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### Running command:
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###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:pareg.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings pareg_1.9.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.20-bioc/meat/pareg.Rcheck’
* using R version 4.4.1 (2024-06-14)
* using platform: x86_64-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 Monterey 12.7.1
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘pareg/DESCRIPTION’ ... OK
* this is package ‘pareg’ version ‘1.9.0’
* 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 ... NOTE
Found the following non-portable file paths:
  pareg/inst/scripts/synthetic_benchmark/resources/multi_config_workflow/config_ablation_study/config.yaml
  pareg/inst/scripts/synthetic_benchmark/resources/multi_config_workflow/config_ablation_study/params.csv
  pareg/inst/scripts/synthetic_benchmark/resources/multi_config_workflow/config_dispersion_fitting/config.yaml
  pareg/inst/scripts/synthetic_benchmark/resources/multi_config_workflow/config_dispersion_fitting/params.csv
  pareg/inst/scripts/synthetic_benchmark/resources/multi_config_workflow/config_real_datasets/config.yaml
  pareg/inst/scripts/synthetic_benchmark/resources/multi_config_workflow/config_real_datasets/params.csv
  pareg/inst/scripts/synthetic_benchmark/resources/multi_config_workflow/config_regularization_effect/config.yaml
  pareg/inst/scripts/synthetic_benchmark/resources/multi_config_workflow/config_regularization_effect/params.csv
  pareg/inst/scripts/synthetic_benchmark/resources/multi_config_workflow/config_regularization_parameter/config.yaml
  pareg/inst/scripts/synthetic_benchmark/resources/multi_config_workflow/config_regularization_parameter/params.csv
  pareg/inst/scripts/synthetic_benchmark/resources/multi_config_workflow/config_response_distribution/config.yaml
  pareg/inst/scripts/synthetic_benchmark/resources/multi_config_workflow/config_response_distribution/params.csv
  pareg/inst/scripts/synthetic_benchmark/resources/multi_config_workflow/config_similarity_measures/config.yaml
  pareg/inst/scripts/synthetic_benchmark/resources/multi_config_workflow/config_similarity_measures/params.csv
  pareg/inst/scripts/synthetic_benchmark/resources/multi_config_workflow/workflow/scripts/compare_rocauc_vs_loss.R
  pareg/inst/scripts/synthetic_benchmark/resources/multi_config_workflow/config_regularization_parameter

Tarballs are only required to store paths of up to 100 bytes and cannot
store those of more than 256 bytes, with restrictions including to 100
bytes for the final component.
See section ‘Package structure’ in the ‘Writing R Extensions’ manual.
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘pareg’ can be installed ... NOTE
Found the following notes/warnings:
  Non-staged installation was used
See ‘/Users/biocbuild/bbs-3.20-bioc/meat/pareg.Rcheck/00install.out’ for details.
* 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 line endings in shell scripts ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                      user system elapsed
as.data.frame.pareg 10.731  3.195  16.455
cvedgenet-methods    6.679  0.092   6.819
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’
 OK
* 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: 2 NOTEs
See
  ‘/Users/biocbuild/bbs-3.20-bioc/meat/pareg.Rcheck/00check.log’
for details.

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### Running command:
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###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL pareg
###
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* installing to library ‘/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library’
* installing *source* package ‘pareg’ ...
** using non-staged installation via StagedInstall field
** 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
* DONE (pareg)

R version 4.4.1 (2024-06-14) -- "Race for Your Life"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-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)
> library(pareg)
Loading required package: tensorflow
Loading required package: tfprobability


Attaching package: 'pareg'

The following objects are masked from 'package:stats':

    family, gaussian

The following object is masked from 'package:base':

    beta

> 
> cl <- basilisk::basiliskStart(
+   pareg::pareg_env,
+   testload = c("tensorflow", "tensorflow_probability")
+ )
2024-07-24 23:23:53.545438: I tensorflow/core/platform/cpu_feature_guard.cc:193] This TensorFlow binary is optimized with oneAPI Deep Neural Network Library (oneDNN) to use the following CPU instructions in performance-critical operations:  SSE4.1 SSE4.2 AVX AVX2 AVX512F AVX512_VNNI FMA
To enable them in other operations, rebuild TensorFlow with the appropriate compiler flags.
> basilisk::basiliskRun(
+   proc = cl,
+   fun = test_check,
+   "pareg"
+ )
2024-07-24 23:24:00.410330: I tensorflow/core/platform/cpu_feature_guard.cc:193] This TensorFlow binary is optimized with oneAPI Deep Neural Network Library (oneDNN) to use the following CPU instructions in performance-critical operations:  SSE4.1 SSE4.2 AVX AVX2 AVX512F AVX512_VNNI FMA
To enable them in other operations, rebuild TensorFlow with the appropriate compiler flags.
[ FAIL 0 | WARN 8 | SKIP 10 | PASS 14 ]

