Package: nmarank Check: tests New result: ERROR Running ‘testthat.R’ [92s/93s] Running the tests in ‘tests/testthat.R’ failed. Complete output: > library(testthat) > library(nmarank) Loading required package: meta Loading required package: metadat Loading 'meta' package (version 8.0-1). Type 'help(meta)' for a brief overview. Loading required package: netmeta Loading 'netmeta' package (version 2.9-0). Type 'help("netmeta-package")' for a brief overview. Readers of 'Meta-Analysis with R (Use R!)' should install older version of 'netmeta' package: https://tinyurl.com/kyz6wjbb Attaching package: 'netmeta' The following object is masked from 'package:meta': pairwise > > test_check("nmarank") [ FAIL 1 | WARN 0 | SKIP 0 | PASS 10 ] ══ Failed tests ════════════════════════════════════════════════════════════════ ── Failure ('test-arm.R:185:3'): arm gives correct probs ─────────────────────── abs(p1 - p2) is not less than 0.02. Difference: 0.0045 [ FAIL 1 | WARN 0 | SKIP 0 | PASS 10 ] Error: Test failures Execution halted Package: ref.ICAR Check: re-building of vignette outputs New result: ERROR Error(s) in re-building vignettes: ... --- re-building ‘ref-icar-vignette.Rmd’ using rmarkdown Warning in eng_r(options) : Failed to tidy R code in chunk 'unnamed-chunk-1'. Reason: Error : The formatR package is required by the chunk option tidy = TRUE but not installed; tidy = TRUE will be ignored. Warning in eng_r(options) : Failed to tidy R code in chunk 'unnamed-chunk-2'. Reason: Error : The formatR package is required by the chunk option tidy = TRUE but not installed; tidy = TRUE will be ignored. Warning in eng_r(options) : Failed to tidy R code in chunk 'unnamed-chunk-3'. Reason: Error : The formatR package is required by the chunk option tidy = TRUE but not installed; tidy = TRUE will be ignored. ** Processing: /home/hornik/tmp/CRAN_recheck/ref.ICAR.Rcheck/vign_test/ref.ICAR/vignettes/ref-icar-vignette_files/figure-html/unnamed-chunk-3-1.png 672x528 pixels, 3x8 bits/pixel, RGB Input IDAT size = 55347 bytes Input file size = 55497 bytes Trying: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 45467 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 = 45467 Output IDAT size = 45467 bytes (9880 bytes decrease) Output file size = 45545 bytes (9952 bytes = 17.93% decrease) Warning in eng_r(options) : Failed to tidy R code in chunk 'unnamed-chunk-4'. Reason: Error : The formatR package is required by the chunk option tidy = TRUE but not installed; tidy = TRUE will be ignored. ** Processing: /home/hornik/tmp/CRAN_recheck/ref.ICAR.Rcheck/vign_test/ref.ICAR/vignettes/ref-icar-vignette_files/figure-html/unnamed-chunk-4-1.png 672x528 pixels, 3x8 bits/pixel, RGB Input IDAT size = 51884 bytes Input file size = 52034 bytes Trying: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 43075 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 = 43075 Output IDAT size = 43075 bytes (8809 bytes decrease) Output file size = 43153 bytes (8881 bytes = 17.07% decrease) Warning in eng_r(options) : Failed to tidy R code in chunk 'unnamed-chunk-5'. Reason: Error : The formatR package is required by the chunk option tidy = TRUE but not installed; tidy = TRUE will be ignored. Warning in eng_r(options) : Failed to tidy R code in chunk 'unnamed-chunk-6'. Reason: Error : The formatR package is required by the chunk option tidy = TRUE but not installed; tidy = TRUE will be ignored. Warning in eng_r(options) : Failed to tidy R code in chunk 'unnamed-chunk-7'. Reason: Error : The formatR package is required by the chunk option tidy = TRUE but not installed; tidy = TRUE will be ignored. Warning in eng_r(options) : Failed to tidy R code in chunk 'unnamed-chunk-8'. Reason: Error : The formatR package is required by the chunk option tidy = TRUE but not installed; tidy = TRUE will be ignored. ** Processing: /home/hornik/tmp/CRAN_recheck/ref.ICAR.Rcheck/vign_test/ref.ICAR/vignettes/ref-icar-vignette_files/figure-html/unnamed-chunk-8-1.png 672x480 pixels, 8 bits/pixel, 