| Back to Multiple platform build/check report for BioC 3.18: simplified long |
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This page was generated on 2024-03-04 11:37:10 -0500 (Mon, 04 Mar 2024).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | 4.3.2 Patched (2023-11-13 r85521) -- "Eye Holes" | 4692 |
| palomino4 | Windows Server 2022 Datacenter | x64 | 4.3.2 (2023-10-31 ucrt) -- "Eye Holes" | 4445 |
| lconway | macOS 12.7.1 Monterey | x86_64 | 4.3.2 Patched (2023-11-01 r85457) -- "Eye Holes" | 4466 |
| 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 211/2266 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| BioNAR 1.4.2 (landing page) Anatoly Sorokin
| nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | OK | ERROR | |||||||||
| palomino4 | Windows Server 2022 Datacenter / x64 | OK | OK | ERROR | OK | |||||||||
| lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | ERROR | OK | |||||||||
| kjohnson1 | macOS 13.6.1 Ventura / arm64 | see weekly results here | ||||||||||||
|
To the developers/maintainers of the BioNAR package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/BioNAR.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: BioNAR |
| Version: 1.4.2 |
| Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:BioNAR.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings BioNAR_1.4.2.tar.gz |
| StartedAt: 2024-03-03 19:15:52 -0500 (Sun, 03 Mar 2024) |
| EndedAt: 2024-03-03 19:24:28 -0500 (Sun, 03 Mar 2024) |
| EllapsedTime: 516.2 seconds |
| RetCode: 1 |
| Status: ERROR |
| CheckDir: BioNAR.Rcheck |
| Warnings: NA |
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### Running command:
###
### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:BioNAR.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings BioNAR_1.4.2.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.18-bioc/meat/BioNAR.Rcheck’
* using R version 4.3.2 Patched (2023-11-01 r85457)
* using platform: x86_64-apple-darwin20 (64-bit)
* R was compiled by
Apple clang version 14.0.3 (clang-1403.0.22.14.1)
GNU Fortran (GCC) 12.2.0
* running under: macOS Monterey 12.7.1
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘BioNAR/DESCRIPTION’ ... OK
* this is package ‘BioNAR’ version ‘1.4.2’
* package encoding: UTF-8
* 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 ‘BioNAR’ can be installed ... OK
* checking installed package size ... NOTE
installed size is 6.8Mb
sub-directories of 1Mb or more:
extdata 6.1Mb
* 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
Package in Depends field not imported from: ‘Rdpack’
These packages need to be imported from (in the NAMESPACE file)
for when this namespace is loaded but not attached.
There are ::: calls to the package's namespace in its code. A package
almost never needs to use ::: for its own objects:
‘addNoise’ ‘gofs’ ‘highlightRate’ ‘plotSigmoid’
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
clusterORA : forafun: no visible binding for global variable ‘pathway’
clusterORA : forafun: no visible binding for global variable ‘size’
clusterORA : forafun: no visible binding for global variable ‘overlap’
clusterORA : forafun: no visible binding for global variable ‘pval’
clusterORA : forafun: no visible binding for global variable ‘padj’
clusterORA : forafun: no visible binding for global variable
‘overlapGenes’
clusterORA : forafun: no visible binding for global variable ‘FL’
clusterORA : forafun: no visible binding for global variable ‘N’
clusterORA : forafun: no visible binding for global variable ‘Fn’
clusterORA : forafun: no visible binding for global variable ‘Cn’
clusterORA : forafun: no visible binding for global variable ‘Mu’
clusterORA : forafun: no visible binding for global variable ‘OR’
clusterORA : forafun: no visible binding for global variable ‘CIw’
clusterORA : forafun: no visible binding for global variable ‘Fe’
clusterORA : forafun: no visible binding for global variable ‘Fc’
clusterORA : forafun: no visible binding for global variable ‘palt’
plotSigmoid: no visible binding for global variable ‘yiR1’
plotSigmoid: no visible binding for global variable ‘yiR2’
plotSigmoid: no visible binding for global variable ‘yiR3’
plotSigmoid: no visible binding for global variable ‘yiR4’
plotSigmoid: no visible binding for global variable ‘yiR5’
Undefined global functions or variables:
CIw Cn FL Fc Fe Fn Mu N OR overlap overlapGenes padj palt pathway
pval size yiR1 yiR2 yiR3 yiR4 yiR5
* 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 LazyData ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
addEdgeAtts 11.648 2.056 13.906
calcEntropy 12.439 0.829 13.402
getCentralityMatrix 12.338 0.637 13.135
getEntropy 11.909 0.815 12.884
clusteringSummary 12.506 0.185 12.843
plotEntropy 11.462 0.876 12.513
getGraphCentralityECDF 11.595 0.611 12.317
annotateTopOntoOVG 10.158 0.632 10.922
annotateSCHanno 7.463 0.539 8.186
runPermDisease 6.972 0.182 7.217
normModularity 5.610 0.630 6.307
annotateGOont 5.222 0.846 6.838
calcSparsness 5.087 0.626 5.816
FitDegree 1.136 0.057 6.306
getRandomGraphCentrality 0.784 0.031 14.263
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘testthat.R’
ERROR
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
`actual`: 16 0
`expected`: 6 15
── Failure ('test_centrality.R:103:5'): Layouts ────────────────────────────────
isomorphic(cg, graph_from_literal(A - B - C)) is not TRUE
`actual`: FALSE
`expected`: TRUE
[ FAIL 7 | WARN 1417 | SKIP 2 | PASS 121 ]
Deleting unused snapshots:
• bridgeness/entropyplot.svg
• fitdegree/powerfitplot.svg
Error: Test failures
Execution halted
* 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: 1 ERROR, 3 NOTEs
See
‘/Users/biocbuild/bbs-3.18-bioc/meat/BioNAR.Rcheck/00check.log’
for details.
