Frank Kramer
| Snapshot Date: 2022-03-17 13:55:23 -0400 (Thu, 17 Mar 2022) |
| git_url: https://git.bioconductor.org/packages/rBiopaxParser |
| git_branch: master |
| git_last_commit: fc7c9cf |
| git_last_commit_date: 2021-10-26 12:06:39 -0400 (Tue, 26 Oct 2021) |
| Back to Multiple platform build/check report for BioC 3.15 |
|
This page was generated on 2022-03-18 11:08:25 -0400 (Fri, 18 Mar 2022).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 20.04.4 LTS) | x86_64 | R Under development (unstable) (2022-02-17 r81757) -- "Unsuffered Consequences" | 4334 |
| riesling1 | Windows Server 2019 Standard | x64 | R Under development (unstable) (2021-11-21 r81221) -- "Unsuffered Consequences" | 4097 |
| palomino3 | Windows Server 2022 Datacenter | x64 | R Under development (unstable) (2022-02-17 r81757 ucrt) -- "Unsuffered Consequences" | 4083 |
| merida1 | macOS 10.14.6 Mojave | x86_64 | R Under development (unstable) (2022-03-02 r81842) -- "Unsuffered Consequences" | 4134 |
| 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 | ||||
|
To the developers/maintainers of the rBiopaxParser package: - Please 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 How and When does the builder pull? When will my changes propagate? here for more information. - Make sure to use the following settings in order to reproduce any error or warning you see on this page. |
| Package 1542/2090 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| rBiopaxParser 2.35.0 (landing page) Frank Kramer
| nebbiolo1 | Linux (Ubuntu 20.04.4 LTS) / x86_64 | OK | OK | OK | | ||||||||
| riesling1 | Windows Server 2019 Standard / x64 | OK | OK | OK | OK | |||||||||
| palomino3 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | | ||||||||
| merida1 | macOS 10.14.6 Mojave / x86_64 | OK | OK | OK | OK | | ||||||||
| Package: rBiopaxParser |
| Version: 2.35.0 |
| Command: D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:rBiopaxParser.install-out.txt --library=D:\biocbuild\bbs-3.15-bioc\R\library --no-vignettes --timings rBiopaxParser_2.35.0.tar.gz |
| StartedAt: 2022-03-17 20:00:50 -0400 (Thu, 17 Mar 2022) |
| EndedAt: 2022-03-17 20:01:50 -0400 (Thu, 17 Mar 2022) |
| EllapsedTime: 59.9 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: rBiopaxParser.Rcheck |
| Warnings: 0 |
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###
### Running command:
###
### D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:rBiopaxParser.install-out.txt --library=D:\biocbuild\bbs-3.15-bioc\R\library --no-vignettes --timings rBiopaxParser_2.35.0.tar.gz
###
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* using log directory 'D:/biocbuild/bbs-3.15-bioc/meat/rBiopaxParser.Rcheck'
* using R Under development (unstable) (2021-11-21 r81221)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'rBiopaxParser/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'rBiopaxParser' version '2.35.0'
* 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 '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 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 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 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 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: 3 NOTEs
See
'D:/biocbuild/bbs-3.15-bioc/meat/rBiopaxParser.Rcheck/00check.log'
for details.
rBiopaxParser.Rcheck/00install.out
##############################################################################
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###
### Running command:
###
### D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD INSTALL rBiopaxParser
###
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* installing to library 'D:/biocbuild/bbs-3.15-bioc/R/library'
* installing *source* package 'rBiopaxParser' ...
** using staged installation
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
converting help for package 'rBiopaxParser'
finding HTML links ... done
CLASS_INHERITANCE_BP2 html
CLASS_INHERITANCE_BP3 html
CLASS_PROPERTIES_BP2 html
CLASS_PROPERTIES_BP3 html
DATABASE_BIOPAX html
addBiochemicalReaction html
addBiopaxInstance html
addBiopaxInstances html
addControl html
addPathway html
addPathwayComponents html
addPhysicalEntity html
addPhysicalEntityParticipant html
addPropertiesToBiopaxInstance html
addhash html
addns html
biopax html
calcGraphOverlap html
checkValidity html
colorGraphNodes html
combineNodes html
createBiopax html
diffGraphs html
downloadBiopaxData html
generateNewUniqueID html
getClassProperties html
getInstanceClass html
getInstanceProperty html
getNeighborhood html
getParticipants html
getReferencedIDs html
getReferencingIDs html
getSubClasses html
getSuperClasses html
getXrefAnnotations html
hasProperty html
internal_NrOfXMLNodes html
internal_XMLInstance2DF html
internal_checkArguments html
internal_generateXMLfromBiopax html
internal_getBiopaxModelAsDataFrame html
internal_propertyListToDF html
internal_resolvePhysicalEntityParticipant
html
intersectGraphs html
isOfClass html
isOfNamespace html
isURL html
layoutRegulatoryGraph html
listComplexComponents html
listInstances html
listInteractionComponents html
listPathwayComponents html
listPathways html
mergePathways html
pathway2AdjacancyMatrix html
pathway2Geneset html
pathway2Graph html
pathway2RegulatoryGraph html
plotRegulatoryGraph html
print.biopax html
rBiopaxParser-package html
readBiopax html
removeDisconnectedParts html
removeInstance html
removeNodes html
removeProperties html
selectInstances html
splitComplex html
striphash html
stripns html
transitiveClosure html
transitiveReduction html
unfactorize html
uniteGraphs html
writeBiopax 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
* DONE (rBiopaxParser)
Making 'packages.html' ...Warning in packageDescription(i, lib.loc = lib, fields = "Title", encoding = "UTF-8") :
DESCRIPTION file of package 'tweeDEseq' is missing or broken
done
rBiopaxParser.Rcheck/tests/runTests.Rout
R Under development (unstable) (2021-11-21 r81221) -- "Unsuffered Consequences"
Copyright (C) 2021 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64 (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.
