Frank Kramer
| Snapshot Date: 2019-04-15 17:01:12 -0400 (Mon, 15 Apr 2019) |
| URL: https://git.bioconductor.org/packages/rBiopaxParser |
| Branch: RELEASE_3_8 |
| Last Commit: 789779b |
| Last Changed Date: 2018-10-30 11:41:50 -0400 (Tue, 30 Oct 2018) |
| Back to Multiple platform build/check report for BioC 3.8 |
|
This page was generated on 2019-04-16 11:49:54 -0400 (Tue, 16 Apr 2019).
| Package 1255/1649 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| rBiopaxParser 2.22.0 Frank Kramer
| malbec1 | Linux (Ubuntu 16.04.6 LTS) / x86_64 | OK | OK | [ OK ] | | ||||||
| merida1 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | OK | OK | |
| Package: rBiopaxParser |
| Version: 2.22.0 |
| Command: /home/biocbuild/bbs-3.8-bioc/R/bin/R CMD check --install=check:rBiopaxParser.install-out.txt --library=/home/biocbuild/bbs-3.8-bioc/R/library --no-vignettes --timings rBiopaxParser_2.22.0.tar.gz |
| StartedAt: 2019-04-16 02:24:22 -0400 (Tue, 16 Apr 2019) |
| EndedAt: 2019-04-16 02:29:48 -0400 (Tue, 16 Apr 2019) |
| EllapsedTime: 326.4 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: rBiopaxParser.Rcheck |
| Warnings: 0 |
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### Running command:
###
### /home/biocbuild/bbs-3.8-bioc/R/bin/R CMD check --install=check:rBiopaxParser.install-out.txt --library=/home/biocbuild/bbs-3.8-bioc/R/library --no-vignettes --timings rBiopaxParser_2.22.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.8-bioc/meat/rBiopaxParser.Rcheck’
* using R version 3.5.3 (2019-03-11)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘rBiopaxParser/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘rBiopaxParser’ version ‘2.22.0’
* 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 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’ ‘nem’
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’
transitiveReduction: no visible global function definition for ‘as’
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
Examples with CPU or elapsed time > 5s
user system elapsed
uniteGraphs 143.652 0.444 39.691
intersectGraphs 143.276 0.400 39.838
diffGraphs 142.968 0.364 40.521
calcGraphOverlap 123.184 0.424 23.479
removeNodes 83.084 0.272 22.764
pathway2AdjacancyMatrix 82.944 0.292 24.743
pathway2RegulatoryGraph 82.564 0.216 24.023
plotRegulatoryGraph 82.264 0.276 23.794
colorGraphNodes 76.260 0.236 15.580
pathway2Geneset 63.932 0.252 18.950
pathway2Graph 36.424 0.088 10.945
getXrefAnnotations 13.972 0.040 3.916
addPathwayComponents 5.100 0.008 0.955
* 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
‘/home/biocbuild/bbs-3.8-bioc/meat/rBiopaxParser.Rcheck/00check.log’
for details.
rBiopaxParser.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.8-bioc/R/bin/R CMD INSTALL rBiopaxParser ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.8-bioc/R/library’ * installing *source* package ‘rBiopaxParser’ ... ** 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 * DONE (rBiopaxParser)
rBiopaxParser.Rcheck/tests/runTests.Rout
R version 3.5.3 (2019-03-11) -- "Great Truth"
Copyright (C) 2019 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.
> BiocGenerics:::testPackage("rBiopaxParser")
RUNIT TEST PROTOCOL -- Tue Apr 16 02:29:44 2019
***********************************************
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
0.604 0.028 0.645
rBiopaxParser.Rcheck/rBiopaxParser-Ex.timings
| name | user | system | elapsed | |
| addBiochemicalReaction | 2.940 | 0.008 | 0.692 | |
| addBiopaxInstance | 0.588 | 0.000 | 0.101 | |
| addBiopaxInstances | 1.016 | 0.004 | 0.215 | |
| addControl | 4.472 | 0.020 | 0.745 | |
| addPathway | 4.404 | 0.008 | 0.799 | |
| addPathwayComponents | 5.100 | 0.008 | 0.955 | |
| addPhysicalEntity | 1.236 | 0.004 | 0.226 | |
| addPhysicalEntityParticipant | 2.624 | 0.020 | 0.464 | |
| addPropertiesToBiopaxInstance | 1.132 | 0.004 | 0.192 | |
| biopax | 0.168 | 0.000 | 0.041 | |
| calcGraphOverlap | 123.184 | 0.424 | 23.479 | |
| colorGraphNodes | 76.260 | 0.236 | 15.580 | |
| combineNodes | 0.004 | 0.000 | 0.005 | |
| createBiopax | 0.188 | 0.000 | 0.036 | |
| diffGraphs | 142.968 | 0.364 | 40.521 | |
| downloadBiopaxData | 0 | 0 | 0 | |
| getClassProperties | 0.000 | 0.000 | 0.002 | |
| getInstanceClass | 0.340 | 0.000 | 0.117 | |
| getInstanceProperty | 0.348 | 0.000 | 0.109 | |
| getReferencedIDs | 3.216 | 0.008 | 0.939 | |
| getReferencingIDs | 1.672 | 0.000 | 0.474 | |
| getSubClasses | 0.000 | 0.000 | 0.001 | |
| getSuperClasses | 0.000 | 0.000 | 0.001 | |
| getXrefAnnotations | 13.972 | 0.040 | 3.916 | |
| intersectGraphs | 143.276 | 0.400 | 39.838 | |
| listComplexComponents | 1.244 | 0.008 | 0.376 | |
| listInstances | 1.676 | 0.012 | 0.503 | |
| listInteractionComponents | 3.000 | 0.004 | 0.797 | |
| listPathwayComponents | 1.748 | 0.000 | 0.495 | |
| listPathways | 0.484 | 0.004 | 0.135 | |
| pathway2AdjacancyMatrix | 82.944 | 0.292 | 24.743 | |
| pathway2Geneset | 63.932 | 0.252 | 18.950 | |
| pathway2Graph | 36.424 | 0.088 | 10.945 | |
| pathway2RegulatoryGraph | 82.564 | 0.216 | 24.023 | |
| plotRegulatoryGraph | 82.264 | 0.276 | 23.794 | |
| print.biopax | 0.088 | 0.000 | 0.043 | |
| rBiopaxParser-package | 0 | 0 | 0 | |
| readBiopax | 0 | 0 | 0 | |
| removeNodes | 83.084 | 0.272 | 22.764 | |
| selectInstances | 0.180 | 0.000 | 0.077 | |
| splitComplex | 3.792 | 0.004 | 1.032 | |
| uniteGraphs | 143.652 | 0.444 | 39.691 | |
| writeBiopax | 0.000 | 0.000 | 0.003 | |