BioNAR.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL BioNAR ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library’ * installing *source* package ‘BioNAR’ ... ** using staged installation ** R ** data *** moving datasets to lazyload DB ** 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 (BioNAR)
BioNAR.Rcheck/tests/testthat.Rout.fail
R version 4.3.2 Patched (2023-11-01 r85457) -- "Eye Holes"
Copyright (C) 2023 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin20 (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.
> library(testthat)
> library(BioNAR)
Loading required package: igraph
Attaching package: 'igraph'
The following object is masked from 'package:testthat':
compare
The following objects are masked from 'package:stats':
decompose, spectrum
The following object is masked from 'package:base':
union
Loading required package: poweRlaw
Loading required package: latex2exp
Loading required package: RSpectra
Loading required package: Rdpack
Attaching package: 'BioNAR'
The following object is masked from 'package:igraph':
permute
>
> test_check("BioNAR")
This graph was created by an old(er) igraph version.
Call upgrade_graph() on it to use with the current igraph version
For now we convert it on the fly...
This graph was created by an old(er) igraph version.
Call upgrade_graph() on it to use with the current igraph version
For now we convert it on the fly...
This graph was created by an old(er) igraph version.
Call upgrade_graph() on it to use with the current igraph version
For now we convert it on the fly...
This graph was created by an old(er) igraph version.
Call upgrade_graph() on it to use with the current igraph version
For now we convert it on the fly...
This graph was created by an old(er) igraph version.
Call upgrade_graph() on it to use with the current igraph version
For now we convert it on the fly...
This graph was created by an old(er) igraph version.
Call upgrade_graph() on it to use with the current igraph version
For now we convert it on the fly...
[ FAIL 7 | WARN 1417 | SKIP 2 | PASS 121 ]
══ Skipped tests (2) ═══════════════════════════════════════════════════════════
• On CRAN (2): 'test_bridgeness.R:34:5', 'test_bridgeness.R:75:5'
══ Failed tests ════════════════════════════════════════════════════════════════
── Failure ('test_bridgeness.R:19:5'): Karate getBridgenes ─────────────────────
br$BRIDGENESS.louvain[br$ID == "John A"] (`actual`) not equal to 0.2407267 (`expected`).
`actual`: 0.3
`expected`: 0.2
── Failure ('test_bridgeness.R:66:5'): Presynaptic Bridgenes ───────────────────
br$BRIDGENESS.louvain[br$GENE.NAME == "ACTN2"] (`actual`) not equal to 0.2385256 (`expected`).
`actual`: 0.4
`expected`: 0.2
── Failure ('test_bridgeness.R:95:5'): Norm Modularity ─────────────────────────
`nm` (`actual`) not equal to 0.01347063 (`expected`).
`actual`: 0.007
`expected`: 0.013
── Failure ('test_centrality.R:95:5'): Layouts ─────────────────────────────────
lay[1, ] (`actual`) not equal to c(-10.16347, 9.7602631) (`expected`).
`actual`: -8.5 9.2
`expected`: -10.2 9.8
── Failure ('test_centrality.R:98:5'): Layouts ─────────────────────────────────
unlist(remem[34, c(2, 3)]) (`actual`) not equal to c(3, 4) (`expected`).
`actual`: 3 5
`expected`: 3 4
── Failure ('test_centrality.R:101:5'): Layouts ────────────────────────────────
lay[1, ] (`actual`) not equal to c(6.0216997, 14.6233495) (`expected`).
