Last updated on 2023-03-20 05:52:15 CET.
| Flavor | Version | Tinstall | Tcheck | Ttotal | Status | Flags |
|---|---|---|---|---|---|---|
| r-devel-linux-x86_64-debian-clang | 1.22 | OK | ||||
| r-devel-linux-x86_64-debian-gcc | 1.22 | 7.06 | 50.53 | 57.59 | ERROR | |
| r-devel-linux-x86_64-fedora-clang | 1.22 | 114.02 | OK | |||
| r-devel-linux-x86_64-fedora-gcc | 1.22 | 127.04 | OK | |||
| r-devel-windows-x86_64 | 1.22 | 126.00 | 153.00 | 279.00 | OK | |
| r-patched-linux-x86_64 | 1.22 | 10.57 | 73.24 | 83.81 | OK | |
| r-release-linux-x86_64 | 1.22 | 8.64 | 72.40 | 81.04 | OK | |
| r-release-macos-arm64 | 1.22 | 38.00 | OK | |||
| r-release-macos-x86_64 | 1.22 | 50.00 | OK | |||
| r-release-windows-x86_64 | 1.22 | 120.00 | 140.00 | 260.00 | OK | |
| r-oldrel-macos-arm64 | 1.22 | 39.00 | OK | |||
| r-oldrel-macos-x86_64 | 1.22 | 56.00 | OK | |||
| r-oldrel-windows-ix86+x86_64 | 1.22 | 25.00 | 146.00 | 171.00 | OK |
Version: 1.22
Check: examples
Result: ERROR
Running examples in ‘MALDIquant-Ex.R’ failed
The error most likely occurred in:
> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: alignSpectra
> ### Title: Align MassSpectrum objects.
> ### Aliases: alignSpectra
> ### Keywords: methods
>
> ### ** Examples
>
> ## load package
> library("MALDIquant")
>
> ## load example data
> data("fiedler2009subset", package="MALDIquant")
>
> ## running typical workflow
>
> ## transform intensities
> spectra <- transformIntensity(fiedler2009subset, method="sqrt")
>
> ## smooth spectra
> spectra <- smoothIntensity(spectra, method="MovingAverage")
>
> ## baseline correction
> spectra <- removeBaseline(spectra)
Error in .estimateBaselineSnip(x, y, ...) :
DLL requires the use of native symbols
Calls: removeBaseline ... .local -> .estimateBaseline -> .estimateBaselineSnip
Execution halted
Flavor: r-devel-linux-x86_64-debian-gcc
Version: 1.22
Check: tests
Result: ERROR
Running ‘testthat.R’ [6s/11s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
> library("testthat")
> test_check("MALDIquant")
Loading required package: MALDIquant
This is MALDIquant version 1.22
Quantitative Analysis of Mass Spectrometry Data
See '?MALDIquant' for more information about this package.
[ FAIL 19 | WARN 0 | SKIP 0 | PASS 505 ]
══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test_alignSpectra-functions.R:12:3'): alignSpectra ──────────────────
Error in `.localMaxima(object@intensity, halfWindowSize = halfWindowSize)`: DLL requires the use of native symbols
Backtrace:
▆
1. ├─MALDIquant::detectPeaks(...) at test_alignSpectra-functions.R:12:2
2. └─MALDIquant::detectPeaks(...)
3. └─MALDIquant:::.mapply(detectPeaks, object, ...)
4. └─parallel::mcmapply(...)
5. └─parallel::mclapply(...)
6. └─base::lapply(X = X, FUN = FUN, ...)
7. └─parallel (local) FUN(X[[i]], ...)
8. └─base::.mapply(FUN, dots, MoreArgs)
9. ├─MALDIquant (local) `<stndrdGn>`(...)
10. └─MALDIquant (local) `<stndrdGn>`(...)
11. └─MALDIquant (local) .local(object, ...)
