Last updated on 2020-03-27 00:49:16 CET.
| Flavor | Version | Tinstall | Tcheck | Ttotal | Status | Flags |
|---|---|---|---|---|---|---|
| r-devel-linux-x86_64-debian-clang | 0.3.7 | 12.99 | 135.27 | 148.26 | NOTE | |
| r-devel-linux-x86_64-debian-gcc | 0.3.7 | 12.04 | 103.80 | 115.84 | NOTE | |
| r-devel-linux-x86_64-fedora-clang | 0.3.7 | 158.89 | ERROR | |||
| r-devel-linux-x86_64-fedora-gcc | 0.3.7 | 152.98 | ERROR | |||
| r-devel-windows-ix86+x86_64 | 0.3.7 | 47.00 | 172.00 | 219.00 | NOTE | |
| r-devel-windows-ix86+x86_64-gcc8 | 0.3.7 | 49.00 | 184.00 | 233.00 | NOTE | |
| r-patched-linux-x86_64 | 0.3.7 | 10.50 | 123.10 | 133.60 | OK | |
| r-patched-solaris-x86 | 0.3.7 | 241.30 | NOTE | |||
| r-release-linux-x86_64 | 0.3.7 | 11.51 | 120.57 | 132.08 | OK | |
| r-release-windows-ix86+x86_64 | 0.3.7 | 83.00 | 291.00 | 374.00 | NOTE | |
| r-release-osx-x86_64 | 0.3.7 | NOTE | ||||
| r-oldrel-windows-ix86+x86_64 | 0.3.7 | 62.00 | 234.00 | 296.00 | NOTE | |
| r-oldrel-osx-x86_64 | 0.3.7 | NOTE |
Version: 0.3.7
Check: for non-standard things in the check directory
Result: NOTE
Found the following files/directories:
'GRCh37_MT_ensGene.txt'
Flavors: r-devel-linux-x86_64-debian-clang, r-devel-linux-x86_64-debian-gcc, r-devel-linux-x86_64-fedora-clang, r-devel-linux-x86_64-fedora-gcc, r-patched-solaris-x86
Version: 0.3.7
Check: installed package size
Result: NOTE
installed size is 11.7Mb
sub-directories of 1Mb or more:
doc 2.5Mb
extdata 8.7Mb
Flavors: r-devel-linux-x86_64-fedora-clang, r-devel-windows-ix86+x86_64, r-devel-windows-ix86+x86_64-gcc8, r-patched-solaris-x86, r-release-windows-ix86+x86_64, r-release-osx-x86_64, r-oldrel-windows-ix86+x86_64, r-oldrel-osx-x86_64
Version: 0.3.7
Check: tests
Result: ERROR
Running ‘testthat.R’
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
> library(testthat)
> library(BioInstaller)
>
>
> test_check("BioInstaller")
cloning into '/tmp/RtmpgkVlJq/working_dir/Rtmpw1YlZE/github_demo0'...
*** caught segfault ***
address 0xc800010009, cause 'memory not mapped'
Traceback:
1: git2r::clone(github_url, destdir)
2: git.download(name, download.dir, version, github_url, use_git2r, recursive_clone, verbose)
3: install.github(name = "github_demo", destdir = destdir, download.dir = destdir, verbose = F)
4: eval(code, test_env)
5: eval(code, test_env)
6: withCallingHandlers({ eval(code, test_env) if (!handled && !is.null(test)) { skip_empty() }}, expectation = handle_expectation, skip = handle_skip, warning = handle_warning, message = handle_message, error = handle_error)
7: doTryCatch(return(expr), name, parentenv, handler)
8: tryCatchOne(expr, names, parentenv, handlers[[1L]])
9: tryCatchList(expr, names[-nh], parentenv, handlers[-nh])
10: doTryCatch(return(expr), name, parentenv, handler)
11: tryCatchOne(tryCatchList(expr, names[-nh], parentenv, handlers[-nh]), names[nh], parentenv, handlers[[nh]])
12: tryCatchList(expr, classes, parentenv, handlers)
13: tryCatch(withCallingHandlers({ eval(code, test_env) if (!handled && !is.null(test)) { skip_empty() }}, expectation = handle_expectation, skip = handle_skip, warning = handle_warning, message = handle_message, error = handle_error), error = handle_fatal, skip = function(e) { })
14: test_code(desc, code, env = parent.frame())
15: test_that("install.github", { x <- tryCatch(RCurl::getURL("https://github.com"), error = function(e) { message("Connect Github failed. Please check the network.") NULL }) if (!is.null(x)) { destdir <- sprintf("%s/github_demo0", tempdir()) destdir <- normalizePath(destdir, "/", FALSE) x <- install.github(name = "github_demo", destdir = destdir, download.dir = destdir, verbose = F) expect_that(x, equals(TRUE)) unlink(destdir, recursive = T, TRUE) destdir <- sprintf("%s/github_demo1", tempdir()) destdir <- normalizePath(destdir, "/", FALSE) x <- suppressWarnings(install.github(show.all.versions = T, verbose = F)) expect_that(x, equals(FALSE)) destdir <- sprintf("%s/bwa", tempdir()) destdir <- normalizePath(destdir, "/", FALSE) x <- install.github(name = "bwa", show.all.versions = T, verbose = F) expect_that(is.character(x), equals(TRUE)) unlink(destdir, recursive = T, TRUE) x <- tryCatch(install.github(name = list(), show.all.versions = T, verbose = F), error = function(e) { return(FALSE) }) expect_that(is.character(x), equals(FALSE)) unlink(destdir, recursive = T, TRUE) destdir <- sprintf("%s/github_demo2", tempdir()) destdir <- normalizePath(destdir, "/", FALSE) x <- install.github(name = "github_demo", destdir = destdir, download.dir = destdir, verbose = F, download.only = TRUE) expect_that(x, equals(TRUE)) unlink(destdir, recursive = T, TRUE) } else { message("Please check RCurl::getURL('https://github.com')") }})
16: eval(code, test_env)
17: eval(code, test_env)
18: withCallingHandlers({ eval(code, test_env) if (!handled && !is.null(test)) { skip_empty() }}, expectation = handle_expectation, skip = handle_skip, warning = handle_warning, message = handle_message, error = handle_error)
19: doTryCatch(return(expr), name, parentenv, handler)
20: tryCatchOne(expr, names, parentenv, handlers[[1L]])
21: tryCatchList(expr, names[-nh], parentenv, handlers[-nh])
22: doTryCatch(return(expr), name, parentenv, handler)
23: tryCatchOne(tryCatchList(expr, names[-nh], parentenv, handlers[-nh]), names[nh], parentenv, handlers[[nh]])
24: tryCatchList(expr, classes, parentenv, handlers)
25: tryCatch(withCallingHandlers({ eval(code, test_env) if (!handled && !is.null(test)) { skip_empty() }}, expectation = handle_expectation, skip = handle_skip, warning = handle_warning, message = handle_message, error = handle_error), error = handle_fatal, skip = function(e) { })
26: test_code(NULL, exprs, env)
27: source_file(path, new.env(parent = env), chdir = TRUE, wrap = wrap)
28: force(code)
29: doWithOneRestart(return(expr), restart)
30: withOneRestart(expr, restarts[[1L]])
31: withRestarts(testthat_abort_reporter = function() NULL, force(code))
32: with_reporter(reporter = reporter, start_end_reporter = start_end_reporter, { reporter$start_file(basename(path)) lister$start_file(basename(path)) source_file(path, new.env(parent = env), chdir = TRUE, wrap = wrap) reporter$.end_context() reporter$end_file() })
33: FUN(X[[i]], ...)
34: lapply(paths, test_file, env = env, reporter = current_reporter, start_end_reporter = FALSE, load_helpers = FALSE, wrap = wrap)
35: force(code)
36: doWithOneRestart(return(expr), restart)
37: withOneRestart(expr, restarts[[1L]])
38: withRestarts(testthat_abort_reporter = function() NULL, force(code))
39: with_reporter(reporter = current_reporter, results <- lapply(paths, test_file, env = env, reporter = current_reporter, start_end_reporter = FALSE, load_helpers = FALSE, wrap = wrap))
40: test_files(paths, reporter = reporter, env = env, stop_on_failure = stop_on_failure, stop_on_warning = stop_on_warning, wrap = wrap)
41: test_dir(path = test_path, reporter = reporter, env = env, filter = filter, ..., stop_on_failure = stop_on_failure, stop_on_warning = stop_on_warning, wrap = wrap)
42: test_package_dir(package = package, test_path = test_path, filter = filter, reporter = reporter, ..., stop_on_failure = stop_on_failure, stop_on_warning = stop_on_warning, wrap = wrap)
43: test_check("BioInstaller")
An irrecoverable exception occurred. R is aborting now ...
Flavor: r-devel-linux-x86_64-fedora-clang
Version: 0.3.7
Check: re-building of vignette outputs
Result: WARN
Error(s) in re-building vignettes:
sh: line 1: 19126 Segmentation fault (core dumped) R_LIBS=/tmp/RtmpgkVlJq/RLIBS_ade8406df629 R_ENVIRON_USER='' R_LIBS_USER='' R_LIBS_SITE='no_such_dir' '/data/gannet/ripley/R/R-clang/bin/R' --vanilla --no-echo > '/tmp/RtmpgkVlJq/working_dir/RtmpxGTX7j/file4a7174562fb5' 2>&1 < '/tmp/RtmpgkVlJq/working_dir/RtmpxGTX7j/file4a716dce68e6'
--- re-building ‘BioInstaller.Rmd’ using rmarkdown
trying URL 'https://raw.githubusercontent.com/Miachol/ftp/master/files/GRCh37_MT_ensGene.txt'
Content type 'text/plain; charset=utf-8' length 3131 bytes
==================================================
downloaded 3131 bytes
trying URL 'https://raw.githubusercontent.com/Miachol/ftp/master/files/GRCh37_MT_ensGene.txt'
Content type 'text/plain; charset=utf-8' length 3131 bytes
==================================================
downloaded 3131 bytes
trying URL 'https://raw.githubusercontent.com/Miachol/ftp/master/files/GRCh37_MT_ensGene.txt'
Content type 'text/plain; charset=utf-8' length 3131 bytes
==================================================
downloaded 3131 bytes
trying URL 'https://raw.githubusercontent.com/Miachol/ftp/master/files/GRCh37_MT_ensGene.txt'
Content type 'text/plain; charset=utf-8' length 3131 bytes
==================================================
downloaded 3131 bytes
*** caught segfault ***
address 0xc800010009, cause 'memory not mapped'
Traceback:
1: git2r::clone(github_url, destdir)
2: git.download(name, download.dir, version, github_url, use_git2r, recursive_clone, verbose)
3: install.github(name = i, destdir = destdir[count], download.dir = download.dir[count], github.cfg = github.cfg, name.saved = name.saved[count], version = version[count], local.source = local.source[count], show.all.versions = show.all.versions, db = db, download.only = download.only, verbose = verbose, showWarnings = showWarnings, dependence.need = dependence.need, extra.list = extra.list, rmcd.parse = rcmd.parse, bash.parse = bash.parse, glue.parse = glue.parse, glue.flag = glue.flag, save.to.db = save.to.db, overwrite = overwrite, ...)
4: install.bioinfo("github_demo", download.dir = download.dir, download.only = TRUE, verbose = FALSE)
5: doTryCatch(return(expr), name, parentenv, handler)
6: tryCatchOne(expr, names, parentenv, handlers[[1L]])
7: tryCatchList(expr, classes, parentenv, handlers)
8: tryCatch({ install.bioinfo("github_demo", download.dir = download.dir, download.only = TRUE, verbose = FALSE) install.bioinfo("github_demo", local.source = download.dir)}, error = function(e) { message("Please check the SSL or connection with GitHub")})
9: eval(expr, envir, enclos)
10: eval(expr, envir, enclos)
11: withVisible(eval(expr, envir, enclos))
12: withCallingHandlers(withVisible(eval(expr, envir, enclos)), warning = wHandler, error = eHandler, message = mHandler)
13: handle(ev <- withCallingHandlers(withVisible(eval(expr, envir, enclos)), warning = wHandler, error = eHandler, message = mHandler))
14: timing_fn(handle(ev <- withCallingHandlers(withVisible(eval(expr, envir, enclos)), warning = wHandler, error = eHandler, message = mHandler)))
15: evaluate_call(expr, parsed$src[[i]], envir = envir, enclos = enclos, debug = debug, last = i == length(out), use_try = stop_on_error != 2L, keep_warning = keep_warning, keep_message = keep_message, output_handler = output_handler, include_timing = include_timing)
16: evaluate::evaluate(...)
17: evaluate(code, envir = env, new_device = FALSE, keep_warning = !isFALSE(options$warning), keep_message = !isFALSE(options$message), stop_on_error = if (options$error && options$include) 0L else 2L, output_handler = knit_handlers(options$render, options))
18: in_dir(input_dir(), evaluate(code, envir = env, new_device = FALSE, keep_warning = !isFALSE(options$warning), keep_message = !isFALSE(options$message), stop_on_error = if (options$error && options$include) 0L else 2L, output_handler = knit_handlers(options$render, options)))
19: block_exec(params)
20: call_block(x)
21: process_group.block(group)
22: process_group(group)
23: withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), error = function(e) { setwd(wd) cat(res, sep = "\n", file = output %n% "") message("Quitting from lines ", paste(current_lines(i), collapse = "-"), " (", knit_concord$get("infile"), ") ") })
24: process_file(text, output)
25: knitr::knit(knit_input, knit_output, envir = envir, quiet = quiet)
26: rmarkdown::render(file, encoding = encoding, quiet = quiet, envir = globalenv(), output_dir = getwd(), ...)
27: vweave_rmarkdown(...)
28: engine$weave(file, quiet = quiet, encoding = enc)
29: doTryCatch(return(expr), name, parentenv, handler)
30: tryCatchOne(expr, names, parentenv, handlers[[1L]])
31: tryCatchList(expr, classes, parentenv, handlers)
32: tryCatch({ engine$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)))})
33: tools:::.buildOneVignette("BioInstaller.Rmd", "/data/gannet/ripley/R/packages/tests-clang/BioInstaller.Rcheck/vign_test/BioInstaller", TRUE, FALSE, "BioInstaller", "UTF-8", "/tmp/RtmpgkVlJq/working_dir/RtmpxGTX7j/file4a715abd2596.rds")
An irrecoverable exception occurred. R is aborting now ...
--- re-building ‘download.Rmd’ using rmarkdown
--- finished re-building ‘download.Rmd’
--- re-building ‘items_description.Rmd’ using rmarkdown
--- finished re-building ‘items_description.Rmd’
--- re-building ‘plugins_of_BioInstaller_shiny.Rmd’ using rmarkdown
--- finished re-building ‘plugins_of_BioInstaller_shiny.Rmd’
--- re-building ‘start_shiny_of_BioInstaller.Rmd’ using rmarkdown
--- finished re-building ‘start_shiny_of_BioInstaller.Rmd’
--- re-building ‘write_configuration_file.Rmd’ using rmarkdown
--- finished re-building ‘write_configuration_file.Rmd’
SUMMARY: processing the following file failed:
‘BioInstaller.Rmd’
Error: Vignette re-building failed.
Execution halted
Flavor: r-devel-linux-x86_64-fedora-clang
Version: 0.3.7
Check: tests
Result: ERROR
Running ‘testthat.R’
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
> library(testthat)
> library(BioInstaller)
>
>
> test_check("BioInstaller")
cloning into '/tmp/RtmpoR0Zxj/working_dir/Rtmpwb7IWL/github_demo0'...
*** caught segfault ***
address 0xc800010009, cause 'memory not mapped'
Traceback:
1: git2r::clone(github_url, destdir)
2: git.download(name, download.dir, version, github_url, use_git2r, recursive_clone, verbose)
3: install.github(name = "github_demo", destdir = destdir, download.dir = destdir, verbose = F)
4: eval(code, test_env)
5: eval(code, test_env)
6: withCallingHandlers({ eval(code, test_env) if (!handled && !is.null(test)) { skip_empty() }}, expectation = handle_expectation, skip = handle_skip, warning = handle_warning, message = handle_message, error = handle_error)
7: doTryCatch(return(expr), name, parentenv, handler)
8: tryCatchOne(expr, names, parentenv, handlers[[1L]])
9: tryCatchList(expr, names[-nh], parentenv, handlers[-nh])
10: doTryCatch(return(expr), name, parentenv, handler)
11: tryCatchOne(tryCatchList(expr, names[-nh], parentenv, handlers[-nh]), names[nh], parentenv, handlers[[nh]])
12: tryCatchList(expr, classes, parentenv, handlers)
13: tryCatch(withCallingHandlers({ eval(code, test_env) if (!handled && !is.null(test)) { skip_empty() }}, expectation = handle_expectation, skip = handle_skip, warning = handle_warning, message = handle_message, error = handle_error), error = handle_fatal, skip = function(e) { })
14: test_code(desc, code, env = parent.frame())
15: test_that("install.github", { x <- tryCatch(RCurl::getURL("https://github.com"), error = function(e) { message("Connect Github failed. Please check the network.") NULL }) if (!is.null(x)) { destdir <- sprintf("%s/github_demo0", tempdir()) destdir <- normalizePath(destdir, "/", FALSE) x <- install.github(name = "github_demo", destdir = destdir, download.dir = destdir, verbose = F) expect_that(x, equals(TRUE)) unlink(destdir, recursive = T, TRUE) destdir <- sprintf("%s/github_demo1", tempdir()) destdir <- normalizePath(destdir, "/", FALSE) x <- suppressWarnings(install.github(show.all.versions = T, verbose = F)) expect_that(x, equals(FALSE)) destdir <- sprintf("%s/bwa", tempdir()) destdir <- normalizePath(destdir, "/", FALSE) x <- install.github(name = "bwa", show.all.versions = T, verbose = F) expect_that(is.character(x), equals(TRUE)) unlink(destdir, recursive = T, TRUE) x <- tryCatch(install.github(name = list(), show.all.versions = T, verbose = F), error = function(e) { return(FALSE) }) expect_that(is.character(x), equals(FALSE)) unlink(destdir, recursive = T, TRUE) destdir <- sprintf("%s/github_demo2", tempdir()) destdir <- normalizePath(destdir, "/", FALSE) x <- install.github(name = "github_demo", destdir = destdir, download.dir = destdir, verbose = F, download.only = TRUE) expect_that(x, equals(TRUE)) unlink(destdir, recursive = T, TRUE) } else { message("Please check RCurl::getURL('https://github.com')") }})
16: eval(code, test_env)
17: eval(code, test_env)
18: withCallingHandlers({ eval(code, test_env) if (!handled && !is.null(test)) { skip_empty() }}, expectation = handle_expectation, skip = handle_skip, warning = handle_warning, message = handle_message, error = handle_error)
19: doTryCatch(return(expr), name, parentenv, handler)
20: tryCatchOne(expr, names, parentenv, handlers[[1L]])
21: tryCatchList(expr, names[-nh], parentenv, handlers[-nh])
22: doTryCatch(return(expr), name, parentenv, handler)
23: tryCatchOne(tryCatchList(expr, names[-nh], parentenv, handlers[-nh]), names[nh], parentenv, handlers[[nh]])
24: tryCatchList(expr, classes, parentenv, handlers)
25: tryCatch(withCallingHandlers({ eval(code, test_env) if (!handled && !is.null(test)) { skip_empty() }}, expectation = handle_expectation, skip = handle_skip, warning = handle_warning, message = handle_message, error = handle_error), error = handle_fatal, skip = function(e) { })
26: test_code(NULL, exprs, env)
27: source_file(path, new.env(parent = env), chdir = TRUE, wrap = wrap)
28: force(code)
29: doWithOneRestart(return(expr), restart)
30: withOneRestart(expr, restarts[[1L]])
31: withRestarts(testthat_abort_reporter = function() NULL, force(code))
32: with_reporter(reporter = reporter, start_end_reporter = start_end_reporter, { reporter$start_file(basename(path)) lister$start_file(basename(path)) source_file(path, new.env(parent = env), chdir = TRUE, wrap = wrap) reporter$.end_context() reporter$end_file() })
33: FUN(X[[i]], ...)
