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BioC 3.2: CHECK report for ChIPpeakAnno on zin1

This page was generated on 2016-04-23 10:11:14 -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: /home/biocbuild/bbs-3.2-bioc/R/bin/R CMD check --no-vignettes --timings ChIPpeakAnno_3.4.6.tar.gz
StartedAt: 2016-04-22 23:01:40 -0700 (Fri, 22 Apr 2016)
EndedAt: 2016-04-22 23:06:29 -0700 (Fri, 22 Apr 2016)
EllapsedTime: 288.2 seconds
RetCode: 0
Status:  OK 
CheckDir: ChIPpeakAnno.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.2-bioc/R/bin/R CMD check --no-vignettes --timings ChIPpeakAnno_3.4.6.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.2-bioc/meat/ChIPpeakAnno.Rcheck’
* using R version 3.2.4 Revised (2016-03-16 r70336)
* 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 ‘3.4.6’
* 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 ... [21s/21s] OK
* checking installed package size ... NOTE
  installed size is 18.4Mb
  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 ... [28s/28s] OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘runTests.R’ [50s/50s]
 [50s/50s] 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-3.2-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
BED2RangedData0.0380.0000.038
ChIPpeakAnno-package000
ExonPlusUtr.human.GRCh373.6530.0363.701
GFF2RangedData0.0150.0000.015
HOT.spots0.140.000.14
Peaks.Ste12.Replicate10.0220.0040.027
Peaks.Ste12.Replicate20.0160.0080.024
Peaks.Ste12.Replicate30.0200.0040.025
TSS.human.GRCh370.1640.0080.171
TSS.human.GRCh380.9580.0040.966
TSS.human.NCBI360.1250.0000.125
TSS.mouse.GRCm380.1180.0000.118
TSS.mouse.NCBIM370.1070.0040.111
TSS.rat.RGSC3.40.090.000.09
TSS.rat.Rnor_5.00.0840.0000.083
TSS.zebrafish.Zv80.0860.0000.086
TSS.zebrafish.Zv90.1000.0080.108
addAncestors1.6530.0321.686
addGeneIDs2.0920.0282.136
annoGR000
annotatePeakInBatch1.8890.0761.976
annotatedPeak0.0880.0120.100
assignChromosomeRegion0.0240.0000.024
binOverFeature0.4060.0040.409
condenseMatrixByColnames0.0190.0000.019
convert2EntrezID0.3780.0000.381
countPatternInSeqs0.1090.0040.113
egOrgMap0.0010.0000.001
enrichedGO0.0030.0000.003
featureAlignedDistribution1.0110.0001.010
featureAlignedHeatmap1.0970.0001.096
featureAlignedSignal0.9190.0160.935
findOverlappingPeaks0.0020.0000.003
findOverlapsOfPeaks0.5160.0000.515
getAllPeakSequence0.6130.0000.612
getAnnotation0.0010.0000.001
getEnrichedGO0.0150.0000.015
getEnrichedPATH0.0010.0000.001
getGeneSeq0.0030.0000.002
getUniqueGOidCount0.0010.0000.001
getVennCounts0.0020.0000.002
hyperGtest0.0020.0000.002
makeVennDiagram0.0040.0000.004
mergePlusMinusPeaks0.0010.0000.001
myPeakList0.020.000.02
peakPermTest0.0030.0000.003
peaksNearBDP0.0010.0000.001
pie10.010.000.01
preparePool0.0010.0000.002
summarizePatternInPeaks0.5630.0080.570
toGRanges0.0250.0000.025
translatePattern0.0010.0000.001
wgEncodeTfbsV30.2210.0040.226
write2FASTA0.010.000.01