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CHECK report for sigaR on malbec1

This page was generated on 2020-04-15 12:06:43 -0400 (Wed, 15 Apr 2020).

Package 1583/1823HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
sigaR 1.34.0
Wessel N. van Wieringen
Snapshot Date: 2020-04-14 16:46:13 -0400 (Tue, 14 Apr 2020)
URL: https://git.bioconductor.org/packages/sigaR
Branch: RELEASE_3_10
Last Commit: 8c164ca
Last Changed Date: 2019-10-29 13:08:25 -0400 (Tue, 29 Oct 2019)
malbec1 Linux (Ubuntu 18.04.4 LTS) / x86_64  OK  OK [ OK ]UNNEEDED, same version exists in internal repository
tokay1 Windows Server 2012 R2 Standard / x64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository
merida1 OS X 10.11.6 El Capitan / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: sigaR
Version: 1.34.0
Command: /home/biocbuild/bbs-3.10-bioc/R/bin/R CMD check --install=check:sigaR.install-out.txt --library=/home/biocbuild/bbs-3.10-bioc/R/library --no-vignettes --timings sigaR_1.34.0.tar.gz
StartedAt: 2020-04-15 01:12:50 -0400 (Wed, 15 Apr 2020)
EndedAt: 2020-04-15 01:15:59 -0400 (Wed, 15 Apr 2020)
EllapsedTime: 188.7 seconds
RetCode: 0
Status:  OK 
CheckDir: sigaR.Rcheck
Warnings: 0

Command output

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### Running command:
###
###   /home/biocbuild/bbs-3.10-bioc/R/bin/R CMD check --install=check:sigaR.install-out.txt --library=/home/biocbuild/bbs-3.10-bioc/R/library --no-vignettes --timings sigaR_1.34.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.10-bioc/meat/sigaR.Rcheck’
* using R version 3.6.3 (2020-02-29)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘sigaR/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘sigaR’ version ‘1.34.0’
* 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 for sufficient/correct file permissions ... 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
* 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 files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
                user system elapsed
mutInfTest    80.096  1.112  83.279
cisEffectTune  9.488  0.000   9.499
* 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-3.10-bioc/meat/sigaR.Rcheck/00check.log’
for details.



Installation output

sigaR.Rcheck/00install.out

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###
### Running command:
###
###   /home/biocbuild/bbs-3.10-bioc/R/bin/R CMD INSTALL sigaR
###
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* installing to library ‘/home/biocbuild/bbs-3.10-bioc/R/library’
* installing *source* package ‘sigaR’ ...
** using staged installation
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (sigaR)

Tests output


Example timings

sigaR.Rcheck/sigaR-Ex.timings

nameusersystemelapsed
CNGEheatmaps0.6880.0280.716
ExpressionSet2order0.0080.0000.009
ExpressionSet2subset0.0120.0000.011
ExpressionSet2weightedSubset0.260.000.26
RCMestimation0.6280.0320.662
RCMrandom0.5200.0001.109
RCMtest1.9760.0082.661
cghCall2cghSeg0.0520.0000.049
cghCall2maximumSubset0.2720.0000.875
cghCall2order0.0160.0000.014
cghCall2subset0.0360.0000.035
cghCall2weightedSubset0.2640.0000.264
cghSeg2order0.0320.0000.029
cghSeg2subset0.0400.0040.044
cghSeg2weightedSubset0.2240.0000.227
cisEffectPlot0.040.000.04
cisEffectTable1.0760.0081.085
cisEffectTest1.1080.0041.114
cisEffectTune9.4880.0009.499
cisTest-class000
entTest-class000
entropyTest0.2080.0040.209
expandMatching2singleIDs0.0120.0080.019
getSegFeatures0.0000.0040.005
hdEntropy0.0080.0000.006
hdMI0.4840.0000.487
matchAnn2Ann0.0160.0000.015
matchCGHcall2ExpressionSet0.0240.0000.024
merge2ExpressionSets0.0240.0000.027
merge2cghCalls0.0320.0000.035
miTest-class000
mutInfTest80.096 1.11283.279
nBreakpoints0.1040.0040.108
pathway1sample0.0720.0040.126
pathway2sample2.5520.2762.829
pathwayFit-class0.0000.0000.001
pathwayPlot0.0920.0000.091
pollackCN160.0080.0000.006
pollackGE160.0000.0040.003
profilesPlot0.1080.0000.107
rcmFit-class000
rcmTest-class000
splitMatchingAtBreakpoints0.1080.0000.110
uniqGenomicInfo0.0040.0000.004