Back to Multiple platform build/check report for BioC 3.19:   simplified   long
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This page was generated on 2024-07-12 17:42 -0400 (Fri, 12 Jul 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 22.04.3 LTS)x86_644.4.1 (2024-06-14) -- "Race for Your Life" 4741
palomino7Windows Server 2022 Datacenterx644.4.1 (2024-06-14 ucrt) -- "Race for Your Life" 4483
merida1macOS 12.7.4 Montereyx86_644.4.1 (2024-06-14) -- "Race for Your Life" 4512
kjohnson1macOS 13.6.6 Venturaarm644.4.1 (2024-06-14) -- "Race for Your Life" 4461
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 213/2300HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
BioNAR 1.6.0  (landing page)
Anatoly Sorokin
Snapshot Date: 2024-07-10 14:00 -0400 (Wed, 10 Jul 2024)
git_url: https://git.bioconductor.org/packages/BioNAR
git_branch: RELEASE_3_19
git_last_commit: 61eee62
git_last_commit_date: 2024-04-30 11:45:27 -0400 (Tue, 30 Apr 2024)
nebbiolo1Linux (Ubuntu 22.04.3 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino7Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  
merida1macOS 12.7.4 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kjohnson1macOS 13.6.6 Ventura / arm64  OK    OK    OK    OK  UNNEEDED, same version is already published


CHECK results for BioNAR on kjohnson1

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.

raw results


Summary

Package: BioNAR
Version: 1.6.0
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_1.6.0.tar.gz
StartedAt: 2024-07-11 12:34:18 -0400 (Thu, 11 Jul 2024)
EndedAt: 2024-07-11 12:41:01 -0400 (Thu, 11 Jul 2024)
EllapsedTime: 403.7 seconds
RetCode: 0
Status:   OK  
CheckDir: BioNAR.Rcheck
Warnings: 0

Command output

##############################################################################
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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_1.6.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.19-bioc/meat/BioNAR.Rcheck’
* using R version 4.4.1 (2024-06-14)
* using platform: aarch64-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 Ventura 13.6.6
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘BioNAR/DESCRIPTION’ ... OK
* this is package ‘BioNAR’ version ‘1.6.0’
* 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 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
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 ... NOTE
checkRd: (-1) FitDegree.Rd:34: Lost braces
    34 | \item{legpos}{position of the legend @seealso{legend}}
       |                                              ^
checkRd: (-1) calcEntropy.Rd:52: Lost braces; missing escapes or markup?
    52 | Other {Entropy Functions}: 
       |       ^
checkRd: (-1) getEntropy.Rd:66: Lost braces; missing escapes or markup?
    66 | Other {Entropy Functions}: 
       |       ^
checkRd: (-1) getEntropyRate.Rd:41: Lost braces; missing escapes or markup?
    41 | Other {Entropy Functions}: 
       |       ^
checkRd: (-1) getRobustness.Rd:49: Lost braces; missing escapes or markup?
    49 | Other {Robustness functions}: 
       |       ^
checkRd: (-1) makeConsensusMatrix.Rd:69: Lost braces; missing escapes or markup?
    69 | Other {Robustness functions}: 
       |       ^
checkRd: (-1) plotEntropy.Rd:57: Lost braces; missing escapes or markup?
    57 | Other {Entropy Functions}: 
       |       ^
* 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              11.789  2.435  14.272
plotEntropy              10.989  1.890  12.892
getEntropy               10.405  1.717  12.141
calcEntropy              10.626  1.306  11.966
clusteringSummary        10.911  0.032  10.954
annotateTopOntoOVG        8.898  1.093  10.028
getCentralityMatrix       8.795  1.126   9.932
getGraphCentralityECDF    8.040  1.150   9.244
runPermDisease            8.129  0.190   8.338
annotateSCHanno           6.049  0.929   7.000
normModularity            5.509  1.100   6.625
calcSparsness             5.552  0.968   6.531
annotateGOont             4.954  0.619   5.585
calcAllClustering         5.373  0.016   5.393
FitDegree                 0.908  0.048   5.532
getRandomGraphCentrality  0.364  0.025  12.052
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.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: 4 NOTEs
See
  ‘/Users/biocbuild/bbs-3.19-bioc/meat/BioNAR.Rcheck/00check.log’
for details.


