Last updated on 2024-11-27 19:49:13 CET.
| Flavor | Version | Tinstall | Tcheck | Ttotal | Status | Flags |
|---|---|---|---|---|---|---|
| r-devel-linux-x86_64-debian-clang | 1.23.2 | 5.50 | 80.94 | 86.44 | OK | |
| r-devel-linux-x86_64-debian-gcc | 1.23.2 | 4.12 | 56.79 | 60.91 | ERROR | |
| r-devel-linux-x86_64-fedora-clang | 1.23.2 | 145.97 | OK | |||
| r-devel-linux-x86_64-fedora-gcc | 1.23.2 | 148.88 | OK | |||
| r-devel-windows-x86_64 | 1.23.2 | 7.00 | 140.00 | 147.00 | OK | |
| r-patched-linux-x86_64 | 1.23.2 | 6.37 | 77.02 | 83.39 | OK | |
| r-release-linux-x86_64 | 1.23.2 | 4.82 | 79.42 | 84.24 | OK | |
| r-release-macos-arm64 | 1.23.2 | 46.00 | OK | |||
| r-release-macos-x86_64 | 1.23.2 | 85.00 | WARN | |||
| r-release-windows-x86_64 | 1.23.2 | 8.00 | 141.00 | 149.00 | OK | |
| r-oldrel-macos-arm64 | 1.23.2 | 55.00 | OK | |||
| r-oldrel-macos-x86_64 | 1.23.2 | 83.00 | OK | |||
| r-oldrel-windows-x86_64 | 1.23.2 | 7.00 | 148.00 | 155.00 | OK |
Version: 1.23.2
Check: examples
Result: ERROR
Running examples in ‘biogas-Ex.R’ failed
The error most likely occurred in:
> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: calcBgGD
> ### Title: Calculate Biogas Production from Gas Density Data (GD-BMP)
> ### Aliases: calcBgGD
> ### Keywords: chron manip
>
> ### ** Examples
>
>
> data("UQGDBiogas")
> data("UQGDSetup")
>
> head(UQGDBiogas)
id time.d vol mass.init mass.final
1 I1 0 0 183.2661 183.2661
2 I2 0 0 183.8875 183.8875
3 I3 0 0 183.7484 183.7484
4 L1 0 0 185.2874 185.2874
5 L2 0 0 188.5043 188.5043
6 L3 0 0 184.1758 184.1758
> head(UQGDSetup)
id descrip m.inoc m.sub m.tot vol.hs m.sub.vs isr
1 I1 Inoculum 80.004 0.0000 80.0040 79.9960 0.0000000 NA
2 I2 Inoculum 80.032 0.0000 80.0320 79.9680 0.0000000 NA
3 I3 Inoculum 80.011 0.0000 80.0110 79.9890 0.0000000 NA
4 L1 Cellulose 80.030 0.8515 80.8631 79.1400 0.8293398 1.834052
5 L2 Cellulose 80.012 0.8511 80.8600 79.0236 0.8289503 1.834502
6 L3 Cellulose 80.008 0.8520 80.9764 79.0116 0.8298268 1.832472
>
> cbg <- calcBgGD(UQGDBiogas,
+ temp.vol = 20, pres.vol = 1013.25,
+ temp.grav = 30, pres.grav = 1500,
+ id.name = 'id', vol.name = 'vol',
+ m.pre.name = 'mass.init', m.post.name = 'mass.final',
+ time.name = 'time.d', unit.pres = 'mbar')
Using a standard pressure of 1013.25 mbar and standard temperature of 0 C for standardizing volume.
