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BioC 3.5: CHECK report for minfi on tokay2

This page was generated on 2017-10-18 14:21:30 -0400 (Wed, 18 Oct 2017).

Package 822/1381HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
minfi 1.22.1
Kasper Daniel Hansen
Snapshot Date: 2017-10-17 17:00:52 -0400 (Tue, 17 Oct 2017)
URL: https://git.bioconductor.org/packages/minfi
Branch: RELEASE_3_5
Last Commit: b2faf84
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: rm -rf minfi.buildbin-libdir minfi.Rcheck && mkdir minfi.buildbin-libdir minfi.Rcheck && C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=minfi.buildbin-libdir minfi_1.22.1.tar.gz >minfi.Rcheck\00install.out 2>&1 && cp minfi.Rcheck\00install.out minfi-install.out && C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD check --library=minfi.buildbin-libdir --install="check:minfi-install.out" --force-multiarch --no-vignettes --timings minfi_1.22.1.tar.gz
StartedAt: 2017-10-18 01:22:56 -0400 (Wed, 18 Oct 2017)
EndedAt: 2017-10-18 01:43:42 -0400 (Wed, 18 Oct 2017)
EllapsedTime: 1245.6 seconds
RetCode: 0
Status:  OK  
CheckDir: minfi.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   rm -rf minfi.buildbin-libdir minfi.Rcheck && mkdir minfi.buildbin-libdir minfi.Rcheck && C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=minfi.buildbin-libdir minfi_1.22.1.tar.gz >minfi.Rcheck\00install.out 2>&1 && cp minfi.Rcheck\00install.out minfi-install.out  &&  C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD check --library=minfi.buildbin-libdir --install="check:minfi-install.out" --force-multiarch --no-vignettes --timings minfi_1.22.1.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.5-bioc/meat/minfi.Rcheck'
* using R version 3.4.2 Patched (2017-10-07 r73498)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* 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 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
* loading checks for arch 'i386'
** 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
* loading checks for arch 'x64'
** 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 ...
** running examples for arch 'i386' ... OK
Examples with CPU or elapsed time > 5s
                    user system elapsed
combineArrays      72.60   6.83   88.28
bumphunter         33.42   3.19   36.64
read.metharray.exp 11.25   0.20   11.45
read.metharray      6.98   0.17    7.15
preprocessIllumina  5.38   1.03    6.41
densityPlot         5.34   0.61    5.95
compartments        4.04   1.64    5.69
minfiQC             4.87   0.39    5.27
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
                    user system elapsed
combineArrays      68.38   3.00   71.41
bumphunter         31.01   5.13   36.14
read.metharray.exp  8.44   0.24    8.69
preprocessRaw       6.65   0.29    6.93
densityPlot         5.94   0.64    6.58
densityBeanPlot     5.17   0.59    5.77
compartments        5.08   0.61    5.68
read.metharray      5.31   0.06    5.38
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
  Running 'runTests.R'
 OK
** running tests for arch 'x64' ...
  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
  'C:/Users/biocbuild/bbs-3.5-bioc/meat/minfi.Rcheck/00check.log'
for details.


minfi.Rcheck/00install.out:


install for i386

* 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

install for x64

* installing *source* package 'minfi' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'minfi' as minfi_1.22.1.zip
* DONE (minfi)

minfi.Rcheck/examples_i386/minfi-Ex.timings:

nameusersystemelapsed
GenomicMethylSet-class000
GenomicRatioSet-class000
IlluminaMethylationManifest-class2.890.193.08
MethylSet-class000
RGChannelSet-class000
RatioSet-class000
bumphunter33.42 3.1936.64
combineArrays72.60 6.8388.28
compartments4.041.645.69
controlStripPlot3.460.193.64
convertArray1.600.031.64
densityBeanPlot4.500.475.00
densityPlot5.340.615.95
detectionP0.270.000.27
dmpFinder0.270.030.29
estimateCellCounts000
fixMethOutliers1.240.141.37
gaphunter0.120.000.27
getAnnotation2.130.152.28
getGenomicRatioSetFromGEO000
getQC0.340.020.36
getSex1.280.141.42
logit2000
makeGenomicRatioSetFromMatrix1.560.141.70
mapToGenome-methods0.220.030.25
mdsPlot0.170.150.33
minfiQC4.870.395.27
plotBetasByType000
plotCpg0.130.000.13
preprocessFunnorm4.000.964.95
preprocessIllumina5.381.036.41
preprocessNoob1.310.251.56
preprocessQuantile1.950.162.11
preprocessRaw3.740.394.13
preprocessSwan0.460.130.59
qcReport0.080.000.08
ratioConvert-methods0.080.000.08
read.metharray6.980.177.15
read.metharray.exp11.25 0.2011.45
read.metharray.sheet0.080.000.08
readGEORawFile000
readTCGA000
subsetByLoci0.440.000.43
utils0.220.250.47

minfi.Rcheck/examples_x64/minfi-Ex.timings:

nameusersystemelapsed
GenomicMethylSet-class000
GenomicRatioSet-class000
IlluminaMethylationManifest-class2.700.052.75
MethylSet-class000
RGChannelSet-class000
RatioSet-class000
bumphunter31.01 5.1336.14
combineArrays68.38 3.0071.41
compartments5.080.615.68
controlStripPlot2.860.183.05
convertArray2.500.212.70
densityBeanPlot5.170.595.77
densityPlot5.940.646.58
detectionP0.230.000.24
dmpFinder0.360.020.38
estimateCellCounts000
fixMethOutliers1.790.191.99
gaphunter0.080.000.12
getAnnotation1.300.061.36
getGenomicRatioSetFromGEO000
getQC0.200.030.24
getSex2.390.242.62
logit2000
makeGenomicRatioSetFromMatrix0.480.030.51
mapToGenome-methods0.270.010.28
mdsPlot0.810.180.99
minfiQC4.000.434.45
plotBetasByType000
plotCpg0.130.000.13
preprocessFunnorm4.120.194.34
preprocessIllumina4.360.504.88
preprocessNoob0.870.020.89
preprocessQuantile0.50.00.5
preprocessRaw6.650.296.93
preprocessSwan0.390.020.41
qcReport0.040.000.05
ratioConvert-methods0.050.000.04
read.metharray5.310.065.38
read.metharray.exp8.440.248.69
read.metharray.sheet0.090.000.09
readGEORawFile000
readTCGA000
subsetByLoci0.420.000.42
utils1.080.151.23