Last updated on 2023-12-02 12:48:18 CET.
| Flavor | Version | Tinstall | Tcheck | Ttotal | Status | Flags |
|---|---|---|---|---|---|---|
| r-devel-linux-x86_64-debian-clang | 1.0.0 | 7.95 | 88.88 | 96.83 | ERROR | |
| r-devel-linux-x86_64-debian-gcc | 1.0.0 | 6.05 | 63.63 | 69.68 | ERROR | |
| r-devel-linux-x86_64-fedora-clang | 1.0.0 | 117.28 | ERROR | |||
| r-devel-linux-x86_64-fedora-gcc | 1.0.0 | 243.71 | OK | |||
| r-devel-windows-x86_64 | 1.0.0 | 8.00 | 185.00 | 193.00 | OK | |
| r-patched-linux-x86_64 | 1.0.0 | 5.61 | 78.43 | 84.04 | ERROR | |
| r-release-linux-x86_64 | 1.0.0 | 5.14 | 79.19 | 84.33 | ERROR | |
| r-release-macos-arm64 | 1.0.0 | 111.00 | OK | |||
| r-release-macos-x86_64 | 1.0.0 | 168.00 | OK | |||
| r-release-windows-x86_64 | 1.0.0 | 10.00 | 214.00 | 224.00 | OK | |
| r-oldrel-macos-arm64 | 1.0.0 | 112.00 | OK | |||
| r-oldrel-macos-x86_64 | 1.0.0 | 138.00 | OK | |||
| r-oldrel-windows-x86_64 | 1.0.0 | 10.00 | 212.00 | 222.00 | OK |
Version: 1.0.0
Check: re-building of vignette outputs
Result: ERROR
Error(s) in re-building vignettes:
...
--- re-building ‘GenomeAdapt_introduction.Rmd’ using rmarkdown
*** caught segfault ***
address 0x7f64111cc990, cause 'memory not mapped'
Traceback:
1: SNPRelate::snpgdsGRM(genf, sample.id = sample.id, snp.id = snp.id, autosome.only = autosome.only, remove.monosnp = remove.monosnp, maf = maf, missing.rate = missing.rate, method = method, num.thread = num.thread, out.fn = out.fn, out.prec = out.prec, out.compress = out.compress, with.id = with.id, verbose = verbose)
2: GenomeAdapt.gds(genfile = SNPRelate::snpgdsExampleFileName(), method = "EIGMIX", num.thread = 6, autosome.only = TRUE, remove.monosnp = TRUE, maf = 0.01, missing.rate = 0.1)
3: eval(expr, envir, enclos)
4: eval(expr, envir, enclos)
5: eval_with_user_handlers(expr, envir, enclos, user_handlers)
6: withVisible(eval_with_user_handlers(expr, envir, enclos, user_handlers))
7: withCallingHandlers(withVisible(eval_with_user_handlers(expr, envir, enclos, user_handlers)), warning = wHandler, error = eHandler, message = mHandler)
8: handle(ev <- withCallingHandlers(withVisible(eval_with_user_handlers(expr, envir, enclos, user_handlers)), warning = wHandler, error = eHandler, message = mHandler))
9: timing_fn(handle(ev <- withCallingHandlers(withVisible(eval_with_user_handlers(expr, envir, enclos, user_handlers)), warning = wHandler, error = eHandler, message = mHandler)))
10: evaluate_call(expr, parsed$src[[i]], envir = envir, enclos = enclos, debug = debug, