Last updated on 2025-01-11 19:50:36 CET.
| Flavor | Version | Tinstall | Tcheck | Ttotal | Status | Flags |
|---|---|---|---|---|---|---|
| r-devel-linux-x86_64-debian-clang | 0.1.0 | 4.04 | 132.94 | 136.98 | ERROR | |
| r-devel-linux-x86_64-debian-gcc | 0.1.0 | 2.91 | 90.42 | 93.33 | ERROR | |
| r-devel-linux-x86_64-fedora-clang | 0.1.0 | 238.09 | ERROR | |||
| r-devel-linux-x86_64-fedora-gcc | 0.1.0 | 235.61 | ERROR | |||
| r-devel-windows-x86_64 | 0.1.0 | 8.00 | 160.00 | 168.00 | NOTE | |
| r-patched-linux-x86_64 | 0.1.0 | 8.91 | 144.24 | 153.15 | OK | |
| r-release-linux-x86_64 | 0.1.0 | 4.10 | 146.16 | 150.26 | OK | |
| r-release-macos-arm64 | 0.1.0 | 75.00 | OK | |||
| r-release-macos-x86_64 | 0.1.0 | 123.00 | OK | |||
| r-release-windows-x86_64 | 0.1.0 | 6.00 | 140.00 | 146.00 | ERROR | |
| r-oldrel-macos-arm64 | 0.1.0 | 92.00 | OK | |||
| r-oldrel-macos-x86_64 | 0.1.0 | 204.00 | OK | |||
| r-oldrel-windows-x86_64 | 0.1.0 | 7.00 | 196.00 | 203.00 | OK |
Version: 0.1.0
Check: Rd cross-references
Result: NOTE
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
skipTrack.diagnostics.Rd: genDiagnostic
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Flavors: r-devel-linux-x86_64-debian-clang, r-devel-linux-x86_64-debian-gcc, r-devel-windows-x86_64
Version: 0.1.0
Check: examples
Result: ERROR
Running examples in ‘skipTrack-Ex.R’ failed
The error most likely occurred in:
> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: skipTrack.diagnostics
> ### Title: skipTrack MCMC Diagnostics
> ### Aliases: skipTrack.diagnostics
>
> ### ** Examples
>
> #Simulated data
> simDat <- skipTrack.simulate(n = 100, skipProb = c(.7, .2, .1))
>
> #Run model fit (should typically run with much more than 50 reps)
> modFit <- skipTrack.fit(Y = simDat$Y, cluster = simDat$cluster, chains = 2, reps = 50)
>
> #Get diagnostics for cijs
> skipTrack.diagnostics(modFit, 'cijs')
Warning in genMCMCDiag::genDiagnostic(mcmcExt, method = method, distance = genMCMCDiag::hammingDist, :
this proximityMap ignores the argument distance.
Error in proximityMapF(mhDraws = mhDraws, distance = distance, verbose = verbose, :
The chains must be numeric vectors in order to use the standard transformation.
Calls: skipTrack.diagnostics -> <Anonymous> -> proximityMapF
Execution halted
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
plot.skipTrack.model 5.337 0.25 7.536
Flavor: r-devel-linux-x86_64-debian-clang
Version: 0.1.0
Check: tests
Result: ERROR
Running ‘testthat.R’ [9s/14s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
> # This file is part of the standard setup for testthat.
> # It is recommended that you do not modify it.
> #
> # Where should you do additional test configuration?
