Use rSharp instead of rClr #1376

PavelBal · 2024-03-12T13:57:00Z

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- Run docs

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rwmcintosh · 2024-05-22T16:20:49Z

> devtools::test()
ℹ Testing ospsuite
✔ | F W  S  OK | Context
✔ |          4 | aging-data                                                                                                                                                                                                                                                                    
✔ |          3 | application [1.3s]                                                                                                                                                                                                                                                            
✔ |          1 | cache                                                                                                                                                                                                                                                                         
✔ |          9 | container                                                                                                                                                                                                                                                                     
✔ |         11 | data-column                                                                                                                                                                                                                                                                   
✔ |      1   0 | data-combined                                                                                                                                                                                                                                                                 
✔ |     18   0 | data-importer-configuration                                                                                                                                                                                                                                                   
✔ |          9 | data-repository                                                                                                                                                                                                                                                               
✔ |         96 | data-set                                                                                                                                                                                                                                                                      
✔ |          3 | default-plot-configuration                                                                                                                                                                                                                                                    
✔ |          2 | dot-net-wrapper [1.3s]                                                                                                                                                                                                                                                        
✔ |          3 | formula                                                                                                                                                                                                                                                                       
✔ |          1 | interval                                                                                                                                                                                                                                                                      
✔ |          2 | molecule-ontogeny                                                                                                                                                                                                                                                             
✔ |          4 | molecule                                                                                                                                                                                                                                                                      
✔ |          3 | ospsuiteEnv                                                                                                                                                                                                                                                                   
✔ |         22 | output-schema [3.0s]                                                                                                                                                                                                                                                          
✔ |          3 | output-selections                                                                                                                                                                                                                                                             
✔ |         50 | parameter                                                                                                                                                                                                                                                                     
✔ |      1   0 | plot-individual-time-profile                                                                                                                                                                                                                                                  
✖ | 1        0 | plot-observed-vs-simulated                                                                                                                                                                                                                                                    
───────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────
Error (test-plot-observed-vs-simulated.R:14:1): (code run outside of `test_that()`)
Error in `do.call(".External", c(list("r_call_method", self$pointer, methodName), 
    args, PACKAGE = rSharpEnv$nativePkgName))`: Type:    OSPSuite.Infrastructure.Import.Core.InvalidObservedDataFileException
Message: An error occurred while reading the file. Please check the content.
The exception thrown was:

The type initializer for 'NPOI.OpenXml4Net.OPC.PackageRelationshipCollection' threw an exception.

Method:  Void LoadFromFile(System.String)
Stack trace:
   at OSPSuite.Infrastructure.Import.Core.DataSourceFileReaders.ExcelDataSourceFile.LoadFromFile(String path)
   at OSPSuite.Infrastructure.Import.Core.DataSourceFile.set_Path(String value)
   at OSPSuite.Infrastructure.Import.Core.DataSourceFileParser.For(String path)
   at OSPSuite.Infrastructure.Import.Services.Importer.LoadFile(ColumnInfoCache columnInfos, String fileName, IReadOnlyList`1 metaDataCategories)
   at OSPSuite.Infrastructure.Import.Services.Importer.ImportFromConfiguration(ImporterConfiguration configuration, ColumnInfoCache columnInfos, String fileName, IReadOnlyList`1 metaDataCategories, DataImporterSettings dataImporterSettings)
   at 
Backtrace:
    ▆
 1. └─ospsuite::loadDataSetsFromExcel(...) at test-plot-observed-vs-simulated.R:14:1
 2.   └─dataImporterTask$call(...) at OSPSuite-R/R/utilities-data-set.R:186:3
 3.     └─base::do.call(...)
───────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────
✔ |      1   0 | plot-population-time-profile                                                                                                                                                                                                                                                  
✖ | 1        0 | plot-residuals-vs-simulated                                                                                                                                                                                                                                                   
───────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────
Error (test-plot-residuals-vs-simulated.R:16:1): (code run outside of `test_that()`)
Error in `do.call(".External", c(list("r_call_method", self$pointer, methodName), 
    args, PACKAGE = rSharpEnv$nativePkgName))`: Type:    OSPSuite.Infrastructure.Import.Core.InvalidObservedDataFileException
Message: An error occurred while reading the file. Please check the content.
The exception thrown was:

The type initializer for 'NPOI.OpenXml4Net.OPC.PackageRelationshipCollection' threw an exception.

