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BioC 3.1: CHECK report for affyILM on moscato2

This page was generated on 2015-10-09 09:28:51 -0700 (Fri, 09 Oct 2015).

Package 20/1024HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
affyILM 1.20.0
Myriam Kroll and Fabrice Berger
Snapshot Date: 2015-10-08 17:20:21 -0700 (Thu, 08 Oct 2015)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_1/madman/Rpacks/affyILM
Last Changed Rev: 102591 / Revision: 109384
Last Changed Date: 2015-04-16 12:42:01 -0700 (Thu, 16 Apr 2015)
zin2 Linux (Ubuntu 14.04.2 LTS) / x86_64  NotNeeded  OK  OK UNNEEDED, same version exists in internal repository
moscato2 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  NotNeeded  OK [ OK ] OK UNNEEDED, same version exists in internal repository
petty Mac OS X Snow Leopard (10.6.8) / x86_64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository
morelia Mac OS X Mavericks (10.9.5) / x86_64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: affyILM
Version: 1.20.0
Command: rm -rf affyILM.buildbin-libdir affyILM.Rcheck && mkdir affyILM.buildbin-libdir affyILM.Rcheck && E:\biocbld\bbs-3.1-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=affyILM.buildbin-libdir affyILM_1.20.0.tar.gz >affyILM.Rcheck\00install.out 2>&1 && cp affyILM.Rcheck\00install.out affyILM-install.out && E:\biocbld\bbs-3.1-bioc\R\bin\R.exe CMD check --library=affyILM.buildbin-libdir --install="check:affyILM-install.out" --force-multiarch --no-vignettes --timings affyILM_1.20.0.tar.gz
StartedAt: 2015-10-08 23:10:22 -0700 (Thu, 08 Oct 2015)
EndedAt: 2015-10-08 23:13:35 -0700 (Thu, 08 Oct 2015)
EllapsedTime: 193.0 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 && E:\biocbld\bbs-3.1-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=affyILM.buildbin-libdir affyILM_1.20.0.tar.gz >affyILM.Rcheck\00install.out 2>&1 && cp affyILM.Rcheck\00install.out affyILM-install.out  && E:\biocbld\bbs-3.1-bioc\R\bin\R.exe CMD check --library=affyILM.buildbin-libdir --install="check:affyILM-install.out" --force-multiarch --no-vignettes --timings affyILM_1.20.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'E:/biocbld/bbs-3.1-bioc/meat/affyILM.Rcheck'
* using R version 3.2.2 (2015-08-14)
* 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 '1.20.0'
* 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
.getChipInfo: no visible global function definition for
  'getProbePackage'
ilm: no visible global function definition for 'getProbePackage'
* 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' ... [43s] OK
Examples with CPU or elapsed time > 5s
             user system elapsed
ilm-methods 11.29   0.49   30.87
** running examples for arch 'x64' ... [26s] OK
Examples with CPU or elapsed time > 5s
            user system elapsed
ilm-methods 8.31   0.50    9.29
ilm         6.44   0.16    6.61
* 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
  'E:/biocbld/bbs-3.1-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
Creating a generic function for 'nchar' from package 'base' in package 'S4Vectors'
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
Creating a generic function for 'nchar' from package 'base' in package 'S4Vectors'

install for x64

* installing *source* package 'affyILM' ...
** testing if installed package can be loaded
Creating a generic function for 'nchar' from package 'base' in package 'S4Vectors'
* MD5 sums
packaged installation of 'affyILM' as affyILM_1.20.0.zip
* DONE (affyILM)

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

nameusersystemelapsed
ILM-class000
ilm-methods11.29 0.4930.87
ilm4.560.034.74
plotILM2.250.002.25
plotIntens1.950.031.98

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

nameusersystemelapsed
ILM-class000
ilm-methods8.310.509.29
ilm6.440.166.61
plotILM3.320.103.44
plotIntens2.640.042.68