> # Learn more about the roles of various files in:
> # * https://r-pkgs.org/testing-design.html#sec-tests-files-overview
> # * https://testthat.r-lib.org/articles/special-files.html
>
> library(testthat)
> library(skipTrack)
>
> test_check("skipTrack")
-------------------------------------------
SkipTrack Model Output
-------------------------------------------
Number of Observations: 62
Number of Individuals: 10
Dimension of Beta: 1
Dimension of Gamma: 1
-------------------------------------------
Number of MCMC Chains: 2
Model: skipTrack
-------------------------------------------
skipTrack.model S3 Object (also a list)
NChains: 2
Model Type: skipTrack[ FAIL 7 | WARN 7 | SKIP 1 | PASS 9 ]
══ Skipped tests (1) ═══════════════════════════════════════════════════════════
• empty test (1): 'test-visualization.R:1:1'
══ Failed tests ════════════════════════════════════════════════════════════════
── Failure ('test-diagnostics.R:9:3'): skipTrack.diagnostics runs on all options ──
Expected `skipTrack.diagnostics(foo, "Betas")` to run without any errors.
i Actually got a <simpleError> with text:
The chains must be numeric vectors in order to use the standard transformation.
── Failure ('test-diagnostics.R:10:3'): skipTrack.diagnostics runs on all options ──
Expected `skipTrack.diagnostics(foo, "Gammas")` to run without any errors.
i Actually got a <simpleError> with text:
The chains must be numeric vectors in order to use the standard transformation.
── Failure ('test-diagnostics.R:11:3'): skipTrack.diagnostics runs on all options ──
Expected `skipTrack.diagnostics(foo, "muis")` to run without any errors.
i Actually got a <simpleError> with text:
The chains must be numeric vectors in order to use the standard transformation.
── Failure ('test-diagnostics.R:12:3'): skipTrack.diagnostics runs on all options ──
Expected `skipTrack.diagnostics(foo, "tauis")` to run without any errors.
i Actually got a <simpleError> with text:
The chains must be numeric vectors in order to use the standard transformation.
── Failure ('test-diagnostics.R:13:3'): skipTrack.diagnostics runs on all options ──
Expected `skipTrack.diagnostics(foo, "cijs")` to run without any errors.
i Actually got a <simpleError> with text:
The chains must be numeric vectors in order to use the standard transformation.
── Error ('test-results.R:6:3'): results function runs ─────────────────────────
Error in `proximityMapF(mhDraws = mhDraws, distance = distance, verbose = verbose,
...)`: The chains must be numeric vectors in order to use the standard transformation.
Backtrace:
▆
1. └─skipTrack::skipTrack.results(foo, burnIn = 10) at test-results.R:6:3
2. └─base::lapply(...)
3. └─skipTrack (local) FUN(X[[i]], ...)
4. └─skipTrack::skipTrack.diagnostics(stFit = stFit, param)
5. └─genMCMCDiag::genDiagnostic(...)
6. └─genMCMCDiag (local) proximityMapF(...)
── Failure ('test-utils.R:9:3'): Utility functions do not throw errors ─────────
Expected `summary(foo, burnIn = 20)` to run without any errors.
i Actually got a <simpleError> with text:
The chains must be numeric vectors in order to use the standard transformation.
[ FAIL 7 | WARN 7 | SKIP 1 | PASS 9 ]
Error: Test failures
Execution halted
Flavor: r-devel-linux-x86_64-debian-clang
Version: 0.1.0
Check: re-building of vignette outputs
Result: ERROR
Error(s) in re-building vignettes:
...
--- re-building ‘skipTrack_intro.Rmd’ using rmarkdown
** Processing: /home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/skipTrack.Rcheck/vign_test/skipTrack/vignettes/skipTrack_intro_files/figure-html/unnamed-chunk-4-1.png
672x288 pixels, 8 bits/pixel, 256 colors in palette
Reducing image to 8 bits/pixel, grayscale
Input IDAT size = 7208 bytes
Input file size = 8066 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 6555
zc = 9 zm = 8 zs = 1 f = 0
zc = 1 zm = 8 zs = 2 f = 0
zc = 9 zm = 8 zs = 3 f = 0
zc = 9 zm = 8 zs = 0 f = 5
zc = 9 zm = 8 zs = 1 f = 5
zc = 1 zm = 8 zs = 2 f = 5
zc = 9 zm = 8 zs = 3 f = 5
Selecting parameters:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 6555
Output IDAT size = 6555 bytes (653 bytes decrease)
Output file size = 6633 bytes (1433 bytes = 17.77% decrease)
Quitting from lines 122-123 [unnamed-chunk-6] (skipTrack_intro.Rmd)
Error: processing vignette 'skipTrack_intro.Rmd' failed with diagnostics:
The chains must be numeric vectors in order to use the standard transformation.