Method:  Void LoadFromFile(System.String)
Stack trace:
   at OSPSuite.Infrastructure.Import.Core.DataSourceFileReaders.ExcelDataSourceFile.LoadFromFile(String path)
   at OSPSuite.Infrastructure.Import.Core.DataSourceFile.set_Path(String value)
   at OSPSuite.Infrastructure.Import.Core.DataSourceFileParser.For(String path)
   at OSPSuite.Infrastructure.Import.Services.Importer.LoadFile(ColumnInfoCache columnInfos, String fileName, IReadOnlyList`1 metaDataCategories)
   at OSPSuite.Infrastructure.Import.Services.Importer.ImportFromConfiguration(ImporterConfiguration configuration, ColumnInfoCache columnInfos, String fileName, IReadOnlyList`1 metaDataCategories, DataImporterSettings dataImporterSettings)
   at 
Backtrace:
    ▆
 1. └─ospsuite::loadDataSetsFromExcel(...) at test-plot-residuals-vs-simulated.R:16:1
 2.   └─dataImporterTask$call(...) at OSPSuite-R/R/utilities-data-set.R:186:3
 3.     └─base::do.call(...)
───────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────
✖ | 1        0 | plot-residuals-vs-time                                                                                                                                                                                                                                                        
───────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────
Error (test-plot-residuals-vs-time.R:16:1): (code run outside of `test_that()`)
Error in `do.call(".External", c(list("r_call_method", self$pointer, methodName), 
    args, PACKAGE = rSharpEnv$nativePkgName))`: Type:    OSPSuite.Infrastructure.Import.Core.InvalidObservedDataFileException
Message: An error occurred while reading the file. Please check the content.
The exception thrown was:

The type initializer for 'NPOI.OpenXml4Net.OPC.PackageRelationshipCollection' threw an exception.

