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BioC 2.14: CHECK report for affyPara on moscato2

This page was generated on 2014-10-08 08:52:26 -0700 (Wed, 08 Oct 2014).

Package 23/824HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
affyPara 1.24.0
Markus Schmidberger
Snapshot Date: 2014-10-07 17:20:37 -0700 (Tue, 07 Oct 2014)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_14/madman/Rpacks/affyPara
Last Changed Rev: 88838 / Revision: 95116
Last Changed Date: 2014-04-11 14:07:21 -0700 (Fri, 11 Apr 2014)
zin2 Linux (Ubuntu 12.04.4 LTS) / x86_64  NotNeeded  OK  OK 
moscato2 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  NotNeeded  OK [ OK ] OK 
petty Mac OS X Snow Leopard (10.6.8) / x86_64  NotNeeded  OK  OK  OK 
morelia Mac OS X Mavericks (10.9.5) / x86_64  NotNeeded  OK  OK  OK 

Summary

Package: affyPara
Version: 1.24.0
Command: rm -rf affyPara.buildbin-libdir && mkdir affyPara.buildbin-libdir && E:\biocbld\bbs-2.14-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=affyPara.buildbin-libdir affyPara_1.24.0.tar.gz >affyPara-install.out 2>&1 && E:\biocbld\bbs-2.14-bioc\R\bin\R.exe CMD check --library=affyPara.buildbin-libdir --install="check:affyPara-install.out" --force-multiarch --no-vignettes --timings affyPara_1.24.0.tar.gz
StartedAt: 2014-10-07 22:30:05 -0700 (Tue, 07 Oct 2014)
EndedAt: 2014-10-07 22:31:53 -0700 (Tue, 07 Oct 2014)
EllapsedTime: 107.9 seconds
RetCode: 0
Status:  OK  
CheckDir: affyPara.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   rm -rf affyPara.buildbin-libdir && mkdir affyPara.buildbin-libdir && E:\biocbld\bbs-2.14-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=affyPara.buildbin-libdir affyPara_1.24.0.tar.gz >affyPara-install.out 2>&1 && E:\biocbld\bbs-2.14-bioc\R\bin\R.exe CMD check --library=affyPara.buildbin-libdir --install="check:affyPara-install.out" --force-multiarch --no-vignettes --timings affyPara_1.24.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'E:/biocbld/bbs-2.14-bioc/meat/affyPara.Rcheck'
* using R version 3.1.1 (2014-07-10)
* using platform: i386-w64-mingw32 (32-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'affyPara/DESCRIPTION' ... OK
* this is package 'affyPara' version '1.24.0'
* 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 whether package 'affyPara' can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking 'build' directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Package listed in more than one of Depends, Imports, Suggests, Enhances:
  'affy'
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
* loading checks for arch 'i386'
** 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
* loading checks for arch 'x64'
** 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
'library' or 'require' calls to packages already attached by Depends:
  'affy' 'aplpack' 'snow' 'vsn'
  Please remove these calls from your code.
Packages in Depends field not imported from:
  'affyio' 'aplpack' 'methods' 'snow' 'vsn'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
Unexported objects imported by ':::' calls:
  'vsn:::isSmall' 'vsn:::optimparNames' 'vsn:::pstartHeuristic'
  'vsn:::vsnLTS'
  See the note in ?`:::` about the use of this operator.
See the information on DESCRIPTION files in the chapter 'Creating R
packages' of the 'Writing R Extensions' manual.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... NOTE
Foreign function call to a different package:
  .Call("ReadHeader", ..., PACKAGE = "affyio")
See the chapter 'System and foreign language interfaces' of the
'Writing R Extensions' manual.
* checking R code for possible problems ... OK
* 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 installed files from 'inst/doc' ... OK
* checking files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... [5s] OK
** running examples for arch 'x64' ... [5s] 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

NOTE: There were 3 notes.
See
  'E:/biocbld/bbs-2.14-bioc/meat/affyPara.Rcheck/00check.log'
for details.

affyPara.Rcheck/00install.out:


install for i386

* installing *source* package 'affyPara' ...
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded

install for x64

* installing *source* package 'affyPara' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'affyPara' as affyPara_1.24.0.zip
* DONE (affyPara)

affyPara.Rcheck/examples_i386/affyPara-Ex.timings:

nameusersystemelapsed
MAplotPara000
bgcPara000
boxplotPara000
computeExprSetPara000
distributeFiles000
mergeSplitObjects202
normalizeAffyBatchConstantPara000
normalizeAffyBatchInvariantsetPara0.010.000.01
normalizeAffyBatchLoessPara000
normalizeAffyBatchLoessParaIter000
normalizeAffyBatchQuantilesPara000
preproPara000
qa000
readAffybatchPara000
removeDistributedFiles000
rmaPara000
snowReplace000
split0.610.050.66
vsnPara000

affyPara.Rcheck/examples_x64/affyPara-Ex.timings:

nameusersystemelapsed
MAplotPara000
bgcPara000
boxplotPara000
computeExprSetPara000
distributeFiles0.000.000.04
mergeSplitObjects1.800.011.80
normalizeAffyBatchConstantPara000
normalizeAffyBatchInvariantsetPara000
normalizeAffyBatchLoessPara000
normalizeAffyBatchLoessParaIter0.010.000.02
normalizeAffyBatchQuantilesPara000
preproPara000
qa000
readAffybatchPara000
removeDistributedFiles000
rmaPara000
snowReplace000
split0.480.030.51
vsnPara000