Error in options(scipen = oldscipen) : invalid 'scipen'
Calls: calcBgGD ... GDComp -> gasDens -> molMass -> readFormula -> options
Execution halted
Flavor: r-devel-linux-x86_64-debian-gcc
Version: 1.23.2
Check: tests
Result: ERROR
Running ‘testthat.R’ [2s/2s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
> library(testthat)
> library(biogas)
>
> test_check("biogas")
[ FAIL 18 | WARN 2 | SKIP 0 | PASS 17 ]
══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test_HighLevelFunctions.R:9:3'): default methane prediction from COD is stable ──
Error in `options(scipen = oldscipen)`: invalid 'scipen'
Backtrace:
▆
1. ├─testthat::expect_equal(round(predBg(COD = 1), 4), 349.3842) at test_HighLevelFunctions.R:9:3
2. │ └─testthat::quasi_label(enquo(object), label, arg = "object")
3. │ └─rlang::eval_bare(expr, quo_get_env(quo))
4. └─biogas::predBg(COD = 1)
5. └─biogas::molMass("O2")
6. └─biogas:::readFormula(f)
7. └─base::options(scipen = oldscipen)
── Error ('test_HighLevelFunctions.R:13:3'): default methane prediction from COD is stable with fs argument ──
Error in `options(scipen = oldscipen)`: invalid 'scipen'
Backtrace:
▆
1. ├─testthat::expect_equal(...) at test_HighLevelFunctions.R:13:3
2. │ └─testthat::quasi_label(enquo(object), label, arg = "object")
3. │ └─rlang::eval_bare(expr, quo_get_env(quo))
4. └─biogas::predBg(COD = 1, fs = 0.1)
5. └─biogas::molMass("O2")
6. └─biogas:::readFormula(f)
7. └─base::options(scipen = oldscipen)
── Error ('test_HighLevelFunctions.R:17:3'): default methane prediction from COD is stable with fd argument ──
Error in `options(scipen = oldscipen)`: invalid 'scipen'
Backtrace:
▆
1. ├─testthat::expect_equal(...) at test_HighLevelFunctions.R:17:3
2. │ └─testthat::quasi_label(enquo(object), label, arg = "object")
3. │ └─rlang::eval_bare(expr, quo_get_env(quo))
4. └─biogas::predBg(COD = 1, fd = 0.9)
5. └─biogas::molMass("O2")
6. └─biogas:::readFormula(f)
7. └─base::options(scipen = oldscipen)
── Error ('test_HighLevelFunctions.R:21:3'): default methane prediction from COD is stable ──
Error in `options(scipen = oldscipen)`: invalid 'scipen'
Backtrace:
▆
1. ├─testthat::expect_equal(round(predBg(COD = 1), 4), 349.3842) at test_HighLevelFunctions.R:21:3
2. │ └─testthat::quasi_label(enquo(object), label, arg = "object")
3. │ └─rlang::eval_bare(expr, quo_get_env(quo))
4. └─biogas::predBg(COD = 1)
5. └─biogas::molMass("O2")
6. └─biogas:::readFormula(f)
7. └─base::options(scipen = oldscipen)
── Error ('test_HighLevelFunctions.R:25:3'): default methane prediction from predBg using a formula is stable ──
Error in `options(scipen = oldscipen)`: invalid 'scipen'
Backtrace:
▆
1. ├─testthat::expect_equal(...) at test_HighLevelFunctions.R:25:3
2. │ └─testthat::quasi_label(enquo(object), label, arg = "object")
3. │ └─rlang::eval_bare(expr, quo_get_env(quo))
4. └─biogas::predBg("C6H10O6")
5. ├─base::t(...)
6. └─base::mapply(...)
7. └─biogas (local) `<fn>`(form = dots[[1L]][[1L]], elements = `<chr>`, min.elements = `<chr>`)
8. └─base::options(scipen = oldscipen)
── Error ('test_HighLevelFunctions.R:81:3'): cumulative sum, rates and methane volume are corrrectly calculated using mass + one required value for comp, temp and pres ──
Error in `options(scipen = oldscipen)`: invalid 'scipen'
Backtrace:
▆
1. ├─base::data.frame(...) at test_HighLevelFunctions.R:81:3
2. └─biogas::mass2vol(...)
3. └─biogas::molMass("CH4")
4. └─biogas:::readFormula(f)
5. └─base::options(scipen = oldscipen)
── Error ('test_LowLevelFunctions.R:33:3'): readFormula reads correctly the formulas independement from case sensitivity and double letter elements ──
Error in `options(scipen = oldscipen)`: invalid 'scipen'
Backtrace:
▆
1. ├─testthat::expect_equal(...) at test_LowLevelFunctions.R:33:3
2. │ └─testthat::quasi_label(enquo(object), label, arg = "object")
3. │ └─rlang::eval_bare(expr, quo_get_env(quo))
4. └─biogas:::readFormula("c6h12o6")
5. └─base::options(scipen = oldscipen)
── Error ('test_LowLevelFunctions.R:53:3'): molMass results with one letter element are correct ──
Error in `options(scipen = oldscipen)`: invalid 'scipen'
Backtrace:
▆
1. ├─testthat::expect_equal(molMass("C6H12O6"), mmcellu, tolerance = 0.01) at test_LowLevelFunctions.R:53:3
2. │ └─testthat::quasi_label(enquo(object), label, arg = "object")
3. │ └─rlang::eval_bare(expr, quo_get_env(quo))
4. └─biogas::molMass("C6H12O6")
5. └─biogas:::readFormula(f)
6. └─base::options(scipen = oldscipen)
── Error ('test_LowLevelFunctions.R:56:3'): molMass results are not influencend by case sensitivity ──