Method:  Void LoadFromFile(System.String)
Stack trace:
   at OSPSuite.Infrastructure.Import.Core.DataSourceFileReaders.ExcelDataSourceFile.LoadFromFile(String path)
   at OSPSuite.Infrastructure.Import.Core.DataSourceFile.set_Path(String value)
   at OSPSuite.Infrastructure.Import.Core.DataSourceFileParser.For(String path)
   at OSPSuite.Infrastructure.Import.Services.Importer.LoadFile(ColumnInfoCache columnInfos, String fileName, IReadOnlyList`1 metaDataCategories)
   at OSPSuite.Infrastructure.Import.Services.Importer.ImportFromConfiguration(ImporterConfiguration configuration, ColumnInfoCache columnInfos, String fileName, IReadOnlyList`1 metaDataCategories, DataImporterSettings dataImporterSettings)
   at 
Backtrace:
    ▆
 1. └─ospsuite::loadDataSetsFromExcel(...) at test-plot-residuals-vs-time.R:16:1
 2.   └─dataImporterTask$call(...) at OSPSuite-R/R/utilities-data-set.R:186:3
 3.     └─base::do.call(...)
───────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────
✔ |         30 | population                                                                                                                                                                                                                                                                    
✔ |         29 | quantity-pk-parameter [1.6s]                                                                                                                                                                                                                                                  
✔ |          1 | quantity-selection                                                                                                                                                                                                                                                            
✔ |          9 | quantity                                                                                                                                                                                                                                                                      
✔ |          9 | sensitivity-analysis-results                                                                                                                                                                                                                                                  
✔ |          2 | sensitivity-analysis-run-options                                                                                                                                                                                                                                              
✔ |         11 | sensitivity-analysis                                                                                                                                                                                                                                                          
✔ |          7 | simulation-batch-options                                                                                                                                                                                                                                                      
✔ |          7 | simulation-batch                                                                                                                                                                                                                                                              
✔ |          3 | simulation-pk-analyses [1.4s]                                                                                                                                                                                                                                                 
✔ |         17 | simulation-results [1.9s]                                                                                                                                                                                                                                                     
✔ |          4 | simulation-run-options                                                                                                                                                                                                                                                        
✔ |         10 | simulation                                                                                                                                                                                                                                                                    
✔ |         17 | solver-settings                                                                                                                                                                                                                                                               
✔ |         21 | table-formula                                                                                                                                                                                                                                                                 
✔ |          2 | unicode-support                                                                                                                                                                                                                                                               
✔ |      1   0 | user-defined-pk-parameter                                                                                                                                                                                                                                                     
✔ |         16 | utilities-container                                                                                                                                                                                                                                                           
✔ |      1   0 | utilities-data-combined                                                                                                                                                                                                                                                       
✔ |      5   0 | utilities-data-importer-configuration                                                                                                                                                                                                                                         
✔ |          1 | utilities-data-repository                                                                                                                                                                                                                                                     
✔ |      6  18 | utilities-data-set                                                                                                                                                                                                                                                            
✔ |          8 | utilities-entity                                                                                                                                                                                                                                                              
✔ |          3 | utilities-file                                                                                                                                                                                                                                                                
✔ |      1   0 | utilities-individual                                                                                                                                                                                                                                                          
✔ |         18 | utilities-molecule [1.1s]                                                                                                                                                                                                                                                     
✔ |         12 | utilities-output-schema                                                                                                                                                                                                                                                       
✔ |         16 | utilities-output-selections                                                                                                                                                                                                                                                   
✔ |         36 | utilities-parameter [1.7s]                                                                                                                                                                                                                                                    
✔ |          5 | utilities-path                                                                                                                                                                                                                                                                
✔ |   2      7 | utilities-pk-analysis [11.1s]                                                                                                                                                                                                                                                 
─────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────
Warning (test-utilities-pk-analysis.R:31:3): it can return pk analysis for sparse population and only return ids defined in the population file
One or more parsing issues, call `problems()` on your data frame for details, e.g.:
  dat <- vroom(...)
  problems(dat)
Backtrace:
    ▆
 1. ├─ospsuite::pkAnalysesToDataFrame(pkAnalyses) at test-utilities-pk-analysis.R:31:3
 2. │ ├─base::tryCatch(...) at OSPSuite-R/R/utilities-pk-analysis.R:74:3
 3. │ │ └─base (local) tryCatchList(expr, classes, parentenv, handlers)
 4. │ └─readr::read_csv(...) at OSPSuite-R/R/utilities-pk-analysis.R:85:7
 5. │   └─vroom::vroom(...)
 6. │     └─vroom:::vroom_(...)
 7. └─cli (local) `<fn>`(`<chr>`, "vroom_parse_issue")