══ Skipped tests (10) ══════════════════════════════════════════════════════════
• On Bioconductor (10): 'test-netreg.R:2:3', 'test-netreg.R:19:3',
  'test-netreg.R:48:3', 'test-netreg.R:76:3', 'test-netreg.R:108:3',
  'test-pareg.R:2:3', 'test-pareg.R:38:3', 'test-pareg.R:82:3',
  'test-pareg.R:146:3', 'test-pareg.R:196:3'

[ FAIL 0 | WARN 8 | SKIP 10 | PASS 14 ]
                       file context
1             test-netreg.R        
2             test-netreg.R        
3             test-netreg.R        
4             test-netreg.R        
5             test-netreg.R        
6             test-netreg.R        
7              test-pareg.R        
8              test-pareg.R        
9              test-pareg.R        
10             test-pareg.R        
11             test-pareg.R        
12             test-pareg.R        
13 test-term_similarities.R        
14 test-term_similarities.R        
15             test-utils.R        
16             test-utils.R        
17             test-utils.R        
18             test-utils.R        
19             test-utils.R        
                                                             test nb failed
1                                             Gaussian case works  1      0
2                                                 Beta case works  1      0
3                                          Cross-validation works  1      0
4              Cross-validation with network regularization works  1      0
5  Cross-validation with network regularization works in parallel  1      0
6                                     laplacian computation works  1      0
7                          package doesn't crash for trivial case  1      0
8                                   pareg works with term network  1      0
9                                          Bernoulli family works  1      0
10                     term input network mismatch leads to crash  6      0
11                              sequential cross-validation works  1      0
12                            parallelized cross-validation works  1      0
13                              term similarities can be computed  1      0
14                    term similarities can be computed on tibble  1      0
15                    model creation works with only common genes  1      0
16             model creation works with gene which is in no term  1      0
17                                      similarity sampling works  2      0
18                                   enrichplot integration works  7      0
19                                   tensorflow integration works  2      0
   skipped error warning  user system  real passed       result
1     TRUE FALSE       0 0.017  0.005 0.022      0 list(mes....
2     TRUE FALSE       0 0.030  0.004 0.035      0 list(mes....
3     TRUE FALSE       0 0.004  0.002 0.006      0 list(mes....
4     TRUE FALSE       0 0.003  0.001 0.005      0 list(mes....
5     TRUE FALSE       0 0.004  0.002 0.006      0 list(mes....
6    FALSE FALSE       0 0.009  0.002 0.011      1 list(mes....
7     TRUE FALSE       0 0.004  0.002 0.006      0 list(mes....
8     TRUE FALSE       0 0.004  0.001 0.006      0 list(mes....
9     TRUE FALSE       0 0.004  0.001 0.006      0 list(mes....
10   FALSE FALSE       5 3.148  0.098 3.258      1 list(mes....
11    TRUE FALSE       0 0.005  0.001 0.005      0 list(mes....
12    TRUE FALSE       0 0.004  0.001 0.006      0 list(mes....
13   FALSE FALSE       0 0.032  0.002 0.035      1 list(mes....
14   FALSE FALSE       0 0.029  0.002 0.031      1 list(mes....
15   FALSE FALSE       0 0.152  0.002 0.156      1 list(mes....
16   FALSE FALSE       0 0.151  0.002 0.154      1 list(mes....
17   FALSE FALSE       0 0.140  0.005 0.146      2 list(mes....
18   FALSE FALSE       3 2.360  0.128 2.551      4 list(mes....
19   FALSE FALSE       0 0.014  0.004 0.018      2 list(mes....
> basilisk::basiliskStop(cl)
> 
> proc.time()
   user  system elapsed 
 23.176   3.218  26.489