* using log directory ‘/data/gannet/ripley/R/packages/tests-LENGTH1/TSTr.Rcheck’ * using R Under development (unstable) (2022-04-26 r82264) * using platform: x86_64-pc-linux-gnu (64-bit) * using session charset: UTF-8 * using option ‘--no-stop-on-test-error’ * checking for file ‘TSTr/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘TSTr’ version ‘1.2’ * checking package namespace information ... OK * checking package dependencies ... OK * checking if this is a source package ... OK * checking if there is a namespace ... OK * checking for executable files ... OK * checking for hidden files and directories ... OK * checking for portable file names ... OK * checking for sufficient/correct file permissions ... OK * checking whether package ‘TSTr’ can be installed ... OK * checking package directory ... OK * checking ‘build’ directory ... OK * checking DESCRIPTION meta-information ... OK * checking top-level files ... OK * checking for left-over files ... OK * checking index information ... OK * checking package subdirectories ... OK * checking R files for non-ASCII characters ... OK * checking R files for syntax errors ... OK * checking whether the package can be loaded ... OK * checking whether the package can be loaded with stated dependencies ... OK * checking whether the package can be unloaded cleanly ... OK * checking whether the namespace can be loaded with stated dependencies ... OK * checking whether the namespace can be unloaded cleanly ... OK * checking loading without being on the library search path ... OK * checking use of S3 registration ... OK * checking dependencies in R code ... OK * checking S3 generic/method consistency ... OK * checking replacement functions ... OK * checking foreign function calls ... OK * checking R code for possible problems ... [8s/14s] OK * checking Rd files ... OK * checking Rd metadata ... OK * checking Rd line widths ... OK * checking Rd cross-references ... OK * checking for missing documentation entries ... OK * checking for code/documentation mismatches ... OK * checking Rd \usage sections ... OK * checking Rd contents ... OK * checking for unstated dependencies in examples ... OK * checking contents of ‘data’ directory ... OK * checking data for non-ASCII characters ... OK * checking LazyData ... OK * checking data for ASCII and uncompressed saves ... OK * checking installed files from ‘inst/doc’ ... OK * checking files in ‘vignettes’ ... OK * checking examples ... OK * checking for unstated dependencies in vignettes ... OK * checking package vignettes in ‘inst/doc’ ... OK * checking re-building of vignette outputs ... [5s/13s] ERROR Error(s) in re-building vignettes: --- re-building ‘TSTr.Rmd’ using rmarkdown ----------- FAILURE REPORT -------------- --- failure: length > 1 in coercion to logical --- --- srcref --- : --- package (from environment) --- TSTr --- call from context --- Addlist(b, str_sub(string, 2, -1), word, b$C[node]) --- call from argument --- is.na(b$C[node]) && (b$flag == 1) --- R stacktrace --- where 1: Addlist(b, str_sub(string, 2, -1), word, b$C[node]) where 2: Addlist(b, string, word, b$L[node]) where 3: Addlist(b, string, word, b$R[node]) where 4: Addlist(b, string, word, b$R[node]) where 5: Addlist(b, str_sub(string, 2, -1), word, b$C[node]) where 6: Addlist(b, str_sub(string, 2, -1), word, b$C[node]) where 