Back to Multiple platform build/check report for BioC 3.16:   simplified   long
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This page was generated on 2023-04-12 11:06:01 -0400 (Wed, 12 Apr 2023).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 20.04.5 LTS)x86_644.2.3 (2023-03-15) -- "Shortstop Beagle" 4502
palomino4Windows Server 2022 Datacenterx644.2.3 (2023-03-15 ucrt) -- "Shortstop Beagle" 4282
lconwaymacOS 12.5.1 Montereyx86_644.2.3 (2023-03-15) -- "Shortstop Beagle" 4310
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

CHECK results for BioNAR on lconway


To the developers/maintainers of the BioNAR package:
- Please 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 How and When does the builder pull? When will my changes propagate? for more information.
- Make sure to use the following settings in order to reproduce any error or warning you see on this page.

raw results

Package 195/2183HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
BioNAR 1.0.0  (landing page)
Anatoly Sorokin
Snapshot Date: 2023-04-10 14:00:05 -0400 (Mon, 10 Apr 2023)
git_url: https://git.bioconductor.org/packages/BioNAR
git_branch: RELEASE_3_16
git_last_commit: f9c6c3c
git_last_commit_date: 2022-11-01 11:27:44 -0400 (Tue, 01 Nov 2022)
nebbiolo2Linux (Ubuntu 20.04.5 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
lconwaymacOS 12.5.1 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: BioNAR
Version: 1.0.0
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_1.0.0.tar.gz
StartedAt: 2023-04-10 19:04:35 -0400 (Mon, 10 Apr 2023)
EndedAt: 2023-04-10 19:11:07 -0400 (Mon, 10 Apr 2023)
EllapsedTime: 392.7 seconds
RetCode: 0
Status:   OK  
CheckDir: BioNAR.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### 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_1.0.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.16-bioc/meat/BioNAR.Rcheck’
* using R version 4.2.3 (2023-03-15)
* using platform: x86_64-apple-darwin17.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘BioNAR/DESCRIPTION’ ... OK
* this is package ‘BioNAR’ version ‘1.0.0’
* 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 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 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.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* 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        9.992  0.070  10.122
plotEntropy              7.899  0.758   8.778
calcEntropy              7.401  0.886   8.346
getEntropy               6.779  0.721   7.545
runPermDisease           5.837  0.156   6.031
getGraphCentralityECDF   4.931  0.151   5.101
getCentralityMatrix      4.894  0.166   5.117
annotateGOont            4.164  0.888   5.427
FitDegree                1.402  0.052   6.308
getRandomGraphCentrality 0.289  0.022  10.676
* 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 ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 1 NOTE
See
  ‘/Users/biocbuild/bbs-3.16-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/4.2/Resources/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
snapshotDate(): 2023-04-06
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
snapshotDate(): 2023-04-06
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
snapshotDate(): 2023-04-06
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 4.2.3 (2023-03-15) -- "Shortstop Beagle"
Copyright (C) 2023 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin17.0 (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
snapshotDate(): 2023-04-06
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
An object of class "law"
Slot "fit":
Reference class object of class "displ" 
Field "xmin": 
[1] 11
Field "pars": 
[1] 2.634402
Field "no_pars": 
[1] 1

Slot "p":
[1] 0.4

Slot "alpha":
[1] 2.634402

Slot "SDxmin":
[1] 0.8944272

Slot "SDalpha":
[1] 0.08737987

[ FAIL 0 | WARN 15 | SKIP 4 | PASS 104 ]

══ Skipped tests ═══════════════════════════════════════════════════════════════
• On CRAN (4)

[ FAIL 0 | WARN 15 | SKIP 4 | PASS 104 ]
> 
> proc.time()
   user  system elapsed 
 36.921   2.782  54.634 

Example timings

BioNAR.Rcheck/BioNAR-Ex.timings

nameusersystemelapsed
FitDegree1.4020.0526.308
addEdgeAtts0.0640.0040.073
annotateGOont4.1640.8885.427
annotateGeneNames0.1540.0050.164
annotateGoBP4.0070.6634.724
annotateGoCC2.9010.5593.532
annotateGoMF3.3310.6454.031
annotatePresynaptic1.2390.3231.626
annotateSCHanno1.6030.3002.453
annotateTopOntoOVG4.4250.4624.959
annotateVertex0.0050.0010.005
applpMatrixToGraph0.0020.0010.003
buildFromSynaptomeByEntrez0.5390.0200.564
buildFromSynaptomeGeneTable0.3560.0150.381
buildNetwork0.0030.0010.003
calcAllClustering3.6840.0243.739
calcBridgeness0.0700.0070.106
calcCentrality0.0500.0020.052
calcCentralityExternalDistances0.3780.0140.399
calcCentralityInternalDistances0.3090.0050.316
calcClustering0.0030.0010.004
calcDiseasePairs0.3570.0090.366
calcEntropy7.4010.8868.346
calcMembership0.0130.0150.028
calcReclusterMatrix0.0080.0020.034
calcSparsness0.5300.0250.561
clusterORA0.1400.0220.244
clusteringSummary 9.992 0.07010.122
degreeBinnedGDAs0.1770.0070.217
escapeAnnotation0.0000.0000.002
evalCentralitySignificance0.2990.0060.363
findLCC0.0040.0010.006
getAnnotationList0.0500.0050.056
getAnnotationVertexList0.0620.0160.091
getBridgeness0.0580.0060.063
getCentralityMatrix4.8940.1665.117
getClusterSubgraphByID0.0030.0010.004
getClustering0.0120.0140.026
getCommunityGraph0.0050.0010.006
getDType000
getDiseases000
getEntropy6.7790.7217.545
getEntropyRate0.0050.0050.009
getGraphCentralityECDF4.9310.1515.101
getRandomGraphCentrality 0.289 0.02210.676
getRobustness0.4570.0540.526
layoutByCluster0.0550.0060.061
layoutByRecluster0.1030.0100.113
makeConsensusMatrix0.3400.0290.371
normModularity1.4090.0801.497
permute0.0000.0010.000
plotBridgeness0.3300.0160.360
plotEntropy7.8990.7588.778
prepareGDA0.1740.0070.183
recluster0.0080.0020.009
removeVertexTerm0.0020.0010.003
runPermDisease5.8370.1566.031
sampleDegBinnedGDA0.2340.0050.239
sampleGraphClust0.0040.0000.005
unescapeAnnotation0.0000.0010.001
zeroNA0.0000.0010.001