Package: amadeus Check: examples New result: ERROR Running examples in ‘amadeus-Ex.R’ failed The error most likely occurred in: > base::assign(".ptime", proc.time(), pos = "CheckExEnv") > ### Name: download_geos > ### Title: Download atmospheric composition data > ### Aliases: download_geos > > ### ** Examples > > download_geos( + collection = "aqc_tavg_1hr_g1440x721_v1", + date = "2024-01-01", + directory_to_save = tempdir(), + acknowledgement = TRUE, + download = FALSE, # NOTE: download skipped for examples, + remove_command = TRUE + ) Error in download_geos(collection = "aqc_tavg_1hr_g1440x721_v1", date = "2024-01-01", : Invalid date returns HTTP code 404. Check `date` parameter. Execution halted Package: mlr3pipelines Check: tests New result: ERROR Running ‘testthat.R’ [298s/144s] Running the tests in ‘tests/testthat.R’ failed. Complete output: > if (requireNamespace("testthat", quietly = TRUE)) { + library("checkmate") + library("testthat") + library("mlr3") + library("paradox") + library("mlr3pipelines") + test_check("mlr3pipelines") + } Starting 2 test processes [ FAIL 1 | WARN 0 | SKIP 87 | PASS 12484 ] ══ Skipped tests (87) ══════════════════════════════════════════════════════════ • On CRAN (85): 'test_CnfFormula_simplify.R:6:3', 'test_CnfFormula.R:591:3', 'test_Graph.R:281:3', 'test_dictionary.R:7:3', 'test_learner_weightedaverage.R:5:3', 'test_learner_weightedaverage.R:57:3', 'test_learner_weightedaverage.R:105:3', 'test_learner_weightedaverage.R:152:3', 'test_meta.R:39:3', 'test_mlr_graphs_bagging.R:6:3', 'test_mlr_graphs_branching.R:26:3', 'test_GraphLearner.R:5:3', 'test_GraphLearner.R:184:3', 'test_GraphLearner.R:306:3', 'test_GraphLearner.R:371:3', 'test_mlr_graphs_robustify.R:5:3', 'test_pipeop_adas.R:8:3', 'test_pipeop_blsmote.R:8:3', 'test_pipeop_branch.R:4:3', 'test_pipeop_chunk.R:4:3', 'test_pipeop_classbalancing.R:10:3', 'test_pipeop_boxcox.R:9:3', 'test_pipeop_classweights.R:10:3', 'test_pipeop_colroles.R:10:3', 'test_pipeop_colapply.R:9:3', 'test_pipeop_copy.R:5:3', 'test_pipeop_encode.R:21:3', 'test_pipeop_encodeimpact.R:11:3', 'test_pipeop_datefeatures.R:13:3', 'test_pipeop_encodelmer.R:15:3', 'test_pipeop_encodelmer.R:38:3', 'test_pipeop_encodelmer.R:81:3', 'test_pipeop_featureunion.R:9:3', 'test_pipeop_featureunion.R:134:3', 'test_pipeop_filter.R:7:3', 'test_pipeop_fixfactors.R:9:3', 'test_pipeop_ensemble.R:6:3', 'test_pipeop_histbin.R:9:3', 'test_pipeop_ica.R:7:3', 'test_pipeop_impute.R:4:3', 'test_pipeop_kernelpca.R:9:3', 'test_pipeop_imputelearner.R:43:3', 'test_pipeop_learner.R:17:3', 'test_pipeop_missind.R:6:3', 'test_pipeop_modelmatrix.R:7:3', 'test_pipeop_learnercv.R:31:3', 'test_pipeop_multiplicityexply.R:9:3', 'test_pipeop_mutate.R:9:3', 'test_pipeop_multiplicityimply.R:9:3', 'test_pipeop_ovr.R:9:3', 'test_pipeop_ovr.R:48:3', 'test_pipeop_pca.R:8:3', 'test_pipeop_proxy.R:14:3', 'test_pipeop_quantilebin.R:5:3', 'test_pipeop_nmf.R:9:3', 'test_pipeop_randomprojection.R:8:3', 'test_pipeop_randomresponse.R:5:3', 'test_pipeop_renamecolumns.R:11:3', 'test_pipeop_replicate.R:9:3', 'test_pipeop_removeconstants.R:10:3', 'test_pipeop_scale.R:8:3', 'test_pipeop_scale.R:18:3', 'test_pipeop_scalemaxabs.R:7:3', 'test_pipeop_scalerange.R:8:3', 'test_pipeop_select.R:9:3', 'test_pipeop_smote.R:10:3', 'test_pipeop_smotenc.R:8:3', 'test_pipeop_rowapply.R:9:3', 'test_pipeop_subsample.R:10:3', 'test_pipeop_targetinvert.R:4:3', 'test_pipeop_targetmutate.R:5:3', 'test_pipeop_targettrafo.R:4:3', 'test_pipeop_targettrafoscalerange.R:5:3', 'test_pipeop_task_preproc.R:4:3', 'test_pipeop_task_preproc.R:14:3', 'test_pipeop_spatialsign.R:7:3', 'test_pipeop_textvectorizer.R:38:3', 'test_pipeop_textvectorizer.R:190:3', 'test_pipeop_unbranch.R:10:3', 'test_pipeop_updatetarget.R:89:3', 'test_pipeop_vtreat.R:9:3', 'test_pipeop_yeojohnson.R:8:3', 'test_pipeop_tunethreshold.R:111:3', 'test_pipeop_tunethreshold.R:191:3', 'test_typecheck.R:188:3' • empty test (2): 'test_pipeop_missind.R:101:1', 'test_ppl.R:61:1' ══ Failed tests ════════════════════════════════════════════════════════════════ ── Error ('test_pipeop_blsmote.R:86:3'): PipeOpBLSmote - handling of feature named 'class' ── Error in `smotefamily::BLSMOTE(X = dt, target = task$truth())`: K cannot exceed the size of DANGER This happened PipeOp blsmote's $train() Backtrace: ▆ 1. ├─op$train(list(task)) at test_pipeop_blsmote.R:86:3 2. │ └─mlr3pipelines:::.__PipeOp__train(...) 3. │ ├─base::withCallingHandlers(...) 4. │ └─private$.train(input) 5. │ └─mlr3pipelines:::.__PipeOpTaskPreproc__.train(...) 6. │ └─private$.train_task(intask) 7. │ └─mlr3pipelines:::.__PipeOpBLSmote__.train_task(...) 8. │ ├─utils::capture.output(...) 9. │ │ └─base::withVisible(...elt(i)) 10. │ ├─data.table::setDT(...) 11. │ │ └─data.table::is.data.table(x) 12. │ ├─mlr3misc::invoke(...) 13. │ │ └─base::eval.parent(expr, n = 1L) 14. │ │ └─base::eval(expr, p) 15. │ │ └─base::eval(expr, p) 16. │ └─smotefamily::BLSMOTE(X = dt, target = task$truth()) 17. │ └─base::stop("K cannot exceed the size of DANGER") 18. └─base::.handleSimpleError(...) 19. └─mlr3pipelines (local) h(simpleError(msg, call)) [ FAIL 1 | WARN 0 | SKIP 87 | PASS 12484 ] Error: Test failures Execution halted Package: phenofit Check: tests New result: ERROR Running ‘testthat.R’ [62s/62s] Running the tests in ‘tests/testthat.R’ failed. Complete output: > library(testthat) > library(phenofit) > > test_check("phenofit") List of 5 $ AG : tibble [6 × 8] (S3: tbl_df/tbl/data.frame) $ Beck : tibble [6 × 7] (S3: tbl_df/tbl/data.frame) $ Elmore: tibble [6 × 8] (S3: tbl_df/tbl/data.frame) $ Gu : tibble [6 × 10] (S3: tbl_df/tbl/data.frame) $ Zhang : tibble [6 × 8] (S3: tbl_df/tbl/data.frame) NULL # A tibble: 6 × 8 flag t0 mn mx rsp a3 rau a5 1 1999_1 -135. 0.201 0.636 0.00932 2.85 0.00852 2 2 2000_1 189. 0.238 0.635 0.0126 2.47 0.00801 3.21 3 2001_1 569. 0.252 0.626 0.0108 2.96 0.00950 2.96 4 2002_1 892. 0.253 0.614 0.0159 2 0.00724 3.08 5 2003_1 1268. 0.236 0.577 0.0121 2.88 0.00723 2.88 6 2004_1 1677. 0.202 0.576 0.00832 2.84 0.00990 3.48 meth R2 NSE R RMSE pvalue n_sim 1: AG 0.9986908 0.9985845 0.9993452 9.940385e-03 4.489925e-65 46 2: Beck 1.0000000 1.0000000 1.0000000 1.389780e-09 0.000000e+00 46 3: Elmore 1.0000000 1.0000000 1.0000000 4.161813e-10 0.000000e+00 46 4: Gu 1.0000000 1.0000000 1.0000000 4.891365e-11 0.000000e+00 46 5: Zhang 1.0000000 1.0000000 1.0000000 5.529073e-06 8.043461e-208 46 $AG formula: mn + (mx - mn) * exp(-((t0 - t) * rsp)^a3) formula: mn + (mx - mn) * exp(-((t - t0) * rau)^a5) pars: t0 mn mx rsp a3 rau a5 nlminb 149.8926 0.1020656 0.7095242 0.009389263 6 0.009367765 6 warning: solve(): system is singular; attempting approx solution warning: solve(): system is singular (rcond: 1.65502e-16); attempting approx solution warning: solve(): system is singular (rcond: 2.19427e-17); attempting approx solution warning: solve(): system is singular (rcond: 1.65502e-16); attempting approx solution warning: solve(): system is singular; attempting approx solution warning: solve(): system is singular; attempting approx solution warning: solve(): system is singular; attempting approx solution warning: solve(): system is singular (rcond: 1.33432e-17); attempting approx solution warning: solve(): system is singular; attempting approx solution warning: solve(): system is singular; attempting approx solution warning: solve(): system is singular; attempting approx solution warning: solve(): system is singular; attempting approx solution warning: solve(): system is singular; attempting approx solution warning: solve(): system is singular; attempting approx solution warning: solve(): system is singular; attempting approx solution warning: solve(): system is singular; attempting approx solution warning: solve(): system is singular; attempting approx solution warning: solve(): system is singular; attempting approx solution warning: solve(): system is singular; attempting approx solution warning: solve(): system is singular (rcond: 2.38811e-17); attempting approx solution warning: solve(): system is singular; attempting approx solution warning: solve(): system is singular; attempting approx solution warning: solve(): system is singular (rcond: 2.03034e-17); attempting approx solution warning: solve(): system is singular; attempting approx solution warning: solve(): system is singular; attempting approx solution warning: solve(): system is singular; attempting approx solution warning: solve(): system is singular; attempting approx solution warning: solve(): system is singular; attempting approx solution warning: solve(): system is singular; attempting approx solution warning: solve(): system is singular (rcond: 1.33432e-17); attempting approx solution warning: solve(): system is singular (rcond: 3.31005e-17); attempting approx solution warning: solve(): system is singular; attempting approx solution warning: solve(): system is singular; attempting approx solution warning: solve(): system is singular; attempting approx solution warning: solve(): system is singular; attempting approx solution warning: solve(): system is singular; attempting approx solution warning: solve(): system is singular; attempting approx solution warning: solve(): system is singular; attempting approx solution warning: solve(): system is singular; attempting approx solution warning: solve(): system is singular (rcond: 3.08395e-17); attempting approx solution warning: solve(): system is singular; attempting approx solution warning: solve(): system is singular (rcond: 2.36432e-17); attempting approx solution warning: solve(): system is singular; attempting approx solution warning: solve(): system is singular; attempting approx solution warning: solve(): system is singular; attempting approx solution warning: solve(): system is singular; attempting approx solution warning: solve(): system is singular; attempting approx solution warning: solve(): system is singular; attempting approx solution warning: solve(): system is singular; attempting approx solution warning: solve(): system is singular (rcond: 6.97437e-18); attempting approx solution warning: solve(): system is singular; attempting approx solution warning: solve(): system is singular; attempting approx solution warning: solve(): system is singular (rcond: 1.85037e-16); attempting approx solution warning: solve(): system is singular; attempting approx solution warning: solve(): system is singular (rcond: 2.80681e-17); attempting approx solution warning: solve(): system is singular; attempting approx solution warning: solve(): system is singular (rcond: 5.43896e-17); attempting approx solution warning: solve(): system is singular; attempting approx solution warning: solve(): system is singular; attempting approx solution warning: solve(): system is singular; attempting approx solution warning: solve(): system is singular; attempting approx solution warning: solve(): system is singular; attempting approx solution warning: solve(): system is singular; attempting approx solution warning: solve(): system is singular; attempting approx solution warning: solve(): system is singular; attempting approx solution warning: solve(): system is singular (rcond: 2.38811e-17); attempting approx solution warning: solve(): system is singular (rcond: 3.05447e-17); attempting approx solution warning: solve(): system is singular (rcond: 2.11109e-17); attempting approx solution warning: solve(): system is singular; attempting approx solution warning: solve(): system is singular; attempting approx solution warning: solve(): system is singular; attempting approx solution warning: solve(): system is singular; attempting approx solution warning: solve(): system is singular; attempting approx solution warning: solve(): system is singular; attempting approx solution warning: solve(): system is singular (rcond: 6.04329e-17); attempting approx solution warning: solve(): system is singular; attempting approx solution warning: solve(): system is singular; attempting approx solution warning: solve(): system is singular; attempting approx solution warning: solve(): system is singular; attempting approx solution warning: solve(): system is singular; attempting approx solution warning: solve(): system is singular (rcond: 1.85037e-16); attempting approx solution warning: solve(): system is singular; attempting approx solution warning: solve(): system is singular (rcond: 2.80681e-17); attempting approx solution warning: solve(): system is singular; attempting approx solution warning: solve(): system is singular (rcond: 5.43896e-17); attempting approx solution warning: solve(): system is singular; attempting approx solution warning: solve(): system is singular; attempting approx solution warning: solve(): system is singular; attempting approx solution warning: solve(): system is singular; attempting approx solution warning: solve(): system is singular; attempting approx solution warning: solve(): system is singular; attempting approx solution warning: solve(): system is singular (rcond: 3.31005e-17); attempting approx solution warning: solve(): system is singular; attempting approx solution warning: solve(): system is singular; attempting approx solution warning: solve(): system is singular; attempting approx solution warning: solve(): system is singular; attempting approx solution warning: solve(): system is singular; attempting approx solution warning: solve(): system is singular (rcond: 2.38811e-17); attempting approx solution warning: solve(): system is singular; attempting approx solution warning: solve(): system is singular; attempting approx solution warning: solve(): system is singular; attempting approx solution warning: solve(): system is singular; attempting approx solution warning: solve(): system is singular; attempting approx solution warning: solve(): system is singular (rcond: 3.31005e-17); attempting approx solution warning: solve(): system is singular; attempting approx solution warning: solve(): system is singular; attempting approx solution warning: solve(): system is singular; attempting approx solution warning: solve(): system is singular; attempting approx solution warning: solve(): system is singular; attempting approx solution warning: solve(): system is singular; attempting approx solution warning: solve(): system is singular; attempting approx solution warning: solve(): system is singular; attempting approx solution warning: solve(): system is singular (rcond: 2.38811e-17); attempting approx solution warning: solve(): system is singular; attempting approx solution warning: solve(): system is singular; attempting approx solution warning: solve(): system is singular; attempting approx solution warning: solve(): system is singular; attempting approx solution warning: solve(): system is singular; attempting approx solution warning: solve(): system is singular; attempting approx solution warning: solve(): system is singular; attempting approx solution warning: solve(): system is singular; attempting approx solution warning: solve(): system is singular; attempting approx solution warning: solve(): system is singular; attempting approx solution warning: solve(): system is singular; attempting approx solution warning: solve(): system is singular; attempting approx solution warning: solve(): system is singular (rcond: 1.94249e-17); attempting approx solution warning: solve(): system is singular; attempting approx solution warning: solve(): system is singular; attempting approx solution warning: solve(): system is singular; attempting approx solution warning: solve(): system is singular; attempting approx solution warning: solve(): system is singular (rcond: 3.84957e-17); attempting approx solution warning: solve(): system is singular; attempting approx solution warning: solve(): system is singular; attempting approx solution warning: solve(): system is singular; attempting approx solution warning: solve(): system is singular; attempting approx solution warning: solve(): system is singular; attempting approx solution warning: solve(): system is singular; attempting approx solution warning: solve(): system is singular; attempting approx solution warning: solve(): system is singular; attempting approx solution warning: solve(): system is singular (rcond: 3.31005e-17); attempting approx solution warning: solve(): system is singular; attempting approx solution warning: solve(): system is singular (rcond: 8.58712e-17); attempting approx solution warning: solve(): system is singular; attempting approx solution warning: solve(): system is singular; attempting approx solution warning: solve(): system is singular; attempting approx solution warning: solve(): system is singular; attempting approx solution warning: solve(): system is singular; attempting approx solution warning: solve(): system is singular (rcond: 2.38811e-17); attempting approx solution warning: solve(): system is singular; attempting approx solution warning: solve(): system is singular; attempting approx solution warning: solve(): system is singular; attempting approx solution warning: solve(): system is singular (rcond: 2.09346e-17); attempting approx solution warning: solve(): system is singular; attempting approx solution warning: solve(): system is singular; attempting approx solution warning: solve(): system is singular; attempting approx solution warning: solve(): system is singular; attempting approx solution warning: solve(): system is singular (rcond: 3.82199e-17); attempting approx solution warning: solve(): system is singular (rcond: 2.38705e-17); attempting approx solution warning: solve(): system is singular; attempting approx solution warning: solve(): system is singular; attempting approx solution warning: solve(): system is singular; attempting approx solution warning: solve(): system is singular; attempting approx solution warning: solve(): system is singular (rcond: 2.38811e-17); attempting approx solution warning: solve(): system is singular; attempting approx solution warning: solve(): system is singular; attempting approx solution warning: solve(): system is singular (rcond: 5.88785e-17); attempting approx solution warning: solve(): system is singular; attempting approx solution warning: solve(): system is singular; attempting approx solution warning: solve(): system is singular; attempting approx solution warning: solve(): system is singular; attempting approx solution warning: solve(): system is singular (rcond: 1.85037e-16); attempting approx solution warning: solve(): system is singular; attempting approx solution warning: solve(): system is singular; attempting approx solution warning: solve(): system is singular; attempting approx solution warning: solve(): system is singular; attempting approx solution warning: solve(): system is singular (rcond: 7.40149e-17); attempting approx solution warning: solve(): system is singular (rcond: 6.20634e-17); attempting approx solution warning: solve(): system is singular; attempting approx solution warning: solve(): system is singular; attempting approx solution warning: solve(): system is singular; attempting approx solution warning: solve(): system is singular; attempting approx solution warning: solve(): system is singular; attempting approx solution warning: solve(): system is singular (rcond: 2.38811e-17); attempting approx solution warning: solve(): system is singular (rcond: 3.05447e-17); attempting approx solution warning: solve(): system is singular (rcond: 2.11109e-17); attempting approx solution warning: solve(): system is singular; attempting approx solution warning: solve(): system is singular; attempting approx solution warning: solve(): system is singular (rcond: 5.43896e-17); attempting approx solution warning: solve(): system is singular (rcond: 4.38854e-17); attempting approx solution warning: solve(): system is singular; attempting approx solution warning: solve(): system is singular; attempting approx solution warning: solve(): system is singular; attempting approx solution warning: solve(): system is singular; attempting approx solution warning: solve(): system is singular (rcond: 1.00786e-16); attempting approx solution warning: solve(): system is singular (rcond: 1.46031e-17); attempting approx solution warning: solve(): system is singular (rcond: 5.02097e-17); attempting approx solution warning: solve(): system is singular (rcond: 1.25524e-17); attempting approx solution warning: solve(): system is singular; attempting approx solution warning: solve(): system is singular; attempting approx solution warning: solve(): system is singular; attempting approx solution warning: solve(): system is singular; attempting approx solution warning: solve(): system is singular; attempting approx solution warning: solve(): system is singular; attempting approx solution warning: solve(): system is singular (rcond: 3.31005e-17); attempting approx solution warning: solve(): system is singular; attempting approx solution warning: solve(): system is singular; attempting approx solution warning: solve(): system is singular; attempting approx solution warning: solve(): system is singular; attempting approx solution warning: solve(): system is singular; attempting approx solution warning: solve(): system is singular; attempting approx solution warning: solve(): system is singular; attempting approx solution warning: solve(): system is singular; attempting approx solution warning: solve(): system is singular (rcond: 3.31005e-17); attempting approx solution [ FAIL 1 | WARN 2 | SKIP 0 | PASS 69 ] ══ Failed tests ════════════════════════════════════════════════════════════════ ── Failure ('test-curvefit.R:18:5'): curvefit works ──────────────────────────── all.equal(p1, p2, tolerance = 1e-06) is not TRUE `actual` is a character vector ('Component "Elmore": Component "mn": Mean relative difference: 1.990404e-06') `expected` is a logical vector (TRUE) [ FAIL 1 | WARN 2 | SKIP 0 | PASS 69 ] Error: Test failures Execution halted Package: reportRmd Check: tests New result: ERROR Running ‘testthat.R’ [6s/6s] Running the tests in ‘tests/testthat.R’ failed. Complete output: > library(testthat) > library(reportRmd) > > test_check("reportRmd") Using MC sim. Use set.seed() prior to function for reproducible results. Using MC sim. Use set.seed() prior to function for reproducible results. Waiting for profiling to be done... Waiting for profiling to be done... Waiting for profiling to be done... Waiting for profiling to be done... Waiting for profiling to be done... Waiting for profiling to be done... Waiting for profiling to be done... Waiting for profiling to be done... Waiting for profiling to be done... Waiting for profiling to be done... Waiting for profiling to be done... Waiting for profiling to be done... Waiting for profiling to be done... Waiting for profiling to be done... Waiting for profiling to be done... Waiting for profiling to be done... VIF not yet implemented for negative binomial, mixed effects or GEE models. [ FAIL 1 | WARN 42 | SKIP 0 | PASS 56 ] ══ Failed tests ════════════════════════════════════════════════════════════════ ── Failure ('test_calculations.R:156:5'): uvsum logistic regression CIS are correct ── output[, 2] (`actual`) not equal to `expected` (`expected`). `actual`: "0.77 (0.49, 1.16)" "4.74 (2.59, 10.00)" `expected`: "0.77 (0.49, 1.16)" "4.74 ( 2.59, 10.00)" [ FAIL 1 | WARN 42 | SKIP 0 | PASS 56 ] Error: Test failures Execution halted Package: rYWAASB Check: whether the package can be loaded New result: ERROR Loading this package had a fatal error status code 1 Loading log: Error: package or namespace load failed for ‘rYWAASB’ in loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]]): there is no package called ‘Rcpp’ Execution halted Package: samplesizeCMH Check: re-building of vignette outputs New result: ERROR Error(s) in re-building vignettes: ... --- re-building ‘samplesizeCMH-introduction.Rmd’ using rmarkdown Quitting from lines 136-139 [BreslowDay] (samplesizeCMH-introduction.Rmd) Error: processing vignette 'samplesizeCMH-introduction.Rmd' failed with diagnostics: package or namespace load failed for 'DescTools' in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]): there is no package called 'Rcpp' --- failed re-building ‘samplesizeCMH-introduction.Rmd’ --- re-building ‘samplesizeCMH-power.Rmd’ using rmarkdown ** Processing: /home/hornik/tmp/CRAN_recheck/samplesizeCMH.Rcheck/vign_test/samplesizeCMH/vignettes/samplesizeCMH-power_files/figure-html/contraceptives-plot-1.png 576x384 pixels, 3x8 bits/pixel, RGB Input IDAT size = 19329 bytes Input file size = 19431 bytes Trying: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 15462 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 = 15462 Output IDAT size = 15462 bytes (3867 bytes decrease) Output file size = 15540 bytes (3891 bytes = 20.02% decrease) --- finished re-building ‘samplesizeCMH-power.Rmd’ --- re-building ‘samplesizeCMH-samplesize.Rmd’ using rmarkdown --- finished re-building ‘samplesizeCMH-samplesize.Rmd’ SUMMARY: processing the following file failed: ‘samplesizeCMH-introduction.Rmd’ Error: Vignette re-building failed. Execution halted Package: SIBER Check: re-building of vignette outputs New result: ERROR Error(s) in re-building vignettes: ... --- re-building ‘Centroid-Vectors.Rmd’ using rmarkdown ** Processing: /home/hornik/tmp/CRAN_recheck/SIBER.Rcheck/vign_test/SIBER/vignettes/Centroid-Vectors_files/figure-html/ggplot-polar-1.png 864x480 pixels, 8 bits/pixel, 250 colors in palette Reducing image to 8 bits/pixel, grayscale Input IDAT size = 41175 bytes Input file size = 42075 bytes Trying: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 37975 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 = 37975 Output IDAT size = 37975 bytes (3200 bytes decrease) Output file size = 38053 bytes (4022 bytes = 9.56% decrease) ** Processing: /home/hornik/tmp/CRAN_recheck/SIBER.Rcheck/vign_test/SIBER/vignettes/Centroid-Vectors_files/figure-html/polar-density-1.png 960x672 pixels, 3x8 bits/pixel, RGB Input IDAT size = 47794 bytes Input file size = 47932 bytes Trying: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 38111 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 = 38111 Output IDAT size = 38111 bytes (9683 bytes decrease) Output file size = 38189 bytes (9743 bytes = 20.33% decrease) --- finished re-building ‘Centroid-Vectors.Rmd’ --- re-building ‘Customising-Plots-Manually.Rmd’ using rmarkdown ** Processing: /home/hornik/tmp/CRAN_recheck/SIBER.Rcheck/vign_test/SIBER/vignettes/Customising-Plots-Manually_files/figure-html/unnamed-chunk-3-1.png 576x480 pixels, 3x8 bits/pixel, RGB Input IDAT size = 35528 bytes Input file size = 35654 bytes Trying: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 27592 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 = 27592 Output IDAT size = 27592 bytes (7936 bytes decrease) Output file size = 27670 bytes (7984 bytes = 22.39% decrease) --- finished re-building ‘Customising-Plots-Manually.Rmd’ --- re-building ‘Ellipse-Overlap.Rmd’ using rmarkdown ** Processing: /home/hornik/tmp/CRAN_recheck/SIBER.Rcheck/vign_test/SIBER/vignettes/Ellipse-Overlap_files/figure-html/bayesOverlap-1.png 576x480 pixels, 8 bits/pixel, 256 colors in palette Reducing image to 8 bits/pixel, grayscale Input IDAT size = 7441 bytes Input file size = 8299 bytes Trying: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 6543 zc = 9 zm = 8 zs = 1 f = 0 IDAT size = 6494 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 = 1 f = 0 IDAT size = 6494 Output IDAT size = 6494 bytes (947 bytes decrease) Output file size = 6572 bytes (1727 bytes = 20.81% decrease) ** Processing: /home/hornik/tmp/CRAN_recheck/SIBER.Rcheck/vign_test/SIBER/vignettes/Ellipse-Overlap_files/figure-html/bayesOverlap-2.png 576x480 pixels, 8 bits/pixel, 256 colors in palette Reducing image to 8 bits/pixel, grayscale Input IDAT size = 8220 bytes Input file size = 9090 bytes Trying: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 7313 zc = 9 zm = 8 zs = 1 f = 0 IDAT size = 7270 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 = 1 f = 0 IDAT size = 7270 Output IDAT size = 7270 bytes (950 bytes decrease) Output file size = 7348 bytes (1742 bytes = 19.16% decrease) --- finished re-building ‘Ellipse-Overlap.Rmd’ --- re-building ‘Introduction-to-SIBER.Rmd’ using rmarkdown ** Processing: /home/hornik/tmp/CRAN_recheck/SIBER.Rcheck/vign_test/SIBER/vignettes/Introduction-to-SIBER_files/figure-html/plot-data-1.png 576x480 pixels, 3x8 bits/pixel, RGB Input IDAT size = 59176 bytes Input file size = 59338 bytes Trying: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 45829 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 = 45829 Output IDAT size = 45829 bytes (13347 bytes decrease) Output file size = 45907 bytes (13431 bytes = 22.63% decrease) ** Processing: /home/hornik/tmp/CRAN_recheck/SIBER.Rcheck/vign_test/SIBER/vignettes/Introduction-to-SIBER_files/figure-html/summary-stats-1.png 576x480 pixels, 3x8 bits/pixel, RGB Input IDAT size = 53922 bytes Input file size = 54072 bytes Trying: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 41159 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 = 41159 Output IDAT size = 41159 bytes (12763 bytes decrease) Output file size = 41237 bytes (12835 bytes = 23.74% decrease) ** Processing: /home/hornik/tmp/CRAN_recheck/SIBER.Rcheck/vign_test/SIBER/vignettes/Introduction-to-SIBER_files/figure-html/layman-metrics-1.png 576x480 pixels, 3x8 bits/pixel, RGB Input IDAT size = 41844 bytes Input file size = 41982 bytes Trying: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 32782 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 = 32782 Output IDAT size = 32782 bytes (9062 bytes decrease) Output file size = 32860 bytes (9122 bytes = 21.73% decrease) ** Processing: /home/hornik/tmp/CRAN_recheck/SIBER.Rcheck/vign_test/SIBER/vignettes/Introduction-to-SIBER_files/figure-html/density-plots-1.png 576x480 pixels, 3x8 bits/pixel, RGB Input IDAT size = 22827 bytes Input file size = 22929 bytes Trying: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 18077 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 = 18077 Output IDAT size = 18077 bytes (4750 bytes decrease) Output file size = 18155 bytes (4774 bytes = 20.82% decrease) ** Processing: /home/hornik/tmp/CRAN_recheck/SIBER.Rcheck/vign_test/SIBER/vignettes/Introduction-to-SIBER_files/figure-html/bayesian-layman-1.png 576x480 pixels, 3x8 bits/pixel, RGB Input IDAT size = 14041 bytes Input file size = 14131 bytes Trying: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 11025 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 = 11025 Output IDAT size = 11025 bytes (3016 bytes decrease) Output file size = 11103 bytes (3028 bytes = 21.43% decrease) ** Processing: /home/hornik/tmp/CRAN_recheck/SIBER.Rcheck/vign_test/SIBER/vignettes/Introduction-to-SIBER_files/figure-html/bayesian-layman-2.png 576x480 pixels, 3x8 bits/pixel, RGB Input IDAT size = 13939 bytes Input file size = 14029 bytes Trying: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 10889 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 = 10889 Output IDAT size = 10889 bytes (3050 bytes decrease) Output file size = 10967 bytes (3062 bytes = 21.83% decrease) ** Processing: /home/hornik/tmp/CRAN_recheck/SIBER.Rcheck/vign_test/SIBER/vignettes/Introduction-to-SIBER_files/figure-html/bayesian-layman-3.png 576x480 pixels, 8 bits/pixel, 256 colors in palette Reducing image to 8 bits/pixel, grayscale Input IDAT size = 5793 bytes Input file size = 6651 bytes Trying: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 4844 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 = 4844 Output IDAT size = 4844 bytes (949 bytes decrease) Output file size = 4922 bytes (1729 bytes = 26.00% decrease) --- finished re-building ‘Introduction-to-SIBER.Rmd’ --- re-building ‘Plot-SIA-ggplot2.Rmd’ using rmarkdown ** Processing: /home/hornik/tmp/CRAN_recheck/SIBER.Rcheck/vign_test/SIBER/vignettes/Plot-SIA-ggplot2_files/figure-html/first-gg-1.png 864x576 pixels, 3x8 bits/pixel, RGB Input IDAT size = 27597 bytes Input file size = 27711 bytes Trying: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 24703 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 = 24703 Output IDAT size = 24703 bytes (2894 bytes decrease) Output file size = 24781 bytes (2930 bytes = 10.57% decrease) ** Processing: /home/hornik/tmp/CRAN_recheck/SIBER.Rcheck/vign_test/SIBER/vignettes/Plot-SIA-ggplot2_files/figure-html/classic-theme-1.png 864x576 pixels, 3x8 bits/pixel, RGB Input IDAT size = 26911 bytes Input file size = 27025 bytes Trying: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 21364 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 = 21364 Output IDAT size = 21364 bytes (5547 bytes decrease) Output file size = 21442 bytes (5583 bytes = 20.66% decrease) ** Processing: /home/hornik/tmp/CRAN_recheck/SIBER.Rcheck/vign_test/SIBER/vignettes/Plot-SIA-ggplot2_files/figure-html/classic-scatterplot-1.png 864x576 pixels, 3x8 bits/pixel, RGB Input IDAT size = 29818 bytes Input file size = 29932 bytes Trying: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 27248 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 = 27248 Output IDAT size = 27248 bytes (2570 bytes decrease) Output file size = 27326 bytes (2606 bytes = 8.71% decrease) ** Processing: /home/hornik/tmp/CRAN_recheck/SIBER.Rcheck/vign_test/SIBER/vignettes/Plot-SIA-ggplot2_files/figure-html/nice-ellipses-1.png 864x576 pixels, 3x8 bits/pixel, RGB Input IDAT size = 59169 bytes Input file size = 59331 bytes Trying: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 50976 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 = 50976 Output IDAT size = 50976 bytes (8193 bytes decrease) Output file size = 51054 bytes (8277 bytes = 13.95% decrease) --- finished re-building ‘Plot-SIA-ggplot2.Rmd’ --- re-building ‘Plot-posterior-ellipses.Rmd’ using rmarkdown ** Processing: /home/hornik/tmp/CRAN_recheck/SIBER.Rcheck/vign_test/SIBER/vignettes/Plot-posterior-ellipses_files/figure-html/basic-model-1.png 288x288 pixels, 8 bits/pixel, 256 colors in palette Reducing image to 8 bits/pixel, grayscale Input IDAT size = 7026 bytes Input file size = 7884 bytes Trying: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 6431 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 = 6431 Output IDAT size = 6431 bytes (595 bytes decrease) Output file size = 6509 bytes (1375 bytes = 17.44% decrease) ** Processing: /home/hornik/tmp/CRAN_recheck/SIBER.Rcheck/vign_test/SIBER/vignettes/Plot-posterior-ellipses_files/figure-html/plot-data-1.png 288x288 pixels, 3x8 bits/pixel, RGB Input IDAT size = 9306 bytes Input file size = 9396 bytes Trying: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 7205 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 = 7205 Output IDAT size = 7205 bytes (2101 bytes decrease) Output file size = 7283 bytes (2113 bytes = 22.49% decrease) ** Processing: /home/hornik/tmp/CRAN_recheck/SIBER.Rcheck/vign_test/SIBER/vignettes/Plot-posterior-ellipses_files/figure-html/plot-posts-1.png 288x288 pixels, 3x8 bits/pixel, RGB Input IDAT size = 9385 bytes Input file size = 9475 bytes Trying: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 7335 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 = 7335 Output IDAT size = 7335 bytes (2050 bytes decrease) Output file size = 7413 bytes (2062 bytes = 21.76% decrease) ** Processing: /home/hornik/tmp/CRAN_recheck/SIBER.Rcheck/vign_test/SIBER/vignettes/Plot-posterior-ellipses_files/figure-html/plot-posts-2.png 288x288 pixels, 3x8 bits/pixel, RGB Input IDAT size = 11168 bytes Input file size = 11258 bytes Trying: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 8869 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 = 8869 Output IDAT size = 8869 bytes (2299 bytes decrease) Output file size = 8947 bytes (2311 bytes = 