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This page was generated on 2024-06-11 15:40 -0400 (Tue, 11 Jun 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 22.04.3 LTS)x86_644.4.0 RC (2024-04-16 r86468) -- "Puppy Cup" 4679
palomino4Windows Server 2022 Datacenterx644.4.0 RC (2024-04-16 r86468 ucrt) -- "Puppy Cup" 4414
merida1macOS 12.7.4 Montereyx86_644.4.0 Patched (2024-04-24 r86482) -- "Puppy Cup" 4441
kjohnson1macOS 13.6.6 Venturaarm644.4.0 Patched (2024-04-24 r86482) -- "Puppy Cup" 4394
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 209/2239HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
BioNAR 1.7.0  (landing page)
Anatoly Sorokin
Snapshot Date: 2024-06-09 14:00 -0400 (Sun, 09 Jun 2024)
git_url: https://git.bioconductor.org/packages/BioNAR
git_branch: devel
git_last_commit: 8a620ea
git_last_commit_date: 2024-04-30 11:45:27 -0400 (Tue, 30 Apr 2024)
nebbiolo2Linux (Ubuntu 22.04.3 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino4Windows 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 palomino4

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: 1.7.0
Command: F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:BioNAR.install-out.txt --library=F:\biocbuild\bbs-3.20-bioc\R\library --no-vignettes --timings BioNAR_1.7.0.tar.gz
StartedAt: 2024-06-10 00:22:20 -0400 (Mon, 10 Jun 2024)
EndedAt: 2024-06-10 00:30:58 -0400 (Mon, 10 Jun 2024)
EllapsedTime: 517.6 seconds
RetCode: 0
Status:   OK  
CheckDir: BioNAR.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:BioNAR.install-out.txt --library=F:\biocbuild\bbs-3.20-bioc\R\library --no-vignettes --timings BioNAR_1.7.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'F:/biocbuild/bbs-3.20-bioc/meat/BioNAR.Rcheck'
* using R version 4.4.0 RC (2024-04-16 r86468 ucrt)
* using platform: x86_64-w64-mingw32
* R was compiled by
    gcc.exe (GCC) 13.2.0
    GNU Fortran (GCC) 13.2.0
* running under: Windows Server 2022 x64 (build 20348)
* using session charset: UTF-8
* using option '--no-vignettes'
* checking for file 'BioNAR/DESCRIPTION' ... OK
* this is package 'BioNAR' version '1.7.0'
* 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 whether package 'BioNAR' can be installed ... OK
* checking installed package size ... NOTE
  installed size is  6.8Mb
  sub-directories of 1Mb or more:
    extdata   6.0Mb
* 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
clusteringSummary        39.02   0.02   39.05
plotEntropy              11.98   1.67   13.65
calcEntropy              11.44   1.21   12.64
getEntropy               10.53   1.85   12.38
getGraphCentralityECDF    9.48   1.36   10.86
annotateTopOntoOVG        9.83   0.87   10.72
addEdgeAtts              10.41   0.17   10.58
getCentralityMatrix       8.21   1.24    9.43
calcAllClustering         7.77   0.00    7.78
runPermDisease            6.81   0.25    7.07
annotateSCHanno           5.86   0.71    6.58
normModularity            4.98   0.92    5.91
annotateGOont             5.32   0.47    7.28
calcSparsness             4.61   0.89    5.50
annotateGoBP              4.90   0.40    5.34
FitDegree                 1.06   0.05    7.85
getRandomGraphCentrality  0.47   0.01   18.22
* 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
  'F:/biocbuild/bbs-3.20-bioc/meat/BioNAR.Rcheck/00check.log'
for details.


Installation output

BioNAR.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD INSTALL BioNAR
###
##############################################################################
##############################################################################


* installing to library 'F:/biocbuild/bbs-3.20-bioc/R/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 RC (2024-04-16 r86468 ucrt) -- "Puppy Cup"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64

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 
  63.78    2.56   83.73 

Example timings

BioNAR.Rcheck/BioNAR-Ex.timings

nameusersystemelapsed
FitDegree1.060.057.85
addEdgeAtts10.41 0.1710.58
annotateGOont5.320.477.28
annotateGeneNames0.250.020.55
annotateGoBP4.900.405.34
annotateGoCC3.990.524.50
annotateGoMF4.120.584.73
annotatePresynaptic1.440.341.82
annotateSCHanno5.860.716.58
annotateTopOntoOVG 9.83 0.8710.72
annotateVertex0.010.000.01
applpMatrixToGraph000
buildNetwork000
calcAllClustering7.770.007.78
calcBridgeness0.090.010.11
calcCentrality0.060.020.25
calcCentralityExternalDistances0.430.030.45
calcCentralityInternalDistances0.340.000.35
calcClustering000
calcDiseasePairs0.510.010.53
calcEntropy11.44 1.2112.64
calcMembership0.010.000.02
calcReclusterMatrix0.020.000.01
calcSparsness4.610.895.50
clusterORA0.350.040.42
clusteringSummary39.02 0.0239.05
degreeBinnedGDAs0.330.020.34
escapeAnnotation000
evalCentralitySignificance0.330.030.36
findLCC0.000.010.02
getAnnotationList0.110.000.11
getAnnotationVertexList0.120.020.14
getBridgeness0.090.010.11
getCentralityMatrix8.211.249.43
getClusterSubgraphByID000
getClustering0.000.010.02
getCommunityGraph0.010.000.01
getDType000
getDYNAMO0.050.000.05
getDiseases000
getEntropy10.53 1.8512.38
getEntropyRate0.020.000.01
getGNP000
getGraphCentralityECDF 9.48 1.3610.86
getPA000
getRandomGraphCentrality 0.47 0.0118.22
getRobustness0.650.080.73
layoutByCluster0.110.000.11
layoutByRecluster0.060.000.06
makeConsensusMatrix0.520.000.52
metlMatrix0.020.000.01
normModularity4.980.925.91
permute000
plotBridgeness0.440.000.44
plotEntropy11.98 1.6713.65
prepareGDA0.240.020.25
recluster0.010.000.02
removeVertexTerm0.000.020.01
runPermDisease6.810.257.07
sampleDegBinnedGDA0.320.060.37
sampleGraphClust0.010.000.02
unescapeAnnotation000
zeroNA000