34: lapply(paths, test_file, env = env, reporter = current_reporter, start_end_reporter = FALSE, load_helpers = FALSE, wrap = wrap)
35: force(code)
36: doWithOneRestart(return(expr), restart)
37: withOneRestart(expr, restarts[[1L]])
38: withRestarts(testthat_abort_reporter = function() NULL, force(code))
39: with_reporter(reporter = current_reporter, results <- lapply(paths, test_file, env = env, reporter = current_reporter, start_end_reporter = FALSE, load_helpers = FALSE, wrap = wrap))
40: test_files(paths, reporter = reporter, env = env, stop_on_failure = stop_on_failure, stop_on_warning = stop_on_warning, wrap = wrap)
41: test_dir(path = test_path, reporter = reporter, env = env, filter = filter, ..., stop_on_failure = stop_on_failure, stop_on_warning = stop_on_warning, wrap = wrap)
42: test_package_dir(package = package, test_path = test_path, filter = filter, reporter = reporter, ..., stop_on_failure = stop_on_failure, stop_on_warning = stop_on_warning, wrap = wrap)
43: test_check("BioInstaller")
An irrecoverable exception occurred. R is aborting now ...
Flavor: r-devel-linux-x86_64-fedora-gcc
Version: 0.3.7
Check: re-building of vignette outputs
Result: WARN
Error(s) in re-building vignettes:
sh: line 1: 41891 Segmentation fault (core dumped) '/data/gannet/ripley/R/R-devel/bin/R' --vanilla --no-echo > '/tmp/RtmpoR0Zxj/working_dir/Rtmpa6Jkwy/filea344311993b' 2>&1 < '/tmp/RtmpoR0Zxj/working_dir/Rtmpa6Jkwy/filea3443f9c960e'
--- re-building ‘BioInstaller.Rmd’ using rmarkdown
trying URL 'https://raw.githubusercontent.com/Miachol/ftp/master/files/GRCh37_MT_ensGene.txt'
Content type 'text/plain; charset=utf-8' length 3131 bytes
==================================================
downloaded 3131 bytes
trying URL 'https://raw.githubusercontent.com/Miachol/ftp/master/files/GRCh37_MT_ensGene.txt'
Content type 'text/plain; charset=utf-8' length 3131 bytes
==================================================
downloaded 3131 bytes
trying URL 'https://raw.githubusercontent.com/Miachol/ftp/master/files/GRCh37_MT_ensGene.txt'
Content type 'text/plain; charset=utf-8' length 3131 bytes
==================================================
downloaded 3131 bytes
trying URL 'https://raw.githubusercontent.com/Miachol/ftp/master/files/GRCh37_MT_ensGene.txt'
Content type 'text/plain; charset=utf-8' length 3131 bytes
==================================================
downloaded 3131 bytes
*** caught segfault ***
address 0xc800010009, cause 'memory not mapped'
Traceback:
1: git2r::clone(github_url, destdir)
2: git.download(name, download.dir, version, github_url, use_git2r, recursive_clone, verbose)
3: install.github(name = i, destdir = destdir[count], download.dir = download.dir[count], github.cfg = github.cfg, name.saved = name.saved[count], version = version[count], local.source = local.source[count], show.all.versions = show.all.versions, db = db, download.only = download.only, verbose = verbose, showWarnings = showWarnings, dependence.need = dependence.need, extra.list = extra.list, rmcd.parse = rcmd.parse, bash.parse = bash.parse, glue.parse = glue.parse, glue.flag = glue.flag, save.to.db = save.to.db, overwrite = overwrite, ...)