20.53% decrease) --- finished re-building ‘Plot-posterior-ellipses.Rmd’ --- re-building ‘Points-Inside-Outside-Ellipse.Rmd’ using rmarkdown ** Processing: /home/hornik/tmp/CRAN_recheck/SIBER.Rcheck/vign_test/SIBER/vignettes/Points-Inside-Outside-Ellipse_files/figure-html/warpdata-1.png 576x480 pixels, 3x8 bits/pixel, RGB Input IDAT size = 32705 bytes Input file size = 32819 bytes Trying: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 25455 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 = 25455 Output IDAT size = 25455 bytes (7250 bytes decrease) Output file size = 25533 bytes (7286 bytes = 22.20% decrease) ** Processing: /home/hornik/tmp/CRAN_recheck/SIBER.Rcheck/vign_test/SIBER/vignettes/Points-Inside-Outside-Ellipse_files/figure-html/manually-test-points-1.png 576x480 pixels, 3x8 bits/pixel, RGB Input IDAT size = 15205 bytes Input file size = 15295 bytes Trying: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 11841 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 = 11841 Output IDAT size = 11841 bytes (3364 bytes decrease) Output file size = 11919 bytes (3376 bytes = 22.07% decrease) ** Processing: /home/hornik/tmp/CRAN_recheck/SIBER.Rcheck/vign_test/SIBER/vignettes/Points-Inside-Outside-Ellipse_files/figure-html/unnamed-chunk-5-1.png 576x480 pixels, 3x8 bits/pixel, RGB Input IDAT size = 22011 bytes Input file size = 22113 bytes Trying: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 18414 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 = 18414 Output IDAT size = 18414 bytes (3597 bytes decrease) Output file size = 18492 bytes (3621 bytes = 16.37% decrease) --- finished re-building ‘Points-Inside-Outside-Ellipse.Rmd’ --- re-building ‘Test-convergence.Rmd’ using rmarkdown ** Processing: /home/hornik/tmp/CRAN_recheck/SIBER.Rcheck/vign_test/SIBER/vignettes/Test-convergence_files/figure-html/test-convergence-1.png 288x288 pixels, 3x8 bits/pixel, RGB Input IDAT size = 15595 bytes Input file size = 15685 bytes Trying: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 12160 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 = 12160 Output IDAT size = 12160 bytes (3435 bytes decrease) Output file size = 12238 bytes (3447 bytes = 21.98% decrease) ** Processing: /home/hornik/tmp/CRAN_recheck/SIBER.Rcheck/vign_test/SIBER/vignettes/Test-convergence_files/figure-html/test-convergence-2.png 288x288 pixels, 3x8 bits/pixel, RGB Input IDAT size = 16881 bytes Input file size = 16983 bytes Trying: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 13131 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 = 13131 Output IDAT size = 13131 bytes (3750 bytes decrease) Output file size = 13209 bytes (3774 bytes = 22.22% decrease) ** Processing: /home/hornik/tmp/CRAN_recheck/SIBER.Rcheck/vign_test/SIBER/vignettes/Test-convergence_files/figure-html/test-convergence-3.png 288x288 pixels, 3x8 bits/pixel, RGB Input IDAT size = 16898 bytes Input file size = 17000 bytes Trying: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 13128 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 = 13128 Output IDAT size = 13128 bytes (3770 bytes decrease) Output file size = 13206 bytes (3794 bytes = 22.32% decrease) ** Processing: /home/hornik/tmp/CRAN_recheck/SIBER.Rcheck/vign_test/SIBER/vignettes/Test-convergence_files/figure-html/test-convergence-4.png 288x288 pixels, 3x8 bits/pixel, RGB Input IDAT size = 17066 bytes Input file size = 17168 bytes Trying: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 13446 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 = 13446 Output IDAT size = 13446 bytes (3620 bytes decrease) Output file size = 13524 bytes (3644 bytes = 21.23% decrease) ** Processing: /home/hornik/tmp/CRAN_recheck/SIBER.Rcheck/vign_test/SIBER/vignettes/Test-convergence_files/figure-html/test-convergence-5.png 288x288 pixels, 3x8 bits/pixel, RGB Input IDAT size = 14587 bytes Input file size = 14677 bytes Trying: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 11675 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 = 11675 Output IDAT size = 11675 bytes (2912 bytes decrease) Output file size = 11753 bytes (2924 bytes = 19.92% decrease) ** Processing: /home/hornik/tmp/CRAN_recheck/SIBER.Rcheck/vign_test/SIBER/vignettes/Test-convergence_files/figure-html/test-convergence-6.png 288x288 pixels, 3x8 bits/pixel, RGB Input IDAT size = 14128 bytes Input file size = 14218 bytes Trying: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 11147 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 = 11147 Output IDAT size = 11147 bytes (2981 bytes decrease) Output file size = 11225 bytes (2993 bytes = 21.05% decrease) --- finished re-building ‘Test-convergence.Rmd’ --- re-building ‘kapow-example.Rmd’ using rmarkdown ** Processing: /home/hornik/tmp/CRAN_recheck/SIBER.Rcheck/vign_test/SIBER/vignettes/kapow-example_files/figure-html/make-packs-1.png 288x288 pixels, 3x8 bits/pixel, RGB Input IDAT size = 45800 bytes Input file size = 45938 bytes Trying: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 39455 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 = 39455 Output IDAT size = 39455 bytes (6345 bytes decrease) Output file size = 39533 bytes (6405 bytes = 13.94% decrease) ** Processing: /home/hornik/tmp/CRAN_recheck/SIBER.Rcheck/vign_test/SIBER/vignettes/kapow-example_files/figure-html/make-packs-2.png 288x288 pixels, 3x8 bits/pixel, RGB Input IDAT size = 16195 bytes Input file size = 16285 bytes Trying: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 12471 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 = 12471 Output IDAT size = 12471 bytes (3724 bytes decrease) Output file size = 12549 bytes (3736 bytes = 22.94% decrease) ** Processing: /home/hornik/tmp/CRAN_recheck/SIBER.Rcheck/vign_test/SIBER/vignettes/kapow-example_files/figure-html/make-packs-3.png 288x288 pixels, 3x8 bits/pixel, RGB Input IDAT size = 24125 bytes Input file size = 24227 bytes Trying: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 19473 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 = 19473 Output IDAT size = 19473 bytes (4652 bytes decrease) Output file size = 19551 bytes (4676 bytes = 19.30% decrease) ** Processing: /home/hornik/tmp/CRAN_recheck/SIBER.Rcheck/vign_test/SIBER/vignettes/kapow-example_files/figure-html/make-packs-4.png 288x288 pixels, 3x8 bits/pixel, RGB Input IDAT size = 25485 bytes Input file size = 25599 bytes Trying: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 20965 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 = 20965 Output IDAT size = 20965 bytes (4520 bytes decrease) Output file size = 21043 bytes (4556 bytes = 17.80% decrease) ** Processing: /home/hornik/tmp/CRAN_recheck/SIBER.Rcheck/vign_test/SIBER/vignettes/kapow-example_files/figure-html/make-packs-5.png 288x288 pixels, 3x8 bits/pixel, RGB Input IDAT size = 30331 bytes Input file size = 30445 bytes Trying: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 24023 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 = 24023 Output IDAT size = 24023 bytes (6308 bytes decrease) Output file size = 24101 bytes (6344 bytes = 20.84% decrease) ** Processing: /home/hornik/tmp/CRAN_recheck/SIBER.Rcheck/vign_test/SIBER/vignettes/kapow-example_files/figure-html/make-packs-6.png 288x288 pixels, 3x8 bits/pixel, RGB Input IDAT size = 45601 bytes Input file size = 45739 bytes Trying: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 39263 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 = 39263 Output IDAT size = 39263 bytes (6338 bytes decrease) Output file size = 39341 bytes (6398 bytes = 13.99% decrease) ** Processing: /home/hornik/tmp/CRAN_recheck/SIBER.Rcheck/vign_test/SIBER/vignettes/kapow-example_files/figure-html/make-packs-7.png 288x288 pixels, 3x8 bits/pixel, RGB Input IDAT size = 33373 bytes Input file size = 33499 bytes Trying: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 27064 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 = 27064 Output IDAT size = 27064 bytes (6309 bytes decrease) Output file size = 27142 bytes (6357 bytes = 18.98% decrease) ** Processing: /home/hornik/tmp/CRAN_recheck/SIBER.Rcheck/vign_test/SIBER/vignettes/kapow-example_files/figure-html/make-packs-8.png 288x288 pixels, 3x8 bits/pixel, RGB Input IDAT size = 25899 bytes Input file size = 26013 bytes Trying: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 21132 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 = 21132 Output IDAT size = 21132 bytes (4767 bytes decrease) Output file size = 21210 bytes (4803 bytes = 18.46% decrease) ** Processing: /home/hornik/tmp/CRAN_recheck/SIBER.Rcheck/vign_test/SIBER/vignettes/kapow-example_files/figure-html/make-packs-9.png 288x288 pixels, 3x8 bits/pixel, RGB Input IDAT size = 24094 bytes Input file size = 24196 bytes Trying: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 19626 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 = 19626 Output IDAT size = 19626 bytes (4468 bytes decrease) Output file size = 19704 bytes (4492 bytes = 18.57% decrease) ** Processing: /home/hornik/tmp/CRAN_recheck/SIBER.Rcheck/vign_test/SIBER/vignettes/kapow-example_files/figure-html/make-packs-10.png 288x288 pixels, 3x8 bits/pixel, RGB Input IDAT size = 24299 bytes Input file size = 24401 bytes Trying: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 19891 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 = 19891 Output IDAT size = 19891 bytes (4408 bytes decrease) Output file size = 19969 bytes (4432 bytes = 18.16% decrease) --- finished re-building ‘kapow-example.Rmd’ --- re-building ‘siber-comparing-communities.Rmd’ using rmarkdown ** Processing: /home/hornik/tmp/CRAN_recheck/SIBER.Rcheck/vign_test/SIBER/vignettes/siber-comparing-communities_files/figure-html/unnamed-chunk-2-1.png 768x576 pixels, 3x8 bits/pixel, RGB Input IDAT size = 53599 bytes Input file size = 53749 bytes Trying: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 41538 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 = 41538 Output IDAT size = 41538 bytes (12061 bytes decrease) Output file size = 41616 bytes (12133 bytes = 22.57% decrease) ** Processing: /home/hornik/tmp/CRAN_recheck/SIBER.Rcheck/vign_test/SIBER/vignettes/siber-comparing-communities_files/figure-html/unnamed-chunk-4-1.png 576x576 pixels, 3x8 bits/pixel, RGB Input IDAT size = 15249 bytes Input file size = 15339 bytes Trying: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 12006 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 = 12006 Output IDAT size = 12006 bytes (3243 bytes decrease) Output file size = 12084 bytes (3255 bytes = 21.22% decrease) ** Processing: /home/hornik/tmp/CRAN_recheck/SIBER.Rcheck/vign_test/SIBER/vignettes/siber-comparing-communities_files/figure-html/unnamed-chunk-4-2.png 576x576 pixels, 3x8 bits/pixel, RGB Input IDAT size = 15205 bytes Input file size = 15295 bytes Trying: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 12048 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 = 12048 Output IDAT size = 12048 bytes (3157 bytes decrease) Output file size = 12126 bytes (3169 bytes = 20.72% decrease) ** Processing: /home/hornik/tmp/CRAN_recheck/SIBER.Rcheck/vign_test/SIBER/vignettes/siber-comparing-communities_files/figure-html/unnamed-chunk-4-3.png 576x576 pixels, 8 bits/pixel, 256 colors in palette Reducing image to 8 bits/pixel, grayscale Input IDAT size = 6223 bytes Input file size = 7081 bytes Trying: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 5224 zc = 9 zm = 8 zs = 1 f = 0 IDAT size = 5222 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 = 1 f = 0 IDAT size = 5222 Output IDAT size = 5222 bytes (1001 bytes decrease) Output file size = 5300 bytes (1781 bytes = 25.15% decrease) --- finished re-building ‘siber-comparing-communities.Rmd’ --- re-building ‘siber-comparing-populations.Rmd’ using rmarkdown ** Processing: /home/hornik/tmp/CRAN_recheck/SIBER.Rcheck/vign_test/SIBER/vignettes/siber-comparing-populations_files/figure-html/unnamed-chunk-1-1.png 672x672 pixels, 3x8 bits/pixel, RGB Input IDAT size = 43948 bytes Input file size = 44086 bytes Trying: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 34730 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 = 34730 Output IDAT size = 34730 bytes (9218 bytes decrease) Output file size = 34808 bytes (9278 bytes = 21.05% decrease) ** Processing: /home/hornik/tmp/CRAN_recheck/SIBER.Rcheck/vign_test/SIBER/vignettes/siber-comparing-populations_files/figure-html/import-data-1.png 576x576 pixels, 3x8 bits/pixel, RGB Input IDAT size = 74518 bytes Input file size = 74704 bytes Trying: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 56842 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 = 56842 Output IDAT size = 56842 bytes (17676 bytes decrease) Output file size = 56920 bytes (17784 bytes = 23.81% decrease) ** Processing: /home/hornik/tmp/CRAN_recheck/SIBER.Rcheck/vign_test/SIBER/vignettes/siber-comparing-populations_files/figure-html/plot-data-1.png 960x576 pixels, 3x8 bits/pixel, RGB Input IDAT size = 25173 bytes Input file size = 25287 bytes Trying: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 20505 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 = 20505 Output IDAT size = 20505 bytes (4668 bytes decrease) Output file size = 20583 bytes (4704 bytes = 18.60% decrease) *** caught segfault *** address 0x5556, cause 'memory not mapped' Traceback: 1: dev.off(dv) 2: eng_r(options) 3: block_exec(params) 4: call_block(x) 5: process_group(group) 6: withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), error = function(e) if (xfun::pkg_available("rlang", "1.0.0")) rlang::entrace(e)) 7: xfun:::handle_error(withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), error = function(e) if (xfun::pkg_available("rlang", "1.0.0")) rlang::entrace(e)), function(loc) { setwd(wd) write_utf8(res, output %n% stdout()) paste0("\nQuitting from lines ", loc) }, if (labels[i] != "") sprintf(" [%s]", labels[i]), get_loc) 8: process_file(text, output) 9: knitr::knit(knit_input, knit_output, envir = envir, quiet = quiet) 10: rmarkdown::render(file, encoding = encoding, quiet = quiet, envir = globalenv(), output_dir = getwd(), ...) 11: vweave_rmarkdown(...) 12: engine$weave(file, quiet = quiet, encoding = enc) 13: doTryCatch(return(expr), name, parentenv, handler) 14: tryCatchOne(expr, names, parentenv, handlers[[1L]]) 15: tryCatchList(expr, classes, parentenv, handlers) 16: tryCatch({ engine$weave(file, quiet = quiet, encoding = enc) setwd(startdir) output <- find_vignette_product(name, by = "weave", engine = engine) if (!have.makefile && vignette_is_tex(output)) { texi2pdf(file = output, clean = FALSE, quiet = quiet) output <- find_vignette_product(name, by = "texi2pdf", engine = engine) }}, error = function(e) { OK <<- FALSE message(gettextf("Error: processing vignette '%s' failed with diagnostics:\n%s", file, conditionMessage(e)))}) 17: tools:::.buildOneVignette("siber-comparing-populations.Rmd", "/home/hornik/tmp/CRAN_recheck/SIBER.Rcheck/vign_test/SIBER", TRUE, FALSE, "siber-comparing-populations", "UTF-8", "/home/hornik/tmp/scratch/RtmppeelhP/file22ca873ad9f218.rds") An irrecoverable exception occurred. R is aborting now ... Segmentation fault SUMMARY: processing the following file failed: ‘siber-comparing-populations.Rmd’ Error: Vignette re-building failed. Execution halted Package: simDAG Check: examples New result: ERROR Running examples in ‘simDAG-Ex.R’ failed The error most likely occurred in: > base::assign(".ptime", proc.time(), pos = "CheckExEnv") > ### Name: sim_discrete_time > ### Title: Using Discrete-Time Simulation to Generate Complex Data from a > ### Given DAG and Node Information > ### Aliases: sim_discrete_time > > ### ** Examples > > library(simDAG) > > set.seed(454236) > > ## simulating death dependent on age, sex, bmi > ## NOTE: this example is explained in detail in one of the vignettes > > # initializing a DAG with nodes for generating data at t0 > dag <- empty_dag() + + node("age", type="rnorm", mean=50, sd=4) + + node("sex", type="rbernoulli", p=0.5) + + node("bmi", type="gaussian", parents=c("sex", "age"), + betas=c(1.1, 0.4), intercept=12, error=2) > > # a function that increases age as time goes on > node_advance_age <- function(data) { + return(data$age + 1/365) + } > > # a function to calculate the probability of death as a > # linear combination of age, sex and bmi on the log scale > prob_death <- function(data, beta_age, beta_sex, beta_bmi, intercept) { + prob <- intercept + data$age*beta_age + data$sex*beta_sex + data$bmi*beta_bmi + prob <- 1/(1 + exp(-prob)) + return(prob) + } > > # adding time-dependent nodes to the dag > dag <- dag + + node_td("age", type="advance_age", parents="age") + + node_td("death", type="time_to_event", parents=c("age", "sex", "bmi"), + prob_fun=prob_death, beta_age=0.1, beta_bmi=0.3, beta_sex=-0.2, + intercept=-20, event_duration=Inf, save_past_events=FALSE) > > # run simulation for 100 people, 50 days long > sim_dt <- sim_discrete_time(n_sim=100, + dag=dag, + max_t=50, + verbose=FALSE) Loading required namespace: Rfast Failed with error: ‘there is no package called ‘Rcpp’’ Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) : there is no package called ‘Rcpp’ Calls: sim_discrete_time ... loadNamespace -> withRestarts -> withOneRestart -> doWithOneRestart Execution halted Package: simDAG Check: re-building of vignette outputs New result: ERROR Error(s) in re-building vignettes: ... --- re-building ‘v_covid_example.Rmd’ using rmarkdown Failed with error: 'there is no package called 'Rcpp'' Quitting from lines 200-201 [unnamed-chunk-9] (v_covid_example.Rmd) Error: processing vignette 'v_covid_example.Rmd' failed with diagnostics: there is no package called 'Rcpp' --- failed re-building ‘v_covid_example.Rmd’ --- re-building ‘v_sim_discrete_time.Rmd’ using rmarkdown Failed with error: 'there is no package called 'Rcpp'' Quitting from lines 104-105 [unnamed-chunk-8] (v_sim_discrete_time.Rmd) Error: processing