Back to Multiple platform build/check report for BioC 3.16:   simplified   long
A[B]CDEFGHIJKLMNOPQRSTUVWXYZ

This page was generated on 2023-04-12 11:05:26 -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 palomino4


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: F:\biocbuild\bbs-3.16-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:BioNAR.install-out.txt --library=F:\biocbuild\bbs-3.16-bioc\R\library --no-vignettes --timings BioNAR_1.0.0.tar.gz
StartedAt: 2023-04-10 23:23:02 -0400 (Mon, 10 Apr 2023)
EndedAt: 2023-04-10 23:31:28 -0400 (Mon, 10 Apr 2023)
EllapsedTime: 505.4 seconds
RetCode: 0
Status:   OK  
CheckDir: BioNAR.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   F:\biocbuild\bbs-3.16-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:BioNAR.install-out.txt --library=F:\biocbuild\bbs-3.16-bioc\R\library --no-vignettes --timings BioNAR_1.0.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'F:/biocbuild/bbs-3.16-bioc/meat/BioNAR.Rcheck'
* using R version 4.2.3 (2023-03-15 ucrt)
* using platform: x86_64-w64-mingw32 (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 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        37.42   0.02   37.44
plotEntropy               9.21   0.09    9.29
getEntropy                8.02   0.48    8.50
calcEntropy               8.14   0.29    8.44
calcAllClustering         7.70   0.00    7.70
annotateTopOntoOVG        6.84   0.40    7.27
runPermDisease            5.89   0.14    6.03
annotateGoBP              4.45   1.43    5.89
getGraphCentralityECDF    5.29   0.17    5.45
getCentralityMatrix       5.22   0.13    5.34
FitDegree                 1.56   0.01    6.69
getRandomGraphCentrality  0.25   0.02   15.74
* 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
  'F:/biocbuild/bbs-3.16-bioc/meat/BioNAR.Rcheck/00check.log'
for details.



Installation output

BioNAR.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   F:\biocbuild\bbs-3.16-bioc\R\bin\R.exe CMD INSTALL BioNAR
###
##############################################################################
##############################################################################


* installing to library 'F:/biocbuild/bbs-3.16-bioc/R/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 ucrt) -- "Shortstop Beagle"
Copyright (C) 2023 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64 (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] 6.164414

Slot "SDalpha":
[1] 0.1881898

[ 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 
  64.62    3.15   87.71 

Example timings

BioNAR.Rcheck/BioNAR-Ex.timings

nameusersystemelapsed
FitDegree1.560.016.69
addEdgeAtts0.080.000.08
annotateGOont3.850.474.32
annotateGeneNames0.120.030.16
annotateGoBP4.451.435.89
annotateGoCC3.580.824.41
annotateGoMF3.780.934.72
annotatePresynaptic1.610.311.94
annotateSCHanno1.800.322.26
annotateTopOntoOVG6.840.407.27
annotateVertex000
applpMatrixToGraph0.020.000.02
buildFromSynaptomeByEntrez0.580.000.57
buildFromSynaptomeGeneTable0.390.020.41
buildNetwork000
calcAllClustering7.70.07.7
calcBridgeness0.050.010.08
calcCentrality0.060.000.07
calcCentralityExternalDistances0.350.050.39
calcCentralityInternalDistances0.260.020.28
calcClustering000
calcDiseasePairs0.420.000.42
calcEntropy8.140.298.44
calcMembership0.020.000.01
calcReclusterMatrix0.010.000.02
calcSparsness0.610.000.61
clusterORA0.130.000.14
clusteringSummary37.42 0.0237.44
degreeBinnedGDAs0.150.020.17
escapeAnnotation000
evalCentralitySignificance0.440.010.46
findLCC0.020.000.01
getAnnotationList0.040.000.05
getAnnotationVertexList0.080.000.08
getBridgeness0.060.000.06
getCentralityMatrix5.220.135.34
getClusterSubgraphByID000
getClustering0.020.000.02
getCommunityGraph0.010.000.01
getDType000
getDiseases000
getEntropy8.020.488.50
getEntropyRate000
getGraphCentralityECDF5.290.175.45
getRandomGraphCentrality 0.25 0.0215.74
getRobustness0.340.030.37
layoutByCluster0.090.000.10
layoutByRecluster0.160.000.15
makeConsensusMatrix0.340.050.39
normModularity0.830.010.85
permute000
plotBridgeness0.390.050.61
plotEntropy9.210.099.29
prepareGDA0.140.000.14
recluster0.010.000.02
removeVertexTerm000
runPermDisease5.890.146.03
sampleDegBinnedGDA0.240.020.25
sampleGraphClust000
unescapeAnnotation0.010.000.02
zeroNA000