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This page was generated on 2024-12-23 12:06 -0500 (Mon, 23 Dec 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 24.04.1 LTS)x86_644.4.2 (2024-10-31) -- "Pile of Leaves" 4744
palomino8Windows Server 2022 Datacenterx644.4.2 (2024-10-31 ucrt) -- "Pile of Leaves" 4487
merida1macOS 12.7.5 Montereyx86_644.4.2 (2024-10-31) -- "Pile of Leaves" 4515
kjohnson1macOS 13.6.6 Venturaarm644.4.2 (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 215/2289HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
BioNAR 1.8.1  (landing page)
Anatoly Sorokin
Snapshot Date: 2024-12-19 13:00 -0500 (Thu, 19 Dec 2024)
git_url: https://git.bioconductor.org/packages/BioNAR
git_branch: RELEASE_3_20
git_last_commit: 4ba8a84
git_last_commit_date: 2024-12-10 21:43:14 -0500 (Tue, 10 Dec 2024)
nebbiolo2Linux (Ubuntu 24.04.1 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino8Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
merida1macOS 12.7.5 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 merida1

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: 1.8.1
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_1.8.1.tar.gz
StartedAt: 2024-12-20 00:22:25 -0500 (Fri, 20 Dec 2024)
EndedAt: 2024-12-20 00:36:03 -0500 (Fri, 20 Dec 2024)
EllapsedTime: 817.6 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_1.8.1.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.20-bioc/meat/BioNAR.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 ‘BioNAR/DESCRIPTION’ ... OK
* this is package ‘BioNAR’ version ‘1.8.1’
* 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 ... NOTE
Unknown package ‘clusterCons’ in Rd xrefs
* 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
clusteringSummary        21.296  0.079  22.018
calcEntropy              19.452  0.950  21.242
addEdgeAtts              17.501  2.609  20.688
plotEntropy              18.986  0.883  23.560
getEntropy               18.077  1.019  19.946
getGraphCentralityECDF   16.745  0.696  17.899
annotateTopOntoOVG       16.498  0.809  18.260
getCentralityMatrix      16.502  0.756  17.505
annotateSCHanno          11.067  0.699  11.780
runPermDisease           10.774  0.172  11.793
annotateGOont             8.967  1.285  10.414
normModularity            8.624  0.724  10.102
annotateGoBP              8.153  0.603   8.962
calcSparsness             8.092  0.654   9.520
annotateGoMF              6.690  0.422   7.256
annotateGoCC              6.598  0.452   7.197
calcAllClustering         6.648  0.025   6.910
FitDegree                 2.232  0.081  13.393
getRandomGraphCentrality  1.292  0.034  25.739
* 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: 5 NOTEs
See
  ‘/Users/biocbuild/bbs-3.20-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-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)

Tests output

BioNAR.Rcheck/tests/testthat.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.

> 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 
 69.681   3.740 103.722 

Example timings

BioNAR.Rcheck/BioNAR-Ex.timings

nameusersystemelapsed
FitDegree 2.232 0.08113.393
addEdgeAtts17.501 2.60920.688
annotateGOont 8.967 1.28510.414
annotateGeneNames0.4650.0140.492
annotateGoBP8.1530.6038.962
annotateGoCC6.5980.4527.197
annotateGoMF6.6900.4227.256
annotatePresynaptic3.0320.1753.298
annotateSCHanno11.067 0.69911.780
annotateTopOntoOVG16.498 0.80918.260
annotateVertex0.0070.0020.009
applpMatrixToGraph0.0040.0010.005
buildNetwork0.0080.0010.010
calcAllClustering6.6480.0256.910
calcBridgeness0.1820.0050.188
calcCentrality0.2020.0030.207
calcCentralityExternalDistances1.2120.0181.278
calcCentralityInternalDistances1.1390.0071.179
calcClustering0.0070.0010.009
calcDiseasePairs0.9280.0371.084
calcEntropy19.452 0.95021.242
calcMembership0.0110.0010.011
calcReclusterMatrix0.0830.0020.086
calcSparsness8.0920.6549.520
clusterORA0.8260.0710.902
clusteringSummary21.296 0.07922.018
degreeBinnedGDAs0.5250.0150.544
escapeAnnotation0.0010.0010.002
evalCentralitySignificance1.2190.0241.285
findLCC0.0100.0020.012
getAnnotationList0.1170.0040.124
getAnnotationVertexList0.1510.0350.186
getBridgeness0.1620.0050.168
getCentralityMatrix16.502 0.75617.505
getClusterSubgraphByID0.0500.0020.051
getClustering0.0540.0010.055
getCommunityGraph0.0550.0020.057
getDType0.0000.0000.001
getDYNAMO0.0720.0030.074
getDiseases0.0010.0000.001
getEntropy18.077 1.01919.946
getEntropyRate0.0090.0010.010
getGNP0.0430.0030.057
getGraphCentralityECDF16.745 0.69617.899
getPA0.0470.0020.049
getRandomGraphCentrality 1.292 0.03425.739
getRobustness1.3220.0411.378
layoutByCluster0.2420.0030.245
layoutByRecluster0.2160.0070.223
makeConsensusMatrix1.3340.0501.505
makeMembership0.0050.0020.007
metlMatrix0.0170.0030.024
normModularity 8.624 0.72410.102
permute0.0010.0010.001
plotBridgeness0.8360.0150.953
plotEntropy18.986 0.88323.560
prepareGDA0.4840.0130.509
recluster0.0860.0050.188
removeVertexTerm0.0090.0020.011
runPermDisease10.774 0.17211.793
sampleDegBinnedGDA0.6750.0170.725
sampleGraphClust0.0580.0020.061
unescapeAnnotation0.0010.0010.002
zeroNA0.0000.0010.001