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This page was generated on 2024-02-22 11:35:57 -0500 (Thu, 22 Feb 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 22.04.3 LTS)x86_644.3.2 Patched (2023-11-13 r85521) -- "Eye Holes" 4691
palomino4Windows Server 2022 Datacenterx644.3.2 (2023-10-31 ucrt) -- "Eye Holes" 4444
lconwaymacOS 12.7.1 Montereyx86_644.3.2 Patched (2023-11-01 r85457) -- "Eye Holes" 4465
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 808/2266HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
geNetClassifier 1.42.0  (landing page)
Sara Aibar
Snapshot Date: 2024-02-21 14:05:05 -0500 (Wed, 21 Feb 2024)
git_url: https://git.bioconductor.org/packages/geNetClassifier
git_branch: RELEASE_3_18
git_last_commit: d1bee03
git_last_commit_date: 2023-10-24 09:53:42 -0500 (Tue, 24 Oct 2023)
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
lconwaymacOS 12.7.1 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kjohnson1macOS 13.6.1 Ventura / arm64see weekly results here

CHECK results for geNetClassifier on nebbiolo2


To the developers/maintainers of the geNetClassifier package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/geNetClassifier.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: geNetClassifier
Version: 1.42.0
Command: /home/biocbuild/bbs-3.18-bioc/R/bin/R CMD check --install=check:geNetClassifier.install-out.txt --library=/home/biocbuild/bbs-3.18-bioc/R/site-library --timings geNetClassifier_1.42.0.tar.gz
StartedAt: 2024-02-21 22:33:59 -0500 (Wed, 21 Feb 2024)
EndedAt: 2024-02-21 22:34:57 -0500 (Wed, 21 Feb 2024)
EllapsedTime: 58.2 seconds
RetCode: 0
Status:   OK  
CheckDir: geNetClassifier.Rcheck
Warnings: 0

Command output

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### Running command:
###
###   /home/biocbuild/bbs-3.18-bioc/R/bin/R CMD check --install=check:geNetClassifier.install-out.txt --library=/home/biocbuild/bbs-3.18-bioc/R/site-library --timings geNetClassifier_1.42.0.tar.gz
###
##############################################################################
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* using log directory ‘/home/biocbuild/bbs-3.18-bioc/meat/geNetClassifier.Rcheck’
* using R version 4.3.2 Patched (2023-11-13 r85521)
* using platform: x86_64-pc-linux-gnu (64-bit)
* 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 22.04.3 LTS
* using session charset: UTF-8
* checking for file ‘geNetClassifier/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘geNetClassifier’ version ‘1.42.0’
* 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 ‘geNetClassifier’ 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 loading without being on the library search path ... OK
* checking dependencies in R code ... OK
* 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 contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘runTests.R’
 OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ...
  ‘geNetClassifier-vignette.Rnw’... OK
 OK
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: OK


Installation output

geNetClassifier.Rcheck/00install.out

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###
### Running command:
###
###   /home/biocbuild/bbs-3.18-bioc/R/bin/R CMD INSTALL geNetClassifier
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.18-bioc/R/site-library’
* installing *source* package ‘geNetClassifier’ ...
** using staged installation
** R
** data
** 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 (geNetClassifier)

Tests output

geNetClassifier.Rcheck/tests/runTests.Rout


R version 4.3.2 Patched (2023-11-13 r85521) -- "Eye Holes"
Copyright (C) 2023 The R Foundation for Statistical Computing
Platform: x86_64-pc-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.

> BiocGenerics:::testPackage("geNetClassifier")

Attaching package: 'BiocGenerics'

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

Welcome to Bioconductor

    Vignettes contain introductory material; view with
    'browseVignettes()'. To cite Bioconductor, see
    'citation("Biobase")', and for packages 'citation("pkgname")'.

22:34:45 - Filtering data and calculating the genes ranking...
Warning in plotExpressionProfiles(eset = myEset, genes = rownames(myEset),  :
  The argument 'sampleLabels' had to be converted into a factor.
Warning in plotExpressionProfiles(eset = myEset, genes = rownames(myEset),  :
  The data labels vector is not named, it will be assumed the labels are in order: the first label applies to the first sample... 


RUNIT TEST PROTOCOL -- Wed Feb 21 22:34:45 2024 
*********************************************** 
Number of test functions: 3 
Number of errors: 0 
Number of failures: 0 

 
1 Test Suite : 
geNetClassifier RUnit Tests - 3 test functions, 0 errors, 0 failures
Number of test functions: 3 
Number of errors: 0 
Number of failures: 0 
Warning messages:
1: In geNetClassifier(matrix(sample(50000, 5 * 2), 5, 2), c(rep("one",  :
  The argument 'classification sampleLabels' had to be converted into a factor.
2: In geNetClassifier(matrix(sample(50000, 5 * 3), 5, 3), c(rep("one",  :
  The argument 'classification sampleLabels' had to be converted into a factor.
3: In geNetClassifier(matrix(sample(50000, 5 * 3), 5, 3), c(rep("one",  :
  The data labels vector is not named, it is assumed the labels are in order: the first label applies to the first sample... 
4: In geNetClassifier(matrix(sample(50000, 5 * 3), 5, 3), c(rep("one",  :
  It is recommended to have the *same* number of samples in each class in order to obtain balanced external validation stats.
> 
> proc.time()
   user  system elapsed 
  0.869   0.081   0.939 

Example timings

geNetClassifier.Rcheck/geNetClassifier-Ex.timings

nameusersystemelapsed
GeNetClassifierReturn-class0.5260.0360.563
GeneralizationError-class0.3590.0170.375
GenesNetwork-class0.3930.0080.401
GenesRanking-class0.4740.0240.497
calculateGenesRanking0.3840.0160.400
externalValidation.probMatrix0.5100.0080.519
externalValidation.stats0.5610.0080.568
gClasses-methods0.2300.0040.234
geNetClassifier0.1260.0030.129
geneSymbols0.0760.0000.077
genesDetails-methods0.3190.0040.322
getEdges-methods0.2510.0000.251
getNodes-methods0.2420.0030.247
getNumEdges-methods0.2480.0000.248
getNumNodes-methods0.2560.0000.256
getRanking-methods0.2510.0080.260
getSubNetwork-methods0.2510.0080.258
getTopRanking-methods0.2530.0040.257
leukemiasClassifier0.2650.0040.269
network2txt0.3060.0000.305
numGenes-methods0.2550.0000.255
numSignificantGenes-methods0.2580.0000.258
overview-methods0.2770.0040.281
plot.GeNetClassifierReturn0.6770.0240.693
plot.GenesRanking0.2650.0040.269
plotAssignments0.5170.0080.524
plotDiscriminantPower0.5890.0880.676
plotExpressionProfiles0.7220.0520.775
plotNetwork0.3120.0240.336
queryGeNetClassifier0.6340.0200.654
querySummary0.5090.0080.517