--- failed re-building ‘skipTrack_intro.Rmd’
SUMMARY: processing the following file failed:
‘skipTrack_intro.Rmd’
Error: Vignette re-building failed.
Execution halted
Flavor: r-devel-linux-x86_64-debian-clang
Version: 0.1.0
Check: examples
Result: ERROR
Running examples in ‘skipTrack-Ex.R’ failed
The error most likely occurred in:
> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: skipTrack.diagnostics
> ### Title: skipTrack MCMC Diagnostics
> ### Aliases: skipTrack.diagnostics
>
> ### ** Examples
>
> #Simulated data
> simDat <- skipTrack.simulate(n = 100, skipProb = c(.7, .2, .1))
>
> #Run model fit (should typically run with much more than 50 reps)
> modFit <- skipTrack.fit(Y = simDat$Y, cluster = simDat$cluster, chains = 2, reps = 50)
>
> #Get diagnostics for cijs
> skipTrack.diagnostics(modFit, 'cijs')
Warning in genMCMCDiag::genDiagnostic(mcmcExt, method = method, distance = genMCMCDiag::hammingDist, :
this proximityMap ignores the argument distance.
Error in proximityMapF(mhDraws = mhDraws, distance = distance, verbose = verbose, :
The chains must be numeric vectors in order to use the standard transformation.
Calls: skipTrack.diagnostics -> <Anonymous> -> proximityMapF
Execution halted
Flavor: r-devel-linux-x86_64-debian-gcc
Version: 0.1.0
Check: tests
Result: ERROR
Running ‘testthat.R’ [8s/10s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
> # This file is part of the standard setup for testthat.
> # It is recommended that you do not modify it.
> #
> # Where should you do additional test configuration?
> # Learn more about the roles of various files in:
> # * https://r-pkgs.org/testing-design.html#sec-tests-files-overview
> # * https://testthat.r-lib.org/articles/special-files.html
>
> library(testthat)
> library(skipTrack)
>
> test_check("skipTrack")
-------------------------------------------
SkipTrack Model Output
-------------------------------------------
Number of Observations: 62
Number of Individuals: 10
Dimension of Beta: 1
Dimension of Gamma: 1
-------------------------------------------
Number of MCMC Chains: 2
Model: skipTrack
-------------------------------------------
skipTrack.model S3 Object (also a list)
NChains: 2
Model Type: skipTrack[ FAIL 7 | WARN 7 | SKIP 1 | PASS 9 ]
══ Skipped tests (1) ═══════════════════════════════════════════════════════════
• empty test (1): 'test-visualization.R:1:1'
══ Failed tests ════════════════════════════════════════════════════════════════
── Failure ('test-diagnostics.R:9:3'): skipTrack.diagnostics runs on all options ──
Expected `skipTrack.diagnostics(foo, "Betas")` to run without any errors.
i Actually got a <simpleError> with text:
The chains must be numeric vectors in order to use the standard transformation.
── Failure ('test-diagnostics.R:10:3'): skipTrack.diagnostics runs on all options ──
Expected `skipTrack.diagnostics(foo, "Gammas")` to run without any errors.
i Actually got a <simpleError> with text:
The chains must be numeric vectors in order to use the standard transformation.
── Failure ('test-diagnostics.R:11:3'): skipTrack.diagnostics runs on all options ──
Expected `skipTrack.diagnostics(foo, "muis")` to run without any errors.
i Actually got a <simpleError> with text:
The chains must be numeric vectors in order to use the standard transformation.
