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CHECK report for alsace on malbec2

This page was generated on 2019-04-09 11:37:52 -0400 (Tue, 09 Apr 2019).

Package 44/1703HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
alsace 1.19.0
Ron Wehrens
Snapshot Date: 2019-04-08 17:01:18 -0400 (Mon, 08 Apr 2019)
URL: https://git.bioconductor.org/packages/alsace
Branch: master
Last Commit: 3273f76
Last Changed Date: 2018-11-13 03:55:00 -0400 (Tue, 13 Nov 2018)
malbec2 Linux (Ubuntu 18.04.2 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
celaya2 OS X 10.11.6 El Capitan / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository
merida2 OS X 10.11.6 El Capitan / x86_64  OK  OK  OK  OK 

Summary

Package: alsace
Version: 1.19.0
Command: /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD check --install=check:alsace.install-out.txt --library=/home/biocbuild/bbs-3.9-bioc/R/library --no-vignettes --timings alsace_1.19.0.tar.gz
StartedAt: 2019-04-08 22:40:45 -0400 (Mon, 08 Apr 2019)
EndedAt: 2019-04-08 22:41:47 -0400 (Mon, 08 Apr 2019)
EllapsedTime: 61.5 seconds
RetCode: 0
Status:  OK 
CheckDir: alsace.Rcheck
Warnings: 0

Command output

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### Running command:
###
###   /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD check --install=check:alsace.install-out.txt --library=/home/biocbuild/bbs-3.9-bioc/R/library --no-vignettes --timings alsace_1.19.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.9-bioc/meat/alsace.Rcheck’
* using R Under development (unstable) (2019-03-18 r76245)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘alsace/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘alsace’ version ‘1.19.0’
* 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 ‘alsace’ 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
'library' or 'require' call to ‘lattice’ in package code.
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
getPeakTable : clusterPeaks: no visible global function definition for
  ‘stripplot’
getPeakTable : clusterPeaks : <anonymous>: no visible global function
  definition for ‘panel.stripplot’
getPeakTable : clusterPeaks : <anonymous>: no visible global function
  definition for ‘panel.abline’
Undefined global functions or variables:
  panel.abline panel.stripplot stripplot
* 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
components 10.468  0.024  10.505
teaMerged   7.888  0.004   7.892
doALS       5.286  0.000   5.286
* 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
  ‘/home/biocbuild/bbs-3.9-bioc/meat/alsace.Rcheck/00check.log’
for details.



Installation output

alsace.Rcheck/00install.out

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###
### Running command:
###
###   /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD INSTALL alsace
###
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* installing to library ‘/home/biocbuild/bbs-3.9-bioc/R/library’
* installing *source* package ‘alsace’ ...
** using staged installation
** R
** data
** 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 (alsace)

Tests output


Example timings

alsace.Rcheck/alsace-Ex.timings

nameusersystemelapsed
components10.468 0.02410.505
correctPeaks4.6470.0004.650
correctRT1.9480.0001.949
doALS5.2860.0005.286
filterPeaks0.0280.0000.029
fitpeaks4.7120.0044.716
getAllPeaks0.0450.0000.045
getPeakTable2.7880.0002.789
opa1.4190.0041.423
preprocess0.1010.0000.101
showALSresult0.0770.0040.082
tea0.0990.0000.099
teaMerged7.8880.0047.892
windows0.1510.0000.152