Warning (test-utilities-pk-analysis.R:59:3): It can convert valid pk-analysis results to data frame
One or more parsing issues, call `problems()` on your data frame for details, e.g.:
  dat <- vroom(...)
  problems(dat)
Backtrace:
    ▆
 1. ├─ospsuite::pkAnalysesToDataFrame(pkAnalyses = pkAnalyses) at test-utilities-pk-analysis.R:59:3
 2. │ ├─base::tryCatch(...) at OSPSuite-R/R/utilities-pk-analysis.R:74:3
 3. │ │ └─base (local) tryCatchList(expr, classes, parentenv, handlers)
 4. │ └─readr::read_csv(...) at OSPSuite-R/R/utilities-pk-analysis.R:85:7
 5. │   └─vroom::vroom(...)
 6. │     └─vroom:::vroom_(...)
 7. └─cli (local) `<fn>`(`<chr>`, "vroom_parse_issue")
─────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────
✔ |         17 | utilities-pk-parameter [1.6s]                                                                                                                                                                                                                                                 
✔ |         16 | utilities-plotting                                                                                                                                                                                                                                                            
✔ |      1   0 | utilities-population                                                                                                                                                                                                                                                          
⠏ |         10 | utilities-quantity                                                                                                                                                                                                                                                            Warning - Could not find quantity with path 'Organism|Liver|NOPE|Volume'.
Warning - Could not find quantity with path 'Organism|Liver|NOPE|Volume'.
⠼ |         25 | utilities-quantity                                                                                                                                                                                                                                                            Warning - Could not find quantity with path 'Organism|Liver|NOPE|Volume'.
Warning - Could not find quantity with path 'Organism|Liver|NOPE|Volume'.
Warning - Could not find quantity with path 'foo'.
✔ |         36 | utilities-quantity [1.4s]
✔ |          7 | utilities-sensitivity-analysis                                                                                                                                                                                                                                                
✔ |         52 | utilities-simulation-results [13.4s]                                                                                                                                                                                                                                          
✔ |         95 | utilities-simulation [65.1s]                                                                                                                                                                                                                                                  
✔ |        116 | utilities-units [1.5s]                                                                                                                                                                                                                                                        
✔ |          2 | utilities                                                                                                                                                                                                                                                                     
✔ |          1 | value-point                                                                                                                                                                                                                                                                   

══ Results ══════════════════════════════════════════════════════════════════════════════════════════════════════════════════════════════════════════════════════════════════════════════════════════════════════════════════════════════════════════════════════════════════════════════════════════════════════════════════════════════════════════════════════════════════════════════════════════════════════════════════════
Duration: 122.6 s

── Skipped tests (36) ───────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────
• On Linux (34): test-data-combined.R:4:1, test-data-importer-configuration.R:4:3, test-data-importer-configuration.R:25:3, test-data-importer-configuration.R:35:3, test-data-importer-configuration.R:46:3, test-data-importer-configuration.R:61:3, test-data-importer-configuration.R:71:3, test-data-importer-configuration.R:82:3, test-data-importer-configuration.R:99:3, test-data-importer-configuration.R:109:3,
  test-data-importer-configuration.R:120:3, test-data-importer-configuration.R:149:3, test-data-importer-configuration.R:172:3, test-data-importer-configuration.R:184:3, test-data-importer-configuration.R:198:3, test-data-importer-configuration.R:207:3, test-data-importer-configuration.R:220:3, test-data-importer-configuration.R:234:3, test-data-importer-configuration.R:249:3,
  test-plot-individual-time-profile.R:2:1, test-plot-population-time-profile.R:5:1, test-user-defined-pk-parameter.R:5:3, test-utilities-data-combined.R:1:1, test-utilities-data-importer-configuration.R:5:3, test-utilities-data-importer-configuration.R:23:3, test-utilities-data-importer-configuration.R:45:3, test-utilities-data-importer-configuration.R:52:3, test-utilities-data-importer-configuration.R:75:3,
  test-utilities-data-set.R:92:3, test-utilities-data-set.R:117:3, test-utilities-data-set.R:203:3, test-utilities-data-set.R:211:3, test-utilities-data-set.R:222:3, test-utilities-data-set.R:260:3
• Skipping (2): test-utilities-individual.R:1:1, test-utilities-population.R:1:1

── Failed tests ─────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────
Error (test-plot-observed-vs-simulated.R:14:1): (code run outside of `test_that()`)
Error in `do.call(".External", c(list("r_call_method", self$pointer, methodName), 
    args, PACKAGE = rSharpEnv$nativePkgName))`: Type:    OSPSuite.Infrastructure.Import.Core.InvalidObservedDataFileException
Message: An error occurred while reading the file. Please check the content.
The exception thrown was:

The type initializer for 'NPOI.OpenXml4Net.OPC.PackageRelationshipCollection' threw an exception.

