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###
### Running command:
###
###   F:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:ropls.install-out.txt --library=F:\biocbuild\bbs-3.15-bioc\R\library --no-vignettes --timings ropls_1.28.2.tar.gz
###
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* using log directory 'F:/biocbuild/bbs-3.15-bioc/meat/ropls.Rcheck'
* using R version 4.2.1 (2022-06-23 ucrt)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: UTF-8
* using option '--no-vignettes'
* checking for file 'ropls/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'ropls' version '1.28.2'
* 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 whether package 'ropls' 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
opls 6.26   0.15    6.44
* 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:
  • empty test (3)
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error ('test_opls.R:575'): plot ─────────────────────────────────────────────
  Error in `pdf(fig.pdfC)`: cannot open file 'test.pdf'
  Backtrace:
      ▆
   1. ├─base::plot(opLs, typeVc = typeC, fig.pdfC = "test.pdf") at test_opls.R:575:4
   2. └─ropls::plot(opLs, typeVc = typeC, fig.pdfC = "test.pdf")
   3.   └─ropls (local) .local(x, y, ...)
   4.     └─grDevices::pdf(fig.pdfC)
  
  [ FAIL 1 | WARN 4 | SKIP 3 | PASS 61 ]
  Error: Test failures
  Execution halted
* 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: 1 ERROR
See
  'F:/biocbuild/bbs-3.15-bioc/meat/ropls.Rcheck/00check.log'
for details.

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###
### Running command:
###
###   F:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD INSTALL ropls
###
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* installing to library 'F:/biocbuild/bbs-3.15-bioc/R/library'
* installing *source* package 'ropls' ...
** 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 (ropls)

R version 4.2.1 (2022-06-23 ucrt) -- "Funny-Looking Kid"
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("ropls")
Loading required package: ropls
PLS
183 samples x 109 variables and 2 responses
standard scaling of predictors and response(s)
      R2X(cum) R2Y(cum) Q2(cum) RMSEE pre ort
Total    0.293    0.412   0.254  5.72   3   0
PLS-DA
47 samples x 109 variables and 1 response
standard scaling of predictors and response(s)
      R2X(cum) R2Y(cum) Q2(cum) RMSEE pre ort pR2Y  pQ2
Total    0.211     0.47  0.0394 0.338   2   0 0.05 0.05
PLS-DA
47 samples x 109 variables and 1 response
pareto scaling of predictors and standard scaling of response(s)
      R2X(cum) R2Y(cum) Q2(cum) RMSEE pre ort pR2Y  pQ2
Total    0.204    0.442  0.0531 0.353   2   0 0.05 0.05
OPLS-DA
10 samples x 8 variables and 1 response
standard scaling of predictors and response(s)
      R2X(cum) R2Y(cum) Q2(cum)  RMSEE RMSEP pre ort
Total    0.699    0.976    0.94 0.0928 0.244   1   1
PLS-DA
10 samples x 8 variables and 1 response
standard scaling of predictors and response(s)
      R2X(cum) R2Y(cum) Q2(cum)  RMSEE  RMSEP pre ort
Total    0.753     0.99   0.937 0.0636 0.0537   3   0
PCA
183 samples x 109 variables
standard scaling of predictors
      R2X(cum) pre ort
Total    0.501   8   0
PLS-DA
183 samples x 109 variables and 1 response
standard scaling of predictors and response(s)
      R2X(cum) R2Y(cum) Q2(cum) RMSEE pre ort pR2Y  pQ2
Total    0.275     0.73   0.584 0.262   3   0 0.05 0.05
OPLS-DA
183 samples x 109 variables and 1 response
standard scaling of predictors and response(s)
      R2X(cum) R2Y(cum) Q2(cum) RMSEE pre ort pR2Y  pQ2
Total    0.275     0.73   0.602 0.262   1   2 0.05 0.05


Building the model for the 'agilent' dataset:
PLS-DA
16 samples x 300 variables and 1 response
standard scaling of predictors and response(s)
      R2X(cum) R2Y(cum) Q2(cum)  RMSEE pre ort pR2Y  pQ2
Total    0.369    0.996   0.906 0.0326   2   0 0.05 0.05


