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).
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 | | |
tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | [ OK ] | OK | |
veracruz2 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | OK | OK | |
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:
name | user | system | elapsed
|
CNGEheatmaps | 1.38 | 0.06 | 1.44 |
|
ExpressionSet2order | 0.02 | 0.02 | 0.03 |
|
ExpressionSet2subset | 0.01 | 0.00 | 0.01 |
|
ExpressionSet2weightedSubset | 0.3 | 0.0 | 0.3 |
|
RCMestimation | 1.23 | 0.05 | 1.28 |
|
RCMrandom | 1.80 | 0.03 | 1.83 |
|
RCMtest | 2.89 | 0.00 | 2.89 |
|
cghCall2cghSeg | 0.09 | 0.00 | 0.09 |
|
cghCall2maximumSubset | 0.31 | 0.00 | 0.31 |
|
cghCall2order | 0.03 | 0.00 | 0.03 |
|
cghCall2subset | 0.05 | 0.00 | 0.05 |
|
cghCall2weightedSubset | 0.23 | 0.00 | 0.23 |
|
cghSeg2order | 0.07 | 0.00 | 0.06 |
|
cghSeg2subset | 0.04 | 0.00 | 0.05 |
|
cghSeg2weightedSubset | 0.24 | 0.00 | 0.24 |
|
cisEffectPlot | 0.17 | 0.00 | 0.17 |
|
cisEffectTable | 1.30 | 0.01 | 1.31 |
|
cisEffectTest | 1.84 | 0.00 | 1.84 |
|
cisEffectTune | 11.55 | 0.00 | 11.55 |
|
cisTest-class | 0 | 0 | 0 |
|
entTest-class | 0 | 0 | 0 |
|
entropyTest | 0.26 | 0.02 | 0.28 |
|
expandMatching2singleIDs | 0.08 | 0.00 | 0.08 |
|
getSegFeatures | 0.02 | 0.00 | 0.02 |
|
hdEntropy | 0.00 | 0.02 | 0.01 |
|
hdMI | 0.57 | 0.00 | 0.58 |
|
matchAnn2Ann | 0.21 | 0.03 | 0.23 |
|
matchCGHcall2ExpressionSet | 0.20 | 0.00 | 0.21 |
|
merge2ExpressionSets | 0.11 | 0.00 | 0.11 |
|
merge2cghCalls | 0.08 | 0.00 | 0.07 |
|
miTest-class | 0 | 0 | 0 |
|
mutInfTest | 119.61 | 4.11 | 123.72 |
|
nBreakpoints | 0.11 | 0.01 | 0.13 |
|
pathway1sample | 0.42 | 0.00 | 0.42 |
|
pathway2sample | 3.51 | 0.58 | 4.09 |
|
pathwayFit-class | 0 | 0 | 0 |
|
pathwayPlot | 0.19 | 0.00 | 0.19 |
|
pollackCN16 | 0.00 | 0.03 | 0.03 |
|
pollackGE16 | 0.00 | 0.02 | 0.02 |
|
profilesPlot | 0.24 | 0.01 | 0.25 |
|
rcmFit-class | 0 | 0 | 0 |
|
rcmTest-class | 0 | 0 | 0 |
|
splitMatchingAtBreakpoints | 0.16 | 0.00 | 0.16 |
|
uniqGenomicInfo | 0 | 0 | 0 |
|
sigaR.Rcheck/examples_x64/sigaR-Ex.timings:
name | user | system | elapsed
|
CNGEheatmaps | 1 | 0 | 1 |
|
ExpressionSet2order | 0.02 | 0.00 | 0.01 |
|
ExpressionSet2subset | 0 | 0 | 0 |
|
ExpressionSet2weightedSubset | 0.25 | 0.01 | 0.26 |
|
RCMestimation | 1 | 0 | 1 |
|
RCMrandom | 1.23 | 0.02 | 1.25 |
|
RCMtest | 2.88 | 0.00 | 2.88 |
|
cghCall2cghSeg | 0.14 | 0.00 | 0.14 |
|
cghCall2maximumSubset | 0.45 | 0.00 | 0.45 |
|
cghCall2order | 0.05 | 0.00 | 0.05 |
|
cghCall2subset | 0.03 | 0.00 | 0.03 |
|
cghCall2weightedSubset | 0.31 | 0.01 | 0.33 |
|
cghSeg2order | 0.06 | 0.00 | 0.06 |
|
cghSeg2subset | 0.08 | 0.00 | 0.08 |
|
cghSeg2weightedSubset | 0.33 | 0.00 | 0.33 |
|
cisEffectPlot | 0.19 | 0.00 | 0.19 |
|
cisEffectTable | 1.57 | 0.02 | 1.59 |
|
cisEffectTest | 1.90 | 0.01 | 1.91 |
|
cisEffectTune | 16.12 | 0.00 | 16.12 |
|
cisTest-class | 0 | 0 | 0 |
|
entTest-class | 0 | 0 | 0 |
|
entropyTest | 0.45 | 0.00 | 0.45 |
|
expandMatching2singleIDs | 0.08 | 0.02 | 0.10 |
|
getSegFeatures | 0.00 | 0.02 | 0.01 |
|
hdEntropy | 0.02 | 0.00 | 0.02 |
|
hdMI | 0.86 | 0.01 | 0.87 |
|
matchAnn2Ann | 0.17 | 0.00 | 0.18 |
|
matchCGHcall2ExpressionSet | 0.14 | 0.02 | 0.15 |
|
merge2ExpressionSets | 0.08 | 0.00 | 0.08 |
|
merge2cghCalls | 0.08 | 0.00 | 0.08 |
|
miTest-class | 0 | 0 | 0 |
|
mutInfTest | 112.81 | 5.11 | 117.92 |
|
nBreakpoints | 0.14 | 0.00 | 0.14 |
|
pathway1sample | 0.8 | 0.0 | 0.8 |
|
pathway2sample | 4.37 | 0.90 | 5.28 |
|
pathwayFit-class | 0 | 0 | 0 |
|
pathwayPlot | 0.17 | 0.00 | 0.17 |
|
pollackCN16 | 0 | 0 | 0 |
|
pollackGE16 | 0.02 | 0.00 | 0.02 |
|
profilesPlot | 0.14 | 0.03 | 0.17 |
|
rcmFit-class | 0 | 0 | 0 |
|
rcmTest-class | 0 | 0 | 0 |
|
splitMatchingAtBreakpoints | 0.14 | 0.02 | 0.15 |
|
uniqGenomicInfo | 0 | 0 | 0 |
|