7: Addlist(b, string, word, b$L[node]) where 8: Addlist(b, string, word, b$L[node]) where 9: Addlist(arbol, as.character(item), word) where 10: crearFullTree(input, maxdist) where 11: SDkeeper.default(states, 1, useTST = TRUE) where 12: SDkeeper(states, 1, useTST = TRUE) where 13: eval(expr, envir, enclos) where 14: eval(expr, envir, enclos) where 15: eval_with_user_handlers(expr, envir, enclos, user_handlers) where 16: withVisible(eval_with_user_handlers(expr, envir, enclos, user_handlers)) where 17: withCallingHandlers(withVisible(eval_with_user_handlers(expr, envir, enclos, user_handlers)), warning = wHandler, error = eHandler, message = mHandler) where 18: handle(ev <- withCallingHandlers(withVisible(eval_with_user_handlers(expr, envir, enclos, user_handlers)), warning = wHandler, error = eHandler, message = mHandler)) where 19: timing_fn(handle(ev <- withCallingHandlers(withVisible(eval_with_user_handlers(expr, envir, enclos, user_handlers)), warning = wHandler, error = eHandler, message = mHandler))) where 20: evaluate_call(expr, parsed$src[[i]], envir = envir, enclos = enclos, debug = debug, last = i == length(out), use_try = stop_on_error != 2L, keep_warning = keep_warning, keep_message = keep_message, output_handler = output_handler, include_timing = include_timing) where 21: evaluate::evaluate(...) where 22: evaluate(code, envir = env, new_device = FALSE, keep_warning = !isFALSE(options$warning), keep_message = !isFALSE(options$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$render, options)) where 23: in_dir(input_dir(), expr) where 24: in_input_dir(evaluate(code, envir = env, new_device = FALSE, keep_warning = !isFALSE(options$warning), keep_message = !isFALSE(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))) where 25: eng_r(options) where 26: block_exec(params) where 27: call_block(x) where 28: process_group.block(group) where 29: process_group(group) where 30: withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), error = function(e) { setwd(wd) cat(res, sep = "\n", file = output %n% "") message("Quitting from lines ", paste(current_lines(i), collapse = "-"), " (", knit_concord$get("infile"), ") ") }) where 31: process_file(text, output) where 32: knitr::knit(knit_input, knit_output, envir = envir, quiet = quiet) where 33: rmarkdown::render(file, encoding = encoding, quiet = quiet, envir = globalenv(), output_dir = getwd(), ...) where 34: vweave_rmarkdown(...) where 35: engine$weave(file, quiet = quiet, encoding = enc) where 36: doTryCatch(return(expr), name, parentenv, handler) where 37: tryCatchOne(expr, names, parentenv, handlers[[1L]]) where 38: tryCatchList(expr, classes, parentenv, handlers) where 39: 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) } outputs <- c(outputs, output) }, error = function(e) { thisOK <<- FALSE fails <<- c(fails, file) message(gettextf("Error: processing vignette '%s' failed with diagnostics:\n%s", file, conditionMessage(e))) }) where 40: tools:::buildVignettes(dir = "/data/gannet/ripley/R/packages/tests-LENGTH1/TSTr.Rcheck/vign_test/TSTr") --- value of length: 1341 type: logical --- [1] FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE TRUE TRUE FALSE FALSE [13] FALSE FALSE FALSE FALSE FALSE FALSE TRUE FALSE FALSE FALSE FALSE FALSE [25] FALSE FALSE TRUE FALSE FALSE FALSE FALSE FALSE FALSE TRUE FALSE FALSE [37] FALSE FALSE FALSE TRUE FALSE FALSE FALSE FALSE TRUE FALSE FALSE FALSE [49] TRUE FALSE FALSE TRUE FALSE TRUE TRUE FALSE FALSE FALSE FALSE FALSE [61] FALSE FALSE FALSE FALSE FALSE TRUE TRUE FALSE FALSE FALSE FALSE FALSE [73] FALSE FALSE FALSE FALSE FALSE TRUE FALSE FALSE FALSE FALSE FALSE FALSE [85] FALSE FALSE FALSE TRUE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE [97] TRUE FALSE FALSE FALSE FALSE FALSE FALSE FALSE TRUE FALSE FALSE FALSE [109] FALSE FALSE FALSE TRUE FALSE FALSE FALSE FALSE FALSE TRUE FALSE FALSE [121] FALSE FALSE TRUE FALSE FALSE FALSE TRUE FALSE FALSE TRUE FALSE TRUE [133] TRUE FALSE FALSE FALSE FALSE FALSE FALSE TRUE TRUE FALSE FALSE FALSE [145] FALSE FALSE FALSE TRUE FALSE FALSE FALSE FALSE FALSE TRUE FALSE FALSE [157] FALSE FALSE TRUE FALSE FALSE FALSE TRUE FALSE FALSE TRUE FALSE TRUE [169] TRUE FALSE FALSE FALSE FALSE FALSE TRUE TRUE FALSE FALSE FALSE FALSE [181] FALSE TRUE FALSE FALSE FALSE FALSE FALSE TRUE FALSE FALSE FALSE FALSE [193] TRUE FALSE FALSE FALSE TRUE FALSE FALSE TRUE FALSE TRUE TRUE FALSE [205] FALSE FALSE FALSE TRUE TRUE FALSE FALSE FALSE FALSE FALSE TRUE FALSE [217] FALSE FALSE FALSE FALSE TRUE FALSE FALSE FALSE TRUE FALSE FALSE TRUE [229] FALSE TRUE TRUE FALSE FALSE FALSE FALSE TRUE TRUE FALSE FALSE FALSE [241] TRUE FALSE FALSE FALSE TRUE FALSE FALSE TRUE FALSE TRUE FALSE FALSE [253] FALSE FALSE FALSE FALSE FALSE FALSE TRUE TRUE FALSE FALSE FALSE FALSE [265] FALSE FALSE FALSE TRUE FALSE FALSE FALSE FALSE FALSE FALSE FALSE TRUE [277] FALSE FALSE FALSE FALSE FALSE FALSE TRUE FALSE FALSE FALSE FALSE FALSE [289] TRUE FALSE FALSE FALSE FALSE TRUE FALSE FALSE FALSE TRUE FALSE FALSE [301] TRUE FALSE TRUE TRUE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE [313] TRUE TRUE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE TRUE FALSE [325] FALSE FALSE FALSE FALSE FALSE FALSE TRUE FALSE FALSE FALSE FALSE FALSE [337] FALSE TRUE FALSE FALSE FALSE FALSE FALSE TRUE FALSE FALSE FALSE FALSE [349] TRUE FALSE FALSE FALSE TRUE FALSE FALSE TRUE FALSE TRUE TRUE FALSE [361] FALSE FALSE FALSE FALSE FALSE FALSE FALSE TRUE TRUE FALSE FALSE FALSE [373] FALSE FALSE FALSE FALSE FALSE FALSE TRUE FALSE FALSE FALSE FALSE FALSE [385] FALSE FALSE FALSE TRUE FALSE FALSE FALSE FALSE FALSE FALSE TRUE FALSE [397] FALSE FALSE FALSE FALSE TRUE FALSE FALSE FALSE FALSE TRUE FALSE FALSE [409] FALSE TRUE FALSE FALSE TRUE FALSE TRUE TRUE FALSE FALSE FALSE FALSE [421] FALSE TRUE TRUE FALSE FALSE FALSE FALSE TRUE FALSE FALSE FALSE FALSE [433] TRUE FALSE FALSE FALSE TRUE FALSE FALSE TRUE FALSE TRUE TRUE FALSE [445] FALSE FALSE FALSE FALSE FALSE FALSE TRUE TRUE FALSE FALSE FALSE FALSE [457] FALSE FALSE TRUE FALSE FALSE FALSE FALSE FALSE FALSE TRUE FALSE FALSE [469] FALSE FALSE FALSE TRUE FALSE FALSE FALSE FALSE TRUE FALSE FALSE FALSE [481] TRUE FALSE FALSE TRUE FALSE TRUE TRUE FALSE FALSE FALSE FALSE FALSE [493] TRUE TRUE FALSE FALSE FALSE FALSE FALSE TRUE FALSE FALSE FALSE FALSE [505] TRUE FALSE FALSE FALSE TRUE FALSE FALSE TRUE FALSE TRUE TRUE FALSE [517] FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE TRUE TRUE FALSE [529] FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE TRUE FALSE FALSE FALSE [541] FALSE FALSE FALSE FALSE FALSE FALSE TRUE FALSE FALSE FALSE FALSE FALSE [553] FALSE FALSE TRUE FALSE FALSE FALSE FALSE FALSE FALSE TRUE FALSE FALSE [565] FALSE FALSE FALSE TRUE FALSE FALSE FALSE FALSE TRUE FALSE FALSE FALSE [577] TRUE FALSE FALSE TRUE FALSE TRUE TRUE FALSE FALSE FALSE FALSE FALSE [589] TRUE TRUE FALSE FALSE FALSE FALSE TRUE FALSE FALSE FALSE FALSE TRUE [601] FALSE FALSE FALSE TRUE FALSE FALSE TRUE FALSE TRUE TRUE FALSE FALSE [613] FALSE FALSE FALSE TRUE TRUE FALSE FALSE FALSE FALSE FALSE FALSE TRUE [625] FALSE FALSE FALSE FALSE FALSE FALSE TRUE FALSE FALSE FALSE FALSE FALSE [637] FALSE TRUE FALSE FALSE FALSE FALSE FALSE TRUE FALSE FALSE FALSE TRUE [649] FALSE FALSE TRUE TRUE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE [661] FALSE TRUE TRUE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE [673] TRUE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE TRUE FALSE [685] FALSE FALSE FALSE FALSE FALSE FALSE FALSE TRUE FALSE FALSE FALSE FALSE [697] FALSE FALSE FALSE TRUE FALSE FALSE FALSE FALSE FALSE FALSE TRUE FALSE [709] FALSE FALSE FALSE FALSE TRUE FALSE FALSE FALSE FALSE TRUE FALSE FALSE [721] FALSE TRUE FALSE FALSE TRUE FALSE TRUE TRUE FALSE FALSE FALSE TRUE [733] TRUE FALSE FALSE FALSE TRUE FALSE FALSE TRUE FALSE TRUE TRUE FALSE [745] FALSE FALSE FALSE FALSE TRUE TRUE FALSE FALSE FALSE FALSE FALSE TRUE [757] FALSE FALSE FALSE FALSE TRUE FALSE FALSE FALSE TRUE FALSE FALSE TRUE [769] FALSE TRUE TRUE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE [781] TRUE TRUE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE TRUE [793] FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE TRUE FALSE FALSE FALSE [805] FALSE FALSE FALSE FALSE FALSE TRUE FALSE FALSE FALSE FALSE FALSE FALSE [817] FALSE TRUE FALSE FALSE FALSE FALSE FALSE FALSE TRUE FALSE FALSE FALSE [829] FALSE FALSE TRUE FALSE FALSE FALSE FALSE TRUE FALSE FALSE FALSE TRUE [841] FALSE FALSE TRUE TRUE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE [853] FALSE FALSE TRUE TRUE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE [865] FALSE FALSE TRUE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE [877] TRUE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE TRUE FALSE [889] FALSE FALSE FALSE FALSE FALSE FALSE FALSE TRUE FALSE FALSE FALSE FALSE [901] FALSE FALSE FALSE TRUE FALSE FALSE FALSE FALSE FALSE FALSE TRUE FALSE [913] FALSE FALSE FALSE FALSE TRUE FALSE FALSE FALSE FALSE TRUE FALSE FALSE [925] FALSE TRUE FALSE FALSE TRUE FALSE TRUE TRUE FALSE FALSE TRUE TRUE [937] FALSE TRUE FALSE TRUE TRUE FALSE FALSE FALSE FALSE TRUE TRUE FALSE [949] FALSE FALSE FALSE FALSE TRUE FALSE FALSE FALSE FALSE TRUE FALSE FALSE [961] FALSE FALSE TRUE FALSE FALSE FALSE TRUE FALSE FALSE TRUE FALSE TRUE [973] TRUE FALSE TRUE TRUE FALSE TRUE FALSE TRUE TRUE FALSE TRUE TRUE [985] FALSE FALSE TRUE FALSE TRUE FALSE TRUE TRUE FALSE FALSE FALSE FALSE [997] TRUE TRUE FALSE FALSE FALSE FALSE FALSE TRUE FALSE FALSE FALSE FALSE [1009] FALSE TRUE FALSE FALSE FALSE FALSE TRUE FALSE FALSE FALSE TRUE FALSE [1021] FALSE TRUE FALSE TRUE TRUE FALSE FALSE FALSE FALSE TRUE TRUE FALSE [1033] FALSE FALSE TRUE FALSE FALSE FALSE FALSE TRUE FALSE FALSE FALSE TRUE [1045] FALSE FALSE TRUE FALSE TRUE TRUE FALSE FALSE FALSE FALSE TRUE TRUE [1057] FALSE FALSE FALSE FALSE FALSE TRUE FALSE FALSE FALSE FALSE FALSE TRUE [1069] FALSE FALSE FALSE FALSE TRUE FALSE FALSE FALSE TRUE FALSE FALSE TRUE [1081] FALSE TRUE TRUE FALSE FALSE FALSE FALSE FALSE FALSE TRUE TRUE FALSE [1093] FALSE