Back to Multiple platform build/check report for BioC 3.9
ABCDEFGH[I]JKLMNOPQRSTUVWXYZ

CHECK report for ibh on malbec2

This page was generated on 2019-10-16 11:59:37 -0400 (Wed, 16 Oct 2019).

Package 783/1741HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
ibh 1.32.0
Kircicegi Korkmaz
Snapshot Date: 2019-10-15 17:01:26 -0400 (Tue, 15 Oct 2019)
URL: https://git.bioconductor.org/packages/ibh
Branch: RELEASE_3_9
Last Commit: e6ca0f8
Last Changed Date: 2019-05-02 11:53:23 -0400 (Thu, 02 May 2019)
malbec2 Linux (Ubuntu 18.04.2 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
celaya2 OS X 10.11.6 El Capitan / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: ibh
Version: 1.32.0
Command: /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD check --install=check:ibh.install-out.txt --library=/home/biocbuild/bbs-3.9-bioc/R/library --no-vignettes --timings ibh_1.32.0.tar.gz
StartedAt: 2019-10-16 02:25:31 -0400 (Wed, 16 Oct 2019)
EndedAt: 2019-10-16 02:25:57 -0400 (Wed, 16 Oct 2019)
EllapsedTime: 25.8 seconds
RetCode: 0
Status:  OK 
CheckDir: ibh.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD check --install=check:ibh.install-out.txt --library=/home/biocbuild/bbs-3.9-bioc/R/library --no-vignettes --timings ibh_1.32.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.9-bioc/meat/ibh.Rcheck’
* using R version 3.6.1 (2019-07-05)
* using platform: x86_64-pc-linux-gnu (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 ‘1.32.0’
* 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 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 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
  ‘/home/biocbuild/bbs-3.9-bioc/meat/ibh.Rcheck/00check.log’
for details.



Installation output

ibh.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD INSTALL ibh
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.9-bioc/R/library’
* installing *source* package ‘ibh’ ...
** using staged installation
** R
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (ibh)

Tests output


Example timings

ibh.Rcheck/ibh-Ex.timings

nameusersystemelapsed
findEntry0.0270.0040.047
ibh-package1.8870.0362.094
ibh0.0150.0000.014
ibhBioGRID0.3050.0000.309
ibhClusterEval0.3950.0040.401
ibhClusterEvalBioGRID0.9020.0080.913
ibhForMultipleGeneLists0.0150.0000.015
ibhForMultipleGeneListsBioGRID0.3080.0000.311
readDirectedInteractionsFromCsv000
readUndirectedInteractionsFromCsv000