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BioC 3.4: CHECK report for ibh on morelia

This page was generated on 2016-09-21 03:50:58 -0700 (Wed, 21 Sep 2016).

Package 593/1257HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
ibh 1.21.0
Kircicegi Korkmaz
Snapshot Date: 2016-09-19 19:15:14 -0700 (Mon, 19 Sep 2016)
URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/ibh
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  NotNeeded  OK  OK UNNEEDED, same version exists in internal repository
moscato1 Windows Server 2008 R2 Standard (64-bit) / x64  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: ibh
Version: 1.21.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings ibh_1.21.0.tar.gz
StartedAt: 2016-09-20 08:00:35 -0700 (Tue, 20 Sep 2016)
EndedAt: 2016-09-20 08:00:55 -0700 (Tue, 20 Sep 2016)
EllapsedTime: 20.6 seconds
RetCode: 0
Status:  OK 
CheckDir: ibh.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings ibh_1.21.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.4-bioc/meat/ibh.Rcheck’
* using R version 3.3.1 (2016-06-21)
* using platform: x86_64-apple-darwin13.4.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘ibh/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘ibh’ version ‘1.21.0’
* 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 ‘ibh’ 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
* 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: ‘simpIntLists’
  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
ibhBioGRID: no visible global function definition for
  ‘findInteractionList’
ibhForMultipleGeneListsBioGRID: no visible global function definition
  for ‘findInteractionList’
readDirectedInteractionsFromCsv: no visible global function definition
  for ‘read.csv’
readUndirectedInteractionsFromCsv: no visible global function
  definition for ‘read.csv’
Undefined global functions or variables:
  findInteractionList read.csv
Consider adding
  importFrom("utils", "read.csv")
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 sizes of PDF files under ‘inst/doc’ ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
* 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: 2 NOTEs
See
  ‘/Users/biocbuild/bbs-3.4-bioc/meat/ibh.Rcheck/00check.log’
for details.


ibh.Rcheck/00install.out:

* installing *source* package ‘ibh’ ...
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (ibh)

ibh.Rcheck/ibh-Ex.timings:

nameusersystemelapsed
findEntry0.0320.0040.042
ibh-package1.4970.0391.724
ibh0.0070.0010.008
ibhBioGRID0.1510.0030.155
ibhClusterEval0.3020.0100.312
ibhClusterEvalBioGRID0.6510.0150.667
ibhForMultipleGeneLists0.0110.0010.013
ibhForMultipleGeneListsBioGRID0.1840.0050.188
readDirectedInteractionsFromCsv0.0010.0000.000
readUndirectedInteractionsFromCsv0.0010.0000.001