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This page was generated on 2023-10-16 11:36:52 -0400 (Mon, 16 Oct 2023).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 22.04.2 LTS)x86_644.3.1 (2023-06-16) -- "Beagle Scouts" 4626
palomino3Windows Server 2022 Datacenterx644.3.1 (2023-06-16 ucrt) -- "Beagle Scouts" 4379
merida1macOS 12.6.4 Montereyx86_644.3.1 (2023-06-16) -- "Beagle Scouts" 4395
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

Package 215/2230HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
biosigner 1.28.0  (landing page)
Etienne A. Thevenot
Snapshot Date: 2023-10-15 14:00:13 -0400 (Sun, 15 Oct 2023)
git_url: https://git.bioconductor.org/packages/biosigner
git_branch: RELEASE_3_17
git_last_commit: 83d8e8f
git_last_commit_date: 2023-04-25 10:44:49 -0400 (Tue, 25 Apr 2023)
nebbiolo1Linux (Ubuntu 22.04.2 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 12.6.4 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kjohnson2macOS 12.6.1 Monterey / arm64see weekly results here

CHECK results for biosigner on merida1


To the developers/maintainers of the biosigner package:
- 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 Troubleshooting Build Report for more information.
- Use the following Renviron settings to reproduce errors and warnings.
- If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information.

raw results


Summary

Package: biosigner
Version: 1.28.0
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:biosigner.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings biosigner_1.28.0.tar.gz
StartedAt: 2023-10-15 23:10:43 -0400 (Sun, 15 Oct 2023)
EndedAt: 2023-10-15 23:22:46 -0400 (Sun, 15 Oct 2023)
EllapsedTime: 723.2 seconds
RetCode: 0
Status:   OK  
CheckDir: biosigner.Rcheck
Warnings: 0

Command output

##############################################################################
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###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:biosigner.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings biosigner_1.28.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.17-bioc/meat/biosigner.Rcheck’
* using R version 4.3.1 (2023-06-16)
* using platform: x86_64-apple-darwin20 (64-bit)
* R was compiled by
    Apple clang version 14.0.3 (clang-1403.0.22.14.1)
    GNU Fortran (GCC) 12.2.0
* running under: macOS Monterey 12.6.4
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘biosigner/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘biosigner’ version ‘1.28.0’
* 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 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        81.861  1.244 111.947
biosign        33.992  0.625  43.216
plot           14.133  0.211  18.397
biosign-class   6.038  0.161   7.340
getEset         4.921  0.067   6.833
getAccuracyMN   4.777  0.088   6.411
getSignatureLs  4.732  0.085   6.390
predict         4.749  0.058   5.952
show            4.736  0.061   5.640
getBiosign      4.473  0.054   6.240
* 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

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL biosigner
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/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 4.3.1 (2023-06-16) -- "Beagle Scouts"
Copyright (C) 2023 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin20 (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 
101.111   2.297 128.529 

Example timings

biosigner.Rcheck/biosigner-Ex.timings

nameusersystemelapsed
biosign-class6.0380.1617.340
biosign33.992 0.62543.216
biosignMultiDataSet-class0.0000.0000.001
getAccuracyMN4.7770.0886.411
getBiosign4.4730.0546.240
getEset4.9210.0676.833
getMset 81.861 1.244111.947
getSignatureLs4.7320.0856.390
plot14.133 0.21118.397
predict4.7490.0585.952
show4.7360.0615.640