Back to Multiple platform build/check report for BioC 3.19:   simplified   long
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This page was generated on 2024-06-28 17:40 -0400 (Fri, 28 Jun 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 22.04.3 LTS)x86_644.4.0 (2024-04-24) -- "Puppy Cup" 4760
palomino3Windows Server 2022 Datacenterx644.4.0 (2024-04-24 ucrt) -- "Puppy Cup" 4494
merida1macOS 12.7.4 Montereyx86_644.4.0 (2024-04-24) -- "Puppy Cup" 4508
kjohnson1macOS 13.6.6 Venturaarm644.4.0 (2024-04-24) -- "Puppy Cup" 4466
palomino7Windows Server 2022 Datacenterx644.4.1 (2024-06-14 ucrt) -- "Race for Your Life" 4362
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 1706/2300HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
RCy3 2.24.0  (landing page)
Alex Pico
Snapshot Date: 2024-06-26 14:00 -0400 (Wed, 26 Jun 2024)
git_url: https://git.bioconductor.org/packages/RCy3
git_branch: RELEASE_3_19
git_last_commit: ca074c6
git_last_commit_date: 2024-04-30 10:46:27 -0400 (Tue, 30 Apr 2024)
nebbiolo1Linux (Ubuntu 22.04.3 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 12.7.4 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kjohnson1macOS 13.6.6 Ventura / arm64  OK    OK    OK    OK  UNNEEDED, same version is already published
palomino7Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  


CHECK results for RCy3 on nebbiolo1

To the developers/maintainers of the RCy3 package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/RCy3.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: RCy3
Version: 2.24.0
Command: /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD check --install=check:RCy3.install-out.txt --library=/home/biocbuild/bbs-3.19-bioc/R/site-library --timings RCy3_2.24.0.tar.gz
StartedAt: 2024-06-27 02:52:25 -0400 (Thu, 27 Jun 2024)
EndedAt: 2024-06-27 02:53:58 -0400 (Thu, 27 Jun 2024)
EllapsedTime: 93.3 seconds
RetCode: 0
Status:   OK  
CheckDir: RCy3.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD check --install=check:RCy3.install-out.txt --library=/home/biocbuild/bbs-3.19-bioc/R/site-library --timings RCy3_2.24.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.19-bioc/meat/RCy3.Rcheck’
* using R version 4.4.0 (2024-04-24)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
    GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
* running under: Ubuntu 22.04.4 LTS
* using session charset: UTF-8
* checking for file ‘RCy3/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘RCy3’ version ‘2.24.0’
* 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 ... NOTE
Found the following hidden files and directories:
  .travis.yml
These were most likely included in error. See section ‘Package
structure’ in the ‘Writing R Extensions’ manual.
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘RCy3’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
License stub is invalid DCF.
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking code 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 ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
.checkHexColor: no visible global function definition for ‘colors’
.edgeNameToEdgeSUID: no visible binding for global variable ‘SUID’
.nodeNameToNodeSUID: no visible binding for global variable ‘SUID’
createNetworkFromDataFrames: no visible binding for global variable
  ‘SUID’
Undefined global functions or variables:
  SUID colors
Consider adding
  importFrom("grDevices", "colors")
to your NAMESPACE file.
* checking Rd files ... NOTE
checkRd: (-1) importFileFromUrl.Rd:24: Lost braces; missing escapes or markup?
    24 | dict: {'filePath': <new file's absolute path in Cytoscape workstation>, 'fileByteCount': number of bytes read}
       |       ^
checkRd: (-1) sandboxGetFileInfo.Rd:17: Lost braces; missing escapes or markup?
    17 | dict: {'filePath': <full path on Cytoscape workstation>, 'modifiedTime': <last changed time, '' if file doesn't exist>, 'isFile': <True if file, False if directory>}
       |       ^
checkRd: (-1) sandboxRemove.Rd:15: Lost braces; missing escapes or markup?
    15 | dict: {'sandboxPath': <directory on Cytoscape workstation>, 'existed': <True if sandbox existed>}
       |       ^
checkRd: (-1) sandboxRemoveFile.Rd:17: Lost braces; missing escapes or markup?
    17 | dict: {'filePath': <file's absolute path in Cytoscape workstation>, 'existed': True if file existed before being deleted}
       |       ^
checkRd: (-1) sandboxUrlTo.Rd:27: Lost braces; missing escapes or markup?
    27 | dict: {'filePath': <new file's absolute path in Cytoscape workstation>, 'fileByteCount': number of bytes read}
       |       ^
* 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 ‘tests’ ... OK
* checking tests ...
  Running ‘runTests.R’
 OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: 4 NOTEs
See
  ‘/home/biocbuild/bbs-3.19-bioc/meat/RCy3.Rcheck/00check.log’
for details.


Installation output

RCy3.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD INSTALL RCy3
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.19-bioc/R/site-library’
* installing *source* package ‘RCy3’ ...
** 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 (RCy3)

Tests output

RCy3.Rcheck/tests/runTests.Rout


R version 4.4.0 (2024-04-24) -- "Puppy Cup"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu

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.

> # tests disabled as the Bioconductor build system no longer supports interactive sessions
> #require(RCy3) || stop("unable to load RCy3")
> #BiocGenerics:::testPackage('RCy3')
> 
> proc.time()
   user  system elapsed 
  0.149   0.039   0.174 

Example timings

RCy3.Rcheck/RCy3-Ex.timings

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createNetworkFromCytoscapejs000
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createNetworkFromGraph0.0000.0000.001
createNetworkFromIgraph000
createSubnetwork000
createView000
createVisualStyle000
cybrowserClose000
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cyrestGET000
cyrestPOST000
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cytoscapeApiVersions000
cytoscapeFreeMemory000
cytoscapeMemoryStatus000
cytoscapeNumberOfCores0.0000.0010.000
cytoscapePing000
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diffusionAdvanced000
diffusionBasic000
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dockPanel000
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exportNetworkToNDEx0.0000.0010.001
exportPDF000
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fitContent000
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getNetworkViews000
getNetworkZoom000
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getNodeHeight0.0000.0010.001
getNodeLabelPosition000
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getNodeSelectionColorDefault000
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getNodeWidth0.0010.0000.000
getNotebookIsRunning0.0000.0000.001
getSandboxReinitialize000
getSelectedEdgeCount000
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getSelectedNodeCount000
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getTableColumnNames000
getTableColumnTypes0.0000.0000.001
getTableColumns000
getTableValue000
getUninstalledApps000
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getVisualStyleJSON000
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groupAnnotation0.0010.0000.000
hideAllPanels0.0000.0000.001
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hideNodes000
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hideSelectedEdges000
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importFileFromUrl0.0010.0000.000
importFilters0.0000.0000.001
importNetworkFromFile000
importNetworkFromNDEx000
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installApp000
invertEdgeSelection000
invertNodeSelection000
layoutCopycat0.0000.0010.000
layoutNetwork000
listGroups0.0000.0000.001
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makeSimpleIgraph0.0650.0030.068
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mapVisualProperty0.0000.0000.001
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notebookExportShowImage000
notebookShowImage000
openAppStore000
openSession0.0010.0000.000
paletteColorBrewerAccent0.0040.0000.004
paletteColorBrewerBlues0.0000.0000.001
paletteColorBrewerBrBG000
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paletteColorBrewerGnBu000
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renameNetwork000
renameTableColumn000
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