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BioC 3.2: CHECK report for regioneR on perceval

This page was generated on 2015-11-10 14:49:45 -0800 (Tue, 10 Nov 2015).

Package 868/1104HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
regioneR 1.2.0
Bernat Gel
Snapshot Date: 2015-11-09 16:24:09 -0800 (Mon, 09 Nov 2015)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_2/madman/Rpacks/regioneR
Last Changed Rev: 109589 / Revision: 110496
Last Changed Date: 2015-10-13 12:36:05 -0700 (Tue, 13 Oct 2015)
zin1 Linux (Ubuntu 14.04.2 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
perceval Mac OS X Snow Leopard (10.6.8) / x86_64  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: regioneR
Version: 1.2.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings regioneR_1.2.0.tar.gz
StartedAt: 2015-11-10 08:45:53 -0800 (Tue, 10 Nov 2015)
EndedAt: 2015-11-10 08:57:23 -0800 (Tue, 10 Nov 2015)
EllapsedTime: 690.0 seconds
RetCode: 0
Status:  OK 
CheckDir: regioneR.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings regioneR_1.2.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.2-bioc/meat/regioneR.Rcheck’
* using R version 3.2.2 Patched (2015-10-08 r69496)
* using platform: x86_64-apple-darwin10.8.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘regioneR/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘regioneR’ version ‘1.2.0’
* checking package namespace information ... OK
* checking package dependencies ... OK
* 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 ‘regioneR’ can be installed ... [19s/19s] OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Packages listed in more than one of Depends, Imports, Suggests, Enhances:
  ‘memoise’ ‘GenomicRanges’ ‘BSgenome’ ‘rtracklayer’ ‘parallel’
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 ... NOTE
copySeqLevels: no visible global function definition for ‘seqlevels<-’
copySeqLevels: no visible global function definition for ‘seqlevels’
createRandomRegions: no visible global function definition for
  ‘seqlevels’
filterChromosomes: no visible global function definition for
  ‘keepSeqlevels’
randomizeRegions: no visible global function definition for ‘seqlevels’
randomizeRegions: no visible global function definition for ‘IRanges’
resampleRegions: no visible global function definition for ‘seqlevels’
toGRanges: no visible global function definition for ‘IRanges’
* 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 sizes of PDF files under ‘inst/doc’ ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [361s/377s] OK
Examples with CPU or elapsed time > 5s
                           user system elapsed
createRandomRegions      49.251  6.523  55.782
randomizeRegions         49.365  5.536  57.805
filterChromosomes        48.033  6.023  54.060
circularRandomizeRegions 47.794  5.986  63.773
maskFromBSGenome         46.499  6.153  52.665
getMask                  45.768  5.924  51.695
localZScore               3.972  0.370   5.926
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’ [126s/130s]
 [126s/130s] 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/regioneR.Rcheck/00check.log’
for details.


regioneR.Rcheck/00install.out:

* installing *source* package ‘regioneR’ ...
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (regioneR)

regioneR.Rcheck/regioneR-Ex.timings:

nameusersystemelapsed
characterToBSGenome0.6740.1844.861
circularRandomizeRegions47.794 5.98663.773
commonRegions0.2550.0190.274
createFunctionsList1.0210.3831.404
createRandomRegions49.251 6.52355.782
emptyCacheRegioneR0.0010.0000.001
extendRegions0.1310.0010.132
filterChromosomes48.033 6.02354.060
getChromosomesByOrganism0.0020.0000.002
getGenome0.0560.0000.056
getGenomeAndMask0.4070.1330.540
getMask45.768 5.92451.695
joinRegions0.1600.0010.161
listChrTypes0.0190.0000.019
localZScore3.9720.3705.926
maskFromBSGenome46.499 6.15352.665
meanDistance0.1160.0000.116
meanInRegions0.1650.0010.165
mergeRegions0.1340.0010.135
numOverlaps0.1970.0000.198
overlapGraphicalSummary0.1800.0010.181
overlapPermTest0.9820.0030.992
overlapRegions0.0720.0000.072
permTest1.7830.0041.787
plot.localZScoreResults1.4650.1921.659
plot.localZScoreResultsList3.2400.0053.245
plot.permTestResults2.5540.0052.565
plot.permTestResultsList3.1010.2393.425
plotRegions0.0570.0010.058
print.permTestResults1.7200.0021.721
randomizeRegions49.365 5.53657.805
recomputePermTest1.0510.0251.169
resampleRegions0.0790.0010.079
splitRegions0.1170.0010.118
subtractRegions0.1840.0010.185
toDataframe0.0180.0010.018
toGRanges0.0270.0000.026
uniqueRegions0.3620.0020.364