Back to Multiple platform build/check report for BioC 3.15
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This page was generated on 2022-10-19 13:20:02 -0400 (Wed, 19 Oct 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 20.04.5 LTS)x86_644.2.1 (2022-06-23) -- "Funny-Looking Kid" 4386
palomino3Windows Server 2022 Datacenterx644.2.1 (2022-06-23 ucrt) -- "Funny-Looking Kid" 4138
merida1macOS 10.14.6 Mojavex86_644.2.1 (2022-06-23) -- "Funny-Looking Kid" 4205
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 biosigner on nebbiolo1


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.

raw results

Package 197/2140HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
biosigner 1.24.2  (landing page)
Etienne A. Thevenot
Snapshot Date: 2022-10-18 13:55:19 -0400 (Tue, 18 Oct 2022)
git_url: https://git.bioconductor.org/packages/biosigner
git_branch: RELEASE_3_15
git_last_commit: 8f8c386
git_last_commit_date: 2022-06-22 17:09:59 -0400 (Wed, 22 Jun 2022)
nebbiolo1Linux (Ubuntu 20.04.5 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino3Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
merida1macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: biosigner
Version: 1.24.2
Command: /home/biocbuild/bbs-3.15-bioc/R/bin/R CMD check --install=check:biosigner.install-out.txt --library=/home/biocbuild/bbs-3.15-bioc/R/library --no-vignettes --timings biosigner_1.24.2.tar.gz
StartedAt: 2022-10-18 18:47:46 -0400 (Tue, 18 Oct 2022)
EndedAt: 2022-10-18 18:52:14 -0400 (Tue, 18 Oct 2022)
EllapsedTime: 267.2 seconds
RetCode: 0
Status:   OK  
CheckDir: biosigner.Rcheck
Warnings: 0

Command output

##############################################################################
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###
### Running command:
###
###   /home/biocbuild/bbs-3.15-bioc/R/bin/R CMD check --install=check:biosigner.install-out.txt --library=/home/biocbuild/bbs-3.15-bioc/R/library --no-vignettes --timings biosigner_1.24.2.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.15-bioc/meat/biosigner.Rcheck’
* using R version 4.2.1 (2022-06-23)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘biosigner/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘biosigner’ version ‘1.24.2’
* 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 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 30.628  0.020  30.649
biosign 15.213  0.188  15.403
plot     6.054  0.027   6.082
* 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


Installation output

biosigner.Rcheck/00install.out

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##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.15-bioc/R/bin/R CMD INSTALL biosigner
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.15-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)

Tests output

biosigner.Rcheck/tests/testthat.Rout


R version 4.2.1 (2022-06-23) -- "Funny-Looking Kid"
Copyright (C) 2022 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 
 51.889   1.369  53.246 

Example timings

biosigner.Rcheck/biosigner-Ex.timings

nameusersystemelapsed
biosign-class3.5030.1083.612
biosign15.213 0.18815.403
biosignMultiDataSet-class0.0000.0000.001
getAccuracyMN2.3730.0552.428
getBiosign2.6820.0122.694
getEset2.3860.0002.387
getMset30.628 0.02030.649
getSignatureLs2.4390.0002.439
plot6.0540.0276.082
predict2.5130.0002.512
show3.0360.0003.035