Installation output

BioNAR.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL BioNAR
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.4-arm64/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)

Tests output

BioNAR.Rcheck/tests/testthat.Rout


R version 4.4.1 (2024-06-14) -- "Race for Your Life"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: aarch64-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.

> 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")
[ FAIL 0 | WARN 0 | SKIP 2 | PASS 129 ]

══ Skipped tests (2) ═══════════════════════════════════════════════════════════
• On CRAN (2): 'test_bridgeness.R:38:5', 'test_bridgeness.R:81:5'

[ FAIL 0 | WARN 0 | SKIP 2 | PASS 129 ]
> 
> proc.time()
   user  system elapsed 
 37.553   2.191  52.796 

Example timings

BioNAR.Rcheck/BioNAR-Ex.timings

nameusersystemelapsed
FitDegree0.9080.0485.532
addEdgeAtts11.789 2.43514.272
annotateGOont4.9540.6195.585
annotateGeneNames0.2820.0120.294
annotateGoBP3.6120.6904.309
annotateGoCC2.4150.4762.919
annotateGoMF3.0330.6223.658
annotatePresynaptic1.0120.2561.269
annotateSCHanno6.0490.9297.000
annotateTopOntoOVG 8.898 1.09310.028
annotateVertex0.0050.0000.005
applpMatrixToGraph0.0020.0000.002
buildNetwork0.0030.0000.004
calcAllClustering5.3730.0165.393
calcBridgeness0.0610.0020.064
calcCentrality0.0360.0020.039
calcCentralityExternalDistances0.3040.0200.324
calcCentralityInternalDistances0.3140.0180.332
calcClustering0.0030.0010.003
calcDiseasePairs0.6110.0190.630
calcEntropy10.626 1.30611.966
calcMembership0.0080.0010.008
calcReclusterMatrix0.0170.0020.018
calcSparsness5.5520.9686.531
clusterORA0.3250.0250.350
clusteringSummary10.911 0.03210.954
degreeBinnedGDAs0.2970.0150.313
escapeAnnotation0.0000.0000.001
evalCentralitySignificance0.2960.0080.304
findLCC0.0040.0010.005
getAnnotationList0.0590.0060.065
getAnnotationVertexList0.0710.0120.084
getBridgeness0.0590.0120.071
getCentralityMatrix8.7951.1269.932
getClusterSubgraphByID0.0040.0010.005
getClustering0.0060.0010.008
getCommunityGraph0.0060.0010.007
getDType000
getDYNAMO0.0350.0020.037
getDiseases0.0000.0000.001
getEntropy10.405 1.71712.141
getEntropyRate0.0040.0010.005
getGNP0.0020.0010.003
getGraphCentralityECDF8.0401.1509.244
getPA0.0020.0000.002
getRandomGraphCentrality 0.364 0.02512.052
getRobustness0.4590.0400.500
layoutByCluster0.0820.0010.084
layoutByRecluster0.0660.0040.081
makeConsensusMatrix0.4210.0210.442
metlMatrix0.0080.0020.010
normModularity5.5091.1006.625
permute000
plotBridgeness0.3380.0110.349
plotEntropy10.989 1.89012.892
prepareGDA0.2540.0100.265
recluster0.0160.0020.018
removeVertexTerm0.0040.0010.006
runPermDisease8.1290.1908.338
sampleDegBinnedGDA0.3400.0280.368
sampleGraphClust0.0080.0010.009
unescapeAnnotation0.0000.0000.002
zeroNA0.0000.0000.001