256 colors in palette Reducing image to 8 bits/pixel, grayscale Input IDAT size = 30587 bytes Input file size = 31481 bytes Trying: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 28564 zc = 9 zm = 8 zs = 1 f = 0 IDAT size = 28555 zc = 1 zm = 8 zs = 2 f = 0 zc = 9 zm = 8 zs = 3 f = 0 zc = 9 zm = 8 zs = 0 f = 5 IDAT size = 25747 zc = 9 zm = 8 zs = 1 f = 5 IDAT size = 25165 zc = 1 zm = 8 zs = 2 f = 5 zc = 9 zm = 8 zs = 3 f = 5 Selecting parameters: zc = 9 zm = 8 zs = 1 f = 5 IDAT size = 25165 Output IDAT size = 25165 bytes (5422 bytes decrease) Output file size = 25243 bytes (6238 bytes = 19.82% decrease) Warning in eng_r(options) : Failed to tidy R code in chunk 'unnamed-chunk-9'. Reason: Error : The formatR package is required by the chunk option tidy = TRUE but not installed; tidy = TRUE will be ignored. Warning in eng_r(options) : Failed to tidy R code in chunk 'unnamed-chunk-10'. Reason: Error : The formatR package is required by the chunk option tidy = TRUE but not installed; tidy = TRUE will be ignored. ** Processing: /home/hornik/tmp/CRAN_recheck/ref.ICAR.Rcheck/vign_test/ref.ICAR/vignettes/ref-icar-vignette_files/figure-html/unnamed-chunk-10-1.png 672x528 pixels, 3x8 bits/pixel, RGB Input IDAT size = 52560 bytes Input file size = 52710 bytes Trying: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 43044 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 = 43044 Output IDAT size = 43044 bytes (9516 bytes decrease) Output file size = 43122 bytes (9588 bytes = 18.19% decrease) Warning in eng_r(options) : Failed to tidy R code in chunk 'unnamed-chunk-11'. Reason: Error : The formatR package is required by the chunk option tidy = TRUE but not installed; tidy = TRUE will be ignored. ** Processing: /home/hornik/tmp/CRAN_recheck/ref.ICAR.Rcheck/vign_test/ref.ICAR/vignettes/ref-icar-vignette_files/figure-html/unnamed-chunk-11-1.png 672x480 pixels, 8 bits/pixel, 256 colors in palette Reducing image to 8 bits/pixel, grayscale Input IDAT size = 29088 bytes Input file size = 29982 bytes Trying: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 27075 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 IDAT size = 24767 zc = 9 zm = 8 zs = 1 f = 5 IDAT size = 24237 zc = 1 zm = 8 zs = 2 f = 5 zc = 9 zm = 8 zs = 3 f = 5 Selecting parameters: zc = 9 zm = 8 zs = 1 f = 5 IDAT size = 24237 Output IDAT size = 24237 bytes (4851 bytes decrease) Output file size = 24315 bytes (5667 bytes = 18.90% decrease) Warning in eng_r(options) : Failed to tidy R code in chunk 'unnamed-chunk-12'. Reason: Error : The formatR package is required by the chunk option tidy = TRUE but not installed; tidy = TRUE will be ignored. Quitting from lines 269-276 [unnamed-chunk-12] (ref-icar-vignette.Rmd) Error: processing vignette 'ref-icar-vignette.Rmd' failed with diagnostics: `dsn` must point to a source, not an empty string. --- failed re-building ‘ref-icar-vignette.Rmd’ SUMMARY: processing the following file failed: ‘ref-icar-vignette.Rmd’ Error: Vignette re-building failed. Execution halted Package: skipTrack Check: examples New 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 -> -> proximityMapF Execution halted Examples with CPU (user + system) or elapsed time > 5s user system elapsed plot.skipTrack.model 4.969 0.151 5.159 Package: skipTrack Check: re-building of vignette outputs New result: ERROR Error(s) in re-building vignettes: ... --- re-building ‘skipTrack_intro.Rmd’ using rmarkdown ** Processing: /home/hornik/tmp/CRAN_recheck/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 Package: skipTrack Check: tests New result: ERROR Running ‘testthat.R’ [8s/8s] 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 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 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 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 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 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 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