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CHECK report for stepNorm on merida2

This page was generated on 2019-04-09 13:22:48 -0400 (Tue, 09 Apr 2019).

Package 1566/1703HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
stepNorm 1.55.0
Yuanyuan Xiao
Snapshot Date: 2019-04-08 17:01:18 -0400 (Mon, 08 Apr 2019)
URL: https://git.bioconductor.org/packages/stepNorm
Branch: master
Last Commit: 3a48f2f
Last Changed Date: 2018-10-30 11:54:26 -0400 (Tue, 30 Oct 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: stepNorm
Version: 1.55.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:stepNorm.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings stepNorm_1.55.0.tar.gz
StartedAt: 2019-04-09 03:59:23 -0400 (Tue, 09 Apr 2019)
EndedAt: 2019-04-09 04:01:13 -0400 (Tue, 09 Apr 2019)
EllapsedTime: 110.7 seconds
RetCode: 0
Status:  OK 
CheckDir: stepNorm.Rcheck
Warnings: 0

Command output

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:stepNorm.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings stepNorm_1.55.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.9-bioc/meat/stepNorm.Rcheck’
* using R Under development (unstable) (2018-11-27 r75683)
* using platform: x86_64-apple-darwin15.6.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘stepNorm/DESCRIPTION’ ... OK
* this is package ‘stepNorm’ version ‘1.55.0’
* 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 ‘stepNorm’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Packages listed in more than one of Depends, Imports, Suggests, Enhances:
  ‘marray’ ‘methods’
A package should be listed in only one of these fields.
* 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 ... NOTE
loess2Dfit: warning in loess.control(trace.hat = "approximate",
  iteration = 5, surface = "direct"): partial argument match of
  'iteration' to 'iterations'
loessfit: warning in loess.control(trace.hat = "approximate", iteration
  = 5, surface = "direct"): partial argument match of 'iteration' to
  'iterations'
* 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 examples ... OK
Examples with CPU or elapsed time > 5s
                 user system elapsed
stepWithinNorm 32.235  0.170  32.674
fitWithin      30.043  0.106  30.444
fit2DWithin    13.379  0.129  13.620
* checking PDF version of manual ... OK
* DONE

Status: 2 NOTEs
See
  ‘/Users/biocbuild/bbs-3.9-bioc/meat/stepNorm.Rcheck/00check.log’
for details.



Installation output

stepNorm.Rcheck/00install.out

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###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL stepNorm
###
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* installing to library ‘/Library/Frameworks/R.framework/Versions/3.6/Resources/library’
* installing *source* package ‘stepNorm’ ...
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** testing if installed package can be loaded
* DONE (stepNorm)

Tests output


Example timings

stepNorm.Rcheck/stepNorm-Ex.timings

nameusersystemelapsed
calcAIC0.1630.0240.189
calcBIC0.1160.0140.131
fit2DWithin13.379 0.12913.620
fitWithin30.043 0.10630.444
maCompPlate20.0100.0020.012
makeStepList0.0680.0060.074
marrayFitClass0.1090.0130.123
seqWithinNorm0.3260.0370.365
stepWithinNorm32.235 0.17032.674
withinNorm0.0740.0050.080