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CHECK report for biocGraph on tokay1

This page was generated on 2020-08-13 11:34:46 -0400 (Thu, 13 Aug 2020).

TO THE DEVELOPERS/MAINTAINERS OF THE biocGraph PACKAGE: Please make sure to use the following settings in order to reproduce any error or warning you see on this page.
Package 153/1885HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
biocGraph 1.51.0
Florian Hahne
Snapshot Date: 2020-08-12 14:52:00 -0400 (Wed, 12 Aug 2020)
URL: https://git.bioconductor.org/packages/biocGraph
Branch: master
Last Commit: a37dab4
Last Changed Date: 2020-04-27 14:15:24 -0400 (Mon, 27 Apr 2020)
malbec1 Linux (Ubuntu 18.04.4 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
nebbiolo1 Linux (Ubuntu 20.04.1 LTS) / x86_64  OK  OK  OK 
tokay1 Windows Server 2012 R2 Standard / x64  OK  OK [ OK ] OK UNNEEDED, same version exists in internal repository
merida1 macOS 10.14.6 Mojave / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: biocGraph
Version: 1.51.0
Command: C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:biocGraph.install-out.txt --library=C:\Users\biocbuild\bbs-3.12-bioc\R\library --no-vignettes --timings biocGraph_1.51.0.tar.gz
StartedAt: 2020-08-13 00:18:12 -0400 (Thu, 13 Aug 2020)
EndedAt: 2020-08-13 00:20:10 -0400 (Thu, 13 Aug 2020)
EllapsedTime: 117.6 seconds
RetCode: 0
Status:  OK  
CheckDir: biocGraph.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:biocGraph.install-out.txt --library=C:\Users\biocbuild\bbs-3.12-bioc\R\library --no-vignettes --timings biocGraph_1.51.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.12-bioc/meat/biocGraph.Rcheck'
* using R version 4.0.2 (2020-06-22)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'biocGraph/DESCRIPTION' ... OK
* this is package 'biocGraph' version '1.51.0'
* 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 'biocGraph' can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking 'build' directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Packages listed in more than one of Depends, Imports, Suggests, Enhances:
  'Rgraphviz' 'graph' 'geneplotter'
A package should be listed in only one of these fields.
* 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 ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
imageMap,Ragraph-connection-list-character: no visible global function
  definition for 'par'
imageMap,Ragraph-connection-list-character: no visible global function
  definition for 'AgNode'
imageMap,Ragraph-connection-list-character: no visible global function
  definition for 'getNodeXY'
imageMap,Ragraph-connection-list-character: no visible global function
  definition for 'getNodeHeight'
imageMap,Ragraph-connection-list-character: no visible global function
  definition for 'getNodeLW'
imageMap,Ragraph-connection-list-character: no visible global function
  definition for 'getNodeRW'
imageMap,graph-connection-list-character: no visible global function
  definition for 'nodes'
imageMap,graph-connection-list-character: no visible global function
  definition for 'graphRenderInfo'
Undefined global functions or variables:
  AgNode getNodeHeight getNodeLW getNodeRW getNodeXY graphRenderInfo
  nodes par
Consider adding
  importFrom("graphics", "par")
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/biocGraph.Rcheck/00check.log'
for details.



Installation output

biocGraph.Rcheck/00install.out

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###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec1.bioconductor.org/BBS/3.12/bioc/src/contrib/biocGraph_1.51.0.tar.gz && rm -rf biocGraph.buildbin-libdir && mkdir biocGraph.buildbin-libdir && C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=biocGraph.buildbin-libdir biocGraph_1.51.0.tar.gz && C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD INSTALL biocGraph_1.51.0.zip && rm biocGraph_1.51.0.tar.gz biocGraph_1.51.0.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 31466  100 31466    0     0   731k      0 --:--:-- --:--:-- --:--:--  808k

install for i386

* installing *source* package 'biocGraph' ...
** using staged installation
** R
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'biocGraph'
    finding HTML links ... done
    imageMap                                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 'biocGraph' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'biocGraph' as biocGraph_1.51.0.zip
* DONE (biocGraph)
* installing to library 'C:/Users/biocbuild/bbs-3.12-bioc/R/library'
package 'biocGraph' successfully unpacked and MD5 sums checked

Tests output


Example timings

biocGraph.Rcheck/examples_i386/biocGraph-Ex.timings

nameusersystemelapsed
imageMap000

biocGraph.Rcheck/examples_x64/biocGraph-Ex.timings

nameusersystemelapsed
imageMap000