Back to the "Multiple platform build/check report" A  B  C  D  E  F  G  H  I  J  K  L  M  N  O  P  Q [R] S  T  U  V  W  X  Y  Z 

BioC 3.2: CHECK report for regioneR on oaxaca

This page was generated on 2015-06-22 09:09:26 -0700 (Mon, 22 Jun 2015).

Package 820/1040HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
regioneR 1.1.1
Bernat Gel
Snapshot Date: 2015-06-21 16:31:12 -0700 (Sun, 21 Jun 2015)
URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/regioneR
Last Changed Rev: 104558 / Revision: 105281
Last Changed Date: 2015-06-04 06:39:34 -0700 (Thu, 04 Jun 2015)
zin1 Linux (Ubuntu 14.04.2 LTS) / x86_64  NotNeeded  OK  WARNINGS UNNEEDED, same version exists in internal repository
perceval Mac OS X Snow Leopard (10.6.8) / x86_64  NotNeeded  OK  WARNINGS  OK UNNEEDED, same version exists in internal repository
oaxaca Mac OS X Mavericks (10.9.5) / x86_64  NotNeeded  OK [ WARNINGS ] OK UNNEEDED, same version exists in internal repository

Summary

Package: regioneR
Version: 1.1.1
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings regioneR_1.1.1.tar.gz
StartedAt: 2015-06-22 02:07:13 -0700 (Mon, 22 Jun 2015)
EndedAt: 2015-06-22 02:16:35 -0700 (Mon, 22 Jun 2015)
EllapsedTime: 562.7 seconds
RetCode: 0
Status:  WARNINGS 
CheckDir: regioneR.Rcheck
Warnings: 2

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings regioneR_1.1.1.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.2-bioc/meat/regioneR.Rcheck’
* using R version 3.2.1 (2015-06-18)
* using platform: x86_64-apple-darwin13.4.0 (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 ‘1.1.1’
* 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 ... [17s/18s] 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 loading without being on the library search path ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... WARNING
plot:
  function(x, ...)
plot.localZScoreResults:
  function(lz, main, num.x.labels, ...)

See section ‘Generic functions and methods’ in the ‘Writing R
Extensions’ manual.
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
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 ‘seqlevels’
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 ... WARNING
Codoc mismatches from documentation object 'plot.localZScoreResults':
plot.localZScoreResults
  Code: function(lz, main = "", num.x.labels = 5, ...)
  Docs: function(x, ...)
  Argument names in code not in docs:
    lz main num.x.labels
  Argument names in docs not in code:
    x
  Mismatches in argument names:
    Position: 1 Code: lz Docs: x
    Position: 2 Code: main Docs: ...

Codoc mismatches from documentation object 'plot.permTestResults':
plot.permTestResults
  Code: function(x, pvalthres = 0.05, plotType = "Tailed", main = "",
                 xlab = NULL, ylab = "", ...)
  Docs: function(x, pvalthres = 0.05, plotType = "Area", ...)
  Argument names in code not in docs:
    main xlab ylab
  Mismatches in argument names:
    Position: 4 Code: main Docs: ...
  Mismatches in argument default values:
    Name: 'plotType' Code: "Tailed" Docs: "Area"

* 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’ ... NOTE
The following directory looks like a leftover from 'knitr':
  ‘figure’
Please remove from your package.
* checking examples ... [357s/392s] OK
Examples with CPU or elapsed time > 5s
                           user system elapsed
createRandomRegions      53.289  5.179  58.726
filterChromosomes        51.781  4.957  56.855
circularRandomizeRegions 51.811  4.524  76.780
maskFromBSGenome         50.419  4.769  56.197
getMask                  50.050  4.248  60.443
randomizeRegions         48.761  4.666  53.554
characterToBSGenome       0.525  0.083   8.036
* 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 WARNINGs, 3 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
characterToBSGenome0.5250.0838.036
circularRandomizeRegions51.811 4.52476.780
commonRegions0.2750.0220.296
createRandomRegions53.289 5.17958.726
emptyCacheRegioneR0.0010.0010.001
extendRegions0.1380.0010.139
filterChromosomes51.781 4.95756.855
getChromosomesByOrganism0.0010.0000.002
getGenome0.0530.0000.054
getGenomeAndMask0.3280.0940.423
getMask50.050 4.24860.443
joinRegions0.1770.0010.178
listChrTypes0.0220.0000.022
localZScore0.8340.1911.049
maskFromBSGenome50.419 4.76956.197
meanDistance0.1660.1830.358
meanInRegions0.1790.0010.186
mergeRegions0.1400.0010.145
numOverlaps0.1450.0010.150
overlapGraphicalSummary0.2120.0010.215
overlapPermTest0.5170.0030.531
overlapRegions0.0880.0010.092
permTest1.4760.0041.510
plot.localZScoreResults1.2450.3381.139
plot.permTestResults1.9130.0562.044
plotRegions0.0610.0000.063
print.permTestResults1.4910.0041.500
randomizeRegions48.761 4.66653.554
recomputePermTest1.9830.0051.991
resampleRegions0.0620.0010.063
splitRegions0.1150.0010.115
subtractRegions0.1640.0010.165
toDataframe0.0190.0000.018
toGRanges0.0230.0010.023
uniqueRegions0.3580.0010.360