vignette 'v_sim_discrete_time.Rmd' failed with diagnostics: there is no package called 'Rcpp' --- failed re-building ‘v_sim_discrete_time.Rmd’ --- re-building ‘v_sim_from_dag.Rmd’ using rmarkdown Failed with error: 'there is no package called 'Rcpp'' Quitting from lines 112-113 [unnamed-chunk-6] (v_sim_from_dag.Rmd) Error: processing vignette 'v_sim_from_dag.Rmd' failed with diagnostics: there is no package called 'Rcpp' --- failed re-building ‘v_sim_from_dag.Rmd’ --- re-building ‘v_using_formulas.Rmd’ using rmarkdown --- finished re-building ‘v_using_formulas.Rmd’ SUMMARY: processing the following files failed: ‘v_covid_example.Rmd’ ‘v_sim_discrete_time.Rmd’ ‘v_sim_from_dag.Rmd’ Error: Vignette re-building failed. Execution halted Package: simDAG Check: tests New result: ERROR Running ‘testthat.R’ [22s/24s] Running the tests in ‘tests/testthat.R’ failed. Complete output: > library(simDAG) > library(testthat) > library(data.table) > library(igraph) Attaching package: 'igraph' The following object is masked from 'package:testthat': compare The following objects are masked from 'package:stats': decompose, spectrum The following object is masked from 'package:base': union > > test_check("simDAG") Loading required namespace: Rfast Failed with error: 'there is no package called 'Rcpp'' Loading required namespace: MASS Loading required namespace: ggplot2 Loading required namespace: ggforce Failed with error: 'there is no package called 'Rcpp'' Loading required namespace: ggforce Failed with error: 'there is no package called 'Rcpp'' Loading required namespace: ggforce Failed with error: 'there is no package called 'Rcpp'' Loading required namespace: ggforce Failed with error: 'there is no package called 'Rcpp'' Loading required namespace: ggforce Failed with error: 'there is no package called 'Rcpp'' Loading required namespace: ggforce Failed with error: 'there is no package called 'Rcpp'' Loading required namespace: ggforce Failed with error: 'there is no package called 'Rcpp'' Loading required namespace: ggforce Failed with error: 'there is no package called 'Rcpp'' Loading required namespace: ggforce Failed with error: 'there is no package called 'Rcpp'' Loading required namespace: ggforce Failed with error: 'there is no package called 'Rcpp'' Loading required namespace: ggforce Failed with error: 'there is no package called 'Rcpp'' Loading required namespace: ggforce Failed with error: 'there is no package called 'Rcpp'' Loading required namespace: ggforce Failed with error: 'there is no package called 'Rcpp'' Loading required namespace: ggforce Failed with error: 'there is no package called 'Rcpp'' Loading required namespace: ggforce Failed with error: 'there is no package called 'Rcpp'' Loading required namespace: ggforce Failed with error: 'there is no package called 'Rcpp'' Loading required namespace: ggforce Failed with error: 'there is no package called 'Rcpp'' Loading required namespace: ggforce Failed with error: 'there is no package called 'Rcpp'' Loading required namespace: ggforce Failed with error: 'there is no package called 'Rcpp'' Loading required namespace: ggforce Failed with error: 'there is no package called 'Rcpp'' Loading required namespace: ggforce Failed with error: 'there is no package called 'Rcpp'' Loading required namespace: ggforce Failed with error: 'there is no package called 'Rcpp'' Loading required namespace: Rfast Failed with error: 'there is no package called 'Rcpp'' t = 1 node = sickness2 t = 1 node = sickness1 t = 2 node = sickness2 t = 2 node = sickness1 t = 3 node = sickness2 t = 3 node = sickness1 t = 4 node = sickness2 t = 4 node = sickness1 t = 5 node = sickness2 t = 5 node = sickness1 Loading required namespace: Rfast Failed with error: 'there is no package called 'Rcpp'' Loading required namespace: parallel Loading required namespace: doSNOW Loading required namespace: doRNG starting worker pid=2354135 on localhost:11098 at 03:16:12.329 starting worker pid=2354136 on localhost:11098 at 03:16:12.357 | | | 0%Loading required package: simDAG loaded simDAG and set parent environment Loading required package: simDAG loaded simDAG and set parent environment starting worker pid=2354831 on localhost:11098 at 03:16:14.086 starting worker pid=2354832 on localhost:11098 at 03:16:14.105 Loading required package: simDAG loaded simDAG and set parent environment Loading required package: simDAG loaded simDAG and set parent environment starting worker pid=2355295 on localhost:11098 at 03:16:14.814 starting worker pid=2355294 on localhost:11098 at 03:16:14.822 Loading required package: simDAG loaded simDAG and set parent environment Loading required package: simDAG loaded simDAG and set parent environment [ FAIL 22 | WARN 14 | SKIP 27 | PASS 537 ] ══ Skipped tests (27) ══════════════════════════════════════════════════════════ • On CRAN (27): 'test_DAG.node_S3.r:6:3', 'test_DAG.node_S3.r:11:3', 'test_DAG.node_S3.r:16:3', 'test_DAG.node_S3.r:21:3', 'test_DAG.node_S3.r:27:3', 'test_DAG.node_S3.r:34:3', 'test_DAG.node_S3.r:39:3', 'test_DAG.node_S3.r:44:3', 'test_DAG.node_S3.r:49:3', 'test_DAG.node_S3.r:55:3', 'test_dag.r:17:3', 'test_dag.r:30:3', 'test_dag.r:37:3', 'test_dag.r:50:3', 'test_dag.r:66:3', 'test_node.r:519:3', 'test_plot.simDT.r:25:3', 'test_plot.simDT.r:29:3', 'test_plot.simDT.r:33:3', 'test_plot.simDT.r:37:3', 'test_plot.simDT.r:41:3', 'test_plot.simDT.r:49:3', 'test_plot.simDT.r:57:3', 'test_simDT_S3.r:12:3', 'test_simDT_S3.r:17:3', 'test_simDT_S3.r:22:3', 'test_simDT_S3.r:26:3' ══ Failed tests ════════════════════════════════════════════════════════════════ ── Error ('test_dag_from_data.r:15:3'): general test case ────────────────────── Error in `loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]])`: there is no package called 'Rcpp' Backtrace: ▆ 1. ├─base::as.data.frame(sim_from_dag(dag = dag, n_sim = 1000, sort_dag = TRUE)) at test_dag_from_data.r:15:3 2. ├─simDAG::sim_from_dag(dag = dag, n_sim = 1000, sort_dag = TRUE) 3. └─base::loadNamespace(x) 4. ├─base::namespaceImportFrom(...) 5. │ └─base::asNamespace(ns) 6. └─base::loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) 7. └─base::withRestarts(stop(cond), retry_loadNamespace = function() NULL) 8. └─base (local) withOneRestart(expr, restarts[[1L]]) 9. └─base (local) doWithOneRestart(return(expr), restart) ── Error ('test_plot.DAG.r:12:3'): defaults ──────────────────────────────────── Error in `loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]])`: there is no package called 'Rcpp' Backtrace: ▆ 1. ├─testthat::expect_snapshot_output(plot(dag)) at test_plot.DAG.r:12:3 2. │ ├─testthat:::with_is_snapshotting(...) 3. │ └─testthat::capture_output_lines(x, print = TRUE, width = NULL) 4. │ └─testthat:::eval_with_output(code, print = print, width = width) 5. │ ├─withr::with_output_sink(path, withVisible(code)) 6. │ │ └─base::force(code) 7. │ └─base::withVisible(code) 8. ├─base::plot(dag) 9. ├─simDAG:::plot.DAG(dag) 10. └─base::loadNamespace(x) 11. ├─base::namespaceImportFrom(...) 12. │ └─base::asNamespace(ns) 13. └─base::loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) 14. └─base::withRestarts(stop(cond), retry_loadNamespace = function() NULL) 15. └─base (local) withOneRestart(expr, restarts[[1L]]) 16. └─base (local) doWithOneRestart(return(expr), restart) ── Error ('test_plot.DAG.r:16:3'): change layout ─────────────────────────────── Error in `loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]])`: there is no package called 'Rcpp' Backtrace: ▆ 1. ├─testthat::expect_snapshot_output(plot(dag, layout = "in_circle")) at test_plot.DAG.r:16:3 2. │ ├─testthat:::with_is_snapshotting(...) 3. │ └─testthat::capture_output_lines(x, print = TRUE, width = NULL) 4. │ └─testthat:::eval_with_output(code, print = print, width = width) 5. │ ├─withr::with_output_sink(path, withVisible(code)) 6. │ │ └─base::force(code) 7. │ └─base::withVisible(code) 8. ├─base::plot(dag, layout = "in_circle") 9. ├─simDAG:::plot.DAG(dag, layout = "in_circle") 10. └─base::loadNamespace(x) 11. ├─base::namespaceImportFrom(...) 12. │ └─base::asNamespace(ns) 13. └─base::loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) 14. └─base::withRestarts(stop(cond), retry_loadNamespace = function() NULL) 15. └─base (local) withOneRestart(expr, restarts[[1L]]) 16. └─base (local) doWithOneRestart(return(expr), restart) ── Error ('test_plot.DAG.r:20:3'): change layout with extra arguments ────────── Error in `loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]])`: there is no package called 'Rcpp' Backtrace: ▆ 1. ├─testthat::expect_snapshot_output(...) at test_plot.DAG.r:20:3 2. │ ├─testthat:::with_is_snapshotting(...) 3. │ └─testthat::capture_output_lines(x, print = TRUE, width = NULL) 4. │ └─testthat:::eval_with_output(code, print = print, width = width) 5. │ ├─withr::with_output_sink(path, withVisible(code)) 6. │ │ └─base::force(code) 7. │ └─base::withVisible(code) 8. ├─base::plot(dag, layout = "as_tree", flip.y = FALSE) 9. ├─simDAG:::plot.DAG(dag, layout = "as_tree", flip.y = FALSE) 10. └─base::loadNamespace(x) 11. ├─base::namespaceImportFrom(...) 12. │ └─base::asNamespace(ns) 13. └─base::loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) 14. └─base::withRestarts(stop(cond), retry_loadNamespace = function() NULL) 15. └─base (local) withOneRestart(expr, restarts[[1L]]) 16. └─base (local) doWithOneRestart(return(expr), restart) ── Error ('test_plot.DAG.r:24:3'): change node_size ──────────────────────────── Error in `loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]])`: there is no package called 'Rcpp' Backtrace: ▆ 1. ├─testthat::expect_snapshot_output(plot(dag, node_size = 0.1)) at test_plot.DAG.r:24:3 2. │ ├─testthat:::with_is_snapshotting(...) 3. │ └─testthat::capture_output_lines(x, print = TRUE, width = NULL) 4. │ └─testthat:::eval_with_output(code, print = print, width = width) 5. │ ├─withr::with_output_sink(path, withVisible(code)) 6. │ │ └─base::force(code) 7. │ └─base::withVisible(code) 8. ├─base::plot(dag, node_size = 0.1) 9. ├─simDAG:::plot.DAG(dag, node_size = 0.1) 10. └─base::loadNamespace(x) 11. ├─base::namespaceImportFrom(...) 12. │ └─base::asNamespace(ns) 13. └─base::loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) 14. └─base::withRestarts(stop(cond), retry_loadNamespace = function() NULL) 15. └─base (local) withOneRestart(expr, restarts[[1L]]) 16. └─base (local) doWithOneRestart(return(expr), restart) ── Error ('test_plot.DAG.r:28:3'): change node_fill ──────────────────────────── Error in `loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]])`: there is no package called 'Rcpp' Backtrace: ▆ 1. ├─testthat::expect_snapshot_output(plot(dag, node_fill = "lightblue")) at test_plot.DAG.r:28:3 2. │ ├─testthat:::with_is_snapshotting(...) 3. │ └─testthat::capture_output_lines(x, print = TRUE, width = NULL) 4. │ └─testthat:::eval_with_output(code, print = print, width = width) 5. │ ├─withr::with_output_sink(path, withVisible(code)) 6. │ │ └─base::force(code) 7. │ └─base::withVisible(code) 8. ├─base::plot(dag, node_fill = "lightblue") 9. ├─simDAG:::plot.DAG(dag, node_fill = "lightblue") 10. └─base::loadNamespace(x) 11. ├─base::namespaceImportFrom(...) 12. │ └─base::asNamespace(ns) 13. └─base::loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) 14. └─base::withRestarts(stop(cond), retry_loadNamespace = function() NULL) 15. └─base (local) withOneRestart(expr, restarts[[1L]]) 16. └─base (local) doWithOneRestart(return(expr), restart) ── Error ('test_plot.DAG.r:32:3'): change node_names ─────────────────────────── Error in `loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]])`: there is no package called 'Rcpp' Backtrace: ▆ 1. ├─testthat::expect_snapshot_output(...) at test_plot.DAG.r:32:3 2. │ ├─testthat:::with_is_snapshotting(...) 3. │ └─testthat::capture_output_lines(x, print = TRUE, width = NULL) 4. │ └─testthat:::eval_with_output(code, print = print, width = width) 5. │ ├─withr::with_output_sink(path, withVisible(code)) 6. │ │ └─base::force(code) 7. │ └─base::withVisible(code) 8. ├─base::plot(dag, node_names = c("1", "2", "3", "4", "5")) 9. ├─simDAG:::plot.DAG(dag, node_names = c("1", "2", "3", "4", "5")) 10. └─base::loadNamespace(x) 11. ├─base::namespaceImportFrom(...) 12. │ └─base::asNamespace(ns) 13. └─base::loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) 14. └─base::withRestarts(stop(cond), retry_loadNamespace = function() NULL) 15. └─base (local) withOneRestart(expr, restarts[[1L]]) 16. └─base (local) doWithOneRestart(return(expr), restart) ── Error ('test_plot.DAG.r:36:3'): change node outline ───────────────────────── Error in `loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]])`: there is no package called 'Rcpp' Backtrace: ▆ 1. ├─testthat::expect_snapshot_output(...) at test_plot.DAG.r:36:3 2. │ ├─testthat:::with_is_snapshotting(...) 3. │ └─testthat::capture_output_lines(x, print = TRUE, width = NULL) 4. │ └─testthat:::eval_with_output(code, print = print, width = width) 5. │ ├─withr::with_output_sink(path, withVisible(code)) 6. │ │ └─base::force(code) 7. │ └─base::withVisible(code) 8. ├─base::plot(dag, node_color = "green", node_linewidth = 1, node_linetype = "dashed") 9. ├─simDAG:::plot.DAG(...) 10. └─base::loadNamespace(x) 11. ├─base::namespaceImportFrom(...) 12. │ └─base::asNamespace(ns) 13. └─base::loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) 14. └─base::withRestarts(stop(cond), retry_loadNamespace = function() NULL) 15. └─base (local) withOneRestart(expr, restarts[[1L]]) 16. └─base (local) doWithOneRestart(return(expr), restart) ── Error ('test_plot.DAG.r:41:3'): change node insides ───────────────────────── Error in `loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]])`: there is no package called 'Rcpp' Backtrace: ▆ 1. ├─testthat::expect_snapshot_output(...) at test_plot.DAG.r:41:3 2. │ ├─testthat:::with_is_snapshotting(...) 3. │ └─testthat::capture_output_lines(x, print = TRUE, width = NULL) 4. │ └─testthat:::eval_with_output(code, print = print, width = width) 5. │ ├─withr::with_output_sink(path, withVisible(code)) 6. │ │ └─base::force(code) 7. │ └─base::withVisible(code) 8. ├─base::plot(dag, node_fill = "green", node_alpha = 0.3) 9. ├─simDAG:::plot.DAG(dag, node_fill = "green", node_alpha = 0.3) 10. └─base::loadNamespace(x) 11. ├─base::namespaceImportFrom(...) 12. │ └─base::asNamespace(ns) 13. └─base::loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) 14. └─base::withRestarts(stop(cond), retry_loadNamespace = function() NULL) 15. └─base (local) withOneRestart(expr, restarts[[1L]]) 16. └─base (local) doWithOneRestart(return(expr), restart) ── Error ('test_plot.DAG.r:45:3'): change node text ──────────────────────────── Error in `loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]])`: there is no package called 'Rcpp' Backtrace: ▆ 1. ├─testthat::expect_snapshot_output(...) at test_plot.DAG.r:45:3 2. │ ├─testthat:::with_is_snapshotting(...) 3. │ └─testthat::capture_output_lines(x, print = TRUE, width = NULL) 4. │ └─testthat:::eval_with_output(code, print = print, width = width) 5. │ ├─withr::with_output_sink(path, withVisible(code)) 6. │ │ └─base::force(code) 7. │ └─base::withVisible(code) 8. ├─base::plot(...) 9. ├─simDAG:::plot.DAG(...) 10. └─base::loadNamespace(x) 11. ├─base::namespaceImportFrom(...) 12. │ └─base::asNamespace(ns) 13. └─base::loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) 14. └─base::withRestarts(stop(cond), retry_loadNamespace = function() NULL) 15. └─base (local) withOneRestart(expr, restarts[[1L]]) 16. └─base (local) doWithOneRestart(return(expr), restart) ── Error ('test_plot.DAG.r:53:3'): change arrow lines ────────────────────────── Error in `loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]])`: there is no package called 'Rcpp' Backtrace: ▆ 1. ├─testthat::expect_snapshot_output(...) at test_plot.DAG.r:53:3 2. │ ├─testthat:::with_is_snapshotting(...) 3. │ └─testthat::capture_output_lines(x, print = TRUE, width = NULL) 4. │ └─testthat:::eval_with_output(code, print = print, width = width) 5. │ ├─withr::with_output_sink(path, withVisible(code)) 6. │ │ └─base::force(code) 7. │ └─base::withVisible(code) 8. ├─base::plot(...) 9. ├─simDAG:::plot.DAG(...) 10. └─base::loadNamespace(x) 11. ├─base::namespaceImportFrom(...) 12. │ └─base::asNamespace(ns) 13. └─base::loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) 14. └─base::withRestarts(stop(cond), retry_loadNamespace = function() NULL) 15. └─base (local) withOneRestart(expr, restarts[[1L]]) 16. └─base (local) doWithOneRestart(return(expr), restart) ── Error ('test_plot.DAG.r:60:3'): change arrow head ─────────────────────────── Error in `loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]])`: there is no package called 'Rcpp' Backtrace: ▆ 1. ├─testthat::expect_snapshot_output(...) at test_plot.DAG.r:60:3 2. │ ├─testthat:::with_is_snapshotting(...) 3. │ └─testthat::capture_output_lines(x, print = TRUE, width = NULL) 4. │ └─testthat:::eval_with_output(code, print = print, width = width) 5. │ ├─withr::with_output_sink(path, withVisible(code)) 6. │ │ └─base::force(code) 7. │ └─base::withVisible(code) 8. ├─base::plot(...) 9. ├─simDAG:::plot.DAG(...) 10. └─base::loadNamespace(x) 11. ├─base::namespaceImportFrom(...) 12. │ └─base::asNamespace(ns) 13. └─base::loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) 14. └─base::withRestarts(stop(cond), retry_loadNamespace = function() NULL) 15. └─base (local) withOneRestart(expr, restarts[[1L]]) 16. └─base (local) doWithOneRestart(return(expr), restart) ── Error ('test_plot.DAG.r:65:3'): change other paramaters ───────────────────── Error in `loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]])`: there is no package called 'Rcpp' Backtrace: ▆ 1. ├─testthat::expect_snapshot_output(...) at test_plot.DAG.r:65:3 2. │ ├─testthat:::with_is_snapshotting(...) 