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BioC 3.5: CHECK report for sigaR on tokay2

This page was generated on 2017-10-18 14:21:37 -0400 (Wed, 18 Oct 2017).

Package 1213/1381HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
sigaR 1.24.0
Wessel N. van Wieringen
Snapshot Date: 2017-10-17 17:00:52 -0400 (Tue, 17 Oct 2017)
URL: https://git.bioconductor.org/packages/sigaR
Branch: RELEASE_3_5
Last Commit: b68df6f
Last Changed Date: 2017-04-24 15:45:44 -0400 (Mon, 24 Apr 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: sigaR
Version: 1.24.0
Command: rm -rf sigaR.buildbin-libdir sigaR.Rcheck && mkdir sigaR.buildbin-libdir sigaR.Rcheck && C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=sigaR.buildbin-libdir sigaR_1.24.0.tar.gz >sigaR.Rcheck\00install.out 2>&1 && cp sigaR.Rcheck\00install.out sigaR-install.out && C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD check --library=sigaR.buildbin-libdir --install="check:sigaR-install.out" --force-multiarch --no-vignettes --timings sigaR_1.24.0.tar.gz
StartedAt: 2017-10-18 02:59:46 -0400 (Wed, 18 Oct 2017)
EndedAt: 2017-10-18 03:07:10 -0400 (Wed, 18 Oct 2017)
EllapsedTime: 443.7 seconds
RetCode: 0
Status:  OK  
CheckDir: sigaR.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   rm -rf sigaR.buildbin-libdir sigaR.Rcheck && mkdir sigaR.buildbin-libdir sigaR.Rcheck && C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=sigaR.buildbin-libdir sigaR_1.24.0.tar.gz >sigaR.Rcheck\00install.out 2>&1 && cp sigaR.Rcheck\00install.out sigaR-install.out  &&  C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD check --library=sigaR.buildbin-libdir --install="check:sigaR-install.out" --force-multiarch --no-vignettes --timings sigaR_1.24.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.5-bioc/meat/sigaR.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 'sigaR/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'sigaR' version '1.24.0'
* 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 whether package 'sigaR' 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
There are ::: calls to the package's namespace in its code. A package
  almost never needs to use ::: for its own objects:
  '.alphabivariate' '.alphaest' '.pretest'
* 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 contents of 'data' directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... 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
mutInfTest    119.61   4.11  123.72
cisEffectTune  11.55   0.00   11.55
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
                 user system elapsed
mutInfTest     112.81   5.11  117.92
cisEffectTune   16.12   0.00   16.12
pathway2sample   4.37   0.90    5.28
* 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/sigaR.Rcheck/00check.log'
for details.


sigaR.Rcheck/00install.out:

install for i386

* installing *source* package 'sigaR' ...
** R
** data
** 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 'sigaR' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'sigaR' as sigaR_1.24.0.zip
* DONE (sigaR)

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

nameusersystemelapsed
CNGEheatmaps1.380.061.44
ExpressionSet2order0.020.020.03
ExpressionSet2subset0.010.000.01
ExpressionSet2weightedSubset0.30.00.3
RCMestimation1.230.051.28
RCMrandom1.800.031.83
RCMtest2.890.002.89
cghCall2cghSeg0.090.000.09
cghCall2maximumSubset0.310.000.31
cghCall2order0.030.000.03
cghCall2subset0.050.000.05
cghCall2weightedSubset0.230.000.23
cghSeg2order0.070.000.06
cghSeg2subset0.040.000.05
cghSeg2weightedSubset0.240.000.24
cisEffectPlot0.170.000.17
cisEffectTable1.300.011.31
cisEffectTest1.840.001.84
cisEffectTune11.55 0.0011.55
cisTest-class000
entTest-class000
entropyTest0.260.020.28
expandMatching2singleIDs0.080.000.08
getSegFeatures0.020.000.02
hdEntropy0.000.020.01
hdMI0.570.000.58
matchAnn2Ann0.210.030.23
matchCGHcall2ExpressionSet0.200.000.21
merge2ExpressionSets0.110.000.11
merge2cghCalls0.080.000.07
miTest-class000
mutInfTest119.61 4.11123.72
nBreakpoints0.110.010.13
pathway1sample0.420.000.42
pathway2sample3.510.584.09
pathwayFit-class000
pathwayPlot0.190.000.19
pollackCN160.000.030.03
pollackGE160.000.020.02
profilesPlot0.240.010.25
rcmFit-class000
rcmTest-class000
splitMatchingAtBreakpoints0.160.000.16
uniqGenomicInfo000

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

nameusersystemelapsed
CNGEheatmaps101
ExpressionSet2order0.020.000.01
ExpressionSet2subset000
ExpressionSet2weightedSubset0.250.010.26
RCMestimation101
RCMrandom1.230.021.25
RCMtest2.880.002.88
cghCall2cghSeg0.140.000.14
cghCall2maximumSubset0.450.000.45
cghCall2order0.050.000.05
cghCall2subset0.030.000.03
cghCall2weightedSubset0.310.010.33
cghSeg2order0.060.000.06
cghSeg2subset0.080.000.08
cghSeg2weightedSubset0.330.000.33
cisEffectPlot0.190.000.19
cisEffectTable1.570.021.59
cisEffectTest1.900.011.91
cisEffectTune16.12 0.0016.12
cisTest-class000
entTest-class000
entropyTest0.450.000.45
expandMatching2singleIDs0.080.020.10
getSegFeatures0.000.020.01
hdEntropy0.020.000.02
hdMI0.860.010.87
matchAnn2Ann0.170.000.18
matchCGHcall2ExpressionSet0.140.020.15
merge2ExpressionSets0.080.000.08
merge2cghCalls0.080.000.08
miTest-class000
mutInfTest112.81 5.11117.92
nBreakpoints0.140.000.14
pathway1sample0.80.00.8
pathway2sample4.370.905.28
pathwayFit-class000
pathwayPlot0.170.000.17
pollackCN16000
pollackGE160.020.000.02
profilesPlot0.140.030.17
rcmFit-class000
rcmTest-class000
splitMatchingAtBreakpoints0.140.020.15
uniqGenomicInfo000