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BioC 3.5: CHECK report for affyILM on tokay2

This page was generated on 2017-10-18 14:20:47 -0400 (Wed, 18 Oct 2017).

Package 22/1381HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
affyILM 1.28.0
Myriam Kroll and Fabrice Berger
Snapshot Date: 2017-10-17 17:00:52 -0400 (Tue, 17 Oct 2017)
URL: https://git.bioconductor.org/packages/affyILM
Branch: RELEASE_3_5
Last Commit: 307bee3
Last Changed Date: 2017-04-24 15:45:44 -0400 (Mon, 24 Apr 2017)
malbec2 Linux (Ubuntu 16.04.1 LTS) / x86_64  NotNeeded  OK  OK UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  NotNeeded  OK [ OK ] OK UNNEEDED, same version exists in internal repository
veracruz2 OS X 10.11.6 El Capitan / x86_64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: affyILM
Version: 1.28.0
Command: rm -rf affyILM.buildbin-libdir affyILM.Rcheck && mkdir affyILM.buildbin-libdir affyILM.Rcheck && C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=affyILM.buildbin-libdir affyILM_1.28.0.tar.gz >affyILM.Rcheck\00install.out 2>&1 && cp affyILM.Rcheck\00install.out affyILM-install.out && C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD check --library=affyILM.buildbin-libdir --install="check:affyILM-install.out" --force-multiarch --no-vignettes --timings affyILM_1.28.0.tar.gz
StartedAt: 2017-10-17 21:56:28 -0400 (Tue, 17 Oct 2017)
EndedAt: 2017-10-17 21:59:28 -0400 (Tue, 17 Oct 2017)
EllapsedTime: 179.0 seconds
RetCode: 0
Status:  OK  
CheckDir: affyILM.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   rm -rf affyILM.buildbin-libdir affyILM.Rcheck && mkdir affyILM.buildbin-libdir affyILM.Rcheck && C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=affyILM.buildbin-libdir affyILM_1.28.0.tar.gz >affyILM.Rcheck\00install.out 2>&1 && cp affyILM.Rcheck\00install.out affyILM-install.out  &&  C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD check --library=affyILM.buildbin-libdir --install="check:affyILM-install.out" --force-multiarch --no-vignettes --timings affyILM_1.28.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.5-bioc/meat/affyILM.Rcheck'
* using R version 3.4.2 Patched (2017-10-07 r73498)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'affyILM/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'affyILM' version '1.28.0'
* 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 'affyILM' can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking 'build' directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Non-standard license specification:
  GPL version 3
Standardizable: TRUE
Standardized license specification:
  GPL-3
Package listed in more than one of Depends, Imports, Suggests, Enhances:
  '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
* 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
Package in Depends field not imported from: 'gcrma'
  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
.affyILM_scale: no visible binding for global variable 'median'
.affyILM_scale: no visible binding for global variable 'mad'
.affyILM_scale: no visible global function definition for 'median'
.getChipInfo: no visible global function definition for
  'getProbePackage'
.summarizeConcs: no visible binding for global variable 'mad'
.summarizeConcs: no visible binding for global variable 'median'
.summarizeMedpolish: no visible global function definition for
  'medpolish'
.summarizeTrMedpolish: no visible global function definition for
  'medpolish'
ilm: no visible global function definition for 'getProbePackage'
plotILM,ILM: no visible global function definition for 'median'
plotILM,ILM: no visible global function definition for 'mad'
Undefined global functions or variables:
  getProbePackage mad median medpolish
Consider adding
  importFrom("stats", "mad", "median", "medpolish")
to your NAMESPACE file.
* 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' ... OK
Examples with CPU or elapsed time > 5s
            user system elapsed
ilm-methods 8.72   1.11   24.53
ilm         4.69   0.18    5.19
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
            user system elapsed
ilm-methods 6.89   0.75    8.42
ilm         5.00   0.26    5.27
* 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
  'C:/Users/biocbuild/bbs-3.5-bioc/meat/affyILM.Rcheck/00check.log'
for details.


affyILM.Rcheck/00install.out:


install for i386

* installing *source* package 'affyILM' ...
** 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 'affyILM' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'affyILM' as affyILM_1.28.0.zip
* DONE (affyILM)

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

nameusersystemelapsed
ILM-class000
ilm-methods 8.72 1.1124.53
ilm4.690.185.19
plotILM2.190.102.28
plotIntens1.750.141.89

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

nameusersystemelapsed
ILM-class000
ilm-methods6.890.758.42
ilm5.000.265.27
plotILM2.390.112.50
plotIntens2.170.162.32