Back to Multiple platform build/check report for BioC 3.16: simplified long |
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This page was generated on 2023-04-12 11:04:59 -0400 (Wed, 12 Apr 2023).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo2 | Linux (Ubuntu 20.04.5 LTS) | x86_64 | 4.2.3 (2023-03-15) -- "Shortstop Beagle" | 4502 |
palomino4 | Windows Server 2022 Datacenter | x64 | 4.2.3 (2023-03-15 ucrt) -- "Shortstop Beagle" | 4282 |
lconway | macOS 12.5.1 Monterey | x86_64 | 4.2.3 (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 |
To the developers/maintainers of the biosigner package: - Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/biosigner.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. |
Package 200/2183 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
biosigner 1.26.0 (landing page) Etienne A. Thevenot
| nebbiolo2 | Linux (Ubuntu 20.04.5 LTS) / x86_64 | OK | OK | OK | |||||||||
palomino4 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | |||||||||
lconway | macOS 12.5.1 Monterey / x86_64 | OK | OK | OK | OK | |||||||||
Package: biosigner |
Version: 1.26.0 |
Command: /home/biocbuild/bbs-3.16-bioc/R/bin/R CMD check --install=check:biosigner.install-out.txt --library=/home/biocbuild/bbs-3.16-bioc/R/site-library --timings biosigner_1.26.0.tar.gz |
StartedAt: 2023-04-10 19:20:47 -0400 (Mon, 10 Apr 2023) |
EndedAt: 2023-04-10 19:27:19 -0400 (Mon, 10 Apr 2023) |
EllapsedTime: 392.3 seconds |
RetCode: 0 |
Status: OK |
CheckDir: biosigner.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.16-bioc/R/bin/R CMD check --install=check:biosigner.install-out.txt --library=/home/biocbuild/bbs-3.16-bioc/R/site-library --timings biosigner_1.26.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.16-bioc/meat/biosigner.Rcheck’ * using R version 4.2.3 (2023-03-15) * using platform: x86_64-pc-linux-gnu (64-bit) * using session charset: UTF-8 * checking for file ‘biosigner/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘biosigner’ version ‘1.26.0’ * 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 for sufficient/correct file permissions ... OK * checking whether package ‘biosigner’ 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 Examples with CPU (user + system) or elapsed time > 5s user system elapsed getMset 30.017 0.248 30.267 biosign 14.713 0.212 14.925 plot 6.096 0.051 6.148 * 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 ... ‘biosigner-vignette.Rmd’ using ‘UTF-8’... OK NONE * checking re-building of vignette outputs ... OK * checking PDF version of manual ... OK * DONE Status: OK
biosigner.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.16-bioc/R/bin/R CMD INSTALL biosigner ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.16-bioc/R/site-library’ * installing *source* package ‘biosigner’ ... ** 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 (biosigner)
biosigner.Rcheck/tests/testthat.Rout
R version 4.2.3 (2023-03-15) -- "Shortstop Beagle" 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. > library(testthat) > test_check("biosigner") Loading required package: biosigner Selecting features for the plsda model Significant features from 'S' groups: plsda m189.040t01.2 "S" Accuracy: plsda Full 0.718 AS 0.711 S 0.697 Selecting features for the randomforest model Significant features from 'S' groups: randomforest m427.215t07.9 "S" Accuracy: randomforest Full 0.743 AS 0.714 S 0.665 Selecting features for the svm model No significant variable found for the selected classifier(s): 'svm' Selecting features for the plsda model Selecting features for the randomforest model Selecting features for the svm model Significant features from 'S' groups: plsda randomforest svm m189.040t01.2 "A" "S" "B" m427.215t07.9 "A" "S" "B" m539.231t06.6 "A" "S" "B" m164.035t02.1 "A" "D" "S" m557.311t10.9 "S" "C" "B" m511.313t08.7 "E" "E" "S" Accuracy: plsda randomforest svm Full 0.729 0.812 0.729 AS 0.792 0.917 0.583 S 0.708 0.750 0.583 Selecting features for the plsda model Selecting features for the randomforest model Selecting features for the svm model Significant features from 'S' groups: plsda randomforest svm m427.215t07.9 "A" "S" "B" m189.040t01.2 "S" "B" "E" Accuracy: plsda randomforest svm Full 0.718 0.743 0.688 AS 0.711 0.714 0.745 S 0.697 0.665 NA Selecting features for the plsda model Selecting features for the randomforest model Selecting features