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BioC 3.2: CHECK report for affycomp on zin1

This page was generated on 2015-08-24 10:46:39 -0700 (Mon, 24 Aug 2015).

Package 17/1071HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
affycomp 1.45.0
Rafael A. Irizarry
Snapshot Date: 2015-08-23 16:24:14 -0700 (Sun, 23 Aug 2015)
URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/affycomp
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  OK  OK [ OK ]UNNEEDED, same version exists in internal repository
perceval Mac OS X Snow Leopard (10.6.8) / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository
oaxaca Mac OS X Mavericks (10.9.5) / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: affycomp
Version: 1.45.0
Command: /home/biocbuild/bbs-3.2-bioc/R/bin/R CMD check --no-vignettes --timings affycomp_1.45.0.tar.gz
StartedAt: 2015-08-23 21:30:15 -0700 (Sun, 23 Aug 2015)
EndedAt: 2015-08-23 21:30:47 -0700 (Sun, 23 Aug 2015)
EllapsedTime: 31.2 seconds
RetCode: 0
Status:  OK 
CheckDir: affycomp.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.2-bioc/R/bin/R CMD check --no-vignettes --timings affycomp_1.45.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.2-bioc/meat/affycomp.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 ‘affycomp/DESCRIPTION’ ... OK
* this is package ‘affycomp’ version ‘1.45.0’
* 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 ‘affycomp’ can be installed ... [2s/3s] OK
* checking installed package size ... NOTE
  installed size is  8.1Mb
  sub-directories of 1Mb or more:
    data   7.0Mb
* 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 dependencies in R code ... NOTE
'library' or 'require' call to ‘splines’ in package code.
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
Packages in Depends field not imported from:
  ‘Biobase’ ‘methods’
  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
affycomp.figure2b: warning in affycomp.compfig2b(list(l), method.name =
  l$method.name, add.legend = FALSE, main = main): partial argument
  match of 'method.name' to 'method.names'
affycompPlot: warning in vector(mode = "character", len = N): partial
  argument match of 'len' to 'length'
tableAll: warning in vector(mode = "character", len = N): partial
  argument match of 'len' to 'length'
tableOverallSNR: warning in vector(mode = "character", len = N):
  partial argument match of 'len' to 'length'
tableRanks: warning in vector(mode = "character", len = N): partial
  argument match of 'len' to 'length'
.onAttach: no visible global function definition for ‘addVigs2WinMenu’
assessDilution: no visible global function definition for ‘exprs’
assessDilution: no visible global function definition for ‘pData’
assessFC: no visible global function definition for ‘exprs’
assessFC: no visible global function definition for ‘pData’
assessFC2: no visible global function definition for ‘exprs’
assessFC2: no visible global function definition for ‘pData’
assessLS: no visible global function definition for ‘exprs’
assessLS: no visible global function definition for ‘pData’
assessLS: no visible global function definition for ‘featureNames’
assessMA: no visible global function definition for ‘exprs’
assessMA: no visible global function definition for ‘pData’
assessMA2: no visible global function definition for ‘exprs’
assessMA2: no visible global function definition for ‘pData’
assessMA2: no visible global function definition for ‘featureNames’
assessSD: no visible global function definition for ‘exprs’
assessSD: no visible global function definition for ‘assayDataElement’
assessSD: no visible global function definition for ‘pData’
assessSignal: no visible global function definition for ‘exprs’
assessSignal: no visible global function definition for ‘pData’
assessSignal: no visible global function definition for ‘featureNames’
assessSpikeIn2: no visible global function definition for ‘exprs’
assessSpikeInSD: no visible global function definition for ‘pData’
assessSpikeInSD: no visible global function definition for
  ‘featureNames’
assessSpikeInSD: no visible global function definition for ‘esApply’
exprset.log: no visible global function definition for ‘exprs’
exprset.log: no visible global function definition for ‘exprs<-’
read.dilution: no visible global function definition for ‘sampleNames’
read.spikein: no visible global function definition for ‘sampleNames’
remove.hgu133a.xhyb: no visible global function definition for
  ‘featureNames’
* 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 ... [4s/4s] OK
* 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: 3 NOTEs
See
  ‘/home/biocbuild/bbs-3.2-bioc/meat/affycomp.Rcheck/00check.log’
for details.


affycomp.Rcheck/00install.out:

* installing *source* package ‘affycomp’ ...
** 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 (affycomp)

affycomp.Rcheck/affycomp-Ex.timings:

nameusersystemelapsed
SD0.6690.0160.718
affycomp.compfigs.auxiliary0.5070.0040.544
affycomp.figures.auxiliary0.5060.0080.524
affycomp.table0.3480.0000.348
affycompPlot0.7620.0120.773