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BioC 3.5: CHECK report for a4Preproc on tokay2

This page was generated on 2017-08-16 13:21:01 -0400 (Wed, 16 Aug 2017).

Package 5/1382HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
a4Preproc 1.24.0
Tobias Verbeke
Snapshot Date: 2017-08-15 17:17:57 -0400 (Tue, 15 Aug 2017)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_5/madman/Rpacks/a4Preproc
Last Changed Rev: 129126 / Revision: 131943
Last Changed Date: 2017-04-24 15:25:24 -0400 (Mon, 24 Apr 2017)
malbec2 Linux (Ubuntu 16.04.1 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  OK  OK [ OK ] OK UNNEEDED, same version exists in internal repository
veracruz2 OS X 10.11.6 El Capitan / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: a4Preproc
Version: 1.24.0
Command: rm -rf a4Preproc.buildbin-libdir a4Preproc.Rcheck && mkdir a4Preproc.buildbin-libdir a4Preproc.Rcheck && C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=a4Preproc.buildbin-libdir a4Preproc_1.24.0.tar.gz >a4Preproc.Rcheck\00install.out 2>&1 && cp a4Preproc.Rcheck\00install.out a4Preproc-install.out && C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD check --library=a4Preproc.buildbin-libdir --install="check:a4Preproc-install.out" --force-multiarch --no-vignettes --timings a4Preproc_1.24.0.tar.gz
StartedAt: 2017-08-15 21:52:30 -0400 (Tue, 15 Aug 2017)
EndedAt: 2017-08-15 21:55:04 -0400 (Tue, 15 Aug 2017)
EllapsedTime: 153.9 seconds
RetCode: 0
Status:  OK  
CheckDir: a4Preproc.Rcheck
Warnings: 0

Command output

##############################################################################
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###
### Running command:
###
###   rm -rf a4Preproc.buildbin-libdir a4Preproc.Rcheck && mkdir a4Preproc.buildbin-libdir a4Preproc.Rcheck && C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=a4Preproc.buildbin-libdir a4Preproc_1.24.0.tar.gz >a4Preproc.Rcheck\00install.out 2>&1 && cp a4Preproc.Rcheck\00install.out a4Preproc-install.out  &&  C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD check --library=a4Preproc.buildbin-libdir --install="check:a4Preproc-install.out" --force-multiarch --no-vignettes --timings a4Preproc_1.24.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.5-bioc/meat/a4Preproc.Rcheck'
* using R version 3.4.1 (2017-06-30)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'a4Preproc/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'a4Preproc' 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 'a4Preproc' can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Malformed Description field: should contain one or more complete sentences.
* 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 ... NOTE
Package in Depends field not imported from: 'methods'
  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
addGeneInfo: no visible global function definition for 'annotation'
addGeneInfo: no visible global function definition for 'featureNames'
addGeneInfo: no visible global function definition for 'featureData'
addGeneInfo: no visible global function definition for 'pData'
addGeneInfo: no visible global function definition for 'pData<-'
addGeneInfo: no visible global function definition for 'featureData<-'
addGeneInfo: no visible global function definition for 'fvarMetadata'
addGeneInfo: no visible global function definition for 'fvarMetadata<-'
Undefined global functions or variables:
  annotation featureData featureData<- featureNames fvarMetadata
  fvarMetadata<- pData pData<-
* 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 examples ...
** running examples for arch 'i386' ... OK
** running examples for arch 'x64' ... OK
* checking PDF version of manual ... OK
* DONE

Status: 3 NOTEs
See
  'C:/Users/biocbuild/bbs-3.5-bioc/meat/a4Preproc.Rcheck/00check.log'
for details.


a4Preproc.Rcheck/00install.out:


install for i386

* installing *source* package 'a4Preproc' ...
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** testing if installed package can be loaded

install for x64

* installing *source* package 'a4Preproc' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'a4Preproc' as a4Preproc_1.24.0.zip
* DONE (a4Preproc)

a4Preproc.Rcheck/examples_i386/a4Preproc-Ex.timings:

nameusersystemelapsed
addGeneInfo3.220.093.42

a4Preproc.Rcheck/examples_x64/a4Preproc-Ex.timings:

nameusersystemelapsed
addGeneInfo3.310.113.43