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BioC 3.4: CHECK report for AffyCompatible on moscato1

This page was generated on 2016-09-21 03:42:30 -0700 (Wed, 21 Sep 2016).

Package 18/1257HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
AffyCompatible 1.33.0
Martin Morgan
Snapshot Date: 2016-09-19 19:15:14 -0700 (Mon, 19 Sep 2016)
URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/AffyCompatible
Last Changed Rev: 117081 / Revision: 121152
Last Changed Date: 2016-05-03 14:30:44 -0700 (Tue, 03 May 2016)
zin1 Linux (Ubuntu 16.04 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
moscato1 Windows Server 2008 R2 Standard (64-bit) / x64  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: 1.33.0
Command: rm -rf AffyCompatible.buildbin-libdir AffyCompatible.Rcheck && mkdir AffyCompatible.buildbin-libdir AffyCompatible.Rcheck && D:\biocbld\bbs-3.4-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=AffyCompatible.buildbin-libdir AffyCompatible_1.33.0.tar.gz >AffyCompatible.Rcheck\00install.out 2>&1 && cp AffyCompatible.Rcheck\00install.out AffyCompatible-install.out && D:\biocbld\bbs-3.4-bioc\R\bin\R.exe CMD check --library=AffyCompatible.buildbin-libdir --install="check:AffyCompatible-install.out" --force-multiarch --no-vignettes --timings AffyCompatible_1.33.0.tar.gz
StartedAt: 2016-09-20 03:34:14 -0700 (Tue, 20 Sep 2016)
EndedAt: 2016-09-20 03:37:45 -0700 (Tue, 20 Sep 2016)
EllapsedTime: 210.8 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 && D:\biocbld\bbs-3.4-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=AffyCompatible.buildbin-libdir AffyCompatible_1.33.0.tar.gz >AffyCompatible.Rcheck\00install.out 2>&1 && cp AffyCompatible.Rcheck\00install.out AffyCompatible-install.out  && D:\biocbld\bbs-3.4-bioc\R\bin\R.exe CMD check --library=AffyCompatible.buildbin-libdir --install="check:AffyCompatible-install.out" --force-multiarch --no-vignettes --timings AffyCompatible_1.33.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'D:/biocbld/bbs-3.4-bioc/meat/AffyCompatible.Rcheck'
* using R version 3.3.1 (2016-06-21)
* 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 '1.33.0'
* 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
.readAnnotation: no visible global function definition for
  'download.file'
.readAnnotation: no visible global function definition for 'read.csv'
.readAnnotation: no visible global function definition for 'read.delim'
.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'
Undefined global functions or variables:
  download.file read.csv read.delim xmlAttrs xmlDoc xmlName
  xmlTreeParse xpathApply
Consider adding
  importFrom("utils", "download.file", "read.csv", "read.delim")
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 R/sysdata.rda ... 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
NetAffxResource-class 7.84    0.3      23
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
                      user system elapsed
NetAffxResource-class 7.87   0.23    21.1
* 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
  'D:/biocbld/bbs-3.4-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
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded

install for x64

* installing *source* package 'AffyCompatible' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'AffyCompatible' as AffyCompatible_1.33.0.zip
* DONE (AffyCompatible)

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

nameusersystemelapsed
AffyCompatible-class000
NetAffxResource-class 7.84 0.3023.00
readArr0.430.000.42
readMage1.520.001.53
readNetAffx000
readXml0.080.000.07
xclass0.110.020.21
zzz-ARRCompatibility-class000
zzz-DTTCompatibility-class0.050.000.04
zzz-NetAffxCompatibility-class0.010.000.02

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

nameusersystemelapsed
AffyCompatible-class000
NetAffxResource-class 7.87 0.2321.10
readArr0.460.000.47
readMage1.690.001.69
readNetAffx000
readXml0.090.000.09
xclass0.110.020.14
zzz-ARRCompatibility-class000
zzz-DTTCompatibility-class0.040.000.04
zzz-NetAffxCompatibility-class000