4: install.bioinfo("github_demo", download.dir = download.dir, download.only = TRUE, verbose = FALSE)
5: doTryCatch(return(expr), name, parentenv, handler)
6: tryCatchOne(expr, names, parentenv, handlers[[1L]])
7: tryCatchList(expr, classes, parentenv, handlers)
8: tryCatch({ install.bioinfo("github_demo", download.dir = download.dir, download.only = TRUE, verbose = FALSE) install.bioinfo("github_demo", local.source = download.dir)}, error = function(e) { message("Please check the SSL or connection with GitHub")})
9: eval(expr, envir, enclos)
10: eval(expr, envir, enclos)
11: withVisible(eval(expr, envir, enclos))
12: withCallingHandlers(withVisible(eval(expr, envir, enclos)), warning = wHandler, error = eHandler, message = mHandler)
13: handle(ev <- withCallingHandlers(withVisible(eval(expr, envir, enclos)), warning = wHandler, error = eHandler, message = mHandler))
14: timing_fn(handle(ev <- withCallingHandlers(withVisible(eval(expr, envir, enclos)), warning = wHandler, error = eHandler, message = mHandler)))
15: evaluate_call(expr, parsed$src[[i]], envir = envir, enclos = enclos, debug = debug, last = i == length(out), use_try = stop_on_error != 2L, keep_warning = keep_warning, keep_message = keep_message, output_handler = output_handler, include_timing = include_timing)
16: evaluate::evaluate(...)
17: evaluate(code, envir = env, new_device = FALSE, keep_warning = !isFALSE(options$warning), keep_message = !isFALSE(options$message), stop_on_error = if (options$error && options$include) 0L else 2L, output_handler = knit_handlers(options$render, options))
18: in_dir(input_dir(), evaluate(code, envir = env, new_device = FALSE, keep_warning = !isFALSE(options$warning), keep_message = !isFALSE(options$message), stop_on_error = if (options$error && options$include) 0L else 2L, output_handler = knit_handlers(options$render, options)))
19: block_exec(params)
20: call_block(x)
21: process_group.block(group)
22: process_group(group)
23: withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), error = function(e) { setwd(wd) cat(res, sep = "\n", file = output %n% "") message("Quitting from lines ", paste(current_lines(i), collapse = "-"), " (", knit_concord$get("infile"), ") ") })
24: process_file(text, output)
25: knitr::knit(knit_input, knit_output, envir = envir, quiet = quiet)
26: rmarkdown::render(file, encoding = encoding, quiet = quiet, envir = globalenv(), output_dir = getwd(), ...)
27: vweave_rmarkdown(...)
28: engine$weave(file, quiet = quiet, encoding = enc)
29: doTryCatch(return(expr), name, parentenv, handler)
30: tryCatchOne(expr, names, parentenv, handlers[[1L]])
31: tryCatchList(expr, classes, parentenv, handlers)
32: tryCatch({ engine$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)))})
33: tools:::.buildOneVignette("BioInstaller.Rmd", "/data/gannet/ripley/R/packages/tests-devel/BioInstaller.Rcheck/vign_test/BioInstaller", TRUE, FALSE, "BioInstaller", "UTF-8", "/tmp/RtmpoR0Zxj/working_dir/Rtmpa6Jkwy/filea34452227733.rds")
An irrecoverable exception occurred. R is aborting now ...
--- re-building ‘download.Rmd’ using rmarkdown
--- finished re-building ‘download.Rmd’
--- re-building ‘items_description.Rmd’ using rmarkdown
--- finished re-building ‘items_description.Rmd’
--- re-building ‘plugins_of_BioInstaller_shiny.Rmd’ using rmarkdown
--- finished re-building ‘plugins_of_BioInstaller_shiny.Rmd’
--- re-building ‘start_shiny_of_BioInstaller.Rmd’ using rmarkdown
--- finished re-building ‘start_shiny_of_BioInstaller.Rmd’
--- re-building ‘write_configuration_file.Rmd’ using rmarkdown
--- finished re-building ‘write_configuration_file.Rmd’
SUMMARY: processing the following file failed:
‘BioInstaller.Rmd’
Error: Vignette re-building failed.
Execution halted
Flavor: r-devel-linux-x86_64-fedora-gcc