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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_1.34.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.20-bioc/meat/biosigner.Rcheck’
* using R version 4.4.1 (2024-06-14)
* using platform: aarch64-apple-darwin20
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    GNU Fortran (GCC) 12.2.0
* running under: macOS Ventura 13.6.7
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘biosigner/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘biosigner’ version ‘1.34.0’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ...Warning: unable to access index for repository https://CRAN.R-project.org/src/contrib:
  cannot open URL 'https://CRAN.R-project.org/src/contrib/PACKAGES'
 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 code 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 9.957  0.146  10.104
biosign 5.039  0.129   5.170
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’
 ERROR
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
  y[4]: "0.8529397"
  
  x[5]: "0.8908808"
  y[5]: "0.9200604"
  
  x[6]: "0.8449724"
  y[6]: "0.8551306"
  ── Failure ('test_biosigner.R:252:3'): SummarizedExperiment ────────────────────
  sac_accu.mn["AS", "randomforest"] not equivalent to 0.9200604.
  1/1 mismatches
  [1] 0.891 - 0.92 == -0.0292
  
  [ FAIL 2 | WARN 0 | SKIP 0 | PASS 29 ]
  Error: Test failures
  Execution halted
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 1 ERROR
See
  ‘/Users/biocbuild/bbs-3.20-bioc/meat/biosigner.Rcheck/00check.log’
for details.

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###
### Running command:
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###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL biosigner
###
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* installing to library ‘/Library/Frameworks/R.framework/Versions/4.4-arm64/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)

R version 4.4.1 (2024-06-14) -- "Race for Your Life"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: aarch64-apple-darwin20

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        0.840 0.884
AS   0.883        0.891 0.927
S    0.877        0.845 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        0.840 0.884
AS   0.883        0.891 0.927
S    0.877        0.845 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 2 | WARN 0 | SKIP 0 | PASS 29 ]

══ Failed tests ════════════════════════════════════════════════════════════════
── Failure ('test_biosigner.R:187:5'): biosign_sacurine ────────────────────────
`biosignMC` not identical to `accMC`.
3/9 mismatches
x[4]: "0.8397755"
y[4]: "0.8529397"

x[5]: "0.8908808"
y[5]: "0.9200604"

x[6]: "0.8449724"
y[6]: "0.8551306"
── Failure ('test_biosigner.R:252:3'): SummarizedExperiment ────────────────────
sac_accu.mn["AS", "randomforest"] not equivalent to 0.9200604.
1/1 mismatches
[1] 0.891 - 0.92 == -0.0292

[ FAIL 2 | WARN 0 | SKIP 0 | PASS 29 ]
Error: Test failures
Execution halted