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CHECK report for codelink on malbec1

This page was generated on 2020-04-15 12:04:35 -0400 (Wed, 15 Apr 2020).

Package 334/1823HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
codelink 1.54.0
Diego Diez
Snapshot Date: 2020-04-14 16:46:13 -0400 (Tue, 14 Apr 2020)
URL: https://git.bioconductor.org/packages/codelink
Branch: RELEASE_3_10
Last Commit: ea4fead
Last Changed Date: 2019-10-29 13:07:38 -0400 (Tue, 29 Oct 2019)
malbec1 Linux (Ubuntu 18.04.4 LTS) / x86_64  OK  OK [ WARNINGS ]UNNEEDED, same version exists in internal repository
tokay1 Windows Server 2012 R2 Standard / x64  OK  OK  WARNINGS  OK UNNEEDED, same version exists in internal repository
merida1 OS X 10.11.6 El Capitan / x86_64  OK  OK  WARNINGS  OK UNNEEDED, same version exists in internal repository

Summary

Package: codelink
Version: 1.54.0
Command: /home/biocbuild/bbs-3.10-bioc/R/bin/R CMD check --install=check:codelink.install-out.txt --library=/home/biocbuild/bbs-3.10-bioc/R/library --no-vignettes --timings codelink_1.54.0.tar.gz
StartedAt: 2020-04-15 00:17:24 -0400 (Wed, 15 Apr 2020)
EndedAt: 2020-04-15 00:19:08 -0400 (Wed, 15 Apr 2020)
EllapsedTime: 103.4 seconds
RetCode: 0
Status:  WARNINGS 
CheckDir: codelink.Rcheck
Warnings: 1

Command output

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### Running command:
###
###   /home/biocbuild/bbs-3.10-bioc/R/bin/R CMD check --install=check:codelink.install-out.txt --library=/home/biocbuild/bbs-3.10-bioc/R/library --no-vignettes --timings codelink_1.54.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.10-bioc/meat/codelink.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 ‘codelink/DESCRIPTION’ ... OK
* this is package ‘codelink’ version ‘1.54.0’
* 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 ‘codelink’ 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 ... OK
* 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 ... WARNING
Documented arguments not in \usage in documentation object 'normalize':
  ‘...’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
* 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 ... 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 WARNING
See
  ‘/home/biocbuild/bbs-3.10-bioc/meat/codelink.Rcheck/00check.log’
for details.



Installation output

codelink.Rcheck/00install.out

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###
### Running command:
###
###   /home/biocbuild/bbs-3.10-bioc/R/bin/R CMD INSTALL codelink
###
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* installing to library ‘/home/biocbuild/bbs-3.10-bioc/R/library’
* installing *source* package ‘codelink’ ...
** using staged installation
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
   ‘Codelink_Introduction.Rnw’ using ‘UTF-8’ 
   ‘Codelink_Legacy.Rnw’ using ‘UTF-8’ 
** 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 (codelink)

Tests output


Example timings

codelink.Rcheck/codelink-Ex.timings

nameusersystemelapsed
Codelink-class000
CodelinkSet-class000
CodelinkSetUnique-class000
arrayNew0.0040.0000.000
as.matrix.Codelink0.0000.0000.001
averageProbes000
bkgdCorrect0.5880.0160.605
createWeights0.7760.0040.783
cutCV000
dim.Codelink000
imageCodelink000
logCodelink000
mergeArray000
na2false000
normalize0.9440.0200.966
plotCorrelation000
plotDensities000
plotMA000
readCodelink000
readHeader000
readHeaderXLS000
writeCodelink000