12. ├─MALDIquant:::.findLocalMaximaLogical(object, halfWindowSize = halfWindowSize)
13. └─MALDIquant:::.findLocalMaximaLogical(object, halfWindowSize = halfWindowSize)
14. └─MALDIquant:::.localMaxima(object@intensity, halfWindowSize = halfWindowSize)
── Error ('test_averageMassSpectra-functions.R:19:3'): averageMassSpectra ──────
Error in `fun(m, na.rm = TRUE)`: DLL requires the use of native symbols
Backtrace:
▆
1. ├─testthat::expect_equal(...) at test_averageMassSpectra-functions.R:19:2
2. │ └─testthat::quasi_label(enquo(object), label, arg = "object")
3. │ └─rlang::eval_bare(expr, quo_get_env(quo))
4. ├─base::unname(...)
5. └─MALDIquant::averageMassSpectra(...)
6. └─MALDIquant:::.doByLabels(...)
7. └─MALDIquant:::.lapply(...)
8. └─parallel::mclapply(X, FUN, ..., mc.cores = mc.cores)
9. └─base::lapply(X = X, FUN = FUN, ...)
10. └─MALDIquant (local) FUN(X[[i]], ...)
11. └─MALDIquant (local) fun(m, na.rm = TRUE)
── Error ('test_calibrateIntensity-methods.R:52:3'): calibrateIntensity works with PQN ──
Error in `fun(m, na.rm = TRUE)`: DLL requires the use of native symbols
Backtrace:
▆
1. ├─MALDIquant::calibrateIntensity(s, method = "PQN") at test_calibrateIntensity-methods.R:52:2
2. └─MALDIquant::calibrateIntensity(s, method = "PQN")
3. └─MALDIquant (local) .local(object, ...)
4. └─MALDIquant:::.calibrateProbabilisticQuotientNormalization(...)
5. └─MALDIquant:::.averageMassSpectra(l, fun = .colMedians, mergeMetaData = FALSE)
6. └─MALDIquant (local) fun(m, na.rm = TRUE)
── Error ('test_colMedians-functions.R:13:3'): .colMedians ─────────────────────
Error in `MALDIquant:::.colMedians(m)`: DLL requires the use of native symbols
Backtrace:
▆
1. ├─testthat::expect_equal(MALDIquant:::.colMedians(m), colMedians(m)) at test_colMedians-functions.R:13:2
2. │ └─testthat::quasi_label(enquo(object), label, arg = "object")
3. │ └─rlang::eval_bare(expr, quo_get_env(quo))
4. └─MALDIquant:::.colMedians(m)
── Error ('test_detectPeaks-methods.R:7:3'): detectPeaks ───────────────────────
Error in `.localMaxima(object@intensity, halfWindowSize = halfWindowSize)`: DLL requires the use of native symbols
Backtrace:
▆
1. ├─testthat::expect_equal(detectPeaks(s, halfWindowSize = 1), p) at test_detectPeaks-methods.R:7:2
2. │ └─testthat::quasi_label(enquo(object), label, arg = "object")
3. │ └─rlang::eval_bare(expr, quo_get_env(quo))
4. ├─MALDIquant::detectPeaks(s, halfWindowSize = 1)
5. └─MALDIquant::detectPeaks(s, halfWindowSize = 1)
6. └─MALDIquant (local) .local(object, ...)
7. ├─MALDIquant:::.findLocalMaximaLogical(object, halfWindowSize = halfWindowSize)
8. └─MALDIquant:::.findLocalMaximaLogical(object, halfWindowSize = halfWindowSize)
9. └─MALDIquant:::.localMaxima(object@intensity, halfWindowSize = halfWindowSize)
── Error ('test_detectPeaks-methods.R:20:3'): detectPeaks works with list of MassSpectrum objects ──
Error in `.localMaxima(object@intensity, halfWindowSize = halfWindowSize)`: DLL requires the use of native symbols
Backtrace:
▆
1. ├─testthat::expect_equal(...) at test_detectPeaks-methods.R:20:2
2. │ └─testthat::quasi_label(enquo(object), label, arg = "object")
3. │ └─rlang::eval_bare(expr, quo_get_env(quo))
4. ├─MALDIquant::detectPeaks(list(s, s), halfWindowSize = 1)
5. └─MALDIquant::detectPeaks(list(s, s), halfWindowSize = 1)
6. └─MALDIquant:::.mapply(detectPeaks, object, ...)
