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This page was generated on 2023-01-02 09:00:31 -0500 (Mon, 02 Jan 2023).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| palomino5 | Windows Server 2022 Datacenter | x64 | R Under development (unstable) (2022-12-25 r83502 ucrt) -- "Unsuffered Consequences" | 4165 |
| 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 | ||||
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To the developers/maintainers of the geNetClassifier package: Make sure to use the following settings in order to reproduce any error or warning you see on this page. |
| Package 758/2158 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| geNetClassifier 1.39.0 (landing page) Sara Aibar
| palomino5 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | ||||||||
| Package: geNetClassifier |
| Version: 1.39.0 |
| Command: F:\biocbuild\bbs-3.17-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:geNetClassifier.install-out.txt --library=F:\biocbuild\bbs-3.17-bioc\R\library --no-vignettes --timings geNetClassifier_1.39.0.tar.gz |
| StartedAt: 2022-12-29 00:03:03 -0500 (Thu, 29 Dec 2022) |
| EndedAt: 2022-12-29 00:04:10 -0500 (Thu, 29 Dec 2022) |
| EllapsedTime: 66.8 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: geNetClassifier.Rcheck |
| Warnings: 0 |
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### Running command:
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### F:\biocbuild\bbs-3.17-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:geNetClassifier.install-out.txt --library=F:\biocbuild\bbs-3.17-bioc\R\library --no-vignettes --timings geNetClassifier_1.39.0.tar.gz
###
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* using log directory 'F:/biocbuild/bbs-3.17-bioc-rtools43/meat/geNetClassifier.Rcheck'
* using R Under development (unstable) (2022-12-25 r83502 ucrt)
* using platform: x86_64-w64-mingw32 (64-bit)
* R was compiled by
gcc.exe (GCC) 10.4.0
GNU Fortran (GCC) 10.4.0
* running under: Windows Server x64 (build 20348)
* using session charset: UTF-8
* using option '--no-vignettes'
* checking for file 'geNetClassifier/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'geNetClassifier' version '1.39.0'
* 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
* 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 sizes of PDF files under 'inst/doc' ... 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
geNetClassifier.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### F:\biocbuild\bbs-3.17-bioc\R\bin\R.exe CMD INSTALL geNetClassifier ### ############################################################################## ############################################################################## * installing to library 'F:/biocbuild/bbs-3.17-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)
geNetClassifier.Rcheck/tests/runTests.Rout
R Under development (unstable) (2022-12-25 r83502 ucrt) -- "Unsuffered Consequences"
Copyright (C) 2022 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, 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")'.
00:03:57 - 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 Dec 29 00:03:57 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
0.75 0.18 0.92
geNetClassifier.Rcheck/geNetClassifier-Ex.timings
| name | user | system | elapsed | |
| GeNetClassifierReturn-class | 0.63 | 0.08 | 0.76 | |
| GeneralizationError-class | 0.32 | 0.03 | 0.34 | |
| GenesNetwork-class | 2.02 | 1.11 | 3.31 | |
| GenesRanking-class | 0.48 | 0.02 | 0.50 | |
| calculateGenesRanking | 0.31 | 0.06 | 0.38 | |
| externalValidation.probMatrix | 0.50 | 0.03 | 0.53 | |
| externalValidation.stats | 0.46 | 0.03 | 0.48 | |
| gClasses-methods | 0.18 | 0.00 | 0.19 | |
| geNetClassifier | 0.10 | 0.02 | 0.11 | |
| geneSymbols | 0.04 | 0.00 | 0.05 | |
| genesDetails-methods | 0.32 | 0.03 | 0.34 | |
| getEdges-methods | 0.18 | 0.00 | 0.19 | |
| getNodes-methods | 0.18 | 0.00 | 0.17 | |
| getNumEdges-methods | 0.17 | 0.02 | 0.18 | |
| getNumNodes-methods | 0.18 | 0.00 | 0.17 | |
| getRanking-methods | 0.18 | 0.01 | 0.21 | |
| getSubNetwork-methods | 0.19 | 0.00 | 0.19 | |
| getTopRanking-methods | 0.27 | 0.00 | 0.26 | |
| leukemiasClassifier | 0.20 | 0.03 | 0.24 | |
| network2txt | 0.41 | 0.02 | 0.42 | |
| numGenes-methods | 0.18 | 0.00 | 0.18 | |
| numSignificantGenes-methods | 0.19 | 0.01 | 0.21 | |
| overview-methods | 0.24 | 0.00 | 0.23 | |
| plot.GeNetClassifierReturn | 2.00 | 0.10 | 2.14 | |
| plot.GenesRanking | 0.23 | 0.03 | 0.27 | |
| plotAssignments | 0.5 | 0.0 | 0.5 | |
| plotDiscriminantPower | 0.50 | 0.01 | 0.53 | |
| plotExpressionProfiles | 0.59 | 0.08 | 0.67 | |
| plotNetwork | 1.58 | 0.10 | 1.67 | |
| queryGeNetClassifier | 0.75 | 0.03 | 0.78 | |
| querySummary | 0.53 | 0.00 | 0.54 | |