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This page was generated on 2023-05-31 05:44:30 -0000 (Wed, 31 May 2023).

HostnameOSArch (*)R versionInstalled pkgs
kunpeng1Linux (Ubuntu 22.04.1 LTS)aarch644.3.0 (2023-04-21) -- "Already Tomorrow" 4219
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CHECK results for BioNAR on kunpeng1


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.

Note: If "R CMD check" recently failed on the Linux builder over a missing dependency, add the missing dependency to "Suggests" in your DESCRIPTION file. See the Renviron.bioc for details.

raw results

Package 206/2197HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
BioNAR 1.3.0  (landing page)
Anatoly Sorokin
Snapshot Date: 2023-05-29 10:19:22 -0000 (Mon, 29 May 2023)
git_url: https://git.bioconductor.org/packages/BioNAR
git_branch: devel
git_last_commit: c21e57f
git_last_commit_date: 2023-04-26 02:05:33 -0000 (Wed, 26 Apr 2023)
kunpeng1Linux (Ubuntu 22.04.1 LTS) / aarch64  OK    OK    OK  

Summary

Package: BioNAR
Version: 1.3.0
Command: /home/biocbuild/R/R-4.3.0/bin/R CMD check --install=check:BioNAR.install-out.txt --library=/home/biocbuild/R/R-4.3.0/site-library --timings BioNAR_1.3.0.tar.gz
StartedAt: 2023-05-30 01:56:13 -0000 (Tue, 30 May 2023)
EndedAt: 2023-05-30 02:08:43 -0000 (Tue, 30 May 2023)
EllapsedTime: 749.7 seconds
RetCode: 0
Status:   OK  
CheckDir: BioNAR.Rcheck
Warnings: 0

Command output

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###
### Running command:
###
###   /home/biocbuild/R/R-4.3.0/bin/R CMD check --install=check:BioNAR.install-out.txt --library=/home/biocbuild/R/R-4.3.0/site-library --timings BioNAR_1.3.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.18-bioc/meat/BioNAR.Rcheck’
* using R version 4.3.0 (2023-04-21)
* using platform: aarch64-unknown-linux-gnu (64-bit)
* R was compiled by
    gcc (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0
    GNU Fortran (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0
* running under: Ubuntu 22.04.2 LTS
* using session charset: UTF-8
* checking for file ‘BioNAR/DESCRIPTION’ ... OK
* this is package ‘BioNAR’ version ‘1.3.0’
* 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  6.7Mb
  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 R 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 ... OK
* 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 files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                           user system elapsed
clusteringSummary        13.783  0.024  13.808
plotEntropy              12.344  0.096  12.440
calcEntropy              11.376  0.060  11.437
getEntropy               11.044  0.076  11.121
getGraphCentralityECDF   10.268  0.060  10.328
getCentralityMatrix       9.530  0.012   9.543
runPermDisease            7.953  0.000   7.952
annotateTopOntoOVG        6.760  0.024   6.785
annotateGoBP              5.718  0.040   5.759
annotateGOont             5.406  0.172   5.579
calcAllClustering         5.119  0.012   5.133
FitDegree                 2.044  0.027   8.608
getRandomGraphCentrality  0.462  0.020  15.336
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’
 OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ...
  ‘BioNAR_overview.Rmd’ using ‘UTF-8’... OK
 NONE
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: 3 NOTEs
See
  ‘/home/biocbuild/bbs-3.18-bioc/meat/BioNAR.Rcheck/00check.log’
for details.



Installation output

BioNAR.Rcheck/00install.out

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###
### Running command:
###
###   /home/biocbuild/R/R-4.3.0/bin/R CMD INSTALL BioNAR
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/R/R-4.3.0/site-library’
* installing *source* package ‘BioNAR’ ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
Using 'localHub=TRUE'
  If offline, please also see BiocManager vignette section on offline use
loading from cache
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
Using 'localHub=TRUE'
  If offline, please also see BiocManager vignette section on offline use
loading from cache
** testing if installed package can be loaded from final location
Using 'localHub=TRUE'
  If offline, please also see BiocManager vignette section on offline use
loading from cache
** testing if installed package keeps a record of temporary installation path
* DONE (BioNAR)

Tests output

BioNAR.Rcheck/tests/testthat.Rout


R version 4.3.0 (2023-04-21) -- "Already Tomorrow"
Copyright (C) 2023 The R Foundation for Statistical Computing
Platform: aarch64-unknown-linux-gnu (64-bit)