3. │ └─testthat::capture_output_lines(x, print = TRUE, width = NULL) 4. │ └─testthat:::eval_with_output(code, print = print, width = width) 5. │ ├─withr::with_output_sink(path, withVisible(code)) 6. │ │ └─base::force(code) 7. │ └─base::withVisible(code) 8. ├─base::plot(dag, arrow_node_dist = 0.01, gg_theme = ggplot2::theme_bw()) 9. ├─simDAG:::plot.DAG(dag, arrow_node_dist = 0.01, gg_theme = ggplot2::theme_bw()) 10. └─base::loadNamespace(x) 11. ├─base::namespaceImportFrom(...) 12. │ └─base::asNamespace(ns) 13. └─base::loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) 14. └─base::withRestarts(stop(cond), retry_loadNamespace = function() NULL) 15. └─base (local) withOneRestart(expr, restarts[[1L]]) 16. └─base (local) doWithOneRestart(return(expr), restart) ── Error ('test_plot.DAG.r:70:3'): change everything ─────────────────────────── Error in `loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]])`: there is no package called 'Rcpp' Backtrace: ▆ 1. ├─testthat::expect_snapshot_output(...) at test_plot.DAG.r:70:3 2. │ ├─testthat:::with_is_snapshotting(...) 3. │ └─testthat::capture_output_lines(x, print = TRUE, width = NULL) 4. │ └─testthat:::eval_with_output(code, print = print, width = width) 5. │ ├─withr::with_output_sink(path, withVisible(code)) 6. │ │ └─base::force(code) 7. │ └─base::withVisible(code) 8. ├─base::plot(...) 9. ├─simDAG:::plot.DAG(...) 10. └─base::loadNamespace(x) 11. ├─base::namespaceImportFrom(...) 12. │ └─base::asNamespace(ns) 13. └─base::loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) 14. └─base::withRestarts(stop(cond), retry_loadNamespace = function() NULL) 15. └─base (local) withOneRestart(expr, restarts[[1L]]) 16. └─base (local) doWithOneRestart(return(expr), restart) ── Error ('test_plot.DAG.r:101:3'): with time-varying nodes, include = FALSE ─── Error in `loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]])`: there is no package called 'Rcpp' Backtrace: ▆ 1. ├─testthat::expect_snapshot_output(plot(dag, include_td_nodes = FALSE)) at test_plot.DAG.r:101:3 2. │ ├─testthat:::with_is_snapshotting(...) 3. │ └─testthat::capture_output_lines(x, print = TRUE, width = NULL) 4. │ └─testthat:::eval_with_output(code, print = print, width = width) 5. │ ├─withr::with_output_sink(path, withVisible(code)) 6. │ │ └─base::force(code) 7. │ └─base::withVisible(code) 8. ├─base::plot(dag, include_td_nodes = FALSE) 9. ├─simDAG:::plot.DAG(dag, include_td_nodes = FALSE) 10. └─base::loadNamespace(x) 11. ├─base::namespaceImportFrom(...) 12. │ └─base::asNamespace(ns) 13. └─base::loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) 14. └─base::withRestarts(stop(cond), retry_loadNamespace = function() NULL) 15. └─base (local) withOneRestart(expr, restarts[[1L]]) 16. └─base (local) doWithOneRestart(return(expr), restart) ── Error ('test_plot.DAG.r:105:3'): with time-varying nodes, include = TRUE ──── Error in `loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]])`: there is no package called 'Rcpp' Backtrace: ▆ 1. ├─testthat::expect_snapshot_output(plot(dag, include_td_nodes = TRUE)) at test_plot.DAG.r:105:3 2. │ ├─testthat:::with_is_snapshotting(...) 3. │ └─testthat::capture_output_lines(x, print = TRUE, width = NULL) 4. │ └─testthat:::eval_with_output(code, print = print, width = width) 5. │ ├─withr::with_output_sink(path, withVisible(code)) 6. │ │ └─base::force(code) 7. │ └─base::withVisible(code) 8. ├─base::plot(dag, include_td_nodes = TRUE) 9. ├─simDAG:::plot.DAG(dag, include_td_nodes = TRUE) 10. └─base::loadNamespace(x) 11. ├─base::namespaceImportFrom(...) 12. │ └─base::asNamespace(ns) 13. └─base::loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) 14. └─base::withRestarts(stop(cond), retry_loadNamespace = function() NULL) 15. └─base (local) withOneRestart(expr, restarts[[1L]]) 16. └─base (local) doWithOneRestart(return(expr), restart) ── Error ('test_plot.DAG.r:109:3'): with time-varying nodes, include = TRUE & mark_td_nodes = FALSE ── Error in `loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]])`: there is no package called 'Rcpp' Backtrace: ▆ 1. ├─testthat::expect_snapshot_output(...) at test_plot.DAG.r:109:3 2. │ ├─testthat:::with_is_snapshotting(...) 3. │ └─testthat::capture_output_lines(x, print = TRUE, width = NULL) 4. │ └─testthat:::eval_with_output(code, print = print, width = width) 5. │ ├─withr::with_output_sink(path, withVisible(code)) 6. │ │ └─base::force(code) 7. │ └─base::withVisible(code) 8. ├─base::plot(dag, include_td_nodes = TRUE, mark_td_nodes = FALSE) 9. ├─simDAG:::plot.DAG(dag, include_td_nodes = TRUE, mark_td_nodes = FALSE) 10. └─base::loadNamespace(x) 11. ├─base::namespaceImportFrom(...) 12. │ └─base::asNamespace(ns) 13. └─base::loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) 14. └─base::withRestarts(stop(cond), retry_loadNamespace = function() NULL) 15. └─base (local) withOneRestart(expr, restarts[[1L]]) 16. └─base (local) doWithOneRestart(return(expr), restart) ── Error ('test_sim2data.r:24:1'): (code run outside of `test_that()`) ───────── Error in `loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]])`: there is no package called 'Rcpp' Backtrace: ▆ 1. ├─simDAG::sim_discrete_time(...) at test_sim2data.r:24:1 2. │ └─simDAG::sim_from_dag(...) 3. └─base::loadNamespace(x) 4. ├─base::namespaceImportFrom(...) 5. │ └─base::asNamespace(ns) 6. └─base::loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) 7. └─base::withRestarts(stop(cond), retry_loadNamespace = function() NULL) 8. └─base (local) withOneRestart(expr, restarts[[1L]]) 9. └─base (local) doWithOneRestart(return(expr), restart) ── Error ('test_sim_from_dag.r:59:3'): sort_dag working ──────────────────────── Error in `loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]])`: there is no package called 'Rcpp' Backtrace: ▆ 1. ├─simDAG::sim_from_dag(n_sim = 20, dag = dag, sort_dag = TRUE) at test_sim_from_dag.r:59:3 2. └─base::loadNamespace(x) 3. ├─base::namespaceImportFrom(...) 4. │ └─base::asNamespace(ns) 5. └─base::loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) 6. └─base::withRestarts(stop(cond), retry_loadNamespace = function() NULL) 7. └─base (local) withOneRestart(expr, restarts[[1L]]) 8. └─base (local) doWithOneRestart(return(expr), restart) ── Error ('test_sim_n_datasets.r:16:3'): without td, parallel ────────────────── Error in `e$fun(obj, substitute(ex), parent.frame(), e$data)`: worker initialization failed: package ‘Rcpp’ required by ‘Rfast’ could not be found Backtrace: ▆ 1. └─simDAG::sim_n_datasets(...) at test_sim_n_datasets.r:16:3 2. ├─... %dorng% ... 3. │ └─base::do.call(`%dopar%`, list(obj, ex), envir = parent.frame()) 4. └─foreach (local) ``(...) 5. └─e$fun(obj, substitute(ex), parent.frame(), e$data) ── Error ('test_sim_n_datasets.r:43:3'): with td, parallel ───────────────────── Error in `e$fun(obj, substitute(ex), parent.frame(), e$data)`: worker initialization failed: package ‘Rcpp’ required by ‘Rfast’ could not be found Backtrace: ▆ 1. └─simDAG::sim_n_datasets(...) at test_sim_n_datasets.r:43:3 2. ├─... %dorng% ... 3. │ └─base::do.call(`%dopar%`, list(obj, ex), envir = parent.frame()) 4. └─foreach (local) ``(...) 5. └─e$fun(obj, substitute(ex), parent.frame(), e$data) ── Error ('test_sim_n_datasets.r:50:3'): with td, parallel ───────────────────── Error in `e$fun(obj, substitute(ex), parent.frame(), e$data)`: worker initialization failed: package ‘Rcpp’ required by ‘Rfast’ could not be found Backtrace: ▆ 1. ├─testthat::expect_output(...) at test_sim_n_datasets.r:50:3 2. │ └─testthat:::quasi_capture(...) 3. │ ├─testthat (local) .capture(...) 4. │ │ └─testthat::capture_output_lines(code, print, width = width) 5. │ │ └─testthat:::eval_with_output(code, print = print, width = width) 6. │ │ ├─withr::with_output_sink(path, withVisible(code)) 7. │ │ │ └─base::force(code) 8. │ │ └─base::withVisible(code) 9. │ └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo)) 10. └─simDAG::sim_n_datasets(...) 11. ├─... %dorng% ... 12. │ └─base::do.call(`%dopar%`, list(obj, ex), envir = parent.frame()) 13. └─foreach (local) ``(...) 14. └─e$fun(obj, substitute(ex), parent.frame(), e$data) [ FAIL 22 | WARN 14 | SKIP 27 | PASS 537 ] Error: Test failures In addition: Warning messages: 1: In for (i in seq_len(n)) { : closing unused connection 8 (<-localhost:11098) 2: In for (i in seq_len(n)) { : closing unused connection 7 (<-localhost:11098) 3: In for (i in seq_len(n)) { : closing unused connection 6 (<-localhost:11098) 4: In for (i in seq_len(n)) { : closing unused connection 5 (<-localhost:11098) Execution halted Error in unserialize(node$con) : error reading from connection Calls: ... doTryCatch -> recvData -> recvData.SOCKnode -> unserialize Execution halted Error in unserialize(node$con) : error reading from connection Calls: ... doTryCatch -> recvData -> recvData.SOCKnode -> unserialize Execution halted Package: simhelpers Check: re-building of vignette outputs New result: ERROR Error(s) in re-building vignettes: ... --- re-building ‘MCSE.Rmd’ using rmarkdown --- finished re-building ‘MCSE.Rmd’ --- re-building ‘simulation_workflow.Rmd’ using rmarkdown ** Processing: /home/hornik/tmp/CRAN_recheck/simhelpers.Rcheck/vign_test/simhelpers/vignettes/simulation_workflow_files/figure-html/unnamed-chunk-7-1.png 672x288 pixels, 3x8 bits/pixel, RGB Input IDAT size = 24217 bytes Input file size = 24319 bytes Trying: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 20579 zc = 9 zm = 8 zs = 1 f = 0 zc = 1 zm = 8 zs = 2 f = 0 zc = 9 zm = 8 zs = 3 f = 0 zc = 9 zm = 8 zs = 0 f = 5 zc = 9 zm = 8 zs = 1 f = 5 zc = 1 zm = 8 zs = 2 f = 5 zc = 9 zm = 8 zs = 3 f = 5 Selecting parameters: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 20579 Output IDAT size = 20579 bytes (3638 bytes decrease) Output file size = 20657 bytes (3662 bytes = 15.06% decrease) *** caught segfault *** address 0x5556, cause 'memory not mapped' Traceback: 1: dev.off(dv) 2: eng_r(options) 3: block_exec(params) 4: call_block(x) 5: process_group(group) 6: withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), error = function(e) if (xfun::pkg_available("rlang", "1.0.0")) rlang::entrace(e)) 7: xfun:::handle_error(withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), error = function(e) if (xfun::pkg_available("rlang", "1.0.0")) rlang::entrace(e)), function(loc) { setwd(wd) write_utf8(res, output %n% stdout()) paste0("\nQuitting from lines ", loc) }, if (labels[i] != "") sprintf(" [%s]", labels[i]), get_loc) 8: process_file(text, output) 9: knitr::knit(knit_input, knit_output, envir = envir, quiet = quiet) 10: rmarkdown::render(file, encoding = encoding, quiet = quiet, envir = globalenv(), output_dir = getwd(), ...) 11: vweave_rmarkdown(...) 12: engine$weave(file, quiet = quiet, encoding = enc) 13: doTryCatch(return(expr), name, parentenv, handler) 14: tryCatchOne(expr, names, parentenv, handlers[[1L]]) 15: tryCatchList(expr, classes, parentenv, handlers) 16: tryCatch({ engine$weave(file, quiet = quiet, encoding = enc) setwd(startdir) output <- find_vignette_product(name, by = "weave", engine = engine) if (!have.makefile && vignette_is_tex(output)) { texi2pdf(file = output, clean = FALSE, quiet = quiet) output <- find_vignette_product(name, by = "texi2pdf", engine = engine) }}, error = function(e) { OK <<- FALSE message(gettextf("Error: processing vignette '%s' failed with diagnostics:\n%s", file, conditionMessage(e)))}) 17: tools:::.buildOneVignette("simulation_workflow.Rmd", "/home/hornik/tmp/CRAN_recheck/simhelpers.Rcheck/vign_test/simhelpers", TRUE, FALSE, "simulation_workflow", "UTF-8", "/home/hornik/tmp/scratch/RtmpTGi19s/file2348e834b15209.rds") An irrecoverable exception occurred. R is aborting now ... Segmentation fault --- re-building ‘visualization.Rmd’ using rmarkdown ** Processing: /home/hornik/tmp/CRAN_recheck/simhelpers.Rcheck/vign_test/simhelpers/vignettes/visualization_files/figure-html/unnamed-chunk-4-1.png 768x528 pixels, 3x8 bits/pixel, RGB Input IDAT size = 68519 bytes Input file size = 68693 bytes Trying: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 52441 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 = 52441 Output IDAT size = 52441 bytes (16078 bytes decrease) Output file size = 52519 bytes (16174 bytes = 23.55% decrease) --- finished re-building ‘visualization.Rmd’ SUMMARY: processing the following file failed: ‘simulation_workflow.Rmd’ Error: Vignette re-building failed. Execution halted Package: summclust Check: whether package can be installed New result: ERROR Installation failed. Package: SynthETIC Check: HTML version of manual New result: NOTE Skipping checking math rendering: package 'V8' unavailable Package: SynthETIC Check: re-building of vignette outputs New result: ERROR Error(s) in re-building vignettes: ... --- re-building ‘SynthETIC-covariates-demo.Rmd’ using rmarkdown --- finished re-building ‘SynthETIC-covariates-demo.Rmd’ --- re-building ‘SynthETIC-demo.Rmd’ using rmarkdown ** Processing: /home/hornik/tmp/CRAN_recheck/SynthETIC.Rcheck/vign_test/SynthETIC/vignettes/SynthETIC-demo_files/figure-html/unnamed-chunk-10-1.png 1050x600 pixels, 8 bits/pixel, 256 colors in palette Reducing image to 8 bits/pixel, grayscale Input IDAT size = 26550 bytes Input file size = 27444 bytes Trying: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 24649 zc = 9 zm = 8 zs = 1 f = 0 IDAT size = 24637 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 = 1 f = 0 IDAT size = 24637 Output IDAT size = 24637 bytes (1913 bytes decrease) Output file size = 24715 bytes (2729 bytes = 9.94% decrease) ** Processing: /home/hornik/tmp/CRAN_recheck/SynthETIC.Rcheck/vign_test/SynthETIC/vignettes/SynthETIC-demo_files/figure-html/unnamed-chunk-14-1.png 1050x600 pixels, 3x8 bits/pixel, RGB Input IDAT size = 43709 bytes Input file size = 43847 bytes Trying: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 36191 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 = 36191 Output IDAT size = 36191 bytes (7518 bytes decrease) Output file size = 36269 bytes (7578 bytes = 17.28% decrease) ** Processing: /home/hornik/tmp/CRAN_recheck/SynthETIC.Rcheck/vign_test/SynthETIC/vignettes/SynthETIC-demo_files/figure-html/unnamed-chunk-15-1.png 1050x600 pixels, 8 bits/pixel, 256 colors in palette Reducing image to 8 bits/pixel, grayscale Input IDAT size = 14630 bytes Input file size = 15500 bytes Trying: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 13187 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 = 13187 Output IDAT size = 13187 bytes (1443 bytes decrease) Output file size = 13265 bytes (2235 bytes = 14.42% decrease) ** Processing: /home/hornik/tmp/CRAN_recheck/SynthETIC.Rcheck/vign_test/SynthETIC/vignettes/SynthETIC-demo_files/figure-html/unnamed-chunk-19-1.png 1050x600 pixels, 3x8 bits/pixel, RGB Input IDAT size = 42456 bytes Input file size = 42594 bytes Trying: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 34330 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 = 34330 Output IDAT size = 34330 bytes (8126 bytes decrease) Output file size = 34408 bytes (8186 bytes = 19.22% decrease) ** Processing: /home/hornik/tmp/CRAN_recheck/SynthETIC.Rcheck/vign_test/SynthETIC/vignettes/SynthETIC-demo_files/figure-html/unnamed-chunk-45-1.png 1050x900 pixels, 3x8 bits/pixel, RGB Input IDAT size = 225341 bytes Input file size = 225743 bytes Trying: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 220613 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 = 220613 Output IDAT size = 220613 bytes (4728 bytes decrease) Output file size = 220691 bytes (5052 bytes = 2.24% decrease) ** Processing: /home/hornik/tmp/CRAN_recheck/SynthETIC.Rcheck/vign_test/SynthETIC/vignettes/SynthETIC-demo_files/figure-html/unnamed-chunk-45-2.png 1050x900 pixels, 3x8 bits/pixel, RGB Input IDAT size = 192102 bytes Input file size = 192456 bytes Trying: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 190146 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 IDAT size = 188226 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 = 188226 Output IDAT size = 188226 bytes (3876 bytes decrease) Output file size = 188304 bytes (4152 bytes = 2.16% decrease) ** Processing: /home/hornik/tmp/CRAN_recheck/SynthETIC.Rcheck/vign_test/SynthETIC/vignettes/SynthETIC-demo_files/figure-html/unnamed-chunk-46-1.png 1050x900 pixels, 3x8 bits/pixel, RGB Input IDAT size = 115131 bytes Input file size = 115377 bytes Trying: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 107123 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 = 107123 Output IDAT size = 107123 bytes (8008 bytes decrease) Output file size = 107201 bytes (8176 bytes = 7.09% decrease) *** caught segfault *** address 0x5b46, cause 'memory not mapped' Traceback: 1: grid.newpage() 2: print.ggplot(x) 3: print(x) 4: normal_print(x) 5: knit_print.default(x, ...) 6: knit_print(x, ...) 7: withVisible(knit_print(x, ...)) 8: fun(x, options = options) 9: handler$value(value, visible) 10: handle_value(handler, value, visible, envir) 11: withVisible(handle_value(handler, value, visible, envir)) 12: watcher$print_value(ev$value, ev$visible, envir) 13: withCallingHandlers(code, message = function (cnd) { watcher$capture_plot_and_output() if (on_message$capture) { watcher$push(cnd) } if (on_message$silence) { invokeRestart("muffleMessage") }}, warning = function (cnd) { if (getOption("warn") >= 2 || getOption("warn") < 0) { return() } watcher$capture_plot_and_output() if (on_warning$capture) { cnd <- sanitize_call(cnd) watcher$push(cnd) } if (on_warning$silence) { invokeRestart("muffleWarning") }}, error = function (cnd) { watcher$capture_plot_and_output() cnd <- sanitize_call(cnd) watcher$push(cnd) switch(on_error, continue = invokeRestart("eval_continue"), stop = invokeRestart("eval_stop"), error = invokeRestart("eval_error", cnd))}) 14: eval(call) 15: eval(call) 16: with_handlers({ for (expr in tle$exprs) { ev <- withVisible(eval(expr, envir)) watcher$capture_plot_and_output() watcher$print_value(ev$value, ev$visible, envir) } TRUE}, handlers) 17: doWithOneRestart(return(expr), restart) 18: withOneRestart(expr, restarts[[1L]]) 19: withRestartList(expr, restarts[-nr]) 20: doWithOneRestart(return(expr), restart) 21: withOneRestart(withRestartList(expr, restarts[-nr]), restarts[[nr]]) 22: withRestartList(expr, restarts[-nr]) 23: doWithOneRestart(return(expr), restart) 24: withOneRestart(withRestartList(expr, restarts[-nr]), restarts[[nr]]) 25: withRestartList(expr, restarts) 26: withRestarts(with_handlers({ for (expr in tle$exprs) { ev <- withVisible(eval(expr, envir)) watcher$capture_plot_and_output() watcher$print_value(ev$value, ev$visible, envir) } TRUE}, handlers), eval_continue = function() TRUE, eval_stop = function() FALSE, eval_error = function(cnd) { signalCondition(cnd) stop(cnd) }) 27: evaluate::evaluate(...) 