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CHECK report for stepNorm on veracruz1

This page was generated on 2018-04-12 13:31:31 -0400 (Thu, 12 Apr 2018).

Package 1360/1472HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
stepNorm 1.50.0
Yuanyuan Xiao
Snapshot Date: 2018-04-11 16:45:18 -0400 (Wed, 11 Apr 2018)
URL: https://git.bioconductor.org/packages/stepNorm
Branch: RELEASE_3_6
Last Commit: d325b25
Last Changed Date: 2017-10-30 12:39:03 -0400 (Mon, 30 Oct 2017)
malbec1 Linux (Ubuntu 16.04.1 LTS) / x86_64  NotNeeded  OK  OK UNNEEDED, same version exists in internal repository
tokay1 Windows Server 2012 R2 Standard / x64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository
veracruz1 OS X 10.11.6 El Capitan / x86_64  NotNeeded  OK [ OK ] OK UNNEEDED, same version exists in internal repository

Summary

Package: stepNorm
Version: 1.50.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings stepNorm_1.50.0.tar.gz
StartedAt: 2018-04-12 10:04:01 -0400 (Thu, 12 Apr 2018)
EndedAt: 2018-04-12 10:05:35 -0400 (Thu, 12 Apr 2018)
EllapsedTime: 93.6 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 --no-vignettes --timings stepNorm_1.50.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.6-bioc/meat/stepNorm.Rcheck’
* using R version 3.4.4 (2018-03-15)
* 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 ‘1.50.0’
* 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 loading without being on the library search path ... 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 23.548  0.111  23.986
fitWithin      22.094  0.070  22.515
fit2DWithin    10.345  0.072  10.604
* checking PDF version of manual ... OK
* DONE

Status: 2 NOTEs
See
  ‘/Users/biocbuild/bbs-3.6-bioc/meat/stepNorm.Rcheck/00check.log’
for details.



Installation output

stepNorm.Rcheck/00install.out

* installing *source* package ‘stepNorm’ ...
** R
** inst
** preparing 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
calcAIC0.2280.0130.251
calcBIC0.2220.0180.242
fit2DWithin10.345 0.07210.604
fitWithin22.094 0.07022.515
maCompPlate20.0380.0010.039
makeStepList0.1110.0060.116
marrayFitClass0.0830.0050.088
seqWithinNorm0.2850.0190.309
stepWithinNorm23.548 0.11123.986
withinNorm0.0450.0020.048