Frank Kramer
| Snapshot Date: 2025-10-20 13:45 -0400 (Mon, 20 Oct 2025) |
| git_url: https://git.bioconductor.org/packages/rBiopaxParser |
| git_branch: devel |
| git_last_commit: 2f5f7e4 |
| git_last_commit_date: 2025-04-15 10:17:44 -0400 (Tue, 15 Apr 2025) |
| Back to Multiple platform build/check report for BioC 3.22: simplified long |
|
This page was generated on 2025-10-21 12:05 -0400 (Tue, 21 Oct 2025).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 24.04.3 LTS) | x86_64 | 4.5.1 Patched (2025-08-23 r88802) -- "Great Square Root" | 4887 |
| lconway | macOS 12.7.6 Monterey | x86_64 | 4.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" | 4677 |
| kjohnson3 | macOS 13.7.7 Ventura | arm64 | 4.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" | 4622 |
| taishan | Linux (openEuler 24.03 LTS) | aarch64 | 4.5.0 (2025-04-11) -- "How About a Twenty-Six" | 4642 |
| 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 1710/2353 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| rBiopaxParser 2.49.0 (landing page) Frank Kramer
| nebbiolo2 | Linux (Ubuntu 24.04.3 LTS) / x86_64 | OK | OK | OK | | ||||||||
| lconway | macOS 12.7.6 Monterey / x86_64 | OK | OK | OK | OK | | ||||||||
| kjohnson3 | macOS 13.7.7 Ventura / arm64 | OK | OK | OK | OK | | ||||||||
| taishan | Linux (openEuler 24.03 LTS) / aarch64 | OK | OK | OK | ||||||||||
|
To the developers/maintainers of the rBiopaxParser package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/rBiopaxParser.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. |
| Package: rBiopaxParser |
| Version: 2.49.0 |
| Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:rBiopaxParser.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings rBiopaxParser_2.49.0.tar.gz |
| StartedAt: 2025-10-21 01:02:24 -0400 (Tue, 21 Oct 2025) |
| EndedAt: 2025-10-21 01:03:29 -0400 (Tue, 21 Oct 2025) |
| EllapsedTime: 65.5 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: rBiopaxParser.Rcheck |
| Warnings: 0 |
##############################################################################
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###
### Running command:
###
### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:rBiopaxParser.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings rBiopaxParser_2.49.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/Users/biocbuild/bbs-3.22-bioc/meat/rBiopaxParser.Rcheck’
* using R version 4.5.1 Patched (2025-09-10 r88807)
* using platform: x86_64-apple-darwin20
* R was compiled by
Apple clang version 14.0.0 (clang-1400.0.29.202)
GNU Fortran (GCC) 14.2.0
* running under: macOS Monterey 12.7.6
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘rBiopaxParser/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘rBiopaxParser’ version ‘2.49.0’
* 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 ‘rBiopaxParser’ 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 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 dependencies in R code ... NOTE
'library' or 'require' calls in package code:
‘RBGL’ ‘RCurl’ ‘Rgraphviz’ ‘graph’ ‘igraph’
Please use :: or requireNamespace() instead.
See section 'Suggested packages' in the 'Writing R Extensions' manual.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
addBiopaxInstance: no visible binding for global variable ‘property’
addBiopaxInstances: no visible binding for global variable ‘id’
addBiopaxInstances: no visible binding for global variable ‘property’
addPropertiesToBiopaxInstance: no visible binding for global variable
‘property’
colorGraphNodes: no visible global function definition for ‘hcl’
createBiopax: no visible binding for global variable ‘id’
createBiopax: no visible binding for global variable ‘property’
getReferencedIDs: no visible binding for global variable
‘property_attr’
getReferencedIDs: no visible binding for global variable ‘property’
getReferencingIDs: no visible binding for global variable
‘property_attr’
getReferencingIDs: no visible binding for global variable ‘property’
internal_XMLInstance2DF: no visible binding for global variable ‘i’
internal_XMLInstance2DF: no visible binding for global variable ‘p’
internal_generateXMLfromBiopax: no visible binding for global variable
‘id’
internal_getBiopaxModelAsDataFrame: no visible binding for global
variable ‘property’
internal_propertyListToDF: no visible binding for global variable
‘property’
layoutRegulatoryGraph: no visible global function definition for
‘nodes’
listInstances: no visible binding for global variable ‘property_value’
listInstances: no visible binding for global variable ‘property’
pathway2AdjacancyMatrix: no visible global function definition for ‘as’
pathway2Graph: no visible global function definition for ‘new’
pathway2Graph: no visible global function definition for ‘getClassDef’
pathway2Graph: no visible binding for global variable ‘id’
pathway2Graph: no visible binding for global variable ‘property’
pathway2RegulatoryGraph: no visible global function definition for
‘new’
pathway2RegulatoryGraph: no visible global function definition for
‘getClassDef’
pathway2RegulatoryGraph: no visible binding for global variable ‘id’
pathway2RegulatoryGraph: no visible binding for global variable
‘property’
plotRegulatoryGraph: no visible global function definition for ‘nodes’
removeDisconnectedParts: no visible global function definition for
‘removeNode’
removeNodes: no visible global function definition for ‘edgeWeights’
removeNodes: no visible global function definition for ‘na.omit’
removeNodes: no visible global function definition for ‘removeNode’
removeNodes: no visible global function definition for ‘addEdge’
removeProperties: no visible binding for global variable ‘property’
selectInstances: no visible binding for global variable
‘property_value’
Undefined global functions or variables:
addEdge as edgeWeights getClassDef hcl i id na.omit new nodes p
property property_attr property_value removeNode
Consider adding
importFrom("grDevices", "hcl")
importFrom("methods", "as", "getClassDef", "new")
importFrom("stats", "na.omit")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
* 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 contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking sizes of PDF files under ‘inst/doc’ ... 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 running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE
Status: 2 NOTEs
See
‘/Users/biocbuild/bbs-3.22-bioc/meat/rBiopaxParser.Rcheck/00check.log’
for details.