── Failure ('test-diagnostics.R:12:3'): skipTrack.diagnostics runs on all options ──
Expected `skipTrack.diagnostics(foo, "tauis")` to run without any errors.
i Actually got a <simpleError> with text:
The chains must be numeric vectors in order to use the standard transformation.
── Failure ('test-diagnostics.R:13:3'): skipTrack.diagnostics runs on all options ──
Expected `skipTrack.diagnostics(foo, "cijs")` to run without any errors.
i Actually got a <simpleError> with text:
The chains must be numeric vectors in order to use the standard transformation.
── Error ('test-results.R:6:3'): results function runs ─────────────────────────
Error in `proximityMapF(mhDraws = mhDraws, distance = distance, verbose = verbose,
...)`: The chains must be numeric vectors in order to use the standard transformation.
Backtrace:
▆
1. └─skipTrack::skipTrack.results(foo, burnIn = 10) at test-results.R:6:3
2. └─base::lapply(...)
3. └─skipTrack (local) FUN(X[[i]], ...)
4. └─skipTrack::skipTrack.diagnostics(stFit = stFit, param)
5. └─genMCMCDiag::genDiagnostic(...)
6. └─genMCMCDiag (local) proximityMapF(...)
── Failure ('test-utils.R:9:3'): Utility functions do not throw errors ─────────
Expected `summary(foo, burnIn = 20)` to run without any errors.
i Actually got a <simpleError> with text:
The chains must be numeric vectors in order to use the standard transformation.
[ FAIL 7 | WARN 7 | SKIP 1 | PASS 9 ]
Error: Test failures
Execution halted
Flavor: r-devel-linux-x86_64-debian-gcc
Version: 0.1.0
Check: re-building of vignette outputs
Result: ERROR
Error(s) in re-building vignettes:
...
--- re-building ‘skipTrack_intro.Rmd’ using rmarkdown
** Processing: /home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/skipTrack.Rcheck/vign_test/skipTrack/vignettes/skipTrack_intro_files/figure-html/unnamed-chunk-4-1.png
672x288 pixels, 8 bits/pixel, 256 colors in palette
Reducing image to 8 bits/pixel, grayscale
Input IDAT size = 7208 bytes
Input file size = 8066 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 6555
zc = 9 zm = 8 zs = 1 f = 0
zc = 1 zm = 8 zs = 2 f = 0
zc = 9 zm = 8 zs = 3 f = 0
zc = 9 zm = 8 zs = 0 f = 5
zc = 9 zm = 8 zs = 1 f = 5
zc = 1 zm = 8 zs = 2 f = 5
zc = 9 zm = 8 zs = 3 f = 5
Selecting parameters:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 6555
Output IDAT size = 6555 bytes (653 bytes decrease)
Output file size = 6633 bytes (1433 bytes = 17.77% decrease)
Quitting from lines 122-123 [unnamed-chunk-6] (skipTrack_intro.Rmd)
Error: processing vignette 'skipTrack_intro.Rmd' failed with diagnostics:
The chains must be numeric vectors in order to use the standard transformation.
--- failed re-building ‘skipTrack_intro.Rmd’
SUMMARY: processing the following file failed:
‘skipTrack_intro.Rmd’
Error: Vignette re-building failed.
Execution halted
Flavor: r-devel-linux-x86_64-debian-gcc
Version: 0.1.0
Check: examples
Result: ERROR
Running examples in ‘skipTrack-Ex.R’ failed
The error most likely occurred in:
> ### Name: skipTrack.diagnostics
> ### Title: skipTrack MCMC Diagnostics
> ### Aliases: skipTrack.diagnostics
>
> ### ** Examples
>
> #Simulated data
> simDat <- skipTrack.simulate(n = 100, skipProb = c(.7, .2, .1))
>
> #Run model fit (should typically run with much more than 50 reps)
> modFit <- skipTrack.fit(Y = simDat$Y, cluster = simDat$cluster, chains = 2, reps = 50)
>
> #Get diagnostics for cijs
> skipTrack.diagnostics(modFit, 'cijs')
Warning in genMCMCDiag::genDiagnostic(mcmcExt, method = method, distance = genMCMCDiag::hammingDist, :
this proximityMap ignores the argument distance.