Error in `options(scipen = oldscipen)`: invalid 'scipen'
Backtrace:
▆
1. ├─testthat::expect_equal(molMass("c6h12o6"), molMass("C6H12O6")) at test_LowLevelFunctions.R:56:3
2. │ └─testthat::quasi_label(enquo(object), label, arg = "object")
3. │ └─rlang::eval_bare(expr, quo_get_env(quo))
4. └─biogas::molMass("c6h12o6")
5. └─biogas:::readFormula(f)
6. └─base::options(scipen = oldscipen)
── Error ('test_LowLevelFunctions.R:60:3'): molMass results is correct for non organic formula - two letter elements ──
Error in `options(scipen = oldscipen)`: invalid 'scipen'
Backtrace:
▆
1. ├─testthat::expect_equal(molMass("NaCl"), mmNaCl, tolerance = 0.01) at test_LowLevelFunctions.R:60:3
2. │ └─testthat::quasi_label(enquo(object), label, arg = "object")
3. │ └─rlang::eval_bare(expr, quo_get_env(quo))
4. └─biogas::molMass("NaCl")
5. └─biogas:::readFormula(f)
6. └─base::options(scipen = oldscipen)
── Error ('test_LowLevelFunctions.R:64:3'): molMass result is correct for formula mixing one and two letter elements ──
Error in `options(scipen = oldscipen)`: invalid 'scipen'
Backtrace:
▆
1. ├─testthat::expect_equal(molMass("CHONNaClSPK"), mm, tolerance = 0.01) at test_LowLevelFunctions.R:64:3
2. │ └─testthat::quasi_label(enquo(object), label, arg = "object")
3. │ └─rlang::eval_bare(expr, quo_get_env(quo))
4. └─biogas::molMass("CHONNaClSPK")
5. └─biogas:::readFormula(f)
6. └─base::options(scipen = oldscipen)
── Error ('test_LowLevelFunctions.R:67:3'): molMass result is correct for formula with parentheses ──
Error in `options(scipen = oldscipen)`: invalid 'scipen'
Backtrace:
▆
1. ├─testthat::expect_equal(molMass("FeSO4(H2O)7"), 278.0146, tolerance = 0.01) at test_LowLevelFunctions.R:67:3
2. │ └─testthat::quasi_label(enquo(object), label, arg = "object")
3. │ └─rlang::eval_bare(expr, quo_get_env(quo))
4. └─biogas::molMass("FeSO4(H2O)7")
5. └─biogas:::readFormula(f)
6. └─base::options(scipen = oldscipen)
── Error ('test_LowLevelFunctions.R:74:3'): calcCOD results with one letter elelement are correct ──
Error in `options(scipen = oldscipen)`: invalid 'scipen'
Backtrace:
▆
1. └─biogas::molMass("C6H12O6") at test_LowLevelFunctions.R:74:3
2. └─biogas:::readFormula(f)
3. └─base::options(scipen = oldscipen)
── Error ('test_LowLevelFunctions.R:78:3'): calcCOD results are not influenced by case sensitivity ──
Error in `options(scipen = oldscipen)`: invalid 'scipen'
Backtrace:
▆
1. ├─testthat::expect_equal(calcCOD("c6h12o6"), calcCOD("C6H12O6")) at test_LowLevelFunctions.R:78:3
2. │ └─testthat::quasi_label(enquo(object), label, arg = "object")
3. │ └─rlang::eval_bare(expr, quo_get_env(quo))
4. └─biogas::calcCOD("c6h12o6")
5. └─biogas::molMass(form)
6. └─biogas:::readFormula(f)
7. └─base::options(scipen = oldscipen)
── Error ('test_LowLevelFunctions.R:81:3'): calcCOD result is null for non organic formula - two letter elements ──
Error in `options(scipen = oldscipen)`: invalid 'scipen'
Backtrace:
▆
1. ├─testthat::expect_equal(calcCOD("NaCl"), 0) at test_LowLevelFunctions.R:81:3
2. │ └─testthat::quasi_label(enquo(object), label, arg = "object")
3. │ └─rlang::eval_bare(expr, quo_get_env(quo))
4. └─biogas::calcCOD("NaCl")
5. └─biogas::molMass(form)
6. └─biogas:::readFormula(f)
7. └─base::options(scipen = oldscipen)
── Error ('test_LowLevelFunctions.R:84:3'): calcCOD gives correct vectorized results ──
Error in `options(scipen = oldscipen)`: invalid 'scipen'
Backtrace:
▆
1. ├─testthat::expect_equal(...) at test_LowLevelFunctions.R:84:3
2. │ └─testthat::quasi_label(enquo(object), label, arg = "object")
3. │ └─rlang::eval_bare(expr, quo_get_env(quo))
4. └─biogas::calcCOD("CH3CH2OH")
5. └─biogas::molMass(form)
6. └─biogas:::readFormula(f)
7. └─base::options(scipen = oldscipen)
── Error ('test_LowLevelFunctions.R:102:3'): vol2mass results are stables ──────
Error in `options(scipen = oldscipen)`: invalid 'scipen'
Backtrace:
▆
1. └─biogas::molMass("CH4") at test_LowLevelFunctions.R:102:3
2. └─biogas:::readFormula(f)
3. └─base::options(scipen = oldscipen)
── Error ('test_LowLevelFunctions.R:117:3'): mass2vol non vectorised result is correct ──
Error in `options(scipen = oldscipen)`: invalid 'scipen'
Backtrace:
▆
1. └─biogas::molMass("CH4") at test_LowLevelFunctions.R:117:3
2. └─biogas:::readFormula(f)
3. └─base::options(scipen = oldscipen)
[ FAIL 18 | WARN 2 | SKIP 0 | PASS 17 ]
Error: Test failures
Execution halted
Flavor: r-devel-linux-x86_64-debian-gcc
Version: 1.23.2
Check: re-building of vignette outputs
Result: ERROR
Error(s) in re-building vignettes:
...
