Back to Multiple platform build/check report for BioC 3.20: simplified long |
|
This page was generated on 2024-12-23 12:06 -0500 (Mon, 23 Dec 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo2 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4744 |
palomino8 | Windows Server 2022 Datacenter | x64 | 4.4.2 (2024-10-31 ucrt) -- "Pile of Leaves" | 4487 |
merida1 | macOS 12.7.5 Monterey | x86_64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4515 |
kjohnson1 | macOS 13.6.6 Ventura | arm64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4467 |
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 1672/2289 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
rBiopaxParser 2.46.0 (landing page) Frank Kramer
| nebbiolo2 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | OK | |||||||||
palomino8 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | |||||||||
merida1 | macOS 12.7.5 Monterey / x86_64 | OK | OK | OK | OK | |||||||||
kjohnson1 | macOS 13.6.6 Ventura / arm64 | OK | 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: 2.46.0 |
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_2.46.0.tar.gz |
StartedAt: 2024-12-20 08:13:29 -0500 (Fri, 20 Dec 2024) |
EndedAt: 2024-12-20 08:15:13 -0500 (Fri, 20 Dec 2024) |
EllapsedTime: 103.3 seconds |
RetCode: 0 |
Status: OK |
CheckDir: rBiopaxParser.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### 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_2.46.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.20-bioc/meat/rBiopaxParser.Rcheck’ * using R version 4.4.2 (2024-10-31) * using platform: x86_64-apple-darwin20 * R was compiled by Apple clang version 14.0.0 (clang-1400.0.29.202) GNU Fortran (GCC) 12.2.0 * 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 ‘2.46.0’ * 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 ... NOTE Note: found 1 marked UTF-8 string * 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: 3 NOTEs See ‘/Users/biocbuild/bbs-3.20-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/4.4-x86_64/Resources/library’ * installing *source* package ‘rBiopaxParser’ ... ** 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 4.4.2 (2024-10-31) -- "Pile of Leaves" Copyright (C) 2024 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 -- Fri Dec 20 08:14:56 2024 *********************************************** 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 0.899 0.156 1.064
rBiopaxParser.Rcheck/rBiopaxParser-Ex.timings
name | user | system | elapsed | |
addBiochemicalReaction | 0.082 | 0.011 | 0.094 | |
addBiopaxInstance | 0.016 | 0.001 | 0.017 | |
addBiopaxInstances | 0.022 | 0.004 | 0.025 | |
addControl | 0.040 | 0.003 | 0.043 | |
addPathway | 0.050 | 0.003 | 0.054 | |
addPathwayComponents | 0.058 | 0.004 | 0.063 | |
addPhysicalEntity | 0.021 | 0.003 | 0.024 | |
addPhysicalEntityParticipant | 0.032 | 0.002 | 0.036 | |
addPropertiesToBiopaxInstance | 0.022 | 0.002 | 0.024 | |
biopax | 0.039 | 0.011 | 0.050 | |
calcGraphOverlap | 4.234 | 0.122 | 4.573 | |
colorGraphNodes | 2.477 | 0.048 | 2.551 | |
combineNodes | 0.004 | 0.002 | 0.005 | |
createBiopax | 0.002 | 0.001 | 0.003 | |
diffGraphs | 3.634 | 0.060 | 3.845 | |
downloadBiopaxData | 0.001 | 0.000 | 0.001 | |
getClassProperties | 0.001 | 0.001 | 0.003 | |
getInstanceClass | 0.010 | 0.003 | 0.014 | |
getInstanceProperty | 0.014 | 0.003 | 0.028 | |
getReferencedIDs | 0.046 | 0.004 | 0.050 | |
getReferencingIDs | 0.035 | 0.004 | 0.041 | |
getSubClasses | 0.001 | 0.000 | 0.001 | |
getSuperClasses | 0.000 | 0.001 | 0.001 | |
getXrefAnnotations | 0.268 | 0.006 | 0.285 | |
hasProperty | 0.006 | 0.002 | 0.008 | |
intersectGraphs | 3.517 | 0.039 | 4.328 | |
isOfClass | 0.005 | 0.003 | 0.007 | |
layoutRegulatoryGraph | 2.174 | 0.022 | 2.258 | |
listComplexComponents | 0.024 | 0.003 | 0.026 | |
listInstances | 0.041 | 0.019 | 0.061 | |
listInteractionComponents | 0.038 | 0.005 | 0.043 | |
listPathwayComponents | 0.040 | 0.013 | 0.055 | |
listPathways | 0.015 | 0.003 | 0.018 | |
pathway2AdjacancyMatrix | 1.993 | 0.039 | 2.143 | |
pathway2Geneset | 0.829 | 0.015 | 0.875 | |
pathway2Graph | 1.946 | 0.056 | 2.111 | |
pathway2RegulatoryGraph | 2.352 | 0.024 | 2.432 | |
plotRegulatoryGraph | 2.100 | 0.049 | 2.325 | |
print.biopax | 0.016 | 0.004 | 0.024 | |
rBiopaxParser-package | 0 | 0 | 0 | |
readBiopax | 0.005 | 0.002 | 0.008 | |
removeInstance | 0.007 | 0.002 | 0.009 | |
removeNodes | 2.207 | 0.039 | 2.380 | |
removeProperties | 0.008 | 0.002 | 0.009 | |
selectInstances | 0.036 | 0.007 | 0.045 | |
splitComplex | 0.065 | 0.005 | 0.069 | |
transitiveClosure | 2.011 | 0.035 | 2.151 | |
transitiveReduction | 1.924 | 0.029 | 2.079 | |
uniteGraphs | 3.737 | 0.072 | 4.179 | |
writeBiopax | 0.002 | 0.003 | 0.005 | |