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


Using 'localHub=TRUE'
  If offline, please also see BiocManager vignette section on offline use
loading from cache

Attaching package: 'BioNAR'

The following object is masked from 'package:igraph':

    permute

> 
> test_check("BioNAR")
Loading required package: synaptome.data
Loading required package: AnnotationHub
Loading required package: BiocGenerics

Attaching package: 'BiocGenerics'

The following objects are masked from 'package:igraph':

    normalize, path, union

The following objects are masked from 'package:stats':

    IQR, mad, sd, var, xtabs

The following objects are masked from 'package:base':

    Filter, Find, Map, Position, Reduce, anyDuplicated, aperm, append,
    as.data.frame, basename, cbind, colnames, dirname, do.call,
    duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
    lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin,
    pmin.int, rank, rbind, rownames, sapply, setdiff, sort, table,
    tapply, union, unique, unsplit, which.max, which.min

Loading required package: BiocFileCache
Loading required package: dbplyr
[ FAIL 0 | WARN 0 | SKIP 2 | PASS 109 ]

══ Skipped tests ═══════════════════════════════════════════════════════════════
• On CRAN (2)

[ FAIL 0 | WARN 0 | SKIP 2 | PASS 109 ]
Deleting unused snapshots:
• bridgeness/entropyplot.svg
• fitdegree/powerfitplot.svg
> 
> proc.time()
   user  system elapsed 
 48.129   1.979  67.302 

Example timings

BioNAR.Rcheck/BioNAR-Ex.timings

nameusersystemelapsed
FitDegree2.0440.0278.608
addEdgeAtts0.0730.0040.077
annotateGOont5.4060.1725.579
annotateGeneNames0.2640.0040.268
annotateGoBP5.7180.0405.759
annotateGoCC4.1900.0004.191
annotateGoMF4.7990.0124.812
annotatePresynaptic1.9110.0001.912
annotateSCHanno2.3720.0202.451
annotateTopOntoOVG6.7600.0246.785
annotateVertex0.0050.0000.005
applpMatrixToGraph0.0020.0000.002
buildFromSynaptomeByEntrez0.700.020.72
buildFromSynaptomeGeneTable0.5230.0040.526
buildNetwork0.0000.0030.004
calcAllClustering5.1190.0125.133
calcBridgeness0.1100.0120.123
calcCentrality0.0810.0000.082
calcCentralityExternalDistances0.5650.0160.581
calcCentralityInternalDistances0.5150.0040.518
calcClustering0.0070.0000.007
calcDiseasePairs0.6030.0280.631
calcEntropy11.376 0.06011.437
calcMembership0.0080.0120.020
calcReclusterMatrix0.0150.0000.015
calcSparsness0.6890.0080.698
clusterORA0.4030.0130.418
clusteringSummary13.783 0.02413.808
degreeBinnedGDAs0.3290.0080.337
escapeAnnotation0.0010.0000.001
evalCentralitySignificance0.5160.0040.520
findLCC0.0050.0000.005
getAnnotationList0.0700.0040.074
getAnnotationVertexList0.0840.0080.092
getBridgeness0.0950.0040.098
getCentralityMatrix9.5300.0129.543
getClusterSubgraphByID0.0060.0000.005
getClustering0.0150.0040.018
getCommunityGraph0.0090.0000.010
getDType0.0010.0000.000
getDiseases0.0000.0000.001
getEntropy11.044 0.07611.121
getEntropyRate0.0090.0000.009
getGraphCentralityECDF10.268 0.06010.328
getRandomGraphCentrality 0.462 0.02015.336
getRobustness0.7330.0080.740
layoutByCluster0.2360.0000.236
layoutByRecluster0.4850.0000.485
makeConsensusMatrix0.7210.0200.742
normModularity1.0350.0081.043
permute0.0000.0000.001
plotBridgeness0.5750.0050.580
plotEntropy12.344 0.09612.440
prepareGDA0.280.000.28
recluster0.0140.0000.013
removeVertexTerm0.0020.0000.002
runPermDisease7.9530.0007.952
sampleDegBinnedGDA0.4120.0040.416
sampleGraphClust0.010.000.01
unescapeAnnotation0.0010.0000.001
zeroNA0.0010.0000.000