Building the model for the 'hgu95' dataset:
PLS-DA
16 samples x 288 variables and 1 response
standard scaling of predictors and response(s)
      R2X(cum) R2Y(cum) Q2(cum) RMSEE pre ort pR2Y  pQ2
Total    0.371    0.952    0.91 0.113   1   0 0.05 0.05
PCA
183 samples x 109 variables
standard scaling of predictors
      R2X(cum) pre ort
Total    0.501   8   0
PLS-DA
183 samples x 109 variables and 1 response
standard scaling of predictors and response(s)
      R2X(cum) R2Y(cum) Q2(cum) RMSEE pre ort pR2Y  pQ2
Total    0.275     0.73   0.584 0.262   3   0 0.05 0.05
OPLS-DA
183 samples x 109 variables and 1 response
standard scaling of predictors and response(s)
      R2X(cum) R2Y(cum) Q2(cum) RMSEE pre ort pR2Y  pQ2
Total    0.275     0.73   0.602 0.262   1   2 0.05 0.05


Building the model for the 'agilent' dataset:
PCA
16 samples x 300 variables
standard scaling of predictors
      R2X(cum) pre ort
Total    0.521   3   0


Building the model for the 'hgu95' dataset:
PCA
16 samples x 288 variables
standard scaling of predictors
      R2X(cum) pre ort
Total    0.553   3   0

1) Data set:
183 samples x 109 variables
0 (0%) NAs
0 excluded variables (near zero variance)
standard x scaling
Summary of the 3 increasing variance spaced raw variables:
  Citric acid    Ortho-Hydroxyphenylacetic acid Acetaminophen glucuronide
 Min.   :3.978   Min.   :3.516                  Min.   :-0.30001         
 1st Qu.:4.240   1st Qu.:4.260                  1st Qu.: 0.04682         
 Median :4.354   Median :4.465                  Median : 1.23248         
 Mean   :4.352   Mean   :4.438                  Mean   : 1.38781         
 3rd Qu.:4.450   3rd Qu.:4.656                  3rd Qu.: 2.09594         
 Max.   :4.804   Max.   :5.428                  Max.   : 5.56739         

2) Model: PCA
Correlations between variables and first 2 components:
                                       p1    p2 cor_p1 cor_p2
Salicylic acid                    -0.0069    NA -0.028     NA
N-Acetylleucine                    0.0015    NA  0.006     NA
Chenodeoxycholic acid isomer       0.0075    NA  0.030     NA
Pyridylacetylglycine               0.1500    NA  0.590     NA
Dimethylguanosine                  0.1700    NA  0.670     NA
4-Acetamidobutanoic acid isomer 2  0.1800    NA  0.730     NA
FMNH2                                  NA -0.17     NA  -0.56
Testosterone glucuronide               NA -0.16     NA  -0.54
6-(carboxymethoxy)-hexanoic acid       NA -0.16     NA  -0.52
Pyrocatechol sulfate                   NA  0.22     NA   0.72
Fumaric acid                           NA  0.22     NA   0.74
Pentose                                NA  0.24     NA   0.79
     R2X R2X(cum) Iter.
p1 0.149    0.149     0
p2 0.103    0.252     0

1) Data set:
183 samples x 109 variables and 1 response
0 (0%) NAs
0 excluded variables (near zero variance)
standard x and y scaling
Summary of the 3 increasing variance spaced raw variables:
  Citric acid    Ortho-Hydroxyphenylacetic acid Acetaminophen glucuronide
 Min.   :3.978   Min.   :3.516                  Min.   :-0.30001         
 1st Qu.:4.240   1st Qu.:4.260                  1st Qu.: 0.04682         
 Median :4.354   Median :4.465                  Median : 1.23248         
 Mean   :4.352   Mean   :4.438                  Mean   : 1.38781         
 3rd Qu.:4.450   3rd Qu.:4.656                  3rd Qu.: 2.09594         
 Max.   :4.804   Max.   :5.428                  Max.   : 5.56739         

