| Back to Build/check report for BioC 3.17 |
|
This page was generated on 2023-01-02 09:00:21 -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 | ||||
|
To the developers/maintainers of the biosigner package: Make sure to use the following settings in order to reproduce any error or warning you see on this page. |
| Package 198/2158 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| biosigner 1.27.0 (landing page) Etienne A. Thevenot
| palomino5 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | ||||||||
| Package: biosigner |
| Version: 1.27.0 |
| Command: F:\biocbuild\bbs-3.17-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:biosigner.install-out.txt --library=F:\biocbuild\bbs-3.17-bioc\R\library --no-vignettes --timings biosigner_1.27.0.tar.gz |
| StartedAt: 2022-12-28 22:01:33 -0500 (Wed, 28 Dec 2022) |
| EndedAt: 2022-12-28 22:05:39 -0500 (Wed, 28 Dec 2022) |
| EllapsedTime: 245.9 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: biosigner.Rcheck |
| Warnings: 0 |
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### Running command:
###
### F:\biocbuild\bbs-3.17-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:biosigner.install-out.txt --library=F:\biocbuild\bbs-3.17-bioc\R\library --no-vignettes --timings biosigner_1.27.0.tar.gz
###
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* using log directory 'F:/biocbuild/bbs-3.17-bioc-rtools43/meat/biosigner.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 'biosigner/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'biosigner' version '1.27.0'
* 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 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 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 26.81 0.46 27.28
biosign 13.11 0.48 14.71
plot 5.42 0.19 5.61
biosign-class 2.88 0.09 7.05
* 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 ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE
Status: OK
biosigner.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### F:\biocbuild\bbs-3.17-bioc\R\bin\R.exe CMD INSTALL biosigner ### ############################################################################## ############################################################################## * installing to library 'F:/biocbuild/bbs-3.17-bioc/R/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 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.
> 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
40.53 1.50 42.09
biosigner.Rcheck/biosigner-Ex.timings
| name | user | system | elapsed | |
| biosign-class | 2.88 | 0.09 | 7.05 | |
| biosign | 13.11 | 0.48 | 14.71 | |
| biosignMultiDataSet-class | 0 | 0 | 0 | |
| getAccuracyMN | 2.15 | 0.05 | 2.21 | |
| getBiosign | 1.97 | 0.09 | 2.06 | |
| getEset | 2.10 | 0.08 | 2.17 | |
| getMset | 26.81 | 0.46 | 27.28 | |
| getSignatureLs | 2.08 | 0.07 | 2.16 | |
| plot | 5.42 | 0.19 | 5.61 | |
| predict | 1.98 | 0.06 | 2.05 | |
| show | 1.97 | 0.09 | 2.06 | |