> BiocGenerics:::testPackage("rBiopaxParser")
RUNIT TEST PROTOCOL -- Thu Mar 17 20:01:35 2022
***********************************************
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
0.40 0.06 0.45
rBiopaxParser.Rcheck/rBiopaxParser-Ex.timings
| name | user | system | elapsed | |
| addBiochemicalReaction | 0.03 | 0.00 | 0.03 | |
| addBiopaxInstance | 0 | 0 | 0 | |
| addBiopaxInstances | 0.02 | 0.00 | 0.02 | |
| addControl | 0.01 | 0.00 | 0.01 | |
| addPathway | 0.04 | 0.00 | 0.03 | |
| addPathwayComponents | 0.03 | 0.00 | 0.08 | |
| addPhysicalEntity | 0.01 | 0.00 | 0.02 | |
| addPhysicalEntityParticipant | 0.02 | 0.00 | 0.01 | |
| addPropertiesToBiopaxInstance | 0.01 | 0.00 | 0.02 | |
| biopax | 0.00 | 0.02 | 0.01 | |
| calcGraphOverlap | 1.96 | 0.09 | 2.05 | |
| colorGraphNodes | 0.98 | 0.03 | 1.02 | |
| combineNodes | 0 | 0 | 0 | |
| createBiopax | 0 | 0 | 0 | |
| diffGraphs | 1.51 | 0.08 | 1.59 | |
| downloadBiopaxData | 0 | 0 | 0 | |
| getClassProperties | 0 | 0 | 0 | |
| getInstanceClass | 0 | 0 | 0 | |
| getInstanceProperty | 0 | 0 | 0 | |
| getReferencedIDs | 0.03 | 0.00 | 0.03 | |
| getReferencingIDs | 0.02 | 0.00 | 0.02 | |
| getSubClasses | 0 | 0 | 0 | |
| getSuperClasses | 0 | 0 | 0 | |
| getXrefAnnotations | 0.11 | 0.00 | 0.11 | |
| hasProperty | 0.01 | 0.00 | 0.01 | |
| intersectGraphs | 1.50 | 0.07 | 1.58 | |
| isOfClass | 0 | 0 | 0 | |
| layoutRegulatoryGraph | 0.93 | 0.02 | 0.94 | |
| listComplexComponents | 0.03 | 0.00 | 0.03 | |
| listInstances | 0.01 | 0.00 | 0.01 | |
| listInteractionComponents | 0.02 | 0.00 | 0.02 | |
| listPathwayComponents | 0.03 | 0.00 | 0.03 | |
| listPathways | 0 | 0 | 0 | |
| pathway2AdjacancyMatrix | 0.83 | 0.03 | 0.86 | |
| pathway2Geneset | 0.36 | 0.00 | 0.36 | |
| pathway2Graph | 0.62 | 0.06 | 0.69 | |
| pathway2RegulatoryGraph | 0.89 | 0.04 | 0.92 | |
| plotRegulatoryGraph | 0.88 | 0.06 | 0.94 | |
| print.biopax | 0.00 | 0.01 | 0.01 | |
| rBiopaxParser-package | 0 | 0 | 0 | |
| readBiopax | 0 | 0 | 0 | |
| removeInstance | 0.00 | 0.02 | 0.02 | |
| removeNodes | 0.92 | 0.05 | 0.97 | |
| removeProperties | 0 | 0 | 0 | |
| selectInstances | 0.02 | 0.00 | 0.01 | |
| splitComplex | 0.03 | 0.00 | 0.03 | |
| transitiveClosure | 0.92 | 0.03 | 0.96 | |
| transitiveReduction | 0.78 | 0.03 | 0.81 | |
| uniteGraphs | 1.78 | 0.05 | 1.83 | |
| writeBiopax | 0 | 0 | 0 | |