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This page was generated on 2024-12-24 11:43 -0500 (Tue, 24 Dec 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 24.04.1 LTS)x86_64R Under development (unstable) (2024-10-21 r87258) -- "Unsuffered Consequences" 4754
palomino7Windows Server 2022 Datacenterx64R Under development (unstable) (2024-10-26 r87273 ucrt) -- "Unsuffered Consequences" 4472
lconwaymacOS 12.7.1 Montereyx86_64R Under development (unstable) (2024-11-20 r87352) -- "Unsuffered Consequences" 4426
kjohnson3macOS 13.7.1 Venturaarm64R Under development (unstable) (2024-11-20 r87352) -- "Unsuffered Consequences" 4381
kunpeng2Linux (openEuler 22.03 LTS-SP1)aarch64R Under development (unstable) (2024-11-24 r87369) -- "Unsuffered Consequences" 4373
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 211/2274HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
BioNAR 1.9.1  (landing page)
Anatoly Sorokin
Snapshot Date: 2024-12-23 13:40 -0500 (Mon, 23 Dec 2024)
git_url: https://git.bioconductor.org/packages/BioNAR
git_branch: devel
git_last_commit: e9d4e8b
git_last_commit_date: 2024-12-10 21:41:23 -0500 (Tue, 10 Dec 2024)
nebbiolo1Linux (Ubuntu 24.04.1 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino7Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
lconwaymacOS 12.7.1 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kjohnson3macOS 13.7.1 Ventura / arm64  OK    OK    OK    OK  UNNEEDED, same version is already published
kunpeng2Linux (openEuler 22.03 LTS-SP1) / aarch64  OK    ERROR  skipped


CHECK results for BioNAR on lconway

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: 1.9.1
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_1.9.1.tar.gz
StartedAt: 2024-12-23 19:09:30 -0500 (Mon, 23 Dec 2024)
EndedAt: 2024-12-23 19:19:16 -0500 (Mon, 23 Dec 2024)
EllapsedTime: 585.1 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_1.9.1.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.21-bioc/meat/BioNAR.Rcheck’
* using R Under development (unstable) (2024-11-20 r87352)
* 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 ‘1.9.1’
* 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 ... INFO
  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
addEdgeAtts              10.554  3.209  14.394
clusteringSummary        13.007  0.084  13.221
calcEntropy              11.272  0.866  12.273
plotEntropy              10.709  0.959  11.816
getEntropy               10.779  0.868  11.760
annotateTopOntoOVG        9.904  0.789  10.831
getGraphCentralityECDF    9.734  0.763  10.637
getCentralityMatrix       9.575  0.732  10.385
annotateGOont             4.996  2.733  11.132
annotateSCHanno           6.519  0.755   7.441
annotateGoBP              5.149  1.468   7.243
runPermDisease            6.265  0.206   6.533
normModularity            5.390  0.775   6.216
calcSparsness             5.359  0.616   6.055
FitDegree                 1.005  0.050   6.533
getRandomGraphCentrality  0.598  0.024  12.753
* 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-3.21-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/4.5-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 Under development (unstable) (2024-11-20 r87352) -- "Unsuffered Consequences"
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 
 38.948   2.467  56.524 

Example timings

BioNAR.Rcheck/BioNAR-Ex.timings

nameusersystemelapsed
FitDegree1.0050.0506.533
addEdgeAtts10.554 3.20914.394
annotateGOont 4.996 2.73311.132
annotateGeneNames0.3310.0200.356
annotateGoBP5.1491.4687.243
annotateGoCC3.3100.6944.414
annotateGoMF4.1390.4954.748
annotatePresynaptic1.7390.2162.000
annotateSCHanno6.5190.7557.441
annotateTopOntoOVG 9.904 0.78910.831
annotateVertex0.0040.0000.006
applpMatrixToGraph0.0030.0000.003
buildNetwork0.0050.0010.005
calcAllClustering4.7150.0394.791
calcBridgeness0.0970.0060.103
calcCentrality0.1130.0030.119
calcCentralityExternalDistances0.6430.0220.672
calcCentralityInternalDistances0.6190.0090.632
calcClustering0.0040.0010.005
calcDiseasePairs0.5430.0120.559
calcEntropy11.272 0.86612.273
calcMembership0.0070.0010.008
calcReclusterMatrix0.0360.0020.038
calcSparsness5.3590.6166.055
clusterORA0.4290.0240.460
clusteringSummary13.007 0.08413.221
degreeBinnedGDAs0.3650.0400.412
escapeAnnotation0.0030.0010.005
evalCentralitySignificance0.5110.0080.521
findLCC0.0060.0020.007
getAnnotationList0.0720.0060.081
getAnnotationVertexList0.0900.0330.131
getBridgeness0.0810.0050.085
getCentralityMatrix 9.575 0.73210.385
getClusterSubgraphByID0.0250.0010.028
getClustering0.0240.0010.025
getCommunityGraph0.0280.0010.030
getDType000
getDYNAMO0.0370.0020.041
getDiseases000
getEntropy10.779 0.86811.760
getEntropyRate0.0060.0000.006
getGNP0.0230.0010.025
getGraphCentralityECDF 9.734 0.76310.637
getPA0.0250.0010.027
getRandomGraphCentrality 0.598 0.02412.753
getRobustness0.4910.0340.529
layoutByCluster0.1150.0030.118
layoutByRecluster0.1420.0060.149
makeConsensusMatrix0.4790.0320.514
makeMembership0.0020.0010.004
metlMatrix0.0070.0010.009
normModularity5.3900.7756.216
permute0.0000.0010.001
plotBridgeness0.4030.0120.418
plotEntropy10.709 0.95911.816
prepareGDA0.3380.0190.361
recluster0.0420.0020.046
removeVertexTerm0.0050.0020.007
runPermDisease6.2650.2066.533
sampleDegBinnedGDA0.3860.0110.405
sampleGraphClust0.0260.0020.030
unescapeAnnotation0.0010.0010.002
zeroNA0.0000.0000.001