Method:  Void LoadFromFile(System.String)
Stack trace:
   at OSPSuite.Infrastructure.Import.Core.DataSourceFileReaders.ExcelDataSourceFile.LoadFromFile(String path)
   at OSPSuite.Infrastructure.Import.Core.DataSourceFile.set_Path(String value)
   at OSPSuite.Infrastructure.Import.Core.DataSourceFileParser.For(String path)
   at OSPSuite.Infrastructure.Import.Services.Importer.LoadFile(ColumnInfoCache columnInfos, String fileName, IReadOnlyList`1 metaDataCategories)
   at OSPSuite.Infrastructure.Import.Services.Importer.ImportFromConfiguration(ImporterConfiguration configuration, ColumnInfoCache columnInfos, String fileName, IReadOnlyList`1 metaDataCategories, DataImporterSettings dataImporterSettings)
   at 
Backtrace:
    ▆
 1. └─ospsuite::loadDataSetsFromExcel(...) at test-plot-observed-vs-simulated.R:14:1
 2.   └─dataImporterTask$call(...) at OSPSuite-R/R/utilities-data-set.R:186:3
 3.     └─base::do.call(...)

Error (test-plot-residuals-vs-simulated.R:16:1): (code run outside of `test_that()`)
Error in `do.call(".External", c(list("r_call_method", self$pointer, methodName), 
    args, PACKAGE = rSharpEnv$nativePkgName))`: Type:    OSPSuite.Infrastructure.Import.Core.InvalidObservedDataFileException
Message: An error occurred while reading the file. Please check the content.
The exception thrown was:

The type initializer for 'NPOI.OpenXml4Net.OPC.PackageRelationshipCollection' threw an exception.

Method:  Void LoadFromFile(System.String)
Stack trace:
   at OSPSuite.Infrastructure.Import.Core.DataSourceFileReaders.ExcelDataSourceFile.LoadFromFile(String path)
   at OSPSuite.Infrastructure.Import.Core.DataSourceFile.set_Path(String value)
   at OSPSuite.Infrastructure.Import.Core.DataSourceFileParser.For(String path)
   at OSPSuite.Infrastructure.Import.Services.Importer.LoadFile(ColumnInfoCache columnInfos, String fileName, IReadOnlyList`1 metaDataCategories)
   at OSPSuite.Infrastructure.Import.Services.Importer.ImportFromConfiguration(ImporterConfiguration configuration, ColumnInfoCache columnInfos, String fileName, IReadOnlyList`1 metaDataCategories, DataImporterSettings dataImporterSettings)
   at 
Backtrace:
    ▆
 1. └─ospsuite::loadDataSetsFromExcel(...) at test-plot-residuals-vs-simulated.R:16:1
 2.   └─dataImporterTask$call(...) at OSPSuite-R/R/utilities-data-set.R:186:3
 3.     └─base::do.call(...)

Error (test-plot-residuals-vs-time.R:16:1): (code run outside of `test_that()`)
Error in `do.call(".External", c(list("r_call_method", self$pointer, methodName), 
    args, PACKAGE = rSharpEnv$nativePkgName))`: Type:    OSPSuite.Infrastructure.Import.Core.InvalidObservedDataFileException
Message: An error occurred while reading the file. Please check the content.
The exception thrown was:

The type initializer for 'NPOI.OpenXml4Net.OPC.PackageRelationshipCollection' threw an exception.

Method:  Void LoadFromFile(System.String)
Stack trace:
   at OSPSuite.Infrastructure.Import.Core.DataSourceFileReaders.ExcelDataSourceFile.LoadFromFile(String path)
   at OSPSuite.Infrastructure.Import.Core.DataSourceFile.set_Path(String value)
   at OSPSuite.Infrastructure.Import.Core.DataSourceFileParser.For(String path)
   at OSPSuite.Infrastructure.Import.Services.Importer.LoadFile(ColumnInfoCache columnInfos, String fileName, IReadOnlyList`1 metaDataCategories)
   at OSPSuite.Infrastructure.Import.Services.Importer.ImportFromConfiguration(ImporterConfiguration configuration, ColumnInfoCache columnInfos, String fileName, IReadOnlyList`1 metaDataCategories, DataImporterSettings dataImporterSettings)
   at 
Backtrace:
    ▆
 1. └─ospsuite::loadDataSetsFromExcel(...) at test-plot-residuals-vs-time.R:16:1
 2.   └─dataImporterTask$call(...) at OSPSuite-R/R/utilities-data-set.R:186:3
 3.     └─base::do.call(...)

