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This page was generated on 2023-10-16 11:35:40 -0400 (Mon, 16 Oct 2023).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 22.04.2 LTS)x86_644.3.1 (2023-06-16) -- "Beagle Scouts" 4626
palomino3Windows Server 2022 Datacenterx644.3.1 (2023-06-16 ucrt) -- "Beagle Scouts" 4379
merida1macOS 12.6.4 Montereyx86_644.3.1 (2023-06-16) -- "Beagle Scouts" 4395
Click on any hostname to see more info about the system (e.g. compilers)      (*) as reported by 'uname -p', except on Windows and Mac OS X

Package 1655/2230HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
RCX 1.4.0  (landing page)
Florian Auer
Snapshot Date: 2023-10-15 14:00:13 -0400 (Sun, 15 Oct 2023)
git_url: https://git.bioconductor.org/packages/RCX
git_branch: RELEASE_3_17
git_last_commit: 6d4b6ea
git_last_commit_date: 2023-04-25 11:35:30 -0400 (Tue, 25 Apr 2023)
nebbiolo1Linux (Ubuntu 22.04.2 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino3Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
merida1macOS 12.6.4 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kjohnson2macOS 12.6.1 Monterey / arm64see weekly results here

CHECK results for RCX on nebbiolo1


To the developers/maintainers of the RCX package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/RCX.git to reflect on this report. See Troubleshooting Build Report for more information.
- Use the following Renviron settings to reproduce errors and warnings.
- If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information.

raw results


Summary

Package: RCX
Version: 1.4.0
Command: /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:RCX.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/site-library --timings RCX_1.4.0.tar.gz
StartedAt: 2023-10-16 00:16:16 -0400 (Mon, 16 Oct 2023)
EndedAt: 2023-10-16 00:17:11 -0400 (Mon, 16 Oct 2023)
EllapsedTime: 56.0 seconds
RetCode: 0
Status:   OK  
CheckDir: RCX.Rcheck
Warnings: 0

Command output

##############################################################################
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###
### Running command:
###
###   /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:RCX.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/site-library --timings RCX_1.4.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.17-bioc/meat/RCX.Rcheck’
* using R version 4.3.1 (2023-06-16)
* using platform: x86_64-pc-linux-gnu (64-bit)
* R was compiled by
    gcc (Ubuntu 11.3.0-1ubuntu1~22.04.1) 11.3.0
    GNU Fortran (Ubuntu 11.3.0-1ubuntu1~22.04.1) 11.3.0
* running under: Ubuntu 22.04.3 LTS
* using session charset: UTF-8
* checking for file ‘RCX/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘RCX’ version ‘1.4.0’
* package encoding: UTF-8
* 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 ‘RCX’ 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 ... NOTE
Problems with news in ‘NEWS.md’:
No news entries found.
* 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 startup messages can be suppressed ... 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 ... OK
* 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 R/sysdata.rda ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’
 OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ...
  ‘Appendix_The_RCX_and_CX_Data_Model.Rmd’ using ‘UTF-8’... OK
  ‘Creating_RCX_from_scratch.Rmd’ using ‘UTF-8’... OK
  ‘Extending_the_RCX_Data_Model.Rmd’ using ‘UTF-8’... OK
  ‘RCX_an_R_package_implementing_the_Cytoscape_Exchange_format.Rmd’ using ‘UTF-8’... OK
 NONE
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: 1 NOTE
See
  ‘/home/biocbuild/bbs-3.17-bioc/meat/RCX.Rcheck/00check.log’
for details.



Installation output

RCX.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD INSTALL RCX
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.17-bioc/R/site-library’
* installing *source* package ‘RCX’ ...
** using staged installation
** R
** inst
** 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 (RCX)

Tests output

RCX.Rcheck/tests/testthat.Rout


R version 4.3.1 (2023-06-16) -- "Beagle Scouts"
Copyright (C) 2023 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> library(testthat)
> library(RCX)
> 
> test_check("RCX")
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 60 ]
> 
> proc.time()
   user  system elapsed 
  2.401   0.098   2.487 

Example timings

RCX.Rcheck/RCX-Ex.timings

nameusersystemelapsed
CartesianLayout0.0040.0000.005
Convert-Names-and-Classes0.0000.0010.001
CyGroups0.0040.0000.005
CyHiddenAttributes0.1170.0030.121
CyNetworkRelations0.0010.0010.001
CySubNetworks0.0010.0010.003
CyTableColumn0.0030.0030.005
CyVisualProperties0.0140.0000.015
CyVisualProperty0.0100.0030.014
CyVisualPropertyDependencies0.0030.0010.003
CyVisualPropertyMappings0.0040.0000.004
CyVisualPropertyProperties0.0040.0000.003
EdgeAttributes0.0140.0000.014
Edges0.0010.0000.002
Igraph2.2880.0202.309
Meta-data0.0230.0000.024
NetworkAttributes0.0100.0040.014
NodeAttributes0.0130.0000.013
Nodes0.0010.0000.002
RCX-object0.2060.0000.205
aspectClasses0.0010.0000.001
checks000
convert-data-types-and-values0.0010.0000.002
convert2json0.0000.0000.001
countElements0.0080.0000.008
custom-print0.0050.0000.005
dot-addAspectNameToJson0.0000.0000.001
dot-addAttributeData000
dot-aspectClass0.0000.0010.000
dot-convertRawList000
dot-createAttributeAspect0.0000.0000.001
dot-createCyVpPorD000
dot-filterBy0.0010.0000.000
dot-format0.0010.0000.000
dot-infer000
dot-json2RDataType0.0000.0000.001
dot-jsonL0.0000.0000.001
dot-jsonV0.0000.0000.001
dot-log0.0000.0000.001
dot-mergeAttributesAspect000
dot-mergeIdAspect000
dot-modClass0.0000.0000.001
dot-pasteC0.0000.0010.000
dot-renameDF0.0000.0020.001
dot-stop0.0000.0010.000
dot-summaryAspect0.0020.0000.001
dot-transformListLength-set0.0030.0010.002
dot-transformVLD0.0050.0000.005
getCyVisualProperty0.0080.0010.009
graphNEL2.5180.0092.528
hasIds0.0010.0010.001
idProperty0.0010.0000.000
jsonToRCX0.0030.0000.002
markAttributeColumn0.0010.0000.001
markRefColumn0.0040.0000.005
maxId0.0010.0000.001
rcxToJson0.0020.0000.001
readCX0.4500.0120.462
referredBy0.0080.0000.008
refersTo0.0010.0000.001
setExtension000
summary0.0110.0000.011
toCX0.010.000.01
updateCartesianLayout0.0420.0000.042
updateCyGroups0.0210.0040.026
updateCyHiddenAttributes0.0400.0000.041
updateCyNetworkRelations0.0340.0000.034
updateCySubNetworks0.0280.0000.028
updateCyTableColumn0.0400.0000.039
updateCyVisualProperties0.2140.0080.222
updateCyVisualProperty0.0540.0040.059
updateEdgeAttributes0.0450.0000.045
updateEdges0.0230.0000.022
updateMetaDataProperties0.0190.0000.019
updateNetworkAttributes0.0360.0040.041
updateNodeAttributes0.0520.0000.052
updateNodes0.0170.0000.018
validate0.2410.0000.242
visualize0.0060.0020.008
writeCX000
writeHTML0.0590.0160.082