7. └─parallel::mcmapply(...)
8. └─parallel::mclapply(...)
9. └─base::lapply(X = X, FUN = FUN, ...)
10. └─parallel (local) FUN(X[[i]], ...)
11. └─base::.mapply(FUN, dots, MoreArgs)
12. ├─MALDIquant (local) `<stndrdGn>`(dots[[1L]][[1L]], halfWindowSize = dots[[2L]][[1L]])
13. └─MALDIquant (local) `<stndrdGn>`(dots[[1L]][[1L]], halfWindowSize = dots[[2L]][[1L]])
14. └─MALDIquant (local) .local(object, ...)
15. ├─MALDIquant:::.findLocalMaximaLogical(object, halfWindowSize = halfWindowSize)
16. └─MALDIquant:::.findLocalMaximaLogical(object, halfWindowSize = halfWindowSize)
17. └─MALDIquant:::.localMaxima(object@intensity, halfWindowSize = halfWindowSize)
── Error ('test_estimateBaseline-methods.R:19:3'): estimateBaselineConvexHull ──
Error in `MALDIquant:::.estimateBaselineConvexHull(mass(s), intensity(s))`: DLL requires the use of native symbols
Backtrace:
▆
1. ├─testthat::expect_identical(...) at test_estimateBaseline-methods.R:19:2
2. │ └─testthat::quasi_label(enquo(object), label, arg = "object")
3. │ └─rlang::eval_bare(expr, quo_get_env(quo))
4. └─MALDIquant:::.estimateBaselineConvexHull(mass(s), intensity(s))
── Error ('test_estimateBaseline-methods.R:51:3'): estimateBaselineSnip ────────
Error in `MALDIquant:::.estimateBaselineSnip(mass(s), intensity(s), 2)`: DLL requires the use of native symbols
Backtrace:
▆
1. ├─testthat::expect_identical(...) at test_estimateBaseline-methods.R:51:2
2. │ └─testthat::quasi_label(enquo(object), label, arg = "object")
3. │ └─rlang::eval_bare(expr, quo_get_env(quo))
4. └─MALDIquant:::.estimateBaselineSnip(mass(s), intensity(s), 2)
── Error ('test_estimateBaseline-methods.R:78:3'): estimateBaselineTopHat ──────
Error in `.erosion(y, halfWindowSize = halfWindowSize)`: DLL requires the use of native symbols
Backtrace:
▆
1. ├─testthat::expect_identical(...) at test_estimateBaseline-methods.R:78:2
2. │ └─testthat::quasi_label(enquo(object), label, arg = "object")
3. │ └─rlang::eval_bare(expr, quo_get_env(quo))
4. └─MALDIquant:::.estimateBaselineTopHat(mass(s), intensity(s), 1)
5. ├─MALDIquant:::.dilation(...)