FALSE FALSE FALSE FALSE FALSE TRUE FALSE FALSE FALSE FALSE FALSE [1105] FALSE FALSE TRUE FALSE FALSE FALSE FALSE FALSE FALSE FALSE TRUE FALSE [1117] FALSE FALSE FALSE FALSE FALSE FALSE TRUE FALSE FALSE FALSE FALSE FALSE [1129] FALSE FALSE TRUE FALSE FALSE FALSE FALSE FALSE FALSE FALSE TRUE FALSE [1141] FALSE FALSE FALSE FALSE TRUE FALSE FALSE FALSE FALSE FALSE TRUE FALSE [1153] FALSE FALSE FALSE TRUE FALSE FALSE FALSE TRUE FALSE FALSE TRUE FALSE [1165] TRUE TRUE FALSE FALSE FALSE FALSE TRUE TRUE FALSE FALSE FALSE FALSE [1177] FALSE TRUE FALSE FALSE FALSE TRUE FALSE FALSE FALSE TRUE FALSE FALSE [1189] TRUE FALSE TRUE TRUE FALSE FALSE FALSE FALSE TRUE TRUE FALSE FALSE [1201] FALSE FALSE FALSE TRUE FALSE FALSE FALSE FALSE FALSE TRUE FALSE FALSE [1213] FALSE FALSE FALSE TRUE FALSE FALSE FALSE FALSE FALSE TRUE FALSE FALSE [1225] FALSE TRUE FALSE FALSE FALSE TRUE FALSE FALSE TRUE FALSE TRUE TRUE [1237] FALSE FALSE FALSE TRUE TRUE FALSE FALSE FALSE TRUE FALSE FALSE FALSE [1249] TRUE FALSE FALSE TRUE FALSE TRUE TRUE FALSE FALSE FALSE FALSE TRUE [1261] TRUE FALSE FALSE FALSE FALSE TRUE FALSE FALSE FALSE FALSE TRUE FALSE [1273] FALSE FALSE TRUE FALSE FALSE TRUE FALSE TRUE TRUE FALSE FALSE FALSE [1285] FALSE FALSE FALSE TRUE TRUE FALSE FALSE FALSE FALSE FALSE TRUE FALSE [1297] FALSE FALSE FALSE FALSE TRUE FALSE FALSE FALSE FALSE FALSE TRUE FALSE [1309] FALSE FALSE FALSE TRUE FALSE FALSE FALSE TRUE FALSE FALSE TRUE FALSE [1321] TRUE TRUE FALSE FALSE FALSE FALSE FALSE TRUE FALSE FALSE FALSE FALSE [1333] FALSE FALSE TRUE FALSE FALSE FALSE FALSE FALSE TRUE --- function from context --- function (tree, string, word, node = 1) { b <- tree key <- str_sub(string, 1, 1) if (is.na(b$ch[node])) { b$ch[node] <- key b$flag[node] <- 0 } if (key < b$ch[node]) { if (is.na(b$L[node])) { b$L[node] <- length(b$ch) + 1 b <- Addlist(b, string, word, b$L[node]) } else { b <- Addlist(b, string, word, b$L[node]) } } else if (key > b$ch[node]) { if (is.na(b$R[node])) { b$R[node] <- length(b$ch) + 1 b <- Addlist(b, string, word, b$R[node]) } else { b <- Addlist(b, string, word, b$R[node]) } } else { if (nchar(string) == 1) { b$flag[node] <- 1 if (length(b$word) < node) { b$word[[node]] <- word } else { b$word[[node]] <- append(b$word[[node]], word) } } else { if (!is.na(b$C[node]) || !is.na(b$L[node]) || !is.na(b$R[node])) { if (is.na(b$C[node]) && (b$flag == 1)) { b$C[node] <- length(b$ch) + 1 b <- Addlist(b, str_sub(string, 2, -1), word, b$C[node]) } else if (is.na(b$C[node]) && (b$flag == 0)) { b$C[node] <- node + 1 b <- Addlist(b, str_sub(string, 2, -1), word, b$C[node]) } else { b <- Addlist(b, str_sub(string, 2, -1), word, b$C[node]) } } else { b$C[node] <- length(b$ch) + 1 b <- Addlist(b, str_sub(string, 2, -1), word, b$C[node]) } } } return(b) } --- function search by body --- Function Addlist in namespace TSTr has this body. ----------- END OF FAILURE REPORT -------------- Fatal error: length > 1 in coercion to logical * checking PDF version of manual ... OK * checking for non-standard things in the check directory ... NOTE Found the following files/directories: ‘XMIwords.txt’ * checking for detritus in the temp directory ... OK * DONE Status: 1 ERROR, 1 NOTE See ‘/data/gannet/ripley/R/packages/tests-LENGTH1/TSTr.Rcheck/00check.log’ for details. Command exited with non-zero status 1 Time 1:36.03, 46.16 + 7.58