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BioC 3.2: CHECK report for stepNorm on linux1.bioconductor.org

This page was generated on 2015-10-27 17:23:37 -0400 (Tue, 27 Oct 2015).

Package 1025/1104HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
stepNorm 1.42.0
Yuanyuan Xiao
Snapshot Date: 2015-10-26 19:24:07 -0400 (Mon, 26 Oct 2015)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_2/madman/Rpacks/stepNorm
Last Changed Rev: 109589 / Revision: 109947
Last Changed Date: 2015-10-13 15:36:05 -0400 (Tue, 13 Oct 2015)
linux1.bioconductor.org Linux (Ubuntu 14.04.2 LTS) / x86_64  NotNeeded  OK [ OK ]UNNEEDED, same version exists in internal repository
windows1.bioconductor.org Windows Server 2012 R2 Enterprise SP1 (64-bit) / x64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository
perceval Mac OS X Snow Leopard (10.6.8) / x86_64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository
oaxaca Mac OS X Mavericks (10.9.5) / x86_64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: stepNorm
Version: 1.42.0
Command: /home/biocbuild/bbs-3.2-bioc/R/bin/R CMD check --no-vignettes --timings stepNorm_1.42.0.tar.gz
StartedAt: 2015-10-27 08:31:31 -0400 (Tue, 27 Oct 2015)
EndedAt: 2015-10-27 08:33:03 -0400 (Tue, 27 Oct 2015)
EllapsedTime: 92.6 seconds
RetCode: 0
Status:  OK 
CheckDir: stepNorm.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.2-bioc/R/bin/R CMD check --no-vignettes --timings stepNorm_1.42.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.2-bioc/meat/stepNorm.Rcheck’
* using R version 3.2.2 (2015-08-14)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘stepNorm/DESCRIPTION’ ... OK
* this is package ‘stepNorm’ version ‘1.42.0’
* 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 ... [2s/2s] 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 ... [71s/71s] OK
Examples with CPU or elapsed time > 5s
                 user system elapsed
stepWithinNorm 30.964  0.020  30.991
fitWithin      27.118  0.012  27.142
fit2DWithin    10.895  0.007  10.906
* checking PDF version of manual ... OK
* DONE

Status: 2 NOTEs
See
  ‘/home/biocbuild/bbs-3.2-bioc/meat/stepNorm.Rcheck/00check.log’
for details.


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)

stepNorm.Rcheck/stepNorm-Ex.timings:

nameusersystemelapsed
calcAIC0.2780.0120.290
calcBIC0.2000.0000.201
fit2DWithin10.895 0.00710.906
fitWithin27.118 0.01227.142
maCompPlate20.0140.0040.018
makeStepList0.0470.0000.047
marrayFitClass0.0940.0000.094
seqWithinNorm0.3320.0040.340
stepWithinNorm30.964 0.02030.991
withinNorm0.0790.0000.079