6. └─MALDIquant:::.erosion(y, halfWindowSize = halfWindowSize)
── Error ('test_findLocalMaximaLogical-methods.R:25:3'): .findLocalMaximaLogical works with different window sizes ──
Error in `.localMaxima(object@intensity, halfWindowSize = halfWindowSize)`: DLL requires the use of native symbols
Backtrace:
▆
1. ├─testthat::expect_identical(...) at test_findLocalMaximaLogical-methods.R:25:2
2. │ └─testthat::quasi_label(enquo(object), label, arg = "object")
3. │ └─rlang::eval_bare(expr, quo_get_env(quo))
4. ├─MALDIquant:::.findLocalMaximaLogical(s, halfWindowSize = 1)
5. └─MALDIquant:::.findLocalMaximaLogical(s, halfWindowSize = 1)
6. └─MALDIquant:::.localMaxima(object@intensity, halfWindowSize = halfWindowSize)
── Error ('test_findLocalMaximaLogical-methods.R:38:3'): .findLocalMaxima returns matrix ──
Error in `.localMaxima(object@intensity, halfWindowSize = halfWindowSize)`: DLL requires the use of native symbols
Backtrace:
▆
1. ├─testthat::expect_identical(...) at test_findLocalMaximaLogical-methods.R:38:2
2. │ └─testthat::quasi_label(enquo(object), label, arg = "object")
3. │ └─rlang::eval_bare(expr, quo_get_env(quo))
4. ├─MALDIquant:::.findLocalMaxima(s, halfWindowSize = 1)
5. └─MALDIquant:::.findLocalMaxima(s, halfWindowSize = 1)
6. ├─MALDIquant:::.findLocalMaximaLogical(object, halfWindowSize = halfWindowSize)
7. └─MALDIquant:::.findLocalMaximaLogical(object, halfWindowSize = halfWindowSize)
8. └─MALDIquant:::.localMaxima(object@intensity, halfWindowSize = halfWindowSize)
── Error ('test_localMaxima-functions.R:8:3'): .localMaxima ────────────────────
Error in `MALDIquant:::.localMaxima(y, 1)`: DLL requires the use of native symbols
Backtrace:
▆
1. ├─testthat::expect_identical(...) at test_localMaxima-functions.R:8:2
2. │ └─testthat::quasi_label(enquo(object), label, arg = "object")
3. │ └─rlang::eval_bare(expr, quo_get_env(quo))
4. └─MALDIquant:::.localMaxima(y, 1)
── Error ('test_merge-functions.R:34:3'): mergeMassPeaks ───────────────────────
Error in `fun(m, na.rm = TRUE)`: DLL requires the use of native symbols
Backtrace:
▆
1. ├─testthat::expect_equal(...) at test_merge-functions.R:34:2
2. │ └─testthat::quasi_label(enquo(object), label, arg = "object")
3. │ └─rlang::eval_bare(expr, quo_get_env(quo))
4. ├─base::unname(...)
5. └─MALDIquant::mergeMassPeaks(...)
6. └─MALDIquant:::.doByLabels(...)
7. └─MALDIquant (local) FUN(l, ...)
8. └─MALDIquant (local) fun(m, na.rm = TRUE)
── Error ('test_morphologicalFilter-functions.R:14:5'): .erosion ───────────────
Error in `.erosion(x[[i]], halfWindowSize = 2)`: DLL requires the use of native symbols
Backtrace:
▆
1. ├─testthat::expect_equal(...) at test_morphologicalFilter-functions.R:14:4
2. │ └─testthat::quasi_label(enquo(object), label, arg = "object")
3. │ └─rlang::eval_bare(expr, quo_get_env(quo))
4. └─MALDIquant:::.erosion(x[[i]], halfWindowSize = 2)
── Error ('test_morphologicalFilter-functions.R:20:5'): .dilation ──────────────
Error in `.dilation(x[[i]], halfWindowSize = 2)`: DLL requires the use of native symbols
Backtrace:
▆
1. ├─testthat::expect_equal(...) at test_morphologicalFilter-functions.R:20:4
2. │ └─testthat::quasi_label(enquo(object), label, arg = "object")
3. │ └─rlang::eval_bare(expr, quo_get_env(quo))
4. └─MALDIquant:::.dilation(x[[i]], halfWindowSize = 2)
── Error ('test_msiSlices-functions.R:47:3'): .msiSlices ───────────────────────
Error in `.colMedians(t(x), ...)`: DLL requires the use of native symbols
Backtrace:
▆
1. ├─testthat::expect_equal(...) at test_msiSlices-functions.R:47:2
2. │ └─testthat::quasi_label(enquo(object), label, arg = "object")
3. │ └─rlang::eval_bare(expr, quo_get_env(quo))
4. └─MALDIquant:::.msiSlices(...)
5. └─MALDIquant (local) fun(m[, l[i]:r[i], drop = FALSE], na.rm = TRUE)
6. └─MALDIquant:::.colMedians(t(x), ...)
