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 3.1: CHECK report for minfi on morelia

This page was generated on 2015-10-09 09:40:01 -0700 (Fri, 09 Oct 2015).

Package 603/1024HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
minfi 1.14.0
Kasper Daniel Hansen
Snapshot Date: 2015-10-08 17:20:21 -0700 (Thu, 08 Oct 2015)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_1/madman/Rpacks/minfi
Last Changed Rev: 102591 / Revision: 109384
Last Changed Date: 2015-04-16 12:42:01 -0700 (Thu, 16 Apr 2015)
zin2 Linux (Ubuntu 14.04.2 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
moscato2 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository
petty Mac OS X Snow Leopard (10.6.8) / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository
morelia Mac OS X Mavericks (10.9.5) / x86_64  OK  OK [ OK ] OK UNNEEDED, same version exists in internal repository

Summary

Package: minfi
Version: 1.14.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings minfi_1.14.0.tar.gz
StartedAt: 2015-10-09 03:56:50 -0700 (Fri, 09 Oct 2015)
EndedAt: 2015-10-09 04:09:57 -0700 (Fri, 09 Oct 2015)
EllapsedTime: 787.8 seconds
RetCode: 0
Status:  OK 
CheckDir: minfi.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings minfi_1.14.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.1-bioc/meat/minfi.Rcheck’
* using R version 3.2.2 (2015-08-14)
* using platform: x86_64-apple-darwin13.4.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘minfi/DESCRIPTION’ ... OK
* this is package ‘minfi’ version ‘1.14.0’
* checking package namespace information ... OK
* checking package dependencies ... NOTE
Depends: includes the non-default packages:
  ‘BiocGenerics’ ‘Biobase’ ‘lattice’ ‘GenomicRanges’ ‘Biostrings’
  ‘bumphunter’
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 ‘minfi’ can be installed ... [21s/21s] 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 objects imported by ':::' calls:
  ‘GenomicRanges:::.ShallowSimpleListAssays’
  ‘GenomicRanges:::.valid.SummarizedExperiment.colData_dims’
  ‘GenomicRanges:::clone’ ‘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 sizes of PDF files under ‘inst/doc’ ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [394s/396s] OK
Examples with CPU or elapsed time > 5s
                      user system elapsed
gaphunter          194.399  9.704 204.226
bumphunter          36.298  9.387  47.163
preprocessFunnorm   34.010  6.310  40.362
preprocessNoob      15.401  3.079  18.491
preprocessQuantile  13.011  2.007  15.021
detectionP          10.529  1.020  11.555
read.450k.exp        5.998  0.455   6.547
minfiQC              5.500  0.733   6.235
read.450k            4.889  0.375   5.264
densityBeanPlot      4.464  0.535   5.002
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘runTests.R’ [142s/188s]
 [143s/189s] 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-3.1-bioc/meat/minfi.Rcheck/00check.log’
for details.


minfi.Rcheck/00install.out:

* installing *source* package ‘minfi’ ...
** R
** inst
** preparing package for lazy loading
Creating a generic function for ‘nchar’ from package ‘base’ in package ‘S4Vectors’
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
Creating a generic function for ‘nchar’ from package ‘base’ in package ‘S4Vectors’
* DONE (minfi)

minfi.Rcheck/minfi-Ex.timings:

nameusersystemelapsed
GenomicMethylSet-class0.0030.0000.003
GenomicRatioSet-class0.0020.0000.002
IlluminaMethylationManifest-class2.2660.2192.486
MethylSet-class0.0020.0000.002
RGChannelSet-class0.0020.0010.002
RatioSet-class0.0010.0000.001
bumphunter36.298 9.38747.163
controlStripPlot1.4230.1811.902
densityBeanPlot4.4640.5355.002
densityPlot3.6550.5554.246
detectionP10.529 1.02011.555
dmpFinder0.2120.0130.225
estimateCellCounts0.0010.0000.001
fixMethOutliers0.7430.1510.894
gaphunter194.399 9.704204.226
getAnnotation1.5330.2041.737
getGenomicRatioSetFromGEO000
getQC0.1960.0090.205
getSex2.8530.5553.408
logit20.0000.0000.001
makeGenomicRatioSetFromMatrix1.3340.1371.471
mdsPlot0.6600.0760.736
minfiQC5.5000.7336.235
plotBetasByType0.0010.0000.001
plotCpg0.2580.0100.268
preprocessFunnorm34.010 6.31040.362
preprocessIllumina2.9270.3323.260
preprocessNoob15.401 3.07918.491
preprocessQuantile13.011 2.00715.021
preprocessRaw2.3750.3622.738
preprocessSwan0.0010.0010.001
qcReport0.0590.0010.061
read.450k4.8890.3755.264
read.450k.exp5.9980.4556.547
read.450k.sheet0.0790.0020.081
readGEORawFile0.0010.0000.000
readTCGA000
utils1.9840.4212.408