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BioC 3.5: CHECK report for a4Preproc on toluca2

This page was generated on 2017-04-23 14:35:43 -0400 (Sun, 23 Apr 2017).

Package 5/1377HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
a4Preproc 1.23.0
Tobias Verbeke
Snapshot Date: 2017-04-22 17:18:01 -0400 (Sat, 22 Apr 2017)
URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/a4Preproc
Last Changed Rev: 122712 / Revision: 129046
Last Changed Date: 2016-10-17 15:10:43 -0400 (Mon, 17 Oct 2016)
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
toluca2 Mac OS X Mavericks (10.9.5) / x86_64  OK  OK [ OK ] OK 
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: 1.23.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings a4Preproc_1.23.0.tar.gz
StartedAt: 2017-04-23 00:03:40 -0400 (Sun, 23 Apr 2017)
EndedAt: 2017-04-23 00:05:02 -0400 (Sun, 23 Apr 2017)
EllapsedTime: 82.0 seconds
RetCode: 0
Status:  OK 
CheckDir: a4Preproc.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings a4Preproc_1.23.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.5-bioc/meat/a4Preproc.Rcheck’
* using R Under development (unstable) (2017-02-15 r72187)
* using platform: x86_64-apple-darwin13.4.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘a4Preproc/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘a4Preproc’ version ‘1.23.0’
* 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 for sufficient/correct file permissions ... 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
* 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 ... OK
* checking PDF version of manual ... OK
* DONE

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


a4Preproc.Rcheck/00install.out:

* 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
* DONE (a4Preproc)

a4Preproc.Rcheck/a4Preproc-Ex.timings:

nameusersystemelapsed
addGeneInfo3.4930.1273.693