── Error ('test_removeBaseline-methods.R:20:3'): removeBaseline works with ConvexHull ──
Error in `.estimateBaselineConvexHull(x, y, ...)`: DLL requires the use of native symbols
Backtrace:
▆
1. ├─testthat::expect_equal(...) at test_removeBaseline-methods.R:20:2
2. │ └─testthat::quasi_label(enquo(object), label, arg = "object")
3. │ └─rlang::eval_bare(expr, quo_get_env(quo))
4. ├─MALDIquant::removeBaseline(s, method = "ConvexHull")
5. └─MALDIquant::removeBaseline(s, method = "ConvexHull")
6. └─MALDIquant (local) .local(object, ...)
7. └─MALDIquant:::.estimateBaseline(...)
8. └─MALDIquant:::.estimateBaselineConvexHull(x, y, ...)
── Error ('test_removeBaseline-methods.R:36:3'): removeBaseline works with SNIP ──
Error in `.estimateBaselineSnip(x, y, ...)`: DLL requires the use of native symbols
Backtrace:
▆
1. ├─testthat::expect_equal(...) at test_removeBaseline-methods.R:36:2
2. │ └─testthat::quasi_label(enquo(object), label, arg = "object")
3. │ └─rlang::eval_bare(expr, quo_get_env(quo))
4. ├─MALDIquant::removeBaseline(s, iterations = 2)
5. └─MALDIquant::removeBaseline(s, iterations = 2)
6. └─MALDIquant (local) .local(object, ...)
7. └─MALDIquant:::.estimateBaseline(...)
8. └─MALDIquant:::.estimateBaselineSnip(x, y, ...)
── Error ('test_removeBaseline-methods.R:51:3'): removeBaseline works with list of MassSpectrum objects ──
Error in `.estimateBaselineSnip(x, y, ...)`: DLL requires the use of native symbols
Backtrace:
▆
1. ├─testthat::expect_equal(...) at test_removeBaseline-methods.R:51:2
2. │ └─testthat::quasi_label(enquo(object), label, arg = "object")
3. │ └─rlang::eval_bare(expr, quo_get_env(quo))
4. ├─MALDIquant::removeBaseline(list(s, s), iterations = 2)
5. └─MALDIquant::removeBaseline(list(s, s), iterations = 2)
6. └─MALDIquant:::.mapply(removeBaseline, object, ...)
7. └─parallel::mcmapply(...)
8. └─parallel::mclapply(...)
9. └─base::lapply(X = X, FUN = FUN, ...)
10. └─parallel (local) FUN(X[[i]], ...)
11. └─base::.mapply(FUN, dots, MoreArgs)
12. ├─MALDIquant (local) `<stndrdGn>`(dots[[1L]][[1L]], iterations = dots[[2L]][[1L]])
13. └─MALDIquant (local) `<stndrdGn>`(dots[[1L]][[1L]], iterations = dots[[2L]][[1L]])
14. └─MALDIquant (local) .local(object, ...)
15. └─MALDIquant:::.estimateBaseline(...)
16. └─MALDIquant:::.estimateBaselineSnip(x, y, ...)
[ FAIL 19 | WARN 0 | SKIP 0 | PASS 505 ]
Error: Test failures
Execution halted
Flavor: r-devel-linux-x86_64-debian-gcc
Version: 1.22
Check: re-building of vignette outputs
Result: ERROR
Error(s) in re-building vignettes:
...
--- re-building ‘MALDIquant-intro.Rnw’ using knitr
Quitting from lines 230-234 (MALDIquant-intro.Rnw)
Error: processing vignette ‘MALDIquant-intro.Rnw’ failed with diagnostics:
DLL requires the use of native symbols
--- failed re-building ‘MALDIquant-intro.Rnw’
SUMMARY: processing the following file failed:
‘MALDIquant-intro.Rnw’
Error: Vignette re-building failed.
Execution halted
Flavor: r-devel-linux-x86_64-debian-gcc