Error in proximityMapF(mhDraws = mhDraws, distance = distance, verbose = verbose, :
The chains must be numeric vectors in order to use the standard transformation.
Calls: skipTrack.diagnostics -> <Anonymous> -> proximityMapF
Execution halted
Flavors: r-devel-linux-x86_64-fedora-clang, r-devel-linux-x86_64-fedora-gcc, r-release-windows-x86_64
Version: 0.1.0
Check: tests
Result: ERROR
Running ‘testthat.R’ [15s/30s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
> # This file is part of the standard setup for testthat.
> # It is recommended that you do not modify it.
> #
> # Where should you do additional test configuration?
> # Learn more about the roles of various files in:
> # * https://r-pkgs.org/testing-design.html#sec-tests-files-overview
> # * https://testthat.r-lib.org/articles/special-files.html
>
> library(testthat)
> library(skipTrack)
>
> test_check("skipTrack")
-------------------------------------------
SkipTrack Model Output
-------------------------------------------
Number of Observations: 62
Number of Individuals: 10
Dimension of Beta: 1
Dimension of Gamma: 1
-------------------------------------------
Number of MCMC Chains: 2
Model: skipTrack
-------------------------------------------
skipTrack.model S3 Object (also a list)
NChains: 2
Model Type: skipTrack[ FAIL 7 | WARN 7 | SKIP 1 | PASS 9 ]
══ Skipped tests (1) ═══════════════════════════════════════════════════════════
• empty test (1): 'test-visualization.R:1:1'
══ Failed tests ════════════════════════════════════════════════════════════════
── Failure ('test-diagnostics.R:9:3'): skipTrack.diagnostics runs on all options ──
Expected `skipTrack.diagnostics(foo, "Betas")` to run without any errors.
i Actually got a <simpleError> with text:
The chains must be numeric vectors in order to use the standard transformation.
── Failure ('test-diagnostics.R:10:3'): skipTrack.diagnostics runs on all options ──
Expected `skipTrack.diagnostics(foo, "Gammas")` to run without any errors.
i Actually got a <simpleError> with text:
The chains must be numeric vectors in order to use the standard transformation.
── Failure ('test-diagnostics.R:11:3'): skipTrack.diagnostics runs on all options ──
Expected `skipTrack.diagnostics(foo, "muis")` to run without any errors.
i Actually got a <simpleError> with text:
The chains must be numeric vectors in order to use the standard transformation.
── Failure ('test-diagnostics.R:12:3'): skipTrack.diagnostics runs on all options ──
Expected `skipTrack.diagnostics(foo, "tauis")` to run without any errors.
i Actually got a <simpleError> with text:
The chains must be numeric vectors in order to use the standard transformation.
── Failure ('test-diagnostics.R:13:3'): skipTrack.diagnostics runs on all options ──
Expected `skipTrack.diagnostics(foo, "cijs")` to run without any errors.
i Actually got a <simpleError> with text:
The chains must be numeric vectors in order to use the standard transformation.
── Error ('test-results.R:6:3'): results function runs ─────────────────────────
Error in `proximityMapF(mhDraws = mhDraws, distance = distance, verbose = verbose,
...)`: The chains must be numeric vectors in order to use the standard transformation.
Backtrace:
▆
1. └─skipTrack::skipTrack.results(foo, burnIn = 10) at test-results.R:6:3
2. └─base::lapply(...)
3. └─skipTrack (local) FUN(X[[i]], ...)
4. └─skipTrack::skipTrack.diagnostics(stFit = stFit, param)
5. └─genMCMCDiag::genDiagnostic(...)
6. └─genMCMCDiag (local) proximityMapF(...)