[ FAIL 3 | WARN 2 | SKIP 36 | PASS 887 ]
Deleting unused snapshots:
• plot-individual-time-profile/both-custom.svg
• plot-individual-time-profile/both-default.svg
• plot-individual-time-profile/geometric-error.svg
• plot-individual-time-profile/lloq.svg
• plot-individual-time-profile/multiple-obs-and-sim.svg
• plot-individual-time-profile/multiple-obs.svg
• plot-individual-time-profile/multiple-sim.svg
• plot-individual-time-profile/no-lloq.svg
• plot-individual-time-profile/single-obs.svg
• plot-individual-time-profile/single-sim.svg
• plot-observed-vs-simulated/aciclovir.svg
• plot-observed-vs-simulated/custom.svg
• plot-observed-vs-simulated/defaults-1-fold-dist.svg
• plot-observed-vs-simulated/defaults-3-fold-dist.svg
• plot-observed-vs-simulated/defaults-without-lines.svg
• plot-observed-vs-simulated/defaults.svg
• plot-observed-vs-simulated/linear-scale-without-folddistance.svg
• plot-observed-vs-simulated/linear-scale.svg
• plot-observed-vs-simulated/lloq-both-direction.svg
• plot-observed-vs-simulated/lloq-vertical.svg
• plot-observed-vs-simulated/multiple-data-sets-one-group.svg
• plot-observed-vs-simulated/na-past-max-sim-time.svg
• plot-population-time-profile/arithmetic-mean-with-2sd.svg
• plot-population-time-profile/arithmetic-mean.svg
• plot-population-time-profile/default-quantiles.svg
• plot-population-time-profile/geometric-mean-with-2sd.svg
• plot-population-time-profile/geometric-mean.svg
• plot-population-time-profile/modified-quantiles.svg
• plot-population-time-profile/multiple-sim-and-obs.svg
• plot-population-time-profile/multiple-sim.svg
• plot-population-time-profile/obs-and-sim.svg
• plot-population-time-profile/only-sim.svg
• plot-residuals-vs-simulated/custom.svg
• plot-residuals-vs-simulated/defaults.svg
• plot-residuals-vs-simulated/log-residuals.svg
• plot-residuals-vs-simulated/multiple-data-sets-one-group.svg
• plot-residuals-vs-simulated/na-past-max-sim-time.svg
• plot-residuals-vs-time/custom.svg
• plot-residuals-vs-time/defaults.svg
• plot-residuals-vs-time/log-residuals.svg
• plot-residuals-vs-time/multiple-data-sets-one-group.svg

rwmcintosh · 2024-05-22T16:24:25Z

3 failing tests. All because of a thrown exception

OSPSuite.Infrastructure.Import.Core.InvalidObservedDataFileException

That's only thrown when importer is catching another exception. Also from the test log

The type initializer for 'NPOI.OpenXml4Net.OPC.PackageRelationshipCollection' threw an exception.

Doesn't seem related to rSharp though

NEWS.md

Felixmil · 2024-05-23T07:54:12Z

I cannot build the website, it fails for pk-analysis vignette. Now idea why, building the vignette directly works.

Building the website worked on my side.

PavelBal · 2024-05-23T08:29:07Z

3 failing tests. All because of a thrown exception

OSPSuite.Infrastructure.Import.Core.InvalidObservedDataFileException

That's only thrown when importer is catching another exception. Also from the test log

The type initializer for 'NPOI.OpenXml4Net.OPC.PackageRelationshipCollection' threw an exception.

Doesn't seem related to rSharp though

Didn't we also had problems with NPOI and tests reading excel files under Windows at the beginning? Missing dependencies?

