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This page was generated on 2022-01-21 13:06:23 -0500 (Fri, 21 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" 4079
machv2macOS 10.14.6 Mojavex86_644.1.2 (2021-11-01) -- "Bird Hippie" 4140
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 tokay2


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: 2022-01-20 01:55:04 -0500 (Thu, 20 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: C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:geNetClassifier.install-out.txt --library=C:\Users\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings geNetClassifier_1.34.0.tar.gz
StartedAt: 2022-01-20 20:22:58 -0500 (Thu, 20 Jan 2022)
EndedAt: 2022-01-20 20:24:54 -0500 (Thu, 20 Jan 2022)
EllapsedTime: 116.1 seconds
RetCode: 0
Status:   OK  
CheckDir: geNetClassifier.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:geNetClassifier.install-out.txt --library=C:\Users\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings geNetClassifier_1.34.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.14-bioc/meat/geNetClassifier.Rcheck'
* using R version 4.1.2 (2021-11-01)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* 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 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
* loading checks for arch 'i386'
** 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
* loading checks for arch 'x64'
** 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 ...
** running examples for arch 'i386' ... OK
** running examples for arch 'x64' ... OK
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
  Running 'runTests.R'
 OK
** running tests for arch 'x64' ...
  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

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O http://155.52.207.166/BBS/3.14/bioc/src/contrib/geNetClassifier_1.34.0.tar.gz && rm -rf geNetClassifier.buildbin-libdir && mkdir geNetClassifier.buildbin-libdir && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=geNetClassifier.buildbin-libdir geNetClassifier_1.34.0.tar.gz && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL geNetClassifier_1.34.0.zip && rm geNetClassifier_1.34.0.tar.gz geNetClassifier_1.34.0.zip
###
##############################################################################
##############################################################################


  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed

  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
100 2704k  100 2704k    0     0  6254k      0 --:--:-- --:--:-- --:--:-- 6275k

install for i386

* installing *source* package 'geNetClassifier' ...
** using staged installation
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'geNetClassifier'
    finding HTML links ... done
    GeNetClassifierReturn-class             html  
    GeneralizationError-class               html  
    GenesNetwork-class                      html  
    GenesRanking-class                      html  
    calculateGenesRanking                   html  
    externalValidation.probMatrix           html  
    externalValidation.stats                html  
    gClasses-methods                        html  
    geNetClassifier-package                 html  
    geNetClassifier                         html  
    finding level-2 HTML links ... done

    geneSymbols                             html  
    genesDetails-methods                    html  
    getEdges-methods                        html  
    getNodes-methods                        html  
    getNumEdges-methods                     html  
    getNumNodes-methods                     html  
    getRanking-methods                      html  
    getSubNetwork-methods                   html  
    getTopRanking-methods                   html  
    leukemiasClassifier                     html  
    network2txt                             html  
    numGenes-methods                        html  
    numSignificantGenes-methods             html  
    overview-methods                        html  
    plot.GeNetClassifierReturn              html  
    plot.GenesRanking                       html  
    plotAssignments                         html  
    plotDiscriminantPower                   html  
    plotExpressionProfiles                  html  
    plotNetwork                             html  
    queryGeNetClassifier                    html  
    querySummary                            html  
    setProperties-methods                   html  
** 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

install for x64

* installing *source* package 'geNetClassifier' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'geNetClassifier' as geNetClassifier_1.34.0.zip
* DONE (geNetClassifier)
* installing to library 'C:/Users/biocbuild/bbs-3.14-bioc/R/library'
package 'geNetClassifier' successfully unpacked and MD5 sums checked

Tests output

geNetClassifier.Rcheck/tests_i386/runTests.Rout


R version 4.1.2 (2021-11-01) -- "Bird Hippie"
Copyright (C) 2021 The R Foundation for Statistical Computing
Platform: i386-w64-mingw32/i386 (32-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")'.

20:24:44 - 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 -- Thu Jan 20 20:24:44 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 
   1.25    0.07    1.31 

geNetClassifier.Rcheck/tests_x64/runTests.Rout


R version 4.1.2 (2021-11-01) -- "Bird Hippie"
Copyright (C) 2021 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.

> 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")'.

20:24:46 - 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 -- Thu Jan 20 20:24:46 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 
   1.23    0.10    1.32 

Example timings

geNetClassifier.Rcheck/examples_i386/geNetClassifier-Ex.timings

nameusersystemelapsed
GeNetClassifierReturn-class1.030.031.42
GeneralizationError-class0.530.000.54
GenesNetwork-class2.940.923.88
GenesRanking-class0.670.030.70
calculateGenesRanking0.590.000.59
externalValidation.probMatrix0.700.020.72
externalValidation.stats0.570.000.56
gClasses-methods0.310.000.32
geNetClassifier0.140.010.15
geneSymbols0.080.000.08
genesDetails-methods0.390.000.39
getEdges-methods0.340.000.35
getNodes-methods0.330.020.34
getNumEdges-methods0.310.000.33
getNumNodes-methods0.330.000.33
getRanking-methods0.310.000.31
getSubNetwork-methods0.280.020.29
getTopRanking-methods0.280.010.30
leukemiasClassifier0.300.020.31
network2txt0.550.000.55
numGenes-methods0.280.010.29
numSignificantGenes-methods0.280.000.28
overview-methods0.280.030.32
plot.GeNetClassifierReturn2.890.163.04
plot.GenesRanking0.480.020.50
plotAssignments0.680.000.68
plotDiscriminantPower1.010.001.01
plotExpressionProfiles1.110.041.16
plotNetwork2.610.002.61
queryGeNetClassifier0.810.050.86
querySummary0.600.020.61

geNetClassifier.Rcheck/examples_x64/geNetClassifier-Ex.timings

nameusersystemelapsed
GeNetClassifierReturn-class0.660.030.68
GeneralizationError-class0.640.010.66
GenesNetwork-class2.000.913.10
GenesRanking-class0.670.050.72
calculateGenesRanking0.590.030.63
externalValidation.probMatrix0.530.020.55
externalValidation.stats0.490.020.50
gClasses-methods0.230.000.24
geNetClassifier0.110.030.14
geneSymbols0.060.000.06
genesDetails-methods0.300.010.31
getEdges-methods0.250.000.25
getNodes-methods0.240.000.24
getNumEdges-methods0.200.030.23
getNumNodes-methods0.220.040.25
getRanking-methods0.230.010.25
getSubNetwork-methods0.250.000.25
getTopRanking-methods0.420.020.44
leukemiasClassifier0.360.010.37
network2txt0.550.020.56
numGenes-methods0.280.000.29
numSignificantGenes-methods0.270.010.28
overview-methods0.280.000.28
plot.GeNetClassifierReturn3.260.133.40
plot.GenesRanking0.350.000.35
plotAssignments0.530.000.53
plotDiscriminantPower0.670.010.70
plotExpressionProfiles0.750.040.78
plotNetwork2.380.042.44
queryGeNetClassifier0.730.020.75
querySummary0.50.00.5