for the svm model Significant features from 'S' groups: plsda randomforest svm p-Anisic acid "S" "S" "S" Testosterone glucuronide "S" "S" "S" Pantothenic acid "S" "A" "S" Malic acid "S" "A" "A" Oxoglutaric acid "E" "S" "S" Glucuronic acid and/or isomers "B" "E" "S" 2-Isopropylmalic acid "E" "E" "S" 3,7-Dimethyluric acid "E" "E" "S" 4-Acetamidobutanoic acid isomer 3 "E" "E" "S" N-Acetylleucine "E" "E" "S" N2-Acetylaminoadipic acid "E" "E" "S" N4-Acetylcytidine "E" "E" "S" Pyrroledicarboxylic acid "E" "E" "S" Taurine "E" "E" "S" Xanthosine "E" "E" "S" Accuracy: plsda randomforest svm Full 0.871 0.853 0.884 AS 0.883 0.920 0.927 S 0.877 0.855 0.931 Selecting features for the plsda model Selecting features for the randomforest model Selecting features for the svm model Significant features from 'S' groups: plsda randomforest svm m103.040t01.3 "S" "B" "B" m103.040t01.6 "S" "B" "E" m110.985t00.9 "S" "B" "E" m116.072t01.0 "S" "B" "E" m104.043t01.6 "S" "E" "E" m117.055t02.8 "S" "E" "E" Accuracy: plsda randomforest svm Full 0.690 0.606 0.68 AS 0.724 0.606 0.50 S 0.724 NA NA Selecting features for the plsda model Selecting features for the randomforest model Selecting features for the svm model Significant features from 'S' groups: plsda randomforest svm p-Anisic acid "S" "S" "S" Testosterone glucuronide "S" "S" "S" Pantothenic acid "S" "A" "S" Malic acid "S" "A" "A" Oxoglutaric acid "E" "S" "S" Glucuronic acid and/or isomers "B" "E" "S" 2-Isopropylmalic acid "E" "E" "S" 3,7-Dimethyluric acid "E" "E" "S" 4-Acetamidobutanoic acid isomer 3 "E" "E" "S" N-Acetylleucine "E" "E" "S" N2-Acetylaminoadipic acid "E" "E" "S" N4-Acetylcytidine "E" "E" "S" Pyrroledicarboxylic acid "E" "E" "S" Taurine "E" "E" "S" Xanthosine "E" "E" "S" Accuracy: plsda randomforest svm Full 0.871 0.853 0.884 AS 0.883 0.920 0.927 S 0.877 0.855 0.931 Selecting the features for the 'agilent' dataset: Selecting features for the plsda model Selecting features for the randomforest model Selecting features for the svm model Significant features from 'S' groups: plsda randomforest svm VEPH1 "S" "E" "B" LHFP "S" "E" "B" C10orf90 "B" "E" "S" EZH2 "E" "S" "E" Accuracy: plsda randomforest svm Full 1 1.000 1.000 AS 1 0.900 0.983 S 1 0.917 0.983 Selecting the features for the 'hgu95' dataset: Selecting features for the plsda model Selecting features for the randomforest model Selecting features for the svm model Significant features from 'S' groups: plsda randomforest svm TSPAN4 "S" "S" "E" TBC1D16 "S" "E" "B" NASP "S" "E" "E" Accuracy: plsda randomforest svm Full 1 1 1.000 AS 1 1 0.917 S 1 1 NA Selecting features for the plsda model Selecting features for the randomforest model Selecting features for the svm model Significant features from 'S' groups: plsda randomforest svm m495.261t08.7 "A" "B" "S" m497.284t08.1 "S" "S" "C" m497.275t08.1 "S" "A" "E" Accuracy: plsda randomforest svm Full 0.782 0.831 0.738 AS 0.760 0.808 0.708 S 0.823 0.739 0.708 Selecting the features for the 'agilent' dataset: Selecting features for the plsda model Selecting features for the randomforest model Selecting features for the svm model Significant features from 'S' groups: plsda randomforest svm VEPH1 "S" "E" "B" LHFP "S" "E" "B" C10orf90 "B" "E" "S" EZH2 "E" "S" "E" Accuracy: plsda randomforest svm Full 1 1.000 1.000 AS 1 0.900 0.983 S 1 0.917 0.983 Selecting the features for the 'hgu95' dataset: Selecting features for the plsda model Selecting features for the randomforest model Selecting features for the svm model Significant features from 'S' groups: plsda randomforest svm TSPAN4 "S" "S" "E" TBC1D16 "S" "E" "B" NASP "S" "E" "E" Accuracy: plsda randomforest svm Full 1 1 1.000 AS 1 1 0.917 S 1 1 NA Selecting features for the plsda model No significant variable found for the selected classifier(s): 'plsda' [ FAIL 0 | WARN 0 | SKIP 0 | PASS 31 ] > > proc.time() user system elapsed 50.463 1.376 51.826
biosigner.Rcheck/biosigner-Ex.timings
name | user | system | elapsed | |
biosign-class | 3.612 | 0.051 | 3.664 | |
biosign | 14.713 | 0.212 | 14.925 | |
biosignMultiDataSet-class | 0 | 0 | 0 | |
getAccuracyMN | 2.328 | 0.048 | 2.376 | |
getBiosign | 2.168 | 0.016 | 2.185 | |
getEset | 2.891 | 0.054 | 2.946 | |
getMset | 30.017 | 0.248 | 30.267 | |
getSignatureLs | 3.073 | 0.020 | 3.093 | |
plot | 6.096 | 0.051 | 6.148 | |
predict | 2.402 | 0.016 | 2.419 | |
show | 2.388 | 0.019 | 2.408 | |