── Failure ('test-utils.R:9:3'): Utility functions do not throw errors ─────────
Expected `summary(foo, burnIn = 20)` to run without any errors.
i Actually got a <simpleError> with text:
The chains must be numeric vectors in order to use the standard transformation.
[ FAIL 7 | WARN 7 | SKIP 1 | PASS 9 ]
Error: Test failures
Execution halted
Flavor: r-devel-linux-x86_64-fedora-clang
Version: 0.1.0
Check: re-building of vignette outputs
Result: ERROR
Error(s) in re-building vignettes:
--- re-building ‘skipTrack_intro.Rmd’ using rmarkdown
** Processing: /data/gannet/ripley/R/packages/tests-clang/skipTrack.Rcheck/vign_test/skipTrack/vignettes/skipTrack_intro_files/figure-html/unnamed-chunk-4-1.png
672x288 pixels, 8 bits/pixel, 256 colors in palette
Reducing image to 8 bits/pixel, grayscale
Input IDAT size = 7208 bytes
Input file size = 8066 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 6555
zc = 9 zm = 8 zs = 1 f = 0
zc = 1 zm = 8 zs = 2 f = 0
zc = 9 zm = 8 zs = 3 f = 0
zc = 9 zm = 8 zs = 0 f = 5
zc = 9 zm = 8 zs = 1 f = 5
zc = 1 zm = 8 zs = 2 f = 5
zc = 9 zm = 8 zs = 3 f = 5
Selecting parameters:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 6555
Output IDAT size = 6555 bytes (653 bytes decrease)
Output file size = 6633 bytes (1433 bytes = 17.77% decrease)
Quitting from lines 122-123 [unnamed-chunk-6] (skipTrack_intro.Rmd)
Error: processing vignette 'skipTrack_intro.Rmd' failed with diagnostics:
The chains must be numeric vectors in order to use the standard transformation.
--- failed re-building ‘skipTrack_intro.Rmd’
SUMMARY: processing the following file failed:
‘skipTrack_intro.Rmd’
Error: Vignette re-building failed.
Execution halted
Flavor: r-devel-linux-x86_64-fedora-clang
Version: 0.1.0
Check: tests
Result: ERROR
Running ‘testthat.R’ [15s/18s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
> # This file is part of the standard setup for testthat.
> # It is recommended that you do not modify it.
> #
> # Where should you do additional test configuration?
> # Learn more about the roles of various files in:
> # * https://r-pkgs.org/testing-design.html#sec-tests-files-overview
> # * https://testthat.r-lib.org/articles/special-files.html
>
> library(testthat)
> library(skipTrack)
>
> test_check("skipTrack")
-------------------------------------------
SkipTrack Model Output
-------------------------------------------
Number of Observations: 62
Number of Individuals: 10
Dimension of Beta: 1
Dimension of Gamma: 1
-------------------------------------------
Number of MCMC Chains: 2
Model: skipTrack
-------------------------------------------
skipTrack.model S3 Object (also a list)
NChains: 2
Model Type: skipTrack[ FAIL 7 | WARN 7 | SKIP 1 | PASS 9 ]
══ Skipped tests (1) ═══════════════════════════════════════════════════════════
• empty test (1): 'test-visualization.R:1:1'
══ Failed tests ════════════════════════════════════════════════════════════════
── Failure ('test-diagnostics.R:9:3'): skipTrack.diagnostics runs on all options ──
Expected `skipTrack.diagnostics(foo, "Betas")` to run without any errors.
i Actually got a <simpleError> with text:
The chains must be numeric vectors in order to use the standard transformation.
── Failure ('test-diagnostics.R:10:3'): skipTrack.diagnostics runs on all options ──
Expected `skipTrack.diagnostics(foo, "Gammas")` to run without any errors.
i Actually got a <simpleError> with text:
The chains must be numeric vectors in order to use the standard transformation.
