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BioC 3.5: CHECK report for minfi on malbec2

This page was generated on 2017-08-16 13:14:12 -0400 (Wed, 16 Aug 2017).

Package 822/1382HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
minfi 1.22.1
Kasper Daniel Hansen
Snapshot Date: 2017-08-15 17:17:57 -0400 (Tue, 15 Aug 2017)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_5/madman/Rpacks/minfi
Last Changed Rev: 129326 / Revision: 131943
Last Changed Date: 2017-05-01 11:23:50 -0400 (Mon, 01 May 2017)
malbec2 Linux (Ubuntu 16.04.1 LTS) / x86_64  OK  OK [ OK ]UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository
veracruz2 OS X 10.11.6 El Capitan / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: minfi
Version: 1.22.1
Command: /home/biocbuild/bbs-3.5-bioc/R/bin/R CMD check --no-vignettes --timings minfi_1.22.1.tar.gz
StartedAt: 2017-08-16 00:38:51 -0400 (Wed, 16 Aug 2017)
EndedAt: 2017-08-16 00:48:55 -0400 (Wed, 16 Aug 2017)
EllapsedTime: 604.2 seconds
RetCode: 0
Status:  OK 
CheckDir: minfi.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.5-bioc/R/bin/R CMD check --no-vignettes --timings minfi_1.22.1.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.5-bioc/meat/minfi.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 ‘minfi/DESCRIPTION’ ... OK
* this is package ‘minfi’ version ‘1.22.1’
* 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 ‘minfi’ can be installed ... OK
* checking installed package size ... OK
* 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 ... NOTE
Unexported object imported by a ':::' call: ‘bumphunter:::.getEstimate’
  See the note in ?`:::` about the use of this operator.
* 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 installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
                     user system elapsed
combineArrays      62.120 10.700  77.482
bumphunter         31.276  7.460  38.893
densityPlot         8.412  0.056   8.475
read.metharray.exp  7.828  0.028   7.863
read.metharray      5.116  0.012   5.135
densityBeanPlot     4.888  0.212   5.108
* 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: 1 NOTE
See
  ‘/home/biocbuild/bbs-3.5-bioc/meat/minfi.Rcheck/00check.log’
for details.


minfi.Rcheck/00install.out:

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

minfi.Rcheck/minfi-Ex.timings:

nameusersystemelapsed
GenomicMethylSet-class0.0000.0000.002
GenomicRatioSet-class0.0000.0000.001
IlluminaMethylationManifest-class2.7680.0682.834
MethylSet-class0.0000.0000.001
RGChannelSet-class0.0000.0000.001
RatioSet-class000
bumphunter31.276 7.46038.893
combineArrays62.12010.70077.482
compartments3.1320.6163.750
controlStripPlot3.1120.5124.198
convertArray1.2120.0041.216
densityBeanPlot4.8880.2125.108
densityPlot8.4120.0568.475
detectionP0.3400.0040.354
dmpFinder0.2840.0200.306
estimateCellCounts0.0000.0000.001
fixMethOutliers0.8520.6841.537
gaphunter0.1320.0000.157
getAnnotation1.7080.1681.875
getGenomicRatioSetFromGEO0.0000.0000.001
getQC0.2320.0040.235
getSex1.3600.0121.374
logit20.0000.0000.001
makeGenomicRatioSetFromMatrix0.4880.0000.487
mapToGenome-methods0.1800.0000.181
mdsPlot0.1680.0000.168
minfiQC3.0720.1403.217
plotBetasByType0.0000.0000.001
plotCpg0.1000.0000.098
preprocessFunnorm3.1800.0123.200
preprocessIllumina3.2400.0003.243
preprocessNoob0.8440.0000.850
preprocessQuantile0.5080.0000.510
preprocessRaw2.2480.0042.253
preprocessSwan0.420.000.42
qcReport0.0480.0040.050
ratioConvert-methods0.0640.0000.063
read.metharray5.1160.0125.135
read.metharray.exp7.8280.0287.863
read.metharray.sheet0.0680.0000.067
readGEORawFile0.0000.0000.001
readTCGA000
subsetByLoci0.3880.0000.387
utils0.1320.0040.138