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BioC 3.2: CHECK report for ARRmNormalization on zin1

This page was generated on 2015-08-24 10:49:08 -0700 (Mon, 24 Aug 2015).

Package 60/1071HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
ARRmNormalization 1.9.0
Jean-Philippe Fortin
Snapshot Date: 2015-08-23 16:24:14 -0700 (Sun, 23 Aug 2015)
URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/ARRmNormalization
Last Changed Rev: 102594 / Revision: 107696
Last Changed Date: 2015-04-16 13:02:44 -0700 (Thu, 16 Apr 2015)
zin1 Linux (Ubuntu 14.04.2 LTS) / x86_64  NotNeeded  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: ARRmNormalization
Version: 1.9.0
Command: /home/biocbuild/bbs-3.2-bioc/R/bin/R CMD check --no-vignettes --timings ARRmNormalization_1.9.0.tar.gz
StartedAt: 2015-08-23 21:45:24 -0700 (Sun, 23 Aug 2015)
EndedAt: 2015-08-23 21:47:05 -0700 (Sun, 23 Aug 2015)
EllapsedTime: 101.0 seconds
RetCode: 0
Status:  OK 
CheckDir: ARRmNormalization.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.2-bioc/R/bin/R CMD check --no-vignettes --timings ARRmNormalization_1.9.0.tar.gz
###
##############################################################################
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* using log directory ‘/home/biocbuild/bbs-3.2-bioc/meat/ARRmNormalization.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 ‘ARRmNormalization/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘ARRmNormalization’ version ‘1.9.0’
* 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 ‘ARRmNormalization’ can be installed ... [2s/2s] 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 loading without being on the library search path ... OK
* checking dependencies in R code ... NOTE
Package in Depends field not imported from: ‘ARRmData’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
getQuantiles: no visible binding for global variable ‘ProbesType’
normalizeARRm: no visible binding for global variable ‘ProbesType’
* 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 contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking sizes of PDF files under ‘inst/doc’ ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [86s/87s] OK
Examples with CPU or elapsed time > 5s
                  user system elapsed
normalizeARRm   41.069  0.372  41.522
getCoefficients 12.508  0.299  12.828
getQuantiles    10.502  0.140  10.655
quantilePlots   10.177  0.107  10.337
positionPlots    9.699  0.116   9.824
* 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: 2 NOTEs
See
  ‘/home/biocbuild/bbs-3.2-bioc/meat/ARRmNormalization.Rcheck/00check.log’
for details.


ARRmNormalization.Rcheck/00install.out:

* installing *source* package ‘ARRmNormalization’ ...
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (ARRmNormalization)

ARRmNormalization.Rcheck/ARRmNormalization-Ex.timings:

nameusersystemelapsed
ProbesType0.9570.0160.973
getBackground0.1750.0000.175
getCoefficients12.508 0.29912.828
getDesignInfo0.0050.0000.004
getQuantiles10.502 0.14010.655
normalizeARRm41.069 0.37241.522
positionPlots9.6990.1169.824
quantilePlots10.177 0.10710.337