── Failure ('test-diagnostics.R:11:3'): skipTrack.diagnostics runs on all options ──
Expected `skipTrack.diagnostics(foo, "muis")` to run without any errors.
i Actually got a <simpleError> with text:
The chains must be numeric vectors in order to use the standard transformation.
── Failure ('test-diagnostics.R:12:3'): skipTrack.diagnostics runs on all options ──
Expected `skipTrack.diagnostics(foo, "tauis")` to run without any errors.
i Actually got a <simpleError> with text:
The chains must be numeric vectors in order to use the standard transformation.
── Failure ('test-diagnostics.R:13:3'): skipTrack.diagnostics runs on all options ──
Expected `skipTrack.diagnostics(foo, "cijs")` to run without any errors.
i Actually got a <simpleError> with text:
The chains must be numeric vectors in order to use the standard transformation.
── Error ('test-results.R:6:3'): results function runs ─────────────────────────
Error in `proximityMapF(mhDraws = mhDraws, distance = distance, verbose = verbose,
...)`: The chains must be numeric vectors in order to use the standard transformation.
Backtrace:
▆
1. └─skipTrack::skipTrack.results(foo, burnIn = 10) at test-results.R:6:3
2. └─base::lapply(...)
3. └─skipTrack (local) FUN(X[[i]], ...)
4. └─skipTrack::skipTrack.diagnostics(stFit = stFit, param)
5. └─genMCMCDiag::genDiagnostic(...)
6. └─genMCMCDiag (local) proximityMapF(...)
── Failure ('test-utils.R:9:3'): Utility functions do not throw errors ─────────
Expected `summary(foo, burnIn = 20)` to run without any errors.
i Actually got a <simpleError> with text:
The chains must be numeric vectors in order to use the standard transformation.
[ FAIL 7 | WARN 7 | SKIP 1 | PASS 9 ]
Error: Test failures
Execution halted
Flavor: r-devel-linux-x86_64-fedora-gcc
Version: 0.1.0
Check: re-building of vignette outputs
Result: ERROR
Error(s) in re-building vignettes:
--- re-building ‘skipTrack_intro.Rmd’ using rmarkdown
** Processing: /data/gannet/ripley/R/packages/tests-devel/skipTrack.Rcheck/vign_test/skipTrack/vignettes/skipTrack_intro_files/figure-html/unnamed-chunk-4-1.png
672x288 pixels, 8 bits/pixel, 256 colors in palette
Reducing image to 8 bits/pixel, grayscale
Input IDAT size = 7208 bytes
Input file size = 8066 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 6555
zc = 9 zm = 8 zs = 1 f = 0
zc = 1 zm = 8 zs = 2 f = 0
zc = 9 zm = 8 zs = 3 f = 0
zc = 9 zm = 8 zs = 0 f = 5
zc = 9 zm = 8 zs = 1 f = 5
zc = 1 zm = 8 zs = 2 f = 5
zc = 9 zm = 8 zs = 3 f = 5
Selecting parameters:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 6555
Output IDAT size = 6555 bytes (653 bytes decrease)
Output file size = 6633 bytes (1433 bytes = 17.77% decrease)
Quitting from lines 122-123 [unnamed-chunk-6] (skipTrack_intro.Rmd)
Error: processing vignette 'skipTrack_intro.Rmd' failed with diagnostics:
The chains must be numeric vectors in order to use the standard transformation.
--- failed re-building ‘skipTrack_intro.Rmd’
SUMMARY: processing the following file failed:
‘skipTrack_intro.Rmd’
Error: Vignette re-building failed.
Execution halted
Flavor: r-devel-linux-x86_64-fedora-gcc
Version: 0.1.0
Check: tests
Result: ERROR
Running 'testthat.R' [7s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
> # This file is part of the standard setup for testthat.
> # It is recommended that you do not modify it.
> #
> # Where should you do additional test configuration?