28: evaluate(code, envir = env, new_device = FALSE, keep_warning = if (is.numeric(options$warning)) TRUE else options$warning, keep_message = if (is.numeric(options$message)) TRUE else options$message, stop_on_error = if (is.numeric(options$error)) options$error else { if (options$error && options$include) 0L else 2L }, output_handler = knit_handlers(options$render, options)) 29: in_dir(input_dir(), expr) 30: in_input_dir(evaluate(code, envir = env, new_device = FALSE, keep_warning = if (is.numeric(options$warning)) TRUE else options$warning, keep_message = if (is.numeric(options$message)) TRUE else options$message, stop_on_error = if (is.numeric(options$error)) options$error else { if (options$error && options$include) 0L else 2L }, output_handler = knit_handlers(options$render, options))) 31: eng_r(options) 32: block_exec(params) 33: call_block(x) 34: process_group(group) 35: withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), error = function(e) if (xfun::pkg_available("rlang", "1.0.0")) rlang::entrace(e)) 36: xfun:::handle_error(withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), error = function(e) if (xfun::pkg_available("rlang", "1.0.0")) rlang::entrace(e)), function(loc) { setwd(wd) write_utf8(res, output %n% stdout()) paste0("\nQuitting from lines ", loc) }, if (labels[i] != "") sprintf(" [%s]", labels[i]), get_loc) 37: process_file(text, output) 38: knitr::knit(knit_input, knit_output, envir = envir, quiet = quiet) 39: rmarkdown::render(file, encoding = encoding, quiet = quiet, envir = globalenv(), output_dir = getwd(), ...) 40: vweave_rmarkdown(...) 41: engine$weave(file, quiet = quiet, encoding = enc) 42: doTryCatch(return(expr), name, parentenv, handler) 43: tryCatchOne(expr, names, parentenv, handlers[[1L]]) 44: tryCatchList(expr, classes, parentenv, handlers) 45: tryCatch({ engine$weave(file, quiet = quiet, encoding = enc) setwd(startdir) output <- find_vignette_product(name, by = "weave", engine = engine) if (!have.makefile && vignette_is_tex(output)) { texi2pdf(file = output, clean = FALSE, quiet = quiet) output <- find_vignette_product(name, by = "texi2pdf", engine = engine) }}, error = function(e) { OK <<- FALSE message(gettextf("Error: processing vignette '%s' failed with diagnostics:\n%s", file, conditionMessage(e)))}) 46: tools:::.buildOneVignette("SynthETIC-demo.Rmd", "/home/hornik/tmp/CRAN_recheck/SynthETIC.Rcheck/vign_test/SynthETIC", TRUE, FALSE, "SynthETIC-demo", "UTF-8", "/home/hornik/tmp/scratch/RtmpGYn1V9/file230a4153874a9a.rds") An irrecoverable exception occurred. R is aborting now ... Segmentation fault SUMMARY: processing the following file failed: ‘SynthETIC-demo.Rmd’ Error: Vignette re-building failed. Execution halted Package: tidycomm Check: re-building of vignette outputs New result: ERROR Error(s) in re-building vignettes: ... --- re-building ‘v01_univariate.Rmd’ using rmarkdown ** Processing: /home/hornik/tmp/CRAN_recheck/tidycomm.Rcheck/vign_test/tidycomm/vignettes/v01_univariate_files/figure-html/unnamed-chunk-6-1.png 288x288 pixels, 3x8 bits/pixel, RGB Input IDAT size = 20133 bytes Input file size = 20235 bytes Trying: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 13697 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 = 13697 Output IDAT size = 13697 bytes (6436 bytes decrease) Output file size = 13775 bytes (6460 bytes = 31.92% decrease) ** Processing: /home/hornik/tmp/CRAN_recheck/tidycomm.Rcheck/vign_test/tidycomm/vignettes/v01_univariate_files/figure-html/unnamed-chunk-8-1.png 288x288 pixels, 8 bits/pixel, 252 colors in palette Reducing image to 8 bits/pixel, grayscale Input IDAT size = 4996 bytes Input file size = 5842 bytes Trying: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 4560 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 = 4560 Output IDAT size = 4560 bytes (436 bytes decrease) Output file size = 4638 bytes (1204 bytes = 20.61% decrease) ** Processing: /home/hornik/tmp/CRAN_recheck/tidycomm.Rcheck/vign_test/tidycomm/vignettes/v01_univariate_files/figure-html/unnamed-chunk-12-1.png 288x288 pixels, 3x8 bits/pixel, RGB Input IDAT size = 23721 bytes Input file size = 23823 bytes Trying: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 17526 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 = 17526 Output IDAT size = 17526 bytes (6195 bytes decrease) Output file size = 17604 bytes (6219 bytes = 26.11% decrease) ** Processing: /home/hornik/tmp/CRAN_recheck/tidycomm.Rcheck/vign_test/tidycomm/vignettes/v01_univariate_files/figure-html/unnamed-chunk-16-1.png 288x288 pixels, 8 bits/pixel, 206 colors in palette Input IDAT size = 3872 bytes Input file size = 4580 bytes Trying: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 3504 zc = 9 zm = 8 zs = 1 f = 0 IDAT size = 3500 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 = 1 f = 0 IDAT size = 3500 Output IDAT size = 3500 bytes (372 bytes decrease) Output file size = 4208 bytes (372 bytes = 8.12% decrease) --- finished re-building ‘v01_univariate.Rmd’ --- re-building ‘v02_bivariate.Rmd’ using rmarkdown ** Processing: /home/hornik/tmp/CRAN_recheck/tidycomm.Rcheck/vign_test/tidycomm/vignettes/v02_bivariate_files/figure-html/unnamed-chunk-7-1.png 288x288 pixels, 3x8 bits/pixel, RGB Input IDAT size = 18196 bytes Input file size = 18298 bytes Trying: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 13659 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 = 13659 Output IDAT size = 13659 bytes (4537 bytes decrease) Output file size = 13737 bytes (4561 bytes = 24.93% decrease) ** Processing: /home/hornik/tmp/CRAN_recheck/tidycomm.Rcheck/vign_test/tidycomm/vignettes/v02_bivariate_files/figure-html/unnamed-chunk-8-1.png 288x288 pixels, 3x8 bits/pixel, RGB Input IDAT size = 14187 bytes Input file size = 14277 bytes Trying: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 10889 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 = 10889 Output IDAT size = 10889 bytes (3298 bytes decrease) Output file size = 10967 bytes (3310 bytes = 23.18% decrease) ** Processing: /home/hornik/tmp/CRAN_recheck/tidycomm.Rcheck/vign_test/tidycomm/vignettes/v02_bivariate_files/figure-html/unnamed-chunk-13-1.png 288x288 pixels, 3x8 bits/pixel, RGB Input IDAT size = 9766 bytes Input file size = 9856 bytes Trying: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 7386 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 = 7386 Output IDAT size = 7386 bytes (2380 bytes decrease) Output file size = 7464 bytes (2392 bytes = 24.27% decrease) ** Processing: /home/hornik/tmp/CRAN_recheck/tidycomm.Rcheck/vign_test/tidycomm/vignettes/v02_bivariate_files/figure-html/unnamed-chunk-18-1.png 288x288 pixels, 3x8 bits/pixel, RGB Input IDAT size = 10816 bytes Input file size = 10906 bytes Trying: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 8073 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 = 8073 Output IDAT size = 8073 bytes (2743 bytes decrease) Output file size = 8151 bytes (2755 bytes = 25.26% decrease) ** Processing: /home/hornik/tmp/CRAN_recheck/tidycomm.Rcheck/vign_test/tidycomm/vignettes/v02_bivariate_files/figure-html/unnamed-chunk-23-1.png 288x288 pixels, 8 bits/pixel, 256 colors in palette Reducing image to 8 bits/pixel, grayscale Input IDAT size = 13406 bytes Input file size = 14276 bytes Trying: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 12477 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 = 12477 Output IDAT size = 12477 bytes (929 bytes decrease) Output file size = 12555 bytes (1721 bytes = 12.06% decrease) Quitting from lines 215-218 [unnamed-chunk-24] (v02_bivariate.Rmd) Error: processing vignette 'v02_bivariate.Rmd' failed with diagnostics: there is no package called 'Rcpp' --- failed re-building ‘v02_bivariate.Rmd’ --- re-building ‘v03_reliability.Rmd’ using rmarkdown --- finished re-building ‘v03_reliability.Rmd’ --- re-building ‘v04_icr.Rmd’ using rmarkdown --- finished re-building ‘v04_icr.Rmd’ --- re-building ‘v05_scales.Rmd’ using rmarkdown ** Processing: /home/hornik/tmp/CRAN_recheck/tidycomm.Rcheck/vign_test/tidycomm/vignettes/v05_scales_files/figure-html/unnamed-chunk-6-1.png 288x288 pixels, 8 bits/pixel, 221 colors in palette Input IDAT size = 5009 bytes Input file size = 5762 bytes Trying: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 4698 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 = 4698 Output IDAT size = 4698 bytes (311 bytes decrease) Output file size = 5451 bytes (311 bytes = 5.40% decrease) --- finished re-building ‘v05_scales.Rmd’ SUMMARY: processing the following file failed: ‘v02_bivariate.Rmd’ Error: Vignette re-building failed. Execution halted Package: tidymodels Check: whether package can be installed New result: ERROR Installation failed. Package: tidytreatment Check: whether package can be installed New result: ERROR Installation failed. Package: TrafficBDE Check: re-building of vignette outputs New result: ERROR Error(s) in re-building vignettes: ... --- re-building ‘TrafficBDE.Rmd’ using rmarkdown Quitting from lines 59-61 [unnamed-chunk-1] (TrafficBDE.Rmd) Error: processing vignette 'TrafficBDE.Rmd' failed with diagnostics: package or namespace load failed for 'TrafficBDE' in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]): there is no package called 'Rcpp' --- failed re-building ‘TrafficBDE.Rmd’ SUMMARY: processing the following file failed: ‘TrafficBDE.Rmd’ Error: Vignette re-building failed. Execution halted Package: unmarked Check: re-building of vignette outputs New result: ERROR Error(s) in re-building vignettes: ... --- re-building ‘cap-recap.Rmd’ using rmarkdown ** Processing: /home/hornik/tmp/CRAN_recheck/unmarked.Rcheck/vign_test/unmarked/vignettes/cap-recap_files/figure-html/unnamed-chunk-14-1.png 480x480 pixels, 8 bits/pixel, 256 colors in palette Reducing image to 8 bits/pixel, grayscale Input IDAT size = 9349 bytes Input file size = 10219 bytes Trying: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 8381 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 = 8381 Output IDAT size = 8381 bytes (968 bytes decrease) Output file size = 8459 bytes (1760 bytes = 17.22% decrease) --- finished re-building ‘cap-recap.Rmd’ --- re-building ‘colext.Rmd’ using rmarkdown --- finished re-building ‘colext.Rmd’ --- re-building ‘contributing_to_unmarked.Rmd’ using rmarkdown *** caught segfault *** address 0x5556, cause 'memory not mapped' Traceback: 1: dev.off(dv) 2: eng_r(options) 3: block_exec(params) 4: call_block(x) 5: process_group(group) 6: withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), error = function(e) if (xfun::pkg_available("rlang", "1.0.0")) rlang::entrace(e)) 7: xfun:::handle_error(withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), error = function(e) if (xfun::pkg_available("rlang", "1.0.0")) rlang::entrace(e)), function(loc) { setwd(wd) write_utf8(res, output %n% stdout()) paste0("\nQuitting from lines ", loc) }, if (labels[i] != "") sprintf(" [%s]", labels[i]), get_loc) 8: process_file(text, output) 9: knitr::knit(knit_input, knit_output, envir = envir, quiet = quiet) 10: rmarkdown::render(file, encoding = encoding, quiet = quiet, envir = globalenv(), output_dir = getwd(), ...) 11: vweave_rmarkdown(...) 12: engine$weave(file, quiet = quiet, encoding = enc) 13: doTryCatch(return(expr), name, parentenv, handler) 14: tryCatchOne(expr, names, parentenv, handlers[[1L]]) 15: tryCatchList(expr, classes, parentenv, handlers) 16: tryCatch({ engine$weave(file, quiet = quiet, encoding = enc) setwd(startdir) output <- find_vignette_product(name, by = "weave", engine = engine) if (!have.makefile && vignette_is_tex(output)) { texi2pdf(file = output, clean = FALSE, quiet = quiet) output <- find_vignette_product(name, by = "texi2pdf", engine = engine) }}, error = function(e) { OK <<- FALSE message(gettextf("Error: processing vignette '%s' failed with diagnostics:\n%s", file, conditionMessage(e)))}) 17: tools:::.buildOneVignette("contributing_to_unmarked.Rmd", "/home/hornik/tmp/CRAN_recheck/unmarked.Rcheck/vign_test/unmarked", TRUE, FALSE, "contributing_to_unmarked", "UTF-8", "/home/hornik/tmp/scratch/RtmpuNX6l7/file236c0d7b7a0268.rds") An irrecoverable exception occurred. R is aborting now ... Segmentation fault --- re-building ‘distsamp.Rmd’ using rmarkdown ** Processing: /home/hornik/tmp/CRAN_recheck/unmarked.Rcheck/vign_test/unmarked/vignettes/distsamp_files/figure-html/unnamed-chunk-5-1.png 384x384 pixels, 8 bits/pixel, 250 colors in palette Reducing image to 8 bits/pixel, grayscale Input IDAT size = 3557 bytes Input file size = 4397 bytes Trying: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 2889 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 = 2889 Output IDAT size = 2889 bytes (668 bytes decrease) Output file size = 2967 bytes (1430 bytes = 32.52% decrease) ** Processing: /home/hornik/tmp/CRAN_recheck/unmarked.Rcheck/vign_test/unmarked/vignettes/distsamp_files/figure-html/unnamed-chunk-13-1.png 576x288 pixels, 8 bits/pixel, 256 colors in palette Reducing image to 8 bits/pixel, grayscale Input IDAT size = 6383 bytes Input file size = 7241 bytes Trying: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 5700 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 = 5700 Output IDAT size = 5700 bytes (683 bytes decrease) Output file size = 5778 bytes (1463 bytes = 20.20% decrease) ** Processing: /home/hornik/tmp/CRAN_recheck/unmarked.Rcheck/vign_test/unmarked/vignettes/distsamp_files/figure-html/unnamed-chunk-14-1.png 576x288 pixels, 3x8 bits/pixel, RGB Input IDAT size = 20369 bytes Input file size = 20471 bytes Trying: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 15543 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 = 15543 Output IDAT size = 15543 bytes (4826 bytes decrease) Output file size = 15621 bytes (4850 bytes = 23.69% decrease) --- finished re-building ‘distsamp.Rmd’ --- re-building ‘occuMulti.Rmd’ using rmarkdown ** Processing: /home/hornik/tmp/CRAN_recheck/unmarked.Rcheck/vign_test/unmarked/vignettes/occuMulti_files/figure-html/unnamed-chunk-16-1.png 480x480 pixels, 8 bits/pixel, 256 colors in palette Reducing image to 8 bits/pixel, grayscale Input IDAT size = 7285 bytes Input file size = 8143 bytes Trying: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 6276 zc = 9 zm = 8 zs = 1 f = 0 IDAT size = 6260 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 = 1 f = 0 IDAT size = 6260 Output IDAT size = 6260 bytes (1025 bytes decrease) Output file size = 6338 bytes (1805 bytes = 22.17% decrease) ** Processing: /home/hornik/tmp/CRAN_recheck/unmarked.Rcheck/vign_test/unmarked/vignettes/occuMulti_files/figure-html/unnamed-chunk-19-1.png 480x480 pixels, 8 bits/pixel, 256 colors in palette Reducing image to 8 bits/pixel, grayscale Input IDAT size = 7131 bytes Input file size = 7989 bytes Trying: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 6184 zc = 9 zm = 8 zs = 1 f = 0 IDAT size = 6169 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 = 1 f = 0 IDAT size = 6169 Output IDAT size = 6169 bytes (962 bytes decrease) Output file size = 6247 bytes (1742 bytes = 21.80% decrease) ** Processing: /home/hornik/tmp/CRAN_recheck/unmarked.Rcheck/vign_test/unmarked/vignettes/occuMulti_files/figure-html/unnamed-chunk-28-1.png 480x480 pixels, 3x8 bits/pixel, RGB Input IDAT size = 26938 bytes Input file size = 27052 bytes Trying: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 21686 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 = 21686 Output IDAT size = 21686 bytes (5252 bytes decrease) Output file size = 21764 bytes (5288 bytes = 19.55% decrease) --- finished re-building ‘occuMulti.Rmd’ --- re-building ‘powerAnalysis.Rmd’ using rmarkdown --- finished re-building ‘powerAnalysis.Rmd’ --- re-building ‘simulate.Rmd’ using rmarkdown Quitting from lines 62-67 [unnamed-chunk-1] (simulate.Rmd) Error: processing vignette 'simulate.Rmd' failed with diagnostics: package or namespace load failed for 'unmarked' in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]): there is no package called 'Rcpp' --- failed re-building ‘simulate.Rmd’ --- re-building ‘spp-dist.Rmd’ using rmarkdown Quitting from lines 64-73 [unnamed-chunk-2] (spp-dist.Rmd) Error: processing vignette 'spp-dist.Rmd' failed with diagnostics: package or namespace load failed for 'unmarked' in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]): there is no package called 'Rcpp' --- failed re-building ‘spp-dist.Rmd’ --- re-building ‘unmarked.Rmd’ using rmarkdown Quitting from lines 86-94 [unnamed-chunk-3] (unmarked.Rmd) Error: processing vignette 'unmarked.Rmd' failed with diagnostics: package or namespace load failed for 'unmarked' in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]): there is no package called 'Rcpp' --- failed re-building ‘unmarked.Rmd’ SUMMARY: processing the following files failed: ‘contributing_to_unmarked.Rmd’ ‘simulate.Rmd’ ‘spp-dist.Rmd’ ‘unmarked.Rmd’ Error: Vignette re-building failed. Execution halted Package: ursa Check: examples New result: ERROR Running examples in ‘ursa-Ex.R’ failed The error most likely occurred in: > base::assign(".ptime", proc.time(), pos = "CheckExEnv") > ### Name: panel_graticule > ### Title: Add latitude/longitude or metric grid to the image panel. > ### Aliases: