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This page was generated on 2024-06-21 17:38 -0400 (Fri, 21 Jun 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 22.04.3 LTS)x86_644.4.0 (2024-04-24) -- "Puppy Cup" 4758
palomino3Windows Server 2022 Datacenterx644.4.0 (2024-04-24 ucrt) -- "Puppy Cup" 4492
merida1macOS 12.7.4 Montereyx86_644.4.0 (2024-04-24) -- "Puppy Cup" 4506
kjohnson1macOS 13.6.6 Venturaarm644.4.0 (2024-04-24) -- "Puppy Cup" 4464
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: 2024-06-19 14:00 -0400 (Wed, 19 Jun 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
palomino3Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
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 nebbiolo1

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: /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD check --install=check:BioNAR.install-out.txt --library=/home/biocbuild/bbs-3.19-bioc/R/site-library --timings BioNAR_1.6.0.tar.gz
StartedAt: 2024-06-19 21:03:57 -0400 (Wed, 19 Jun 2024)
EndedAt: 2024-06-19 21:11:13 -0400 (Wed, 19 Jun 2024)
EllapsedTime: 436.0 seconds
RetCode: 0
Status:   OK  
CheckDir: BioNAR.Rcheck
Warnings: 0

Command output

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### Running command:
###
###   /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD check --install=check:BioNAR.install-out.txt --library=/home/biocbuild/bbs-3.19-bioc/R/site-library --timings BioNAR_1.6.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.19-bioc/meat/BioNAR.Rcheck’
* using R version 4.4.0 (2024-04-24)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
    GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
* running under: Ubuntu 22.04.4 LTS
* using session charset: UTF-8
* 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 ... 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 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 loading without being on the library search path ... 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
clusteringSummary        11.008  0.008  11.016
plotEntropy               9.058  0.400   9.458
addEdgeAtts               9.151  0.168   9.320
calcEntropy               8.613  0.168   8.783
getEntropy                7.948  0.123   8.071
annotateTopOntoOVG        7.344  0.084   7.428
getGraphCentralityECDF    7.059  0.000   7.058
getCentralityMatrix       6.950  0.047   6.998
runPermDisease            5.935  0.096   6.032
getRandomGraphCentrality  0.424  0.069  11.543
* 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 re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: 3 NOTEs
See
  ‘/home/biocbuild/bbs-3.19-bioc/meat/BioNAR.Rcheck/00check.log’
for details.


Installation output

BioNAR.Rcheck/00install.out

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###
### Running command:
###
###   /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD INSTALL BioNAR
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.19-bioc/R/site-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 4.4.0 (2024-04-24) -- "Puppy Cup"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu

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 
 32.239   0.982  44.546 

Example timings

BioNAR.Rcheck/BioNAR-Ex.timings

nameusersystemelapsed
FitDegree0.7770.0484.790
addEdgeAtts9.1510.1689.320
annotateGOont4.0490.1524.201
annotateGeneNames0.2370.0000.237
annotateGoBP3.1940.0923.287
annotateGoCC2.1740.0282.202
annotateGoMF2.5910.0762.668
annotatePresynaptic0.9330.0000.933
annotateSCHanno4.8750.0334.909
annotateTopOntoOVG7.3440.0847.428
annotateVertex0.0030.0000.004
applpMatrixToGraph0.0010.0000.002
buildNetwork0.0030.0000.003
calcAllClustering4.3590.0164.374
calcBridgeness0.0620.0070.071
calcCentrality0.0360.0040.040
calcCentralityExternalDistances0.2980.0350.334
calcCentralityInternalDistances0.3090.0150.323
calcClustering0.0020.0010.003
calcDiseasePairs0.4690.0110.480
calcEntropy8.6130.1688.783
calcMembership0.0060.0000.005
calcReclusterMatrix0.0120.0040.015
calcSparsness3.9330.0123.944
clusterORA0.2970.0400.337
clusteringSummary11.008 0.00811.016
degreeBinnedGDAs0.2460.0120.258
escapeAnnotation0.0010.0000.000
evalCentralitySignificance0.3190.0380.356
findLCC0.0020.0010.004
getAnnotationList0.0630.0000.063
getAnnotationVertexList0.0710.0090.079
getBridgeness0.0530.0000.053
getCentralityMatrix6.9500.0476.998
getClusterSubgraphByID0.0040.0000.004
getClustering0.0060.0000.006
getCommunityGraph0.0040.0030.006
getDType000
getDYNAMO0.0320.0010.032
getDiseases000
getEntropy7.9480.1238.071
getEntropyRate0.0030.0000.004
getGNP0.0020.0000.002
getGraphCentralityECDF7.0590.0007.058
getPA0.0030.0000.003
getRandomGraphCentrality 0.424 0.06911.543
getRobustness0.4090.0600.469
layoutByCluster0.0880.0000.089
layoutByRecluster0.0670.0080.073
makeConsensusMatrix0.4240.0400.464
metlMatrix0.0010.0070.009
normModularity4.6330.1164.749
permute0.0000.0000.001
plotBridgeness0.3250.0280.353
plotEntropy9.0580.4009.458
prepareGDA0.2510.0080.257
recluster0.0160.0000.016
removeVertexTerm0.0020.0030.005
runPermDisease5.9350.0966.032
sampleDegBinnedGDA0.3050.0120.316
sampleGraphClust0.0080.0000.007
unescapeAnnotation0.0010.0000.001
zeroNA0.0000.0000.001