Back to Multiple platform build/check report for BioC 3.16: simplified long |
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This page was generated on 2023-04-12 11:05:05 -0400 (Wed, 12 Apr 2023).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo2 | Linux (Ubuntu 20.04.5 LTS) | x86_64 | 4.2.3 (2023-03-15) -- "Shortstop Beagle" | 4502 |
palomino4 | Windows Server 2022 Datacenter | x64 | 4.2.3 (2023-03-15 ucrt) -- "Shortstop Beagle" | 4282 |
lconway | macOS 12.5.1 Monterey | x86_64 | 4.2.3 (2023-03-15) -- "Shortstop Beagle" | 4310 |
Click on any hostname to see more info about the system (e.g. compilers) (*) as reported by 'uname -p', except on Windows and Mac OS X |
To the developers/maintainers of the GeneAccord package: - Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/GeneAccord.git to reflect on this report. See How and When does the builder pull? When will my changes propagate? for more information. - Make sure to use the following settings in order to reproduce any error or warning you see on this page. |
Package 751/2183 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
GeneAccord 1.16.0 (landing page) Ariane L. Moore
| nebbiolo2 | Linux (Ubuntu 20.04.5 LTS) / x86_64 | OK | OK | ERROR | |||||||||
palomino4 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | |||||||||
lconway | macOS 12.5.1 Monterey / x86_64 | OK | OK | OK | OK | |||||||||
Package: GeneAccord |
Version: 1.16.0 |
Command: /home/biocbuild/bbs-3.16-bioc/R/bin/R CMD check --install=check:GeneAccord.install-out.txt --library=/home/biocbuild/bbs-3.16-bioc/R/site-library --timings GeneAccord_1.16.0.tar.gz |
StartedAt: 2023-04-10 20:51:18 -0400 (Mon, 10 Apr 2023) |
EndedAt: 2023-04-10 20:53:49 -0400 (Mon, 10 Apr 2023) |
EllapsedTime: 151.7 seconds |
RetCode: 1 |
Status: ERROR |
CheckDir: GeneAccord.Rcheck |
Warnings: NA |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.16-bioc/R/bin/R CMD check --install=check:GeneAccord.install-out.txt --library=/home/biocbuild/bbs-3.16-bioc/R/site-library --timings GeneAccord_1.16.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.16-bioc/meat/GeneAccord.Rcheck’ * using R version 4.2.3 (2023-03-15) * using platform: x86_64-pc-linux-gnu (64-bit) * using session charset: UTF-8 * checking for file ‘GeneAccord/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘GeneAccord’ version ‘1.16.0’ * package encoding: UTF-8 * 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 hidden files and directories ... OK * checking for portable file names ... OK * checking for sufficient/correct file permissions ... OK * checking whether package ‘GeneAccord’ can be installed ... OK * checking installed package size ... NOTE installed size is 10.0Mb sub-directories of 1Mb or more: data 3.0Mb extdata 6.6Mb * 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 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 ... OK * checking Rd files ... OK * checking Rd metadata ... 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 files in ‘vignettes’ ... OK * checking examples ... OK * checking for unstated dependencies in ‘tests’ ... OK * checking tests ... Running ‘testthat.R’ OK * checking for unstated dependencies in vignettes ... OK * checking package vignettes in ‘inst/doc’ ... OK * checking running R code from vignettes ... ‘GeneAccord.Rmd’ using ‘UTF-8’... OK NONE * checking re-building of vignette outputs ... ERROR Error(s) in re-building vignettes: --- re-building ‘GeneAccord.Rmd’ using rmarkdown ----------- FAILURE REPORT -------------- --- failure: length > 1 in coercion to logical --- --- srcref --- : --- package (from environment) --- GeneAccord --- call from context --- FUN(X[[i]], ...) --- call from argument --- this_beta_distored_rate == 0 && num_clon_excl_this_pair[cnt] == num_trees_this_pair[cnt] --- R stacktrace --- where 1: FUN(X[[i]], ...) where 2: vapply(these_rate_this_pair, function(this_rate) { cnt <- which(these_rate_this_pair == this_rate) this_alpha <- this_rate * beta_distortion this_beta <- (1 - this_rate) * beta_distortion this_beta_distored_rate <- rbeta(1, shape1 = this_alpha, shape2 = this_beta) stopifnot(this_beta_distored_rate >= 0 && this_beta_distored_rate <= 1) if (this_beta_distored_rate == 0 && num_clon_excl_this_pair[cnt] == num_trees_this_pair[cnt]) { stop("[Function: build_null_test_statistic]: The beta", " distorted rate is 0,", "\nbut there is a pair