Yuri05 · 2024-05-23T09:18:58Z

R/parameter-range.R

      # Because of weird issue with nullable value in rClr
+      # https://github.com/Open-Systems-Pharmacology/OSPSuite-R/issues/1369
      if (!is.null(min)) {
        self$min <- min
      }


~~The comment refers to rClr.~~
~~Is just the comment obsolete or the code as well?~~

referenced issue says "reevaluate after rSharp migration". let's put a TODO in the comment here so that we can easily find it later

Yuri05 · 2024-05-23T09:33:32Z

README.Rmd

-    [here](https://aka.ms/vs/16/release/vc_redist.x64.exe)
-  - .NET Framework 4.7.2 available
-    [here](https://go.microsoft.com/fwlink/?LinkID=863265)
+- Latest Microsoft Visual C++ Redistributable for Visual Studio 2015, 2017 and 2019 available [here](https://support.microsoft.com/en-us/help/2977003/the-latest-supported-visual-c-downloads) 


please extend the description "... 2015, 2017, 2019 and 2022 ..."

Yuri05 · 2024-05-23T09:39:52Z

install_dependencies.R

+unzip("rsharp.zip")
+rSharp_archive <- list.files( pattern = "rSharp.*\\.zip")
+install.packages(rSharp_archive, repos = NULL, type = "binary")


why do we need these extra steps instead of just
install.packages("rsharp.zip", repos = NULL, type = "binary") ?

Because artifacts built by are zipped. So the package is one level deeper in the archive, and R doesn't expect that.

But it won't be needed once we go to GHactions because it will be able to build from source directly (see https://github.com/Open-Systems-Pharmacology/OSPSuite-R/actions/runs/9204757821/job/25318948079#step:3:5051)

Yuri05 · 2024-05-23T09:50:06Z

@PavelBal We also need to adjust all C++ libs:

Update versions in packages.win.config
Rename packages.ubuntu18.config to packages.ubuntu22.config and update versions
Remove packages.centOS7.config
Update package generation (remove centos package and switch from ubuntu18 to ubuntu22) in appveyor-nightly.yml
Update C++ libs (and corresponding .net libs) in inst/lib (OSPSuite.FuncParser.dll / OSPSuite.FuncParserNative.dll etc.)

If you want, I can do the changes in the next PR - just let me know.

PavelBal · 2024-05-23T10:58:10Z

If you want, I can do the changes in the next PR - just let me know.

Yes please do, I have no idea how to :D

I propose that you create a PR into this branch and we maintain both the develop and the r-sharp-r6 branches for now, and only merge R6 into developed once the full functionality is restored.

rwmcintosh · 2024-05-23T12:02:27Z

3 failing tests. All because of a thrown exception
OSPSuite.Infrastructure.Import.Core.InvalidObservedDataFileException
That's only thrown when importer is catching another exception. Also from the test log
The type initializer for 'NPOI.OpenXml4Net.OPC.PackageRelationshipCollection' threw an exception.
Doesn't seem related to rSharp though

Didn't we also had problems with NPOI and tests reading excel files under Windows at the beginning? Missing dependencies?

IIRC that was when we first tried to load PK-Sim, but yes, that was due to a mismatch in the target runtime. Let me see if I can find it on Linux.

rwmcintosh · 2024-05-23T15:58:18Z

3 failing tests. All because of a thrown exception
OSPSuite.Infrastructure.Import.Core.InvalidObservedDataFileException
That's only thrown when importer is catching another exception. Also from the test log
The type initializer for 'NPOI.OpenXml4Net.OPC.PackageRelationshipCollection' threw an exception.
Doesn't seem related to rSharp though

Didn't we also had problems with NPOI and tests reading excel files under Windows at the beginning? Missing dependencies?

IIRC that was when we first tried to load PK-Sim, but yes, that was due to a mismatch in the target runtime. Let me see if I can find it on Linux.

