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BioC 3.2: CHECK report for ChIPpeakAnno on oaxaca

This page was generated on 2016-04-23 10:24:26 -0700 (Sat, 23 Apr 2016).

Package 165/1103HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
ChIPpeakAnno 3.4.6
Lihua Julie Zhu , Jianhong Ou
Snapshot Date: 2016-04-22 16:20:12 -0700 (Fri, 22 Apr 2016)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_2/madman/Rpacks/ChIPpeakAnno
Last Changed Rev: 113524 / Revision: 116712
Last Changed Date: 2016-02-11 06:19:09 -0800 (Thu, 11 Feb 2016)
zin1 Linux (Ubuntu 14.04.2 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
moscato1 Windows Server 2008 R2 Standard (64-bit) / x64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository
oaxaca Mac OS X Mavericks (10.9.5) / x86_64  OK  OK [ OK ] OK UNNEEDED, same version exists in internal repository

Summary

Package: ChIPpeakAnno
Version: 3.4.6
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings ChIPpeakAnno_3.4.6.tar.gz
StartedAt: 2016-04-22 22:36:09 -0700 (Fri, 22 Apr 2016)
EndedAt: 2016-04-22 22:42:42 -0700 (Fri, 22 Apr 2016)
EllapsedTime: 393.0 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_3.4.6.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.2-bioc/meat/ChIPpeakAnno.Rcheck’
* using R version 3.2.4 (2016-03-10)
* using platform: x86_64-apple-darwin13.4.0 (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 ‘3.4.6’
* 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 ... [28s/28s] OK
* checking installed package size ... NOTE
  installed size is 18.6Mb
  sub-directories of 1Mb or more:
    data     12.7Mb
    extdata   4.7Mb
* 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 ... [39s/40s] OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘runTests.R’ [70s/71s]
 [70s/71s] 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
  ‘/Users/biocbuild/bbs-3.2-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
BED2RangedData0.0680.0010.069
ChIPpeakAnno-package0.0010.0000.001
ExonPlusUtr.human.GRCh374.5090.1144.629
GFF2RangedData0.0210.0010.022
HOT.spots0.7210.0380.759
Peaks.Ste12.Replicate10.0340.0030.037
Peaks.Ste12.Replicate20.0310.0030.034
Peaks.Ste12.Replicate30.0330.0030.036
TSS.human.GRCh370.1820.0270.210
TSS.human.GRCh380.7010.0110.712
TSS.human.NCBI360.1490.0280.178
TSS.mouse.GRCm380.1480.0300.178
TSS.mouse.NCBIM370.1400.0290.168
TSS.rat.RGSC3.40.1150.0300.144
TSS.rat.Rnor_5.00.1150.0280.143
TSS.zebrafish.Zv80.1210.0310.152
TSS.zebrafish.Zv90.1470.0330.179
addAncestors2.2160.1562.374
addGeneIDs2.4650.0992.599
annoGR0.0010.0000.001
annotatePeakInBatch2.7710.2303.436
annotatedPeak0.1170.0100.127
assignChromosomeRegion0.0050.0000.006
binOverFeature0.5210.0300.551
condenseMatrixByColnames0.0280.0010.029
convert2EntrezID0.590.010.60
countPatternInSeqs0.1700.0020.172
egOrgMap0.0010.0000.002
enrichedGO0.0020.0010.004
featureAlignedDistribution1.5600.0081.569
featureAlignedHeatmap1.7210.0051.730
featureAlignedSignal1.3840.0291.415
findOverlappingPeaks0.0040.0000.004
findOverlapsOfPeaks0.7470.0050.752
getAllPeakSequence0.7830.0160.861
getAnnotation0.0010.0010.001
getEnrichedGO0.0270.0020.030
getEnrichedPATH0.0020.0000.002
getGeneSeq0.0060.0000.005
getUniqueGOidCount0.0030.0000.003
getVennCounts0.0040.0000.004
hyperGtest0.0020.0010.002
makeVennDiagram0.0080.0000.009
mergePlusMinusPeaks0.0020.0000.003
myPeakList0.0260.0090.035
peakPermTest0.0040.0010.004
peaksNearBDP0.0030.0000.002
pie10.0150.0010.016
preparePool0.0030.0000.003
summarizePatternInPeaks0.7510.0160.768
toGRanges0.0360.0000.036
translatePattern0.0010.0000.001
wgEncodeTfbsV30.2770.0190.297
write2FASTA0.0160.0000.016