`actual`: 16 0
`expected`: 6 15
── Failure ('test_centrality.R:103:5'): Layouts ────────────────────────────────
isomorphic(cg, graph_from_literal(A - B - C)) is not TRUE
`actual`: FALSE
`expected`: TRUE
[ FAIL 7 | WARN 1417 | SKIP 2 | PASS 121 ]
Deleting unused snapshots:
• bridgeness/entropyplot.svg
• fitdegree/powerfitplot.svg
Error: Test failures
Execution halted
BioNAR.Rcheck/BioNAR-Ex.timings
| name | user | system | elapsed | |
| FitDegree | 1.136 | 0.057 | 6.306 | |
| addEdgeAtts | 11.648 | 2.056 | 13.906 | |
| annotateGOont | 5.222 | 0.846 | 6.838 | |
| annotateGeneNames | 0.289 | 0.009 | 0.324 | |
| annotateGoBP | 3.984 | 0.508 | 4.682 | |
| annotateGoCC | 3.037 | 0.425 | 3.570 | |
| annotateGoMF | 3.615 | 0.388 | 4.150 | |
| annotatePresynaptic | 1.357 | 0.162 | 1.571 | |
| annotateSCHanno | 7.463 | 0.539 | 8.186 | |
| annotateTopOntoOVG | 10.158 | 0.632 | 10.922 | |
| annotateVertex | 0.010 | 0.001 | 0.011 | |
| applpMatrixToGraph | 0.005 | 0.000 | 0.006 | |
| buildNetwork | 0.007 | 0.001 | 0.008 | |
| calcAllClustering | 4.291 | 0.045 | 4.370 | |
| calcBridgeness | 0.150 | 0.006 | 0.158 | |
| calcCentrality | 0.126 | 0.002 | 0.130 | |
| calcCentralityExternalDistances | 0.928 | 0.025 | 0.960 | |
| calcCentralityInternalDistances | 0.940 | 0.014 | 0.963 | |
| calcClustering | 0.012 | 0.002 | 0.013 | |
| calcDiseasePairs | 0.594 | 0.020 | 0.624 | |
| calcEntropy | 12.439 | 0.829 | 13.402 | |
| calcMembership | 0.012 | 0.002 | 0.016 | |
| calcReclusterMatrix | 0.015 | 0.002 | 0.018 | |
| calcSparsness | 5.087 | 0.626 | 5.816 | |
| clusterORA | 0.522 | 0.033 | 0.561 | |
| clusteringSummary | 12.506 | 0.185 | 12.843 | |
| degreeBinnedGDAs | 0.360 | 0.029 | 0.396 | |
| escapeAnnotation | 0 | 0 | 0 | |
| evalCentralitySignificance | 0.908 | 0.021 | 0.942 | |
| findLCC | 0.006 | 0.001 | 0.008 | |
| getAnnotationList | 0.080 | 0.003 | 0.084 | |
| getAnnotationVertexList | 0.095 | 0.015 | 0.113 | |
| getBridgeness | 0.134 | 0.006 | 0.142 | |
| getCentralityMatrix | 12.338 | 0.637 | 13.135 | |
| getClusterSubgraphByID | 0.005 | 0.002 | 0.007 | |
| getClustering | 0.011 | 0.001 | 0.012 | |
| getCommunityGraph | 0.008 | 0.002 | 0.009 | |
| getDType | 0 | 0 | 0 | |
| getDYNAMO | 0.040 | 0.002 | 0.053 | |
| getDiseases | 0.000 | 0.001 | 0.001 | |
| getEntropy | 11.909 | 0.815 | 12.884 | |
| getEntropyRate | 0.007 | 0.001 | 0.007 | |
| getGNP | 0.003 | 0.002 | 0.004 | |
| getGraphCentralityECDF | 11.595 | 0.611 | 12.317 | |
| getPA | 0.002 | 0.001 | 0.004 | |
| getRandomGraphCentrality | 0.784 | 0.031 | 14.263 | |
| getRobustness | 0.731 | 0.042 | 0.780 | |
| layoutByCluster | 0.095 | 0.003 | 0.100 | |
| layoutByRecluster | 0.073 | 0.003 | 0.077 | |
| makeConsensusMatrix | 0.681 | 0.040 | 0.727 | |
| metlMatrix | 0.005 | 0.002 | 0.007 | |
| normModularity | 5.610 | 0.630 | 6.307 | |
| permute | 0.000 | 0.001 | 0.001 | |
| plotBridgeness | 0.554 | 0.013 | 0.572 | |
| plotEntropy | 11.462 | 0.876 | 12.513 | |
| prepareGDA | 0.326 | 0.018 | 0.347 | |
| recluster | 0.015 | 0.002 | 0.018 | |
| removeVertexTerm | 0.004 | 0.001 | 0.005 | |
| runPermDisease | 6.972 | 0.182 | 7.217 | |
| sampleDegBinnedGDA | 0.409 | 0.010 | 0.424 | |
| sampleGraphClust | 0.009 | 0.001 | 0.011 | |
| unescapeAnnotation | 0.001 | 0.001 | 0.002 | |
| zeroNA | 0.001 | 0.000 | 0.000 | |