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CHECK report for ibh on tokay1

This page was generated on 2021-05-06 12:31:47 -0400 (Thu, 06 May 2021).

To the developers/maintainers of the ibh package:
Please make sure to use the following settings in order to reproduce any error or warning you see on this page.
Package 861/1974HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
ibh 1.38.0  (landing page)
Kircicegi Korkmaz
Snapshot Date: 2021-05-05 14:51:38 -0400 (Wed, 05 May 2021)
URL: https://git.bioconductor.org/packages/ibh
Branch: RELEASE_3_12
Last Commit: ad47e92
Last Changed Date: 2020-10-27 10:40:36 -0400 (Tue, 27 Oct 2020)
malbec1Linux (Ubuntu 18.04.5 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version exists in internal repository
tokay1Windows Server 2012 R2 Standard / x64  OK    OK    OK    OK  UNNEEDED, same version exists in internal repository
merida1macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version exists in internal repository

Summary

Package: ibh
Version: 1.38.0
Command: C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:ibh.install-out.txt --library=C:\Users\biocbuild\bbs-3.12-bioc\R\library --no-vignettes --timings ibh_1.38.0.tar.gz
StartedAt: 2021-05-06 03:43:49 -0400 (Thu, 06 May 2021)
EndedAt: 2021-05-06 03:44:47 -0400 (Thu, 06 May 2021)
EllapsedTime: 58.4 seconds
RetCode: 0
Status:   OK   
CheckDir: ibh.Rcheck
Warnings: 0

Command output

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###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:ibh.install-out.txt --library=C:\Users\biocbuild\bbs-3.12-bioc\R\library --no-vignettes --timings ibh_1.38.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.12-bioc/meat/ibh.Rcheck'
* using R version 4.0.5 (2021-03-31)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'ibh/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'ibh' version '1.38.0'
* 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 '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
* 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: '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 ...
** running examples for arch 'i386' ... OK
** running examples for arch 'x64' ... 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
  'C:/Users/biocbuild/bbs-3.12-bioc/meat/ibh.Rcheck/00check.log'
for details.



Installation output

ibh.Rcheck/00install.out

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###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O http://172.29.0.3/BBS/3.12/bioc/src/contrib/ibh_1.38.0.tar.gz && rm -rf ibh.buildbin-libdir && mkdir ibh.buildbin-libdir && C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=ibh.buildbin-libdir ibh_1.38.0.tar.gz && C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD INSTALL ibh_1.38.0.zip && rm ibh_1.38.0.tar.gz ibh_1.38.0.zip
###
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  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed

  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
100  6280  100  6280    0     0   750k      0 --:--:-- --:--:-- --:--:--  876k

install for i386

* installing *source* package 'ibh' ...
** using staged installation
** R
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'ibh'
    finding HTML links ... done
    findEntry                               html  
    ibh-package                             html  
    ibh                                     html  
    ibhBioGRID                              html  
    ibhClusterEval                          html  
    ibhClusterEvalBioGRID                   html  
    ibhForMultipleGeneLists                 html  
    ibhForMultipleGeneListsBioGRID          html  
    readDirectedInteractionsFromCsv         html  
    readUndirectedInteractionsFromCsv       html  
** 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

install for x64

* installing *source* package 'ibh' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'ibh' as ibh_1.38.0.zip
* DONE (ibh)
* installing to library 'C:/Users/biocbuild/bbs-3.12-bioc/R/library'
package 'ibh' successfully unpacked and MD5 sums checked

Tests output


Example timings

ibh.Rcheck/examples_i386/ibh-Ex.timings

nameusersystemelapsed
findEntry0.050.000.17
ibh-package1.450.033.66
ibh000
ibhBioGRID0.200.000.21
ibhClusterEval0.300.000.29
ibhClusterEvalBioGRID0.600.050.66
ibhForMultipleGeneLists0.020.000.02
ibhForMultipleGeneListsBioGRID0.190.020.20
readDirectedInteractionsFromCsv000
readUndirectedInteractionsFromCsv000

ibh.Rcheck/examples_x64/ibh-Ex.timings

nameusersystemelapsed
findEntry0.030.000.04
ibh-package1.250.081.32
ibh0.000.020.02
ibhBioGRID0.180.000.17
ibhClusterEval0.220.010.24
ibhClusterEvalBioGRID0.540.020.56
ibhForMultipleGeneLists0.020.000.01
ibhForMultipleGeneListsBioGRID0.150.010.18
readDirectedInteractionsFromCsv000
readUndirectedInteractionsFromCsv000