> # Learn more about the roles of various files in:
> # * https://r-pkgs.org/testing-design.html#sec-tests-files-overview
> # * https://testthat.r-lib.org/articles/special-files.html
>
> library(testthat)
> library(skipTrack)
>
> test_check("skipTrack")
-------------------------------------------
SkipTrack Model Output
-------------------------------------------
Number of Observations: 62
Number of Individuals: 10
Dimension of Beta: 1
Dimension of Gamma: 1
-------------------------------------------
Number of MCMC Chains: 2
Model: skipTrack
-------------------------------------------
skipTrack.model S3 Object (also a list)
NChains: 2
Model Type: skipTrack[ FAIL 7 | WARN 7 | SKIP 1 | PASS 9 ]
══ Skipped tests (1) ═══════════════════════════════════════════════════════════
• empty test (1): 'test-visualization.R:1:1'
══ Failed tests ════════════════════════════════════════════════════════════════
── Failure ('test-diagnostics.R:9:3'): skipTrack.diagnostics runs on all options ──
Expected `skipTrack.diagnostics(foo, "Betas")` to run without any errors.
i Actually got a <simpleError> with text:
The chains must be numeric vectors in order to use the standard transformation.
── Failure ('test-diagnostics.R:10:3'): skipTrack.diagnostics runs on all options ──
Expected `skipTrack.diagnostics(foo, "Gammas")` to run without any errors.
i Actually got a <simpleError> with text:
The chains must be numeric vectors in order to use the standard transformation.
── Failure ('test-diagnostics.R:11:3'): skipTrack.diagnostics runs on all options ──
Expected `skipTrack.diagnostics(foo, "muis")` to run without any errors.
i Actually got a <simpleError> with text:
The chains must be numeric vectors in order to use the standard transformation.
── Failure ('test-diagnostics.R:12:3'): skipTrack.diagnostics runs on all options ──
Expected `skipTrack.diagnostics(foo, "tauis")` to run without any errors.
i Actually got a <simpleError> with text:
The chains must be numeric vectors in order to use the standard transformation.
── Failure ('test-diagnostics.R:13:3'): skipTrack.diagnostics runs on all options ──
Expected `skipTrack.diagnostics(foo, "cijs")` to run without any errors.
i Actually got a <simpleError> with text:
The chains must be numeric vectors in order to use the standard transformation.
── Error ('test-results.R:6:3'): results function runs ─────────────────────────
Error in `proximityMapF(mhDraws = mhDraws, distance = distance, verbose = verbose,
...)`: The chains must be numeric vectors in order to use the standard transformation.
Backtrace:
▆
1. └─skipTrack::skipTrack.results(foo, burnIn = 10) at test-results.R:6:3
2. └─base::lapply(...)
3. └─skipTrack (local) FUN(X[[i]], ...)
4. └─skipTrack::skipTrack.diagnostics(stFit = stFit, param)
5. └─genMCMCDiag::genDiagnostic(...)
6. └─genMCMCDiag (local) proximityMapF(...)
── Failure ('test-utils.R:9:3'): Utility functions do not throw errors ─────────
Expected `summary(foo, burnIn = 20)` to run without any errors.
i Actually got a <simpleError> with text:
The chains must be numeric vectors in order to use the standard transformation.
[ FAIL 7 | WARN 7 | SKIP 1 | PASS 9 ]
Error: Test failures
Execution halted
Flavor: r-release-windows-x86_64
Version: 0.1.0
Check: re-building of vignette outputs
Result: ERROR
Error(s) in re-building vignettes:
--- re-building 'skipTrack_intro.Rmd' using rmarkdown
Quitting from lines 122-123 [unnamed-chunk-6] (skipTrack_intro.Rmd)
Error: processing vignette 'skipTrack_intro.Rmd' failed with diagnostics:
The chains must be numeric vectors in order to use the standard transformation.
--- failed re-building 'skipTrack_intro.Rmd'
SUMMARY: processing the following file failed:
'skipTrack_intro.Rmd'
Error: Vignette re-building failed.
Execution halted
Flavor: r-release-windows-x86_64