--- re-building ‘biogas_quick_start.Rnw’ using knitr
Quitting from lines 394-395 [unnamed-chunk-14] (biogas_quick_start.Rnw)
Error: processing vignette 'biogas_quick_start.Rnw' failed with diagnostics:
invalid 'scipen'
--- failed re-building ‘biogas_quick_start.Rnw’
--- re-building ‘calcBgMan_function.Rnw’ using knitr
--- finished re-building ‘calcBgMan_function.Rnw’
--- re-building ‘calcBgVol_function.Rnw’ using knitr
--- finished re-building ‘calcBgVol_function.Rnw’
--- re-building ‘predBg_function.Rnw’ using knitr
Quitting from lines 70-71 [cellulose1] (predBg_function.Rnw)
Error: processing vignette 'predBg_function.Rnw' failed with diagnostics:
invalid 'scipen'
--- failed re-building ‘predBg_function.Rnw’
SUMMARY: processing the following files failed:
‘biogas_quick_start.Rnw’ ‘predBg_function.Rnw’
Error: Vignette re-building failed.
Execution halted
Flavor: r-devel-linux-x86_64-debian-gcc
Version: 1.23.2
Check: re-building of vignette outputs
Result: WARN
Error(s) in re-building vignettes:
--- re-building ‘biogas_quick_start.Rnw’ using knitr
Error: processing vignette 'biogas_quick_start.Rnw' failed with diagnostics:
Running 'texi2dvi' on 'biogas_quick_start.tex' failed.
LaTeX errors:
! Undefined control sequence.
l.234 \hlkwd{library}\hldef
{(biogas)}
?
! Emergency stop.
! Emergency stop.
l.234
End of file on the terminal!
! ==> Fatal error occurred, no output PDF file produced!
--- failed re-building ‘biogas_quick_start.Rnw’
--- re-building ‘calcBgMan_function.Rnw’ using knitr
Error: processing vignette 'calcBgMan_function.Rnw' failed with diagnostics:
Running 'texi2dvi' on 'calcBgMan_function.tex' failed.
LaTeX errors:
! Undefined control sequence.
l.163 \hlkwd{data}\hldef
{(}\hlsng{"sludgeTwoBiogas"}\hldef{)}
?
! Emergency stop.
! Emergency stop.
l.163
End of file on the terminal!
! ==> Fatal error occurred, no output PDF file produced!
--- failed re-building ‘calcBgMan_function.Rnw’
--- re-building ‘calcBgVol_function.Rnw’ using knitr
Error: processing vignette 'calcBgVol_function.Rnw' failed with diagnostics:
Running 'texi2dvi' on 'calcBgVol_function.tex' failed.
LaTeX errors:
! Undefined control sequence.
l.146 \hlkwd{data}\hldef
{(}\hlsng{"s3lcombo"}\hldef{)}
?
! Emergency stop.
! Emergency stop.
l.146
End of file on the terminal!
! ==> Fatal error occurred, no output PDF file produced!
--- failed re-building ‘calcBgVol_function.Rnw’
--- re-building ‘predBg_function.Rnw’ using knitr
Error: processing vignette 'predBg_function.Rnw' failed with diagnostics:
Running 'texi2dvi' on 'predBg_function.tex' failed.
LaTeX errors:
! Undefined control sequence.
l.88 \hlkwd{install.packages}\hldef
{(}\hlsng{"biogas"}\hldef{)}
?
! Emergency stop.
! Emergency stop.
l.88
End of file on the terminal!
! ==> Fatal error occurred, no output PDF file produced!
--- failed re-building ‘predBg_function.Rnw’
SUMMARY: processing the following files failed:
‘biogas_quick_start.Rnw’ ‘calcBgMan_function.Rnw’
‘calcBgVol_function.Rnw’ ‘predBg_function.Rnw’
Error: Vignette re-building failed.
Execution halted
Flavor: r-release-macos-x86_64