which is clonally ", "exclusive across ALL trees,\ni.e. num_clon_excl", " == num_trees_pair, which is == ", num_trees_this_pair[cnt], ". The computation of the delta\nwill not be", " possible since the likelihood is zero. ", "Make sure that the rates\nare not distorted too", " much by the beta distribution.", "The original rate of\nthe current simulated pair ", "was ", this_rate) } else if (this_beta_distored_rate == 1 && num_clon_excl_this_pair[cnt] == 0) { stop("[Function: build_null_test_statistic]: ", " The beta distorted rate is 1,", ",\nbut there is a pair which is clonally ", "exclusive across ALL trees,\ni.e. num_clon_excl", " == num_trees_pair, which is == ", num_trees_this_pair[cnt], ". The computation of the delta\nwill not be", " possible since the likelihood is zero. ", "Make sure that the rates\nare not distorted too", " much by the beta distribution.", "The original rate of\nthe current simulated pair ", "was ", this_rate) } return(this_beta_distored_rate) }, numeric(1)) where 3: FUN(newX[, i], ...) where 4: apply(pairs_indices_pats_list, 2, function(x) { this_num_pat_this_pair <- length(x) these_rate_this_pair <- avg_rates_m[x] this_hist_sample <- vapply(x, function(y) { num_pairs_this_pat <- length(list_of_clon_excl_frac_trees_all_pats[[1]][[y]]) hist_entry <- sample(num_pairs_this_pat, 1) num_trees_this_pair <- list_of_clon_excl_frac_trees_all_pats[[1]][[y]][hist_entry] num_clon_excl_this_pair <- list_of_clon_excl_frac_trees_all_pats[[2]][[y]][hist_entry] return(c(num_trees_this_pair, num_clon_excl_this_pair)) }, numeric(2)) stopifnot(is.matrix(this_hist_sample)) stopifnot(dim(this_hist_sample)[1] == 2) stopifnot(dim(this_hist_sample)[2] == this_num_pat_this_pair) num_trees_this_pair <- this_hist_sample[1, ] num_clon_excl_this_pair <- this_hist_sample[2, ] beta_distorted_rates <- vapply(these_rate_this_pair, function(this_rate) { cnt <- which(these_rate_this_pair == this_rate) this_alpha <- this_rate * beta_distortion this_beta <- (1 - this_rate) * beta_distortion this_beta_distored_rate <- rbeta(1, shape1 = this_alpha, shape2 = this_beta) stopifnot(this_beta_distored_rate >= 0 && this_beta_distored_rate <= 1) if (this_beta_distored_rate == 0 && num_clon_excl_this_pair[cnt] == num_trees_this_pair[cnt]) { stop("[Function: build_null_test_statistic]: The beta", " distorted rate is 0,", "\nbut there is a pair which is clonally ", "exclusive across ALL trees,\ni.e. num_clon_excl", " == num_trees_pair, which is == ", num_trees_this_pair[cnt], ". The computation of the delta\nwill not be", " possible since the likelihood is zero. ", "Make sure that the rates\nare not distorted too", " much by the beta distribution.", "The original rate of\nthe current simulated pair ", "was ", this_rate) } else if (this_beta_distored_rate == 1 && num_clon_excl_this_pair[cnt] == 0) { stop("[Function: build_null_test_statistic]: ", " The beta distorted rate is 1,", ",\nbut there is a pair which is clonally ", "exclusive across ALL trees,\ni.e. num_clon_excl", " == num_trees_pair, which is == ", num_trees_this_pair[cnt], ". The computation of the delta\nwill not be", " possible since the likelihood is zero. ", "Make sure that the rates\nare not distorted too", " much by the beta distribution.", "The original rate of\nthe current simulated pair ", "was ", this_rate) } return(this_beta_distored_rate) }, numeric(1)) this_lr_test_res <- suppressMessages(compute_test_stat_avg_rate(beta_distorted_rates, num_trees_this_pair, num_clon_excl_this_pair)) this_test_statistic <- this_lr_test_res[[1]] this_delta <- this_lr_test_res[[2]] return(list(this_test_statistic, this_delta, this_num_pat_this_pair, these_rate_this_pair, num_trees_this_pair, num_clon_excl_this_pair, beta_distorted_rates)) }) where 5: build_null_test_statistic(avg_rates_m, list_of_clon_excl_frac_trees_all_pats, num_pat_pair = i, num_pairs_sim = num_pairs_sim, beta_distortion = beta_distortion) where 6: withCallingHandlers(expr, message = function(c) if (inherits(c, classes)) tryInvokeRestart("muffleMessage")) where 7: suppressMessages(build_null_test_statistic(avg_rates_m, list_of_clon_excl_frac_trees_all_pats, num_pat_pair = i, num_pairs_sim = num_pairs_sim, beta_distortion = beta_distortion)) where 8: generate_ecdf_test_stat(avg_rates_m, list_of_num_trees_all_pats, list_of_clon_excl_all_pats, num_pat_pair_max, num_pairs_sim = 100) where 9: eval(expr, envir, enclos) where 10: eval(expr, envir, enclos) where 11: eval_with_user_handlers(expr, envir, enclos, user_handlers) where 12: withVisible(eval_with_user_handlers(expr, envir, enclos, user_handlers)) where 13: withCallingHandlers(withVisible(eval_with_user_handlers(expr, envir, enclos, user_handlers)), warning = wHandler, error = eHandler, message = mHandler) where 14: handle(ev <- withCallingHandlers(withVisible(eval_with_user_handlers(expr, envir, enclos, user_handlers)), warning = wHandler, error = eHandler, message = mHandler)) where 15: timing_fn(handle(ev <- withCallingHandlers(withVisible(eval_with_user_handlers(expr, envir, enclos, user_handlers)), warning = wHandler, error = eHandler, message = mHandler))) where 16: evaluate_call(expr, parsed$src[[i]], envir = envir, enclos = enclos, debug = debug, last = i == length(out), use_try = stop_on_error != 2L, keep_warning = keep_warning, keep_message = keep_message, output_handler = output_handler, include_timing = include_timing) where 17: evaluate::evaluate(...) where 18: evaluate(code, envir = env, new_device = FALSE, keep_warning = if (is.numeric(options$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)) where 19: in_dir(input_dir(), expr) where 20: 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$render, options))) where 21: eng_r(options) where 22: block_exec(params) where 23: call_block(x) where 24: process_group.block(group) where 25: process_group(group) where 26: withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), error = function(e) { setwd(wd) cat(res, sep = "\n", file = output %n% "") message("Quitting from lines ", paste(current_lines(i), collapse = "-"), " (", knit_concord$get("infile"), ") ") }) where 27: process_file(text, output) where 28: knitr::knit(knit_input, knit_output, envir = envir, quiet = quiet) where 29: rmarkdown::render(file, encoding = encoding, quiet = quiet, envir = globalenv(), output_dir = getwd(), ...) where 30: vweave_rmarkdown(...) where 31: engine$weave(file, quiet = quiet, encoding = enc) where 32: doTryCatch(return(expr), name, parentenv, handler) where 33: tryCatchOne(expr, names, parentenv, handlers[[1L]]) where 34: tryCatchList(expr, classes, parentenv, handlers) where 35: tryCatch({ engine$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 36: tools::buildVignettes(dir = "/home/biocbuild/bbs-3.16-bioc/meat/GeneAccord.Rcheck/vign_test/GeneAccord", ser_elibs = "/tmp/Rtmpjc2nDu/file226bfe8e6e9d7.rds") --- value of length: 2 type: logical --- [1] FALSE FALSE --- function from context --- function (this_rate) { cnt <- which(these_rate_this_pair == this_rate) this_alpha <- this_rate * beta_distortion this_beta <- (1 - this_rate) * beta_distortion this_beta_distored_rate <- rbeta(1, shape1 = this_alpha, shape2 = this_beta) stopifnot(this_beta_distored_rate >= 0 && this_beta_distored_rate <= 1) if (this_beta_distored_rate == 0 && num_clon_excl_this_pair[cnt] == num_trees_this_pair[cnt]) { stop("[Function: build_null_test_statistic]: The beta", " distorted rate is 0,", "\nbut there is a pair which is clonally ", "exclusive across ALL trees,\ni.e. num_clon_excl", " == num_trees_pair, which is == ", num_trees_this_pair[cnt], ". The computation of the delta\nwill not be", " possible since the likelihood is zero. ", "Make sure that the rates\nare not distorted too", " much by the beta distribution.", "The original rate of\nthe current simulated pair ", "was ", this_rate) } else if (this_beta_distored_rate == 1 && num_clon_excl_this_pair[cnt] == 0) { stop("[Function: build_null_test_statistic]: ", " The beta distorted rate is 1,", ",\nbut there is a pair which is clonally ", "exclusive across ALL trees,\ni.e. num_clon_excl", " == num_trees_pair, which is == ", num_trees_this_pair[cnt], ". The computation of the delta\nwill not be", " possible since the likelihood is zero. ", "Make sure that the rates\nare not distorted too", " much by the beta distribution.", "The original rate of\nthe current simulated pair ", "was ", this_rate) } return(this_beta_distored_rate) } <bytecode: 0x55b4a2cce6b0> <environment: 0x55b4a0888fb0> --- function search by body --- ----------- END OF FAILURE REPORT -------------- Fatal error: length > 1 in coercion to logical * checking PDF version of manual ... OK * DONE Status: 1 ERROR, 1 NOTE See ‘/home/biocbuild/bbs-3.16-bioc/meat/GeneAccord.Rcheck/00check.log’ for details.
