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This page was generated on 2022-01-24 13:05:07 -0500 (Mon, 24 Jan 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 20.04.4 LTS)x86_644.1.2 (2021-11-01) -- "Bird Hippie" 4329
tokay2Windows Server 2012 R2 Standardx644.1.2 (2021-11-01) -- "Bird Hippie" 4080
machv2macOS 10.14.6 Mojavex86_644.1.2 (2021-11-01) -- "Bird Hippie" 4141
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 geNetClassifier on nebbiolo2


To the developers/maintainers of the geNetClassifier package:
- Please 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 How and When does the builder pull? When will my changes propagate? here 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 737/2083HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
geNetClassifier 1.34.0  (landing page)
Sara Aibar
Snapshot Date: 2022-01-23 01:55:04 -0500 (Sun, 23 Jan 2022)
git_url: https://git.bioconductor.org/packages/geNetClassifier
git_branch: RELEASE_3_14
git_last_commit: 2aec9d0
git_last_commit_date: 2021-10-26 12:07:41 -0500 (Tue, 26 Oct 2021)
nebbiolo2Linux (Ubuntu 20.04.4 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
tokay2Windows Server 2012 R2 Standard / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
machv2macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: geNetClassifier
Version: 1.34.0
Command: /home/biocbuild/bbs-3.14-bioc/R/bin/R CMD check --install=check:geNetClassifier.install-out.txt --library=/home/biocbuild/bbs-3.14-bioc/R/library --no-vignettes --timings geNetClassifier_1.34.0.tar.gz
StartedAt: 2022-01-23 07:51:08 -0500 (Sun, 23 Jan 2022)
EndedAt: 2022-01-23 07:52:22 -0500 (Sun, 23 Jan 2022)
EllapsedTime: 73.9 seconds
RetCode: 0
Status:   OK  
CheckDir: geNetClassifier.Rcheck
Warnings: 0

Command output

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###
### Running command:
###
###   /home/biocbuild/bbs-3.14-bioc/R/bin/R CMD check --install=check:geNetClassifier.install-out.txt --library=/home/biocbuild/bbs-3.14-bioc/R/library --no-vignettes --timings geNetClassifier_1.34.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.14-bioc/meat/geNetClassifier.Rcheck’
* using R version 4.1.2 (2021-11-01)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘geNetClassifier/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘geNetClassifier’ version ‘1.34.0’
* 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 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 ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: OK


Installation output

geNetClassifier.Rcheck/00install.out

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###
### Running command:
###
###   /home/biocbuild/bbs-3.14-bioc/R/bin/R CMD INSTALL geNetClassifier
###
##############################################################################
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* installing to library ‘/home/biocbuild/bbs-3.14-bioc/R/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 4.1.2 (2021-11-01) -- "Bird Hippie"
Copyright (C) 2021 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, 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")'.

07:52:16 - 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 -- Sun Jan 23 07:52:16 2022 
*********************************************** 
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 
  1.766   0.120   1.869 

Example timings

geNetClassifier.Rcheck/geNetClassifier-Ex.timings

nameusersystemelapsed
GeNetClassifierReturn-class1.1270.0881.215
GeneralizationError-class0.6530.0120.664
GenesNetwork-class2.2430.2652.512
GenesRanking-class0.5390.0410.578
calculateGenesRanking0.6440.0200.662
externalValidation.probMatrix0.7520.0240.775
externalValidation.stats0.8550.0360.889
gClasses-methods0.3520.0160.368
geNetClassifier0.2110.0120.223
geneSymbols0.1160.0000.116
genesDetails-methods0.5050.1360.640
getEdges-methods0.3780.0150.393
getNodes-methods0.3930.0040.397
getNumEdges-methods0.3840.0160.399
getNumNodes-methods0.4200.0040.424
getRanking-methods0.3990.0120.411
getSubNetwork-methods0.2580.0040.262
getTopRanking-methods0.4250.0240.449
leukemiasClassifier0.2760.0000.275
network2txt0.2890.0120.300
numGenes-methods0.2360.0040.241
numSignificantGenes-methods0.2340.0120.246
overview-methods0.2730.0040.276
plot.GeNetClassifierReturn3.9040.1304.039
plot.GenesRanking0.4510.0040.454
plotAssignments0.5530.0120.563
plotDiscriminantPower0.6500.0440.689
plotExpressionProfiles1.0440.0601.100
plotNetwork1.7750.0521.819
queryGeNetClassifier0.8190.0280.844
querySummary0.7640.0080.771