pc-linux-gnu (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 ‘3.11.4’
* 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 19.6Mb
  sub-directories of 1Mb or more:
    data     12.7Mb
    doc       1.1Mb
    extdata   5.2Mb
* 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 ... 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 16.764  0.036  16.814
* 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: 2 NOTEs
See
  ‘/home/biocbuild/bbs-3.6-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
BED2RangedData0.1360.0000.134
ChIPpeakAnno-package0.0000.0000.001
ExonPlusUtr.human.GRCh373.5560.2003.761
GFF2RangedData0.1320.0000.131
HOT.spots0.1560.0240.178
IDRfilter0.0000.0000.001
Peaks.Ste12.Replicate10.0280.0000.026
Peaks.Ste12.Replicate20.0200.0000.022
Peaks.Ste12.Replicate30.0240.0000.022
TSS.human.GRCh370.2120.0200.232
TSS.human.GRCh380.7720.0160.787
TSS.human.NCBI360.1440.0120.153
TSS.mouse.GRCm380.1280.0120.138
TSS.mouse.NCBIM370.2160.0080.225
TSS.rat.RGSC3.40.1040.0080.110
TSS.rat.Rnor_5.00.0840.0120.098
TSS.zebrafish.Zv80.0880.0120.102
TSS.zebrafish.Zv90.7160.0200.734
addAncestors1.5040.0921.625
addGeneIDs1.5560.1041.684
addMetadata1.7400.0401.783
annoGR0.0000.0000.001
annoPeaks2.4640.1082.822
annotatePeakInBatch2.4480.0562.506
annotatedPeak0.1520.0120.167
assignChromosomeRegion0.0040.0000.004
bdp0.0000.0000.001
binOverFeature0.7760.0120.789
binOverGene0.0040.0000.002
binOverRegions0.0040.0000.003
condenseMatrixByColnames0.0880.0000.086
convert2EntrezID0.4880.0000.489
countPatternInSeqs0.3840.0000.385
cumulativePercentage0.0040.0000.001
egOrgMap0.0240.0000.026
enrichedGO0.0040.0000.004
estFragmentLength0.0000.0000.002
estLibSize0.0000.0000.001
featureAlignedDistribution0.7080.0000.706
featureAlignedExtentSignal0.0040.0000.005
featureAlignedHeatmap0.7680.0000.770
featureAlignedSignal0.2840.0080.291
findEnhancers16.764 0.03616.814
findOverlappingPeaks0.0040.0000.002
findOverlapsOfPeaks1.1000.0001.127
getAllPeakSequence0.7040.0161.047
getAnnotation0.0000.0000.001
getEnrichedGO0.0120.0000.011
getEnrichedPATH0.0000.0000.001
getGeneSeq0.0000.0000.002
getUniqueGOidCount0.0040.0000.001
getVennCounts0.0000.0000.002
hyperGtest0.0120.0000.013
makeVennDiagram0.0040.0000.004
mergePlusMinusPeaks0.0040.0000.001
myPeakList0.0120.0040.019
oligoFrequency0.0160.0040.020
oligoSummary000
peakPermTest0.0040.0000.002
peaksNearBDP0.0000.0000.001
pie10.0080.0000.008
plotBinOverRegions0.0000.0000.001
preparePool0.0040.0000.000
reCenterPeaks0.0120.0000.014
summarizeOverlapsByBins0.3440.1440.845
summarizePatternInPeaks0.7880.0280.816
tileCount0.4360.1120.807
tileGRanges0.0480.0040.052
toGRanges0.1000.0040.108
translatePattern0.0000.0000.001
wgEncodeTfbsV30.2320.0280.260
write2FASTA0.0280.0000.027
xget0.1560.0040.161