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BioC 3.1: CHECK report for AffyCompatible on moscato2

This page was generated on 2015-10-09 09:28:16 -0700 (Fri, 09 Oct 2015).

Package 16/1024HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
AffyCompatible 1.28.0
Martin Morgan
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/AffyCompatible
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  OK  OK  ERROR 
moscato2 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  OK  OK [ OK ] OK UNNEEDED, same version exists in internal repository
petty Mac OS X Snow Leopard (10.6.8) / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository
morelia Mac OS X Mavericks (10.9.5) / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: AffyCompatible
Version: 1.28.0
Command: rm -rf AffyCompatible.buildbin-libdir AffyCompatible.Rcheck && mkdir AffyCompatible.buildbin-libdir AffyCompatible.Rcheck && E:\biocbld\bbs-3.1-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=AffyCompatible.buildbin-libdir AffyCompatible_1.28.0.tar.gz >AffyCompatible.Rcheck\00install.out 2>&1 && cp AffyCompatible.Rcheck\00install.out AffyCompatible-install.out && E:\biocbld\bbs-3.1-bioc\R\bin\R.exe CMD check --library=AffyCompatible.buildbin-libdir --install="check:AffyCompatible-install.out" --force-multiarch --no-vignettes --timings AffyCompatible_1.28.0.tar.gz
StartedAt: 2015-10-08 23:08:05 -0700 (Thu, 08 Oct 2015)
EndedAt: 2015-10-08 23:11:57 -0700 (Thu, 08 Oct 2015)
EllapsedTime: 231.3 seconds
RetCode: 0
Status:  OK  
CheckDir: AffyCompatible.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   rm -rf AffyCompatible.buildbin-libdir AffyCompatible.Rcheck && mkdir AffyCompatible.buildbin-libdir AffyCompatible.Rcheck && E:\biocbld\bbs-3.1-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=AffyCompatible.buildbin-libdir AffyCompatible_1.28.0.tar.gz >AffyCompatible.Rcheck\00install.out 2>&1 && cp AffyCompatible.Rcheck\00install.out AffyCompatible-install.out  && E:\biocbld\bbs-3.1-bioc\R\bin\R.exe CMD check --library=AffyCompatible.buildbin-libdir --install="check:AffyCompatible-install.out" --force-multiarch --no-vignettes --timings AffyCompatible_1.28.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'E:/biocbld/bbs-3.1-bioc/meat/AffyCompatible.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 'AffyCompatible/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'AffyCompatible' 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 'AffyCompatible' can be installed ... 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
* 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
* 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 dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
.readXmlAsClass: no visible global function definition for
  'xmlTreeParse'
.xassn: no visible global function definition for 'xpathApply'
.xattrs: no visible global function definition for 'xmlAttrs'
.xclass: no visible global function definition for 'xmlName'
.xclass: no visible global function definition for 'xpathApply'
.xclass: no visible binding for global variable 'xmlName'
.xmlDoc: no visible global function definition for 'xmlDoc'
.xpcdata: no visible global function definition for 'xpathApply'
.xvalue: no visible global function definition for 'xpathApply'
readXml: no visible global function definition for 'xmlTreeParse'
xclass: no visible global function definition for 'xpathApply'
* 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 R/sysdata.rda ... OK
* checking installed files from 'inst/doc' ... OK
* checking files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... [27s] OK
Examples with CPU or elapsed time > 5s
                      user system elapsed
NetAffxResource-class 8.33   0.22   20.53
** running examples for arch 'x64' ... [32s] OK
Examples with CPU or elapsed time > 5s
                      user system elapsed
NetAffxResource-class 8.66   0.16   23.29
* 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: 1 NOTE
See
  'E:/biocbld/bbs-3.1-bioc/meat/AffyCompatible.Rcheck/00check.log'
for details.


AffyCompatible.Rcheck/00install.out:


install for i386

* installing *source* package 'AffyCompatible' ...
** 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 'AffyCompatible' ...
** testing if installed package can be loaded
Creating a generic function for 'nchar' from package 'base' in package 'S4Vectors'
* MD5 sums
packaged installation of 'AffyCompatible' as AffyCompatible_1.28.0.zip
* DONE (AffyCompatible)

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

nameusersystemelapsed
AffyCompatible-class000
NetAffxResource-class 8.33 0.2220.53
readArr0.410.000.40
readMage1.530.001.53
readNetAffx000
readXml0.090.000.10
xclass0.140.000.15
zzz-ARRCompatibility-class000
zzz-DTTCompatibility-class0.050.000.05
zzz-NetAffxCompatibility-class000

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

nameusersystemelapsed
AffyCompatible-class000
NetAffxResource-class 8.66 0.1623.29
readArr0.730.060.80
readMage2.200.022.21
readNetAffx0.020.000.02
readXml0.150.000.15
xclass0.250.000.27
zzz-ARRCompatibility-class000
zzz-DTTCompatibility-class0.080.000.08
zzz-NetAffxCompatibility-class0.000.010.01