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CHECK report for stepNorm on celaya2

This page was generated on 2020-01-16 13:29:22 -0500 (Thu, 16 Jan 2020).

Package 1670/1818HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
stepNorm 1.59.0
Yuanyuan Xiao
Snapshot Date: 2020-01-15 16:46:30 -0500 (Wed, 15 Jan 2020)
URL: https://git.bioconductor.org/packages/stepNorm
Branch: master
Last Commit: 3eaa267
Last Changed Date: 2019-10-29 13:34:37 -0500 (Tue, 29 Oct 2019)
malbec2 Linux (Ubuntu 18.04.3 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  OK  OK  OK  OK 
celaya2 OS X 10.11.6 El Capitan / x86_64  OK  OK [ OK ] OK 

Summary

Package: stepNorm
Version: 1.59.0
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_1.59.0.tar.gz
StartedAt: 2020-01-16 09:16:44 -0500 (Thu, 16 Jan 2020)
EndedAt: 2020-01-16 09:18:55 -0500 (Thu, 16 Jan 2020)
EllapsedTime: 130.6 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_1.59.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.11-bioc/meat/stepNorm.Rcheck’
* using R Under development (unstable) (2019-12-14 r77572)
* 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 ‘1.59.0’
* 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 (user + system) or elapsed time > 5s
                 user system elapsed
stepWithinNorm 33.261  0.313  34.986
fitWithin      27.391  0.131  27.594
fit2DWithin    13.125  0.194  13.853
* checking PDF version of manual ... OK
* DONE

Status: 2 NOTEs
See
  ‘/Users/biocbuild/bbs-3.11-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/4.0/Resources/library’
* installing *source* package ‘stepNorm’ ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** 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 (stepNorm)

Tests output


Example timings

stepNorm.Rcheck/stepNorm-Ex.timings

nameusersystemelapsed
calcAIC0.1770.0410.295
calcBIC0.1290.0300.160
fit2DWithin13.125 0.19413.853
fitWithin27.391 0.13127.594
maCompPlate20.0180.0050.023
makeStepList0.0860.0120.098
marrayFitClass0.1360.0440.180
seqWithinNorm0.4770.0790.566
stepWithinNorm33.261 0.31334.986
withinNorm0.0810.0090.091