2) Model: PLS-DA
Correlations between variables and first 2 components:
                                     p1     p2 cor_p1 cor_p2
Testosterone glucuronide         -0.180     NA  -0.50     NA
6-(carboxymethoxy)-hexanoic acid -0.097     NA  -0.27     NA
Asp-Leu/Ile isomer 1             -0.080     NA  -0.22     NA
Glucuronic acid and/or isomers    0.220     NA   0.62     NA
Phe-Tyr-Asp (and isomers)         0.220     NA   0.63     NA
alpha-N-Phenylacetyl-glutamine    0.220     NA   0.64     NA
Porphobilinogen                      NA -0.200     NA -0.530
1-Methyluric acid                    NA -0.200     NA -0.530
p-Hydroxymandelic acid               NA -0.200     NA -0.520
Malic acid                           NA  0.030     NA  0.078
p-Anisic acid                        NA  0.066     NA  0.180
Acetaminophen glucuronide            NA  0.093     NA  0.240
      R2X R2X(cum)   R2Y R2Y(cum)    Q2 Q2(cum) Signif. Iter.
p1 0.0984   0.0984 0.479    0.479 0.401   0.401      R1     1
p2 0.0861   0.1850 0.189    0.668 0.256   0.555      R1     1
 Country Gr_Coffe ... Yoghurt Crisp_Brea
  factor  numeric ... numeric    numeric
 nRow nCol size NAs
   16   21 0 Mb   3
    Country Gr_Coffe ... Yoghurt Crisp_Brea
1       Ger       90 ...      30         26
2       Ita       82 ...       5         18
...     ...      ... ...     ...        ...
15      Spa       70 ...      16         13
16      Ire       30 ...       3          9
 Country Gr_Coffe Inst_Coffe ... Olive_Oil Yoghurt Crisp_Brea
  factor  numeric    numeric ...   numeric numeric    numeric
 nRow nCol size NAs
   16   21 0 Mb   3
    Country Gr_Coffe Inst_Coffe ... Olive_Oil Yoghurt Crisp_Brea
1       Ger       90         49 ...        74      30         26
2       Ita       82         10 ...        94       5         18
3       Fra       88         42 ...        36      57          3
...     ...      ...        ... ...       ...     ...        ...
14      Fin       98         12 ...        17    <NA>         64
15      Spa       70         40 ...        91      16         13
16      Ire       30         52 ...        31       3          9
       dim  class    mode  typeof size NAs
 1 x 1'000 matrix logical logical 0 Mb   0
    V1   V2 ...   V4   V5
1 TRUE TRUE ... TRUE TRUE
     dim  class      mode    typeof size NAs
 10 x 10 matrix character character 0 Mb   0
     V1  V2 ...  V4  V5
1     a   a ...   a   a
2     a   a ...   a   a
... ... ... ... ... ...
4     a   a ...   a   a
5     a   a ...   a   a
       dim  class    mode typeof   size NAs  min mean median max
 183 x 109 matrix numeric double 0.2 Mb   0 -0.3  4.2    4.3   6
       (2-methoxyethoxy)propanoic acid isomer (gamma)Glu-Leu/Ile ...
HU_011                            3.019766011        3.888479324 ...
HU_014                             3.81433889        4.277148905 ...
...                                       ...                ... ...
HU_208                            3.748127215        4.523763202 ...
HU_209                            4.208859398        4.675880567 ...
       Valerylglycine isomer 2  Xanthosine
HU_011             3.889078716 4.075879575
HU_014             4.181765852 4.195761901
...                        ...         ...
HU_208             4.634338821 4.487781609
HU_209              4.47194762 4.222953354
     age     bmi gender
 numeric numeric factor
 nRow nCol size NAs
  183    3 0 Mb   0
        age   bmi gender
HU_011   29 19.75      M
HU_014   59 22.64      F
...     ...   ...    ...
HU_208   27 18.61      F
HU_209 17.5 21.48      F
[ FAIL 1 | WARN 4 | SKIP 3 | PASS 61 ]

══ Skipped tests ═══════════════════════════════════════════════════════════════
• empty test (3)

══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test_opls.R:575'): plot ─────────────────────────────────────────────
Error in `pdf(fig.pdfC)`: cannot open file 'test.pdf'
Backtrace:
    ▆
 1. ├─base::plot(opLs, typeVc = typeC, fig.pdfC = "test.pdf") at test_opls.R:575:4
 2. └─ropls::plot(opLs, typeVc = typeC, fig.pdfC = "test.pdf")
 3.   └─ropls (local) .local(x, y, ...)
 4.     └─grDevices::pdf(fig.pdfC)

[ FAIL 1 | WARN 4 | SKIP 3 | PASS 61 ]
Error: Test failures
Execution halted