GeneAccord.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.16-bioc/R/bin/R CMD INSTALL GeneAccord ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.16-bioc/R/site-library’ * installing *source* package ‘GeneAccord’ ... ** using staged installation ** R ** data *** moving datasets to lazyload DB ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (GeneAccord)
GeneAccord.Rcheck/tests/testthat.Rout
R version 4.2.3 (2023-03-15) -- "Shortstop Beagle" Copyright (C) 2023 The R Foundation for Statistical Computing Platform: x86_64-pc-linux-gnu (64-bit) 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. > library("testthat") > library("assertthat") > > library("GeneAccord") > # "When R CMD check runs tests, it sets R_TESTS. When the tests > # themeselves run R CMD xxxx, as is the case with the tests in > # devtools, having R_TESTS set causes errors because it confuses > # the R subprocesses. Unsetting it here avoids those problems. > #"R_TESTS" = "" " > Sys.setenv("R_TESTS" = "") > > test_check("GeneAccord") [ FAIL 0 | WARN 9 | SKIP 15 | PASS 27 ] ══ Skipped tests ═══════════════════════════════════════════════════════════════ • empty test (15) [ FAIL 0 | WARN 9 | SKIP 15 | PASS 27 ] > > > proc.time() user system elapsed 13.682 0.465 14.131
GeneAccord.Rcheck/GeneAccord-Ex.timings
name | user | system | elapsed | |
GeneAccord | 1.427 | 0.088 | 1.514 | |
build_null_test_statistic | 1.185 | 0.008 | 1.194 | |
compute_rates_clon_excl | 0.144 | 0.008 | 0.151 | |
compute_test_stat_avg_rate | 0.021 | 0.004 | 0.025 | |
convert_ensembl_to_reactome_pw_tbl | 0.382 | 0.044 | 0.426 | |
create_ensembl_gene_tbl_hg | 0 | 0 | 0 | |
create_tbl_ent_clones | 0.062 | 0.004 | 0.067 | |
create_tbl_tree_collection | 0.244 | 0.012 | 0.260 | |
ecdf_lr_test_clon_excl_avg_rate | 0.506 | 0.000 | 0.507 | |
ensembl_to_hgnc | 0 | 0 | 0 | |
ensembl_to_reactome | 0.016 | 0.000 | 0.015 | |
extract_num_clones_tbl | 0.015 | 0.000 | 0.014 | |
generate_ecdf_test_stat | 0.421 | 0.004 | 0.424 | |
generate_test_stat_hist | 0.553 | 0.004 | 0.556 | |
get_hist_clon_excl | 0.429 | 0.000 | 0.429 | |
get_hist_clon_excl_this_pat_this_pair | 0.016 | 0.000 | 0.016 | |
get_rate_diff_branch_ent_pair | 0.307 | 0.000 | 0.307 | |
heatmap_clones_gene_pat | 0.610 | 0.004 | 0.615 | |
hgnc_to_ensembl | 0 | 0 | 0 | |
is_diff_branch_ent_pair | 0.01 | 0.00 | 0.01 | |
map_pairs_to_hgnc_symbols | 0.001 | 0.000 | 0.000 | |
merge_clones_identical_ents | 0.05 | 0.00 | 0.05 | |
pairs_in_patients_hist | 0.045 | 0.000 | 0.045 | |
plot_ecdf_test_stat | 0.158 | 0.000 | 0.160 | |
plot_rates_clon_excl | 0.208 | 0.000 | 0.208 | |
take_pairs_and_get_patients | 0.162 | 0.000 | 0.162 | |
vis_pval_distr_num_pat | 0.03 | 0.00 | 0.03 | |
write_res_pairs_to_disk | 0.007 | 0.000 | 0.007 | |