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New dataset tests fail on Linux #647

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Yuri05 opened this issue Oct 13, 2021 · 2 comments
Closed

New dataset tests fail on Linux #647

Yuri05 opened this issue Oct 13, 2021 · 2 comments

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@Yuri05
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Yuri05 commented Oct 13, 2021

Some of the newly added tests fail on Linux. All from test-utilities-dataset.R

@msevestre @PavelBal
Is this functionality not supposed to be run under linux? Then we should disable those tests (e.g. with skip_on_os("linux") )
Or is anything missing in the linux installation (what?)?

  • Failing test 1:

    OSPSuite-R/tests/testthat/test-utilities-data-set.R

    Lines 57 to 71 in 1014f04

    test_that("It can convert a data set with metaData", {
    dataSet$addMetaData("Organ", "Blood")
    expect_equal(
    dataSetToDataFrame(dataSet),
    data.frame(
    name = rep(dataSet$name, 5), xValues = dataSet$xValues,
    yValues = dataSet$yValues, yErrorValues = dataSet$yErrorValues,
    xDimension = rep(dataSet$xDimension, 5), xUnit = rep(dataSet$xUnit, 5),
    yDimension = rep(dataSet$yDimension, 5), yUnit = rep(dataSet$yUnit, 5),
    yErrorType = rep(dataSet$yErrorType, 5), yErrorUnit = rep(dataSet$yErrorUnit, 5),
    molWeight = rep(dataSet$molWeight, 5), lloq = rep(dataSet$LLOQ, 5),
    Organ = rep("Blood", 5)
    )
    )
    })
  • Failing test 2:

    OSPSuite-R/tests/testthat/test-utilities-data-set.R

    Lines 73 to 95 in 1014f04

    test_that("It can convert a list of data sets", {
    dataSet2 <- DataSet$new()
    dataSet2$setValues(xValues = c(6, 7, 8), yValues = c(11, 21, 31))
    dataSet2$molWeight <- 456
    dataSet2$addMetaData("Compartment", "Plasma")
    expect_equal(
    dataSetToDataFrame(list(dataSet, dataSet2)),
    data.frame(
    name = c(rep(dataSet$name, 5), rep("", 3)), xValues = c(dataSet$xValues, dataSet2$xValues),
    yValues = c(dataSet$yValues, dataSet2$yValues), yErrorValues = c(dataSet$yErrorValues, rep(NA, 3)),
    xDimension = c(rep(dataSet$xDimension, 5), rep(dataSet2$xDimension, 3)),
    xUnit = c(rep(dataSet$xUnit, 5), rep(dataSet2$xUnit, 3)),
    yDimension = c(rep(dataSet$yDimension, 5), rep(dataSet2$yDimension, 3)),
    yUnit = c(rep(dataSet$yUnit, 5), rep(dataSet2$yUnit, 3)),
    yErrorType = c(rep(dataSet$yErrorType, 5), rep(NA_character_, 3)),
    yErrorUnit = c(rep(dataSet$yErrorUnit, 5), rep(NA_character_, 3)),
    molWeight = c(rep(dataSet$molWeight, 5), rep(dataSet2$molWeight, 3)),
    lloq = c(rep(dataSet$LLOQ, 5), rep(NA, 3)),
    Organ = c(rep("Blood", 5), rep(NA, 3)), Compartment = c(rep(NA, 5), rep("Plasma", 3))
    )
    )
    })
  • Failing test 3:

    OSPSuite-R/tests/testthat/test-utilities-data-set.R

    Lines 152 to 155 in 1014f04

    test_that("it returns an empty list when loading from file with one sheet without
    sheet definition in configuration and importAllSheets == FALSE", {
    expect_named(loadDataSetsFromExcel(xlsFilePath = xlsFilePath, importerConfiguration = importerConfiguration), character())
    })
  • Failing test 4:

    OSPSuite-R/tests/testthat/test-utilities-data-set.R

    Lines 157 to 162 in 1014f04

    test_that("it can load when loading from file with one sheet without
    sheet definition in configuration and importAllSheets == FALSE", {
    dataSets <- loadDataSetsFromExcel(xlsFilePath = xlsFilePath, importerConfiguration = importerConfiguration, importAllSheets = TRUE)
    expect_true(isOfType(dataSets, DataSet))
    expect_equal(length(dataSets), 4)
    })
  • Failing test 5:

    OSPSuite-R/tests/testthat/test-utilities-data-set.R

    Lines 164 to 169 in 1014f04

    test_that("it can convert DataSets loaded from excel to data.frame", {
    dataSets <- loadDataSetsFromExcel(xlsFilePath = xlsFilePath, importerConfiguration = importerConfiguration, importAllSheets = TRUE)
    dataSetsFrame <- dataSetToDataFrame(dataSets)
    expect_equal(names(dataSetsFrame), c(
    "name",
    "xValues",
FAILED TESTS 
#14 424.4 ══ Failed tests ════════════════════════════════════════════════════════════════
#14 424.5 ── Failure (test-utilities-data-set.R:59:3): It can convert a data set with metaData ──
#14 424.5 dataSetToDataFrame(dataSet) not equal to data.frame(...).
#14 424.5 Component “Organ”: Modes: character, numeric
#14 424.5 Component “Organ”: Attributes: < target is NULL, current is list >
#14 424.5 Component “Organ”: target is character, current is factor
#14 424.5 ── Failure (test-utilities-data-set.R:79:3): It can convert a list of data sets ──
#14 424.5 dataSetToDataFrame(list(dataSet, dataSet2)) not equal to data.frame(...).
#14 424.5 Component “Organ”: Modes: character, numeric
#14 424.5 Component “Organ”: Attributes: < target is NULL, current is list >
#14 424.5 Component “Organ”: target is character, current is factor
#14 424.5 Component “Compartment”: Modes: character, numeric
#14 424.5 Component “Compartment”: Attributes: < target is NULL, current is list >
#14 424.5 Component “Compartment”: target is character, current is factor
#14 424.5 ── Error (test-utilities-data-set.R:154:3): it returns an empty list when loading from file with one sheet without
#14 424.5           sheet definition in configuration and importAllSheets == FALSE ──
#14 424.5 Error: Type:    OSPSuite.Infrastructure.Import.Core.InvalidObservedDataFileException
#14 424.5 Message: An error occurred while reading the file. Please check the content.
#14 424.5 The exception thrown was:
#14 424.5 
#14 424.5 Error Initializing the configuration system.
#14 424.5 
#14 424.5 Method:  OSPSuite.Utility.Collections.Cache`2[System.String,OSPSuite.Infrastructure.Import.Core.DataSheet] LoadFromFile(System.String)
#14 424.5 Stack trace:
#14 424.5   at OSPSuite.Infrastructure.Import.Core.DataSourceFileReaders.ExcelDataSourceFile.LoadFromFile (System.String path) [0x0011b] in <93cbb51fbfbe432491d84975ce64ec07>:0 
#14 424.5   at OSPSuite.Infrastructure.Import.Core.DataSourceFile.set_Path (System.String value) [0x00008] in <93cbb51fbfbe432491d84975ce64ec07>:0 
#14 424.5   at OSPSuite.Infrastructure.Import.Core.DataSourceFileParser.For (System.String path) [0x00056] in <93cbb51fbfbe432491d84975ce64ec07>:0 
#14 424.5   at OSPSuite.Infrastructure.Import.Services.Importer.LoadFile (System.Collections.Generic.IReadOnlyList`1[T] columnInfos, System.String fileName, System.Collections.Generic.IRead
#14 424.5 Backtrace:
#14 424.5     █
#14 424.5  1. ├─testthat::expect_named(...) test-utilities-data-set.R:154:2
#14 424.5  2. │ └─testthat::quasi_label(enquo(object), label, arg = "object")
#14 424.5  3. │   └─rlang::eval_bare(expr, quo_get_env(quo))
#14 424.5  4. └─ospsuite::loadDataSetsFromExcel(xlsFilePath = xlsFilePath, importerConfiguration = importerConfiguration)
#14 424.5  5.   └─rClr::clrCall(...)
#14 424.5 ── Error (test-utilities-data-set.R:159:3): it can load when loading from file with one sheet without
#14 424.5           sheet definition in configuration and importAllSheets == FALSE ──
#14 424.5 Error: Type:    OSPSuite.Infrastructure.Import.Core.InvalidObservedDataFileException
#14 424.5 Message: An error occurred while reading the file. Please check the content.
#14 424.5 The exception thrown was:
#14 424.5 
#14 424.5 Error Initializing the configuration system.
#14 424.5 
#14 424.5 Method:  OSPSuite.Utility.Collections.Cache`2[System.String,OSPSuite.Infrastructure.Import.Core.DataSheet] LoadFromFile(System.String)
#14 424.5 Stack trace:
#14 424.5   at OSPSuite.Infrastructure.Import.Core.DataSourceFileReaders.ExcelDataSourceFile.LoadFromFile (System.String path) [0x0011b] in <93cbb51fbfbe432491d84975ce64ec07>:0 