panel_graticule compose_graticule .panel_graticule > ### .compose_graticule > ### Keywords: aplot > > ### ** Examples > > session_grid(NULL) > > # example no.1 > cl <- compose_design(layout=c(2,2),legend=NULL) > session_grid(regrid(lim=3.2*1e6*c(-1,-1,1,1))) > compose_open(cl) > for (i in 1:4) { + panel_new() + panel_graticule(decor=TRUE,trim=i %in% c(2:4)) + panel_annotation(text=as.character(i)) + panel_scalebar(scalebar=i==3) + } > compose_close() Use 'session_pngviewer(TRUE)' to open '/home/hornik/tmp/scratch/Rtmp43qkxt/___ursa57_2f44.png' in external software. > > # example no.2 > session_grid(regrid(lim=1e6*c(-0.5,0.5,1.5,2.5))) > compose_open(layout=c(2,2),legend=NULL,skip=4) > for (i in seq(getOption("ursaPngLayout")$image)) { + panel_new() + if (i==1) + panel_graticule() + else if (i==2) + panel_graticule(decor=TRUE,lon=seq(0,360,by=40)[-1],lat=seq(-90,90,by=10)) + else if (i==3) + panel_graticule(decor=TRUE,lon=seq(0,360,by=20)[-1],lat=seq(-90,90,by=5) + ,trim=TRUE) + else if (i==4) + panel_graticule(gridline=FALSE) + panel_scalebar(scalebar=1) + panel_annotation(text=as.character(i)) + } > compose_close() Use 'session_pngviewer(TRUE)' to open '/home/hornik/tmp/scratch/Rtmp43qkxt/___ursa58_c78a.png' in external software. > > # example no.3 -- indirect usage > session_grid(NULL) > display(pixelsize(),decor=TRUE,grid.col="green3",coast.col="darkgreen",side=2) *** caught segfault *** address 0x5cd6, cause 'memory not mapped' Traceback: 1: box(lwd = 0.5, col = ifelse(bg < 128, "#FFFFFF7F", "#0000007F")) 2: panel_box() 3: .getSide() 4: .legend_colorbar(ct, units = units, labels = labels, align = align, shift = shift, cex = cex, adj = adj, las = las, forceLabel = forceLabel, lomar = lomar, himar = himar, turn = turn, useRaster = useRaster, trim = trim, abbrev = abbrev, opacity = opacity, verbose = verbose) 5: legend_colorbar(obj[[i]], decor = TRUE, grid.col = "green3", coast.col = "darkgreen", side = 2, unit = "") 6: do.call("legend_colorbar", arglist2) 7: compose_legend(list(`Pixel Size (sq.km)` = c(`390` = "#EAF6E8FF", `391` = "#E9F6E7FF", `392` = "#E8F6E6FF", `393` = "#E8F5E5FF", `394` = "#E7F5E4FF", `395` = "#E7F4E3FF", `396` = "#E6F4E2FF", `397` = "#E6F3E1FF", `398` = "#E5F3E0FF", `399` = "#E5F2DEFF", `400` = "#E4F2DDFF", `401` = "#E4F1DCFF", `402` = "#E3F1DBFF", `403` = "#E3F1DAFF", `404` = "#E2F0D9FF", `405` = "#E2EFD8FF", `406` = "#E1EFD7FF", `407` = "#E1EED6FF", `408` = "#E1EED5FF", `409` = "#E0EDD4FF", `410` = "#E0EDD2FF", `411` = "#E0ECD1FF", `412` = "#DFECD0FF", `413` = "#DFEBCFFF", `414` = "#DFEACEFF", `415` = "#DFEACDFF", `416` = "#DEE9CCFF", `417` = "#DEE9CBFF", `418` = "#DEE8CAFF", `419` = "#DEE7C9FF", `420` = "#DEE7C8FF", `421` = "#DEE6C7FF", `422` = "#DDE5C6FF", `423` = "#DDE5C5FF", `424` = "#DDE4C4FF", `425` = "#DDE3C3FF", `426` = "#DDE3C2FF", `427` = "#DDE2C1FF", `428` = "#DDE1C0FF", `429` = "#DDE0BFFF", `430` = "#DDE0BEFF", `431` = "#DDDFBDFF", `432` = "#DDDEBCFF", `433` = "#DDDDBBFF", `434` = "#DDDDBAFF", `435` = "#DDDCB9FF", `436` = "#DDDBB9FF", `437` = "#DDDAB8FF", `438` = "#DDD9B7FF", `439` = "#DDD9B6FF", `440` = "#DDD8B5FF", `441` = "#DDD7B5FF", `442` = "#DDD6B4FF", `443` = "#DDD5B3FF", `444` = "#DED5B2FF", `445` = "#DED4B2FF", `446` = "#DED3B1FF", `447` = "#DED2B0FF", `448` = "#DED1B0FF", `449` = "#DED0AFFF", `450` = "#DECFAEFF", `451` = "#DECEAEFF", `452` = "#DFCDADFF", `453` = "#DFCDADFF", `454` = "#DFCCACFF", `455` = "#DFCBABFF", `456` = "#DFCAABFF", `457` = "#DFC9AAFF", `458` = "#E0C8AAFF", `459` = "#E0C7AAFF", `460` = "#E0C6A9FF", `461` = "#E0C5A9FF", `462` = "#E0C4A8FF", `463` = "#E0C3A8FF", `464` = "#E1C2A8FF", `465` = "#E1C1A7FF", `466` = "#E1C0A7FF", `467` = "#E1C0A7FF", `468` = "#E1BFA6FF", `469` = "#E1BEA6FF", `470` = "#E1BDA6FF", `471` = "#E2BCA6FF", `472` = "#E2BBA6FF", `473` = "#E2BAA5FF", `474` = "#E2B9A5FF", `475` = "#E2B8A5FF", `476` = "#E2B7A5FF", `477` = "#E2B6A5FF", `478` = "#E2B5A5FF", `479` = "#E2B4A5FF", `480` = "#E2B3A5FF", `481` = "#E3B2A5FF", `482` = "#E3B1A5FF", `483` = "#E3B0A5FF", `484` = "#E3AFA5FF", `485` = "#E3AEA5FF", `486` = "#E3ADA5FF", `487` = "#E3ACA5FF", `488` = "#E3ABA5FF", `489` = "#E3ABA6FF", `490` = "#E3AAA6FF", `491` = "#E2A9A6FF", `492` = "#E2A8A6FF", `493` = "#E2A7A6FF", `494` = "#E2A6A6FF", `495` = "#E2A5A7FF", `496` = "#E2A4A7FF", `497` = "#E2A3A7FF", `498` = "#E2A2A7FF", `499` = "#E1A1A8FF", `500` = "#E1A1A8FF", `501` = "#E1A0A8FF", `502` = "#E19FA9FF", `503` = "#E19EA9FF", `504` = "#E09DA9FF", `505` = "#E09CAAFF", `506` = "#E09BAAFF", `507` = "#DF9BABFF", `508` = "#DF9AABFF", `509` = "#DF99ABFF", `510` = "#DE98ACFF", `511` = "#DE97ACFF", `512` = "#DE96ADFF", `513` = "#DD96ADFF", `514` = "#DD95AEFF", `515` = "#DC94AEFF", `516` = "#DC93AFFF", `517` = "#DB93AFFF", `518` = "#DB92AFFF", `519` = "#DA91B0FF", `520` = "#DA90B0FF", `521` = "#D990B1FF", `522` = "#D88FB1FF", `523` = "#D88EB2FF", `524` = "#D78EB2FF", `525` = "#D68DB3FF", `526` = "#D68CB3FF", `527` = "#D58CB4FF", `528` = "#D48BB4FF", `529` = "#D38AB5FF", `530` = "#D38AB5FF", `531` = "#D289B6FF", `532` = "#D188B6FF", `533` = "#D088B7FF", `534` = "#CF87B7FF", `535` = "#CE87B8FF", `536` = "#CE86B8FF", `537` = "#CD86B9FF", `538` = "#CC85B9FF", `539` = "#CB85BAFF", `540` = "#CA84BAFF", `541` = "#C984BBFF", `542` = "#C883BBFF", `543` = "#C783BCFF", `544` = "#C682BCFF", `545` = "#C482BCFF", `546` = "#C381BDFF", `547` = "#C281BDFF", `548` = "#C180BEFF", `549` = "#C080BEFF", `550` = "#BF7FBEFF", `551` = "#BE7FBFFF", `552` = "#BC7FBFFF", `553` = "#BB7EBFFF", `554` = "#BA7EC0FF", `555` = "#B97EC0FF", `556` = "#B77DC0FF", `557` = "#B67DC1FF", `558` = "#B57DC1FF", `559` = "#B47CC1FF", `560` = "#B27CC1FF", `561` = "#B17CC2FF", `562` = "#AF7CC2FF", `563` = "#AE7BC2FF", `564` = "#AD7BC2FF", `565` = "#AB7BC2FF", `566` = "#AA7BC2FF", `567` = "#A87AC3FF", `568` = "#A77AC3FF", `569` = "#A67AC3FF", `570` = "#A47AC3FF", `571` = "#A379C3FF", `572` = "#A179C3FF", `573` = "#A079C3FF", `574` = "#9E79C3FF", `575` = "#9D79C3FF", `576` = "#9B79C3FF", `577` = "#9A79C3FF", `578` = "#9878C3FF", `579` = "#9778C2FF", `580` = "#9578C2FF", `581` = "#9378C2FF", `582` = "#9278C2FF", `583` = "#9078C2FF", `584` = "#8F78C1FF", `585` = "#8D78C1FF", `586` = "#8C78C1FF", `587` = "#8A78C1FF", `588` = "#8878C0FF", `589` = "#8777C0FF", `590` = "#8577BFFF", `591` = "#8477BFFF", `592` = "#8277BFFF", `593` = "#8177BEFF", `594` = "#7F77BEFF", `595` = "#7D77BDFF", `596` = "#7C77BDFF", `597` = "#7A77BCFF", `598` = "#7977BBFF", `599` = "#7777BBFF", `600` = "#7577BAFF", `601` = "#7477BAFF", `602` = "#7277B9FF", `603` = "#7177B8FF", `604` = "#6F77B7FF", `605` = "#6E77B7FF", `606` = "#6C77B6FF", `607` = "#6B77B5FF", `608` = "#6977B4FF", `609` = "#6777B4FF", `610` = "#6677B3FF", `611` = "#6477B2FF", `612` = "#6377B1FF", `613` = "#6177B0FF", `614` = "#6077AFFF", `615` = "#5E77AEFF", `616` = "#5D77ADFF", `617` = "#5C77ACFF", `618` = "#5A77ABFF", `619` = "#5977AAFF", `620` = "#5777A9FF", `621` = "#5677A8FF", `622` = "#5477A7FF", `623` = "#5377A5FF", `624` = "#5277A4FF", `625` = "#5077A3FF", `626` = "#4F77A2FF", `627` = "#4E77A1FF", `628` = "#4C779FFF", `629` = "#4B779EFF", `630` = "#4A779DFF", `631` = "#49779CFF", `632` = "#47779AFF", `633` = "#467799FF", `634` = "#457798FF", `635` = "#447796FF", `636` = "#437795FF", `637` = "#417793FF", `638` = "#407692FF", `639` = "#3F7691FF", `640` = "#3E768FFF", `641` = "#3D768EFF", `642` = "#3C768CFF", `643` = "#3B768BFF", `644` = "#3A7689FF", `645` = "#397688FF", `646` = "#387586FF", `647` = "#377585FF", `648` = "#367583FF", `649` = "#357582FF", `650` = "#347580FF", `651` = "#33757FFF", `652` = "#32747DFF", `653` = "#32747CFF", `654` = "#31747AFF", `655` = "#307479FF", `656` = "#2F7477FF", `657` = "#2E7375FF", `658` = "#2E7374FF", `659` = "#2D7372FF", `660` = "#2C7271FF", `661` = "#2C726FFF", `662` = "#2B726DFF", `663` = "#2A726CFF", `664` = "#2A716AFF")), decor = TRUE, grid.col = "green3", coast.col = "darkgreen", side = 2) 8: do.call("compose_legend", c(list(ct), arglist)) 9: compose_plot(obj, ...) 10: display_brick(obj, ...) 11: display(pixelsize(), decor = TRUE, grid.col = "green3", coast.col = "darkgreen", side = 2) An irrecoverable exception occurred. R is aborting now ... Segmentation fault Package: valr Check: whether package can be installed New result: ERROR Installation failed. Package: varbvs Check: dependencies in R code New result: NOTE Error: there is no package called ‘Rcpp’ Call sequence: 13: doWithOneRestart(return(expr), restart) 12: withOneRestart(expr, restarts[[1L]]) 11: withRestarts(stop(cond), retry_loadNamespace = function() NULL) 10: loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) 9: asNamespace(ns) 8: namespaceImportFrom(ns, loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]), i[[2L]], from = package) 7: loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) 6: asNamespace(ns) 5: namespaceImportFrom(ns, loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]), i[[2L]], from = package) 4: loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) 3: asNamespace(ns) 2: namespaceImportFrom(ns, loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]), i[[2L]], from = package) 1: loadNamespace(package, lib.loc) Execution halted Package: varbvs Check: examples New result: ERROR Running examples in ‘varbvs-Ex.R’ failed The error occurred in: R Under development (unstable) (2024-11-01 r87285) -- "Unsuffered Consequences" Copyright (C) 2024 The R Foundation for Statistical Computing Platform: x86_64-pc-linux-gnu R is free software and comes with ABSOLUTELY NO WARRANTY. You are welcome to redistribute it under certain conditions. Type 'license()' or 'licence()' for distribution details. R is a collaborative project with many contributors. Type 'contributors()' for more information and 'citation()' on how to cite R or R packages in publications. Type 'demo()' for some demos, 'help()' for on-line help, or 'help.start()' for an HTML browser interface to help. Type 'q()' to quit R. > pkgname <- "varbvs" > source(file.path(R.home("share"), "R", "examples-header.R")) > options(warn = 1) > base::assign(".ExTimings", "varbvs-Ex.timings", pos = 'CheckExEnv') > base::cat("name\tuser\tsystem\telapsed\n", file=base::get(".ExTimings", pos = 'CheckExEnv')) > base::assign(".format_ptime", + function(x) { + if(!is.na(x[4L])) x[1L] <- x[1L] + x[4L] + if(!is.na(x[5L])) x[2L] <- x[2L] + x[5L] + options(OutDec = '.') + format(x[1L:3L], digits = 7L) + }, + pos = 'CheckExEnv') > > ### * > library('varbvs') Error: package or namespace load failed for ‘varbvs’ in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]): there is no package called ‘Rcpp’ Execution halted Package: varbvs Check: for code/documentation mismatches New result: WARNING Error: package or namespace load failed for ‘varbvs’ in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]): there is no package called ‘Rcpp’ Call sequence: 6: stop(msg, call. = FALSE, domain = NA) 5: value[[3L]](cond) 4: tryCatchOne(expr, names, parentenv, handlers[[1L]]) 3: tryCatchList(expr, classes, parentenv, handlers) 2: tryCatch({ attr(package, "LibPath") <- which.lib.loc ns <- loadNamespace(package, lib.loc) env <- attachNamespace(ns, pos = pos, deps, exclude, include.only) }, error = function(e) { P <- if (!is.null(cc <- conditionCall(e))) paste(" in", deparse(cc)[1L]) else "" msg <- gettextf("package or namespace load failed for %s%s:\n %s", sQuote(package), P, conditionMessage(e)) if (logical.return && !quietly) message(paste("Error:", msg), domain = NA) else stop(msg, call. = FALSE, domain = NA) }) 1: library(package, lib.loc = lib.loc, charac Execution halted Error: package or namespace load failed for ‘varbvs’ in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]): there is no package called ‘Rcpp’ Call sequence: 6: stop(msg, call. = FALSE, domain = NA) 5: value[[3L]](cond) 4: tryCatchOne(expr, names, parentenv, handlers[[1L]]) 3: tryCatchList(expr, classes, parentenv, handlers) 2: tryCatch({ attr(package, "LibPath") <- which.lib.loc ns <- loadNamespace(package, lib.loc) env <- attachNamespace(ns, pos = pos, deps, exclude, include.only) }, error = function(e) { P <- if (!is.null(cc <- conditionCall(e))) paste(" in", deparse(cc)[1L]) else "" msg <- gettextf("package or namespace load failed for %s%s:\n %s", sQuote(package), P, conditionMessage(e)) if (logical.return && !quietly) message(paste("Error:", msg), domain = NA) else stop(msg, call. = FALSE, domain = NA) }) 1: library(package, lib.loc = lib.loc, charac Execution halted Error: package or namespace load failed for ‘varbvs’ in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]): there is no package called ‘Rcpp’ Call sequence: 6: stop(msg, call. = FALSE, domain = NA) 5: value[[3L]](cond) 4: tryCatchOne(expr, names, parentenv, handlers[[1L]]) 3: tryCatchList(expr, classes, parentenv, handlers) 2: tryCatch({ attr(package, "LibPath") <- which.lib.loc ns <- loadNamespace(package, lib.loc) env <- attachNamespace(ns, pos = pos, deps, exclude, include.only) }, error = function(e) { P <- if (!is.null(cc <- conditionCall(e))) paste(" in", deparse(cc)[1L]) else "" msg <- gettextf("package or namespace load failed for %s%s:\n %s", sQuote(package), P, conditionMessage(e)) if (logical.return && !quietly) message(paste("Error:", msg), domain = NA) else stop(msg, call. = FALSE, domain = NA) }) 1: library(package, lib.loc = lib.loc, charac Execution halted Package: varbvs Check: for missing documentation entries New result: WARNING Error: package or namespace load failed for ‘varbvs’ in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]): there is no package called ‘Rcpp’ Call sequence: 6: stop(msg, call. = FALSE, domain = NA) 5: value[[3L]](cond) 4: tryCatchOne(expr, names, parentenv, handlers[[1L]]) 3: tryCatchList(expr, classes, parentenv, handlers) 2: tryCatch({ attr(package, "LibPath") <- which.lib.loc ns <- loadNamespace(package, lib.loc) env <- attachNamespace(ns, pos = pos, deps, exclude, include.only) }, error = function(e) { P <- if (!is.null(cc <- conditionCall(e))) paste(" in", deparse(cc)[1L]) else "" msg <- gettextf("package or namespace load failed for %s%s:\n %s", sQuote(package), P, conditionMessage(e)) if (logical.return && !quietly) message(paste("Error:", msg), domain = NA) else stop(msg, call. = FALSE, domain = NA) }) 1: library(package, lib.loc = lib.loc, charac Execution halted All user-level objects in a package should have documentation entries. See chapter ‘Writing R documentation files’ in the ‘Writing R Extensions’ manual. Package: varbvs Check: foreign function calls New result: NOTE Error: there is no package called ‘Rcpp’ Call sequence: 13: doWithOneRestart(return(expr), restart) 12: withOneRestart(expr, restarts[[1L]]) 11: withRestarts(stop(cond), retry_loadNamespace = function() NULL) 10: loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) 9: asNamespace(ns) 8: namespaceImportFrom(ns, loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]), i[[2L]], from = package) 7: loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) 6: asNamespace(ns) 5: namespaceImportFrom(ns, loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]), i[[2L]], from = package) 4: loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) 3: asNamespace(ns) 2: namespaceImportFrom(ns, loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]), i[[2L]], from = package) 1: loadNamespace(package, lib.loc) Execution halted See chapter ‘System and foreign language interfaces’ in the ‘Writing R Extensions’ manual. Package: varbvs Check: loading without being on the library search path New result: WARNING Error: package or namespace load failed for ‘varbvs’ in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]): there is no package called ‘Rcpp’ Execution halted It looks like this package has a loading problem when not on .libPaths: see the messages for details. Package: varbvs Check: R code for possible problems New result: NOTE Error: there is no package called ‘Rcpp’ Call sequence: 13: doWithOneRestart(return(expr), restart) 12: withOneRestart(expr, restarts[[1L]]) 11: withRestarts(stop(cond), retry_loadNamespace = function() NULL) 10: loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) 9: asNamespace(ns) 8: namespaceImportFrom(ns, loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]), i[[2L]], from = package) 7: loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) 6: asNamespace(ns) 5: namespaceImportFrom(ns, loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]), i[[2L]], from = package) 4: loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) 3: asNamespace(ns) 2: namespaceImportFrom(ns, loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]), i[[2L]], from = package) 1: loadNamespace(package, lib.loc) Execution halted Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) : there is no package called ‘Rcpp’ Calls: Execution halted Error: there is no package called ‘Rcpp’ Call sequence: 13: doWithOneRestart(return(expr), restart) 12: withOneRestart(expr, restarts[[1L]]) 11: withRestarts(stop(cond), retry_loadNamespace = function() NULL) 10: loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) 9: asNamespace(ns) 8: namespaceImportFrom(ns, loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]), i[[2L]], from = package) 7: loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) 6: asNamespace(ns) 5: namespaceImportFrom(ns, loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]), i[[2L]], from = package) 4: loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) 3: asNamespace(ns) 2: namespaceImportFrom(ns, loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]), i[[2L]], from = package) 1: loadNamespace(package, lib.loc) Execution halted Package: varbvs Check: Rd \usage sections New result: NOTE Error: there is no package called ‘Rcpp’ Call sequence: 13: doWithOneRestart(return(expr), restart) 12: withOneRestart(expr, restarts[[1L]]) 11: withRestarts(stop(cond), retry_loadNamespace = function() NULL) 10: loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) 9: asNamespace(ns) 8: namespaceImportFrom(ns, loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]), i[[2L]], from = package) 7: loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) 6: asNamespace(ns) 5: namespaceImportFrom(ns, loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]), i[[2L]], from = package) 4: loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) 3: asNamespace(ns) 2: namespaceImportFrom(ns, loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]), i[[2L]], from = package) 1: loadNamespace(package, lib.loc) Execution halted The \usage entries for S3 methods should use the \method markup and not their full name. See chapter ‘Writing R documentation files’ in the ‘Writing R Extensions’ manual. Package: varbvs Check: replacement functions New result: WARNING Error: there is no package called ‘Rcpp’ Call sequence: 13: doWithOneRestart(return(expr), restart) 12: withOneRestart(expr, restarts[[1L]]) 11: withRestarts(stop(cond), retry_loadNamespace = function() NULL) 10: loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) 9: asNamespace(ns) 8: namespaceImportFrom(ns, loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]), i[[2L]], from = package) 7: loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) 6: asNamespace(ns) 5: namespaceImportFrom(ns, loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]), i[[2L]], from = package) 4: loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) 3: asNamespace(ns) 2: namespaceImportFrom(ns, loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]), i[[2L]], from = package) 1: loadNamespace(package, lib.loc) Execution halted The argument of a replacement function which corresponds to the right hand side must be named ‘value’. Package: varbvs Check: S3 generic/method consistency New result: WARNING Error: there is no package called ‘Rcpp’ Call sequence: 13: doWithOneRestart(return(expr), restart) 12: withOneRestart(expr, restarts[[1L]]) 11: withRestarts(stop(cond), retry_loadNamespace = function() NULL) 10: loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) 9: asNamespace(ns) 8: namespaceImportFrom(ns, loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]), i[[2L]], from = package) 7: loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) 6: asNamespace(ns) 5: namespaceImportFrom(ns, loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]), i[[2L]], from = package) 4: loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) 3: asNamespace(ns) 2: namespaceImportFrom(ns, loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]), i[[2L]], from = package) 1: loadNamespace(package, lib.loc) Execution halted See section ‘Generic functions and methods’ in the ‘Writing R Extensions’ manual. Package: varbvs Check: tests New result: ERROR Running ‘testthat.R’ [1s/1s] Running the tests in ‘tests/testthat.R’ failed. Complete output: > # Part of the varbvs package, https://github.com/pcarbo/varbvs > # > # Copyright (C) 2012-2018, Peter Carbonetto > # > # This program is free software: you can redistribute it under the > # terms of the GNU General Public License; either version 3 of the > # License, or (at your option) any later version. > # > # This program is distributed in the hope that it will be useful, but > # WITHOUT ANY WARRANY; without even the implied warranty of > # MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. See the GNU > # General Public License for more details. > # > library(testthat) > library(varbvs) Error: package or namespace load failed for 'varbvs' in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]): there is no package called 'Rcpp' Execution halted Package: varycoef Check: HTML version of manual New result: NOTE Skipping checking math rendering: package 'V8' unavailable Package: varycoef Check: re-building of vignette outputs New result: ERROR Error(s) in re-building vignettes: ... --- re-building ‘Introduction.Rmd’ using rmarkdown Quitting from lines 75-83 [help and vignettes] (Introduction.Rmd) Error: processing vignette 'Introduction.Rmd' failed with diagnostics: package or namespace load failed for 'varycoef' in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]): there is no package called 'Rcpp' --- failed re-building ‘Introduction.Rmd’ SUMMARY: processing the following file failed: ‘Introduction.Rmd’ Error: Vignette re-building failed. Execution halted Package: vctsfr Check: re-building of vignette outputs New result: ERROR Error(s) in re-building vignettes: ... --- re-building ‘vctsfr.Rmd’ using rmarkdown ** Processing: /home/hornik/tmp/CRAN_recheck/vctsfr.Rcheck/vign_test/vctsfr/vignettes/vctsfr_files/figure-html/unnamed-chunk-2-1.png 576x288 pixels, 8 bits/pixel, 256 colors in palette Reducing image to 8 bits/pixel, grayscale Input IDAT size = 16837 bytes Input file size = 17719 bytes Trying: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 14960 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 IDAT size = 14891 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 = 14891 Output IDAT size = 14891 bytes (1946 bytes decrease) Output file size = 14969 bytes (2750 bytes = 15.52% decrease) ** Processing: /home/hornik/tmp/CRAN_recheck/vctsfr.Rcheck/vign_test/vctsfr/vignettes/vctsfr_files/figure-html/unnamed-chunk-3-1.png 576x288 pixels, 8 bits/pixel, 256 colors in palette Reducing image to 8 bits/pixel, grayscale Input IDAT size = 15980 bytes Input file size = 16850 bytes Trying: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 14206 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 = 13982 zc = 9 zm = 8 zs = 1 f = 5 IDAT size = 13860 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 = 13860 Output IDAT size = 13860 bytes (2120 bytes decrease) Output file size = 13938 bytes (2912 bytes = 17.28% decrease) Quitting from lines 45-49 [unnamed-chunk-4] (vctsfr.Rmd) Error: processing vignette 'vctsfr.Rmd' failed with diagnostics: package or namespace load failed for 'forecast' in loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]]): there is no package called 'Rcpp' --- failed re-building ‘vctsfr.Rmd’ SUMMARY: processing the following file failed: ‘vctsfr.Rmd’ Error: Vignette re-building failed. Execution halted Package: vsp Check: whether package can be installed New result: ERROR Installation failed. Package: wrapr Check: re-building of vignette outputs New result: ERROR Error(s) in re-building vignettes: ... --- re-building ‘CornerCases.Rmd’ using rmarkdown --- finished re-building ‘CornerCases.Rmd’ --- re-building ‘DebugFnW.Rmd’ using rmarkdown --- finished re-building ‘DebugFnW.Rmd’ --- re-building ‘FrameTools.Rmd’ using rmarkdown --- finished re-building ‘FrameTools.Rmd’ --- re-building ‘Named_Arguments.Rmd’ using rmarkdown --- finished re-building ‘Named_Arguments.Rmd’ --- re-building ‘QuotingConcatinate.Rmd’ using rmarkdown --- finished re-building ‘QuotingConcatinate.Rmd’ +-+QuotingConcatinate.html *** caught segfault *** address 0x5e30, cause 'memory not mapped' An irrecoverable exception occurred. R is aborting now ... Segmentation fault --- re-building ‘SubstitutionModes.Rmd’ using rmarkdown --- finished re-building ‘SubstitutionModes.Rmd’ --- re-building ‘bquote.Rmd’ using rmarkdown ** Processing: /home/hornik/tmp/CRAN_recheck/wrapr.Rcheck/vign_test/wrapr/vignettes/bquote_files/figure-html/unnamed-chunk-2-1.png 288x288 pixels, 8 bits/pixel, 255 colors in palette Reducing image to 8 bits/pixel, grayscale Input IDAT size = 3945 bytes Input file size = 4800 bytes Trying: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 3332 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 = 3332 Output IDAT size = 3332 bytes (613 bytes decrease) Output file size = 3410 bytes (1390 bytes = 28.96% decrease) ** Processing: /home/hornik/tmp/CRAN_recheck/wrapr.Rcheck/vign_test/wrapr/vignettes/bquote_files/figure-html/unnamed-chunk-3-1.png 288x288 pixels, 8 bits/pixel, 255 colors in palette Reducing image to 8 bits/pixel, grayscale Input IDAT size = 3945 bytes Input file size = 4800 bytes Trying: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 3332 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 = 3332 Output IDAT size = 3332 bytes (613 bytes decrease) Output file size = 3410 bytes (1390 bytes = 28.96% decrease) ** Processing: /home/hornik/tmp/CRAN_recheck/wrapr.Rcheck/vign_test/wrapr/vignettes/bquote_files/figure-html/unnamed-chunk-4-1.png 288x288 pixels, 8 bits/pixel, 255 colors in palette Reducing image to 8 bits/pixel, grayscale Input IDAT size = 3945 bytes Input file size = 4800 bytes Trying: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 3332 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 = 3332 Output IDAT size = 3332 bytes (613 bytes decrease) Output file size = 3410 bytes (1390 bytes = 28.96% decrease) --- finished re-building ‘bquote.Rmd’ --- re-building ‘dot_pipe.Rmd’ using rmarkdown --- finished re-building ‘dot_pipe.Rmd’ --- re-building ‘lambda.Rmd’ using rmarkdown --- finished re-building ‘lambda.Rmd’ --- re-building ‘let.Rmd’ using rmarkdown ** Processing: /home/hornik/tmp/CRAN_recheck/wrapr.Rcheck/vign_test/wrapr/vignettes/let_files/figure-html/unnamed-chunk-2-1.png 288x288 pixels, 8 bits/pixel, 256 colors in palette Reducing image to 8 bits/pixel, grayscale Input IDAT size = 5809 bytes Input file size = 6667 bytes Trying: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 5147 zc = 9 zm = 8 zs = 1 f = 0 IDAT size = 5124 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 = 1 f = 0 IDAT size = 5124 Output IDAT size = 5124 bytes (685 bytes decrease) Output file size = 5202 bytes (1465 bytes = 21.97% decrease) ** Processing: /home/hornik/tmp/CRAN_recheck/wrapr.Rcheck/vign_test/wrapr/vignettes/let_files/figure-html/unnamed-chunk-4-1.png 288x288 pixels, 8 bits/pixel, 256 colors in palette Reducing image to 8 bits/pixel, grayscale Input IDAT size = 6458 bytes Input file size = 7316 bytes Trying: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 5791 zc = 9 zm = 8 zs = 1 f = 0 IDAT size = 5734 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 = 1 f = 0 IDAT size = 5734 Output IDAT size = 5734 bytes (724 bytes decrease) Output file size = 5812 bytes (1504 bytes = 20.56% decrease) --- finished re-building ‘let.Rmd’ --- re-building ‘multi_assign.Rmd’ using rmarkdown --- finished re-building ‘multi_assign.Rmd’ --- re-building ‘named_map_builder.Rmd’ using rmarkdown --- finished re-building ‘named_map_builder.Rmd’ --- re-building ‘unpack_multiple_assignment.Rmd’ using rmarkdown --- finished re-building ‘unpack_multiple_assignment.Rmd’ --- re-building ‘wrapr_Eager.Rmd’ using rmarkdown --- finished re-building ‘wrapr_Eager.Rmd’ --- re-building ‘wrapr_applicable.Rmd’ using rmarkdown --- finished re-building ‘wrapr_applicable.Rmd’ --- re-building ‘wrapr_let.pdf.asis’ using asis --- finished re-building ‘wrapr_let.pdf.asis’ --- re-building ‘wrapr_pipe.pdf.asis’ using asis --- finished re-building ‘wrapr_pipe.pdf.asis’ SUMMARY: processing the following file failed: ‘QuotingConcatinate.Rmd’ Error: Vignette re-building failed. Execution halted Package: xesreadR Check: whether package can be installed New result: ERROR Installation failed. Package: yatah Check: whether package can be installed New result: ERROR Installation failed. Package: zonohedra Check: HTML version of manual New result: NOTE Skipping checking math rendering: package 'V8' unavailable Package: zonohedra Check: re-building of vignette outputs New result: ERROR Error(s) in re-building vignettes: ... --- re-building ‘matroids.Rmd’ using rmarkdown --- finished re-building ‘matroids.Rmd’ --- re-building ‘raytrace.Rmd’ using rmarkdown --- finished re-building ‘raytrace.Rmd’ --- re-building ‘transitions.Rmd’ using rmarkdown ** Processing: /home/hornik/tmp/CRAN_recheck/zonohedra.Rcheck/vign_test/zonohedra/vignettes/transitions_files/figure-html/unnamed-chunk-3-1.png 624x384 pixels, 8 bits/pixel, 252 colors in palette Reducing image to 8 bits/pixel, grayscale Input IDAT size = 7037 bytes Input file size = 7883 bytes Trying: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 6286 zc = 9 zm = 8 zs = 1 f = 0 IDAT size = 6264 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 = 1 f = 0 IDAT size = 6264 Output IDAT size = 6264 bytes (773 bytes decrease) Output file size = 6342 bytes (1541 bytes = 19.55% decrease) ** Processing: /home/hornik/tmp/CRAN_recheck/zonohedra.Rcheck/vign_test/zonohedra/vignettes/transitions_files/figure-html/unnamed-chunk-4-1.png 624x384 pixels, 8 bits/pixel, 255 colors in palette Reducing image to 8 bits/pixel, grayscale Input IDAT size = 7978 bytes Input file size = 8833 bytes Trying: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 7014 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 = 7014 Output IDAT size = 7014 bytes (964 bytes decrease) Output file size = 7092 bytes (1741 bytes = 19.71% decrease) Warning in snapshot3d(paste0(name, ".png")) : webshot = TRUE requires the webshot2 package and Chrome browser; using rgl.snapshot() instead ** Processing: /home/hornik/tmp/CRAN_recheck/zonohedra.Rcheck/vign_test/zonohedra/vignettes/transitions_files/figure-html/unnamed-chunk-6-1.png 768x288 pixels, 8 bits/pixel, 256 colors in palette Reducing image to 8 bits/pixel, grayscale Input IDAT size = 11827 bytes Input file size = 12697 bytes Trying: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 10388 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 = 10388 Output IDAT size = 10388 bytes (1439 bytes decrease) Output file size = 10466 bytes (2231 bytes = 17.57% decrease) ** Processing: /home/hornik/tmp/CRAN_recheck/zonohedra.Rcheck/vign_test/zonohedra/vignettes/transitions_files/figure-html/unnamed-chunk-8-1.png 624x288 pixels, 8 bits/pixel, 255 colors in palette Reducing image to 8 bits/pixel, grayscale Input IDAT size = 5790 bytes Input file size = 6645 bytes Trying: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 5069 zc = 9 zm = 8 zs = 1 f = 0 IDAT size = 5059 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 = 1 f = 0 IDAT size = 5059 Output IDAT size = 5059 bytes (731 bytes decrease) Output file size = 5137 bytes (1508 bytes = 22.69% decrease) Warning in snapshot3d(paste0(name, ".png")) : webshot = TRUE requires the webshot2 package and Chrome browser; using rgl.snapshot() instead --- finished re-building ‘transitions.Rmd’ --- re-building ‘zonohedra-guide.Rmd’ using rmarkdown *** caught segfault *** address 0x5556, cause 'memory not mapped' Traceback: 1: dev.off(dv) 2: eng_r(options) 3: block_exec(params) 4: call_block(x) 5: process_group(group) 6: withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), error = function(e) if (xfun::pkg_available("rlang", "1.0.0")) rlang::entrace(e)) 7: xfun:::handle_error(withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), error = function(e) if (xfun::pkg_available("rlang", "1.0.0")) rlang::entrace(e)), function(loc) { setwd(wd) write_utf8(res, output %n% stdout()) paste0("\nQuitting from lines ", loc) }, if (labels[i] != "") sprintf(" [%s]", labels[i]), get_loc) 8: process_file(text, output) 9: knitr::knit(knit_input, knit_output, envir = envir, quiet = quiet) 10: rmarkdown::render(file, encoding = encoding, quiet = quiet, envir = globalenv(), output_dir = getwd(), ...) 11: vweave_rmarkdown(...) 12: engine$weave(file, quiet = quiet, encoding = enc) 13: doTryCatch(return(expr), name, parentenv, handler) 14: tryCatchOne(expr, names, parentenv, handlers[[1L]]) 15: tryCatchList(expr, classes, parentenv, handlers) 16: tryCatch({ engine$weave(file, quiet = quiet, encoding = enc) setwd(startdir) output <- find_vignette_product(name, by = "weave", engine = engine) if (!have.makefile && vignette_is_tex(output)) { texi2pdf(file = output, clean = FALSE, quiet = quiet) output <- find_vignette_product(name, by = "texi2pdf", engine = engine) }}, error = function(e) { OK <<- FALSE message(gettextf("Error: processing vignette '%s' failed with diagnostics:\n%s", file, conditionMessage(e)))}) 17: tools:::.buildOneVignette("zonohedra-guide.Rmd", "/home/hornik/tmp/CRAN_recheck/zonohedra.Rcheck/vign_test/zonohedra", TRUE, FALSE, "zonohedra-guide", "", "/home/hornik/tmp/scratch/Rtmp2kKfYQ/file23695dabb28d6.rds") An irrecoverable exception occurred. R is aborting now ... Segmentation fault During startup - Warning messages: 1: In gzfile(file, "rb") : cannot open compressed file '/home/hornik/tmp/R-d-gcc-14/library/datasets/data/Rdata.rdx', probable reason 'No such file or directory' 2: package ‘datasets’ in options("defaultPackages") was not found --- re-building ‘zonotopes.Rmd’ using rmarkdown ** Processing: /home/hornik/tmp/CRAN_recheck/zonohedra.Rcheck/vign_test/zonohedra/vignettes/zonotopes_files/figure-html/unnamed-chunk-2-1.png 576x384 pixels, 8 bits/pixel, 256 colors in palette Reducing image to 8 bits/pixel, grayscale Input IDAT size = 12933 bytes Input file size = 13803 bytes Trying: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 11806 zc = 9 zm = 8 zs = 1 f = 0 IDAT size = 11793 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 = 1 f = 0 IDAT size = 11793 Output IDAT size = 11793 bytes (1140 bytes decrease) Output file size = 11871 bytes (1932 bytes = 14.00% decrease) ** Processing: /home/hornik/tmp/CRAN_recheck/zonohedra.Rcheck/vign_test/zonohedra/vignettes/zonotopes_files/figure-html/unnamed-chunk-3-1.png 576x384 pixels, 3x8 bits/pixel, RGB Input IDAT size = 36736 bytes Input file size = 36862 bytes Trying: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 29652 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 = 29652 Output IDAT size = 29652 bytes (7084 bytes decrease) Output file size = 29730 bytes (7132 bytes = 19.35% decrease) --- finished re-building ‘zonotopes.Rmd’ SUMMARY: processing the following file failed: ‘zonohedra-guide.Rmd’ Error: Vignette re-building failed. Execution halted Package: ztable Check: whether package can be installed New result: ERROR Installation failed.