We made it work on Windows by placing System.Configuration.ConfigurationManager.dll into inst/lib. That is not working for Ubuntu though. The DLL is not found or not loaded by the runtime.

temporarily disable failing tests Co-authored-by: Yuri05 <Yuri05@github.com>

Yuri05 · 2024-05-24T13:28:50Z

@PavelBal @Felixmil For me good to merge and check if the nightly build runs through and creates the packages.
(I guess it will fail due to PK-Sim based tests (create Individual/Population))

Yuri05 · 2024-05-27T16:44:39Z

@PavelBal @Felixmil @rwmcintosh @msevestre Any objections to merge this PR?

msevestre · 2024-05-27T17:37:20Z

none for me

rwmcintosh · 2024-05-27T21:38:11Z

Merge-away

PavelBal · 2024-05-28T07:33:31Z

NO!!!! Can we revert this, please @msevestre @Yuri05 ? We need a fully functional develop branch and this is NOT fully functional! As long as the create individual / create populations functionalities are not migrated, we need to maintain two branches.

This reverts commit 0fa9efa.

PavelBal and others added 30 commits March 1, 2024 09:40

Added authors to _pkgdown.yml

64b2904

- Exchange rClr for rSharp as dependency

c3aa982

Docs

cb252aa

Replace all calls to rClr by calls to rShapr

a9ff16f

Replace clrLoadAssembly by loadAssembly

afa99c5

- Replace rClrCallStatic by callStatic

5e6ef83

- Run docs

getEnumNames

0900614

Docs

Use correct package reference in test

d17ffd0

- Remove enc2utf, as conversion is done in rSharp

7726ebc

Moved some wrappers to NetObject in rSharp

c4ea6f6

Loading package works

ec28d58

.wrapProperty

4f3f2b5

Replace all clrGet

d2f0e17

Replace all clrSet

44901ff

Replace clrCall

904681c

Replace clrNew

2cfd437

DotNetWrapper expects a NetObject and not a pointer.

ea2db97

Remove ref

7f40e86

Fix all initilialize

c2e4b54

Remove direct pointers

6b78e5b

Styler

58777e4

Documentation

4698e28

Correct calling of private print methods

98da2e8

Prepend '.' to wrapPropertyReadOnly

379610f

Prepend '.' to throwPropertyISREadONly

533aa3d

Fix test for dotNetWrapper

cbd6af7

Fix clrGetType to getType

ddf7295

use NPOI for .NET Core

9d5057e

Fix .wrapProperty

9e35238

Fix print calls in DataCombined

8e8e505

Yuri05 reviewed May 22, 2024

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Felixmil added 4 commits May 23, 2024 09:22

unzip rSharp archive before installing it

052bf1d

correct typo

fd01545

delete and ignore tests/testthat/*.pdf

3b829cd

Tweak test to avoid writing file in package directory

a05bf4a

Yuri05 reviewed May 23, 2024

View reviewed changes

Yuri05 mentioned this pull request May 24, 2024

update c++ libs #1415

Merged

update c++ libs (#1415)

30fa5fd

temporarily disable failing tests Co-authored-by: Yuri05 <Yuri05@github.com>

Yuri05 approved these changes May 24, 2024

View reviewed changes

msevestre merged commit 0fa9efa into develop May 27, 2024
1 check passed

msevestre deleted the r-sharp-r6 branch May 27, 2024 21:40

PavelBal restored the r-sharp-r6 branch May 28, 2024 07:33

Felixmil added a commit that referenced this pull request May 28, 2024

Revert "Use rSharp instead of rClr (#1376)"

f03e031

This reverts commit 0fa9efa.

PavelBal pushed a commit that referenced this pull request May 28, 2024

Revert "Use rSharp instead of rClr (#1376)" (#1416)

66eb79b

This reverts commit 0fa9efa.

Yuri05 mentioned this pull request May 28, 2024

unzip artifacts in release Open-Systems-Pharmacology/rSharp#152

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Use rSharp instead of rClr #1376

Use rSharp instead of rClr #1376

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Use rSharp instead of rClr #1376

Use rSharp instead of rClr #1376

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