#14 424.5   at OSPSuite.Infrastructure.Import.Core.DataSourceFile.set_Path (System.String value) [0x00008] in <93cbb51fbfbe432491d84975ce64ec07>:0 
#14 424.5   at OSPSuite.Infrastructure.Import.Core.DataSourceFileParser.For (System.String path) [0x00056] in <93cbb51fbfbe432491d84975ce64ec07>:0 
#14 424.5   at OSPSuite.Infrastructure.Import.Services.Importer.LoadFile (System.Collections.Generic.IReadOnlyList`1[T] columnInfos, System.String fileName, System.Collections.Generic.IRead
#14 424.5 Backtrace:
#14 424.5     █
#14 424.5  1. └─ospsuite::loadDataSetsFromExcel(...) test-utilities-data-set.R:159:2
#14 424.5  2.   └─rClr::clrCall(...)
#14 424.5 ── Error (test-utilities-data-set.R:165:3): it can convert DataSets loaded from excel to data.frame ──
#14 424.5 Error: Type:    OSPSuite.Infrastructure.Import.Core.InvalidObservedDataFileException
#14 424.5 Message: An error occurred while reading the file. Please check the content.
#14 424.5 The exception thrown was:
#14 424.5 
#14 424.5 Error Initializing the configuration system.
#14 424.5 
#14 424.5 Method:  OSPSuite.Utility.Collections.Cache`2[System.String,OSPSuite.Infrastructure.Import.Core.DataSheet] LoadFromFile(System.String)
#14 424.5 Stack trace:
#14 424.5   at OSPSuite.Infrastructure.Import.Core.DataSourceFileReaders.ExcelDataSourceFile.LoadFromFile (System.String path) [0x0011b] in <93cbb51fbfbe432491d84975ce64ec07>:0 
#14 424.5   at OSPSuite.Infrastructure.Import.Core.DataSourceFile.set_Path (System.String value) [0x00008] in <93cbb51fbfbe432491d84975ce64ec07>:0 
#14 424.5   at OSPSuite.Infrastructure.Import.Core.DataSourceFileParser.For (System.String path) [0x00056] in <93cbb51fbfbe432491d84975ce64ec07>:0 
#14 424.5   at OSPSuite.Infrastructure.Import.Services.Importer.LoadFile (System.Collections.Generic.IReadOnlyList`1[T] columnInfos, System.String fileName, System.Collections.Generic.IRead
#14 424.5 Backtrace:
#14 424.5     █
#14 424.5  1. └─ospsuite::loadDataSetsFromExcel(...) test-utilities-data-set.R:165:2
#14 424.5  2.   └─rClr::clrCall(...)
#14 424.5 
#14 424.5 [ FAIL 5 | WARN 3 | SKIP 36 | PASS 720 ]
#14 425.0 Error: Test failures
#14 425.0 Execution halted
#14 ERROR: executor failed running [/bin/sh -c R --no-save -e "setwd(system.file('tests', package = 'ospsuite')); source('testthat.R')"]: exit code: 1
------
 > [9/9] RUN R --no-save -e "setwd(system.file('tests', package = 'ospsuite')); source('testthat.R')":
#14 424.5   at OSPSuite.Infrastructure.Import.Core.DataSourceFileParser.For (System.String path) [0x00056] in <93cbb51fbfbe432491d84975ce64ec07>:0 
#14 424.5   at OSPSuite.Infrastructure.Import.Services.Importer.LoadFile (System.Collections.Generic.IReadOnlyList`1[T] columnInfos, System.String fileName, System.Collections.Generic.IRead
#14 424.5 Backtrace:
#14 424.5     █
#14 424.5  1. └─ospsuite::loadDataSetsFromExcel(...) test-utilities-data-set.R:165:2
#14 424.5  2.   └─rClr::clrCall(...)
#14 424.5 
#14 424.5 [ FAIL 5 | WARN 3 | SKIP 36 | PASS 720 ]
@msevestre
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msevestre commented Oct 13, 2021 •
edited
Loading

Importer does not work under linux. NPOI (even though it should be .net standard compatible) crashes miserably under linux

@msevestre
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see Open-Systems-Pharmacology/OSPSuite.Core#1288

Yuri05 pushed a commit to Yuri05/Docker-Images-Ospsuite-R that referenced this issue Oct 13, 2021
temporarily remove test-utilities-data-set.R before testing (s. Open-…
b11264a 
…Systems-Pharmacology/OSPSuite-R#647)
Yuri05 added a commit to Open-Systems-Pharmacology/Docker-Images-Ospsuite-R that referenced this issue Oct 13, 2021
@Yuri05
ospsuite 10.0.70 (#3)
61583be 
* ospsuite 10.0.70

* no fail fast

* temporarily remove test-utilities-data-set.R before testing (s. Open-Systems-Pharmacology/OSPSuite-R#647)

Co-authored-by: Yuri05 <Yuri05@github.com>
Yuri05 pushed a commit to Yuri05/OSPSuite-R that referenced this issue Oct 18, 2021
Fixes Open-Systems-Pharmacology#647 New dataset tests fail on Linux (…
f6211f5 
…tests temporarily disabled)
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@msevestre @Yuri05