rBiopaxParser.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL rBiopaxParser ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library’ * installing *source* package ‘rBiopaxParser’ ... ** this is package ‘rBiopaxParser’ version ‘2.49.0’ ** using staged installation ** R ** data ** 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 (rBiopaxParser)
rBiopaxParser.Rcheck/tests/runTests.Rout
R version 4.5.1 Patched (2025-09-10 r88807) -- "Great Square Root"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin20
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.
> BiocGenerics:::testPackage("rBiopaxParser")
RUNIT TEST PROTOCOL -- Tue Oct 21 01:03:16 2025
***********************************************
Number of test functions: 12
Number of errors: 0
Number of failures: 0
1 Test Suite :
rBiopaxParser RUnit Tests - 12 test functions, 0 errors, 0 failures
Number of test functions: 12
Number of errors: 0
Number of failures: 0
>
> proc.time()
user system elapsed
0.540 0.120 0.679
rBiopaxParser.Rcheck/rBiopaxParser-Ex.timings
| name | user | system | elapsed | |
| addBiochemicalReaction | 0.048 | 0.008 | 0.056 | |
| addBiopaxInstance | 0.012 | 0.001 | 0.013 | |
| addBiopaxInstances | 0.012 | 0.002 | 0.014 | |
| addControl | 0.024 | 0.002 | 0.025 | |
| addPathway | 0.028 | 0.002 | 0.030 | |
| addPathwayComponents | 0.029 | 0.003 | 0.031 | |
| addPhysicalEntity | 0.013 | 0.001 | 0.014 | |
| addPhysicalEntityParticipant | 0.021 | 0.001 | 0.021 | |
| addPropertiesToBiopaxInstance | 0.012 | 0.002 | 0.012 | |
| biopax | 0.019 | 0.004 | 0.023 | |
| calcGraphOverlap | 2.199 | 0.071 | 2.288 | |
| colorGraphNodes | 1.372 | 0.033 | 1.421 | |
| combineNodes | 0.003 | 0.002 | 0.005 | |
| createBiopax | 0.002 | 0.001 | 0.002 | |
| diffGraphs | 2.013 | 0.036 | 2.063 | |
| downloadBiopaxData | 0.000 | 0.000 | 0.001 | |
| getClassProperties | 0.001 | 0.000 | 0.002 | |
| getInstanceClass | 0.005 | 0.001 | 0.006 | |
| getInstanceProperty | 0.008 | 0.001 | 0.010 | |
| getReferencedIDs | 0.032 | 0.002 | 0.034 | |
| getReferencingIDs | 0.023 | 0.002 | 0.024 | |
| getSubClasses | 0 | 0 | 0 | |
| getSuperClasses | 0.000 | 0.000 | 0.001 | |
| getXrefAnnotations | 0.150 | 0.003 | 0.155 | |
| hasProperty | 0.004 | 0.001 | 0.005 | |
| intersectGraphs | 1.881 | 0.025 | 1.918 | |
| isOfClass | 0.004 | 0.002 | 0.008 | |
| layoutRegulatoryGraph | 1.267 | 0.020 | 1.304 | |
| listComplexComponents | 0.016 | 0.002 | 0.018 | |
| listInstances | 0.025 | 0.009 | 0.034 | |
| listInteractionComponents | 0.023 | 0.002 | 0.024 | |
| listPathwayComponents | 0.024 | 0.006 | 0.031 | |
| listPathways | 0.009 | 0.002 | 0.012 | |
| pathway2AdjacancyMatrix | 1.045 | 0.021 | 1.073 | |
| pathway2Geneset | 0.468 | 0.008 | 0.479 | |
| pathway2Graph | 1.091 | 0.037 | 1.138 | |
| pathway2RegulatoryGraph | 1.277 | 0.026 | 1.315 | |
| plotRegulatoryGraph | 1.057 | 0.021 | 1.087 | |
| print.biopax | 0.009 | 0.003 | 0.013 | |
| rBiopaxParser-package | 0.000 | 0.000 | 0.001 | |
| readBiopax | 0.004 | 0.001 | 0.006 | |
| removeInstance | 0.005 | 0.002 | 0.006 | |
| removeNodes | 1.213 | 0.029 | 1.253 | |
| removeProperties | 0.005 | 0.001 | 0.007 | |
| selectInstances | 0.019 | 0.004 | 0.022 | |
| splitComplex | 0.047 | 0.003 | 0.050 | |
| transitiveClosure | 0.980 | 0.020 | 1.008 | |
| transitiveReduction | 0.942 | 0.015 | 0.959 | |
| uniteGraphs | 1.993 | 0.038 | 2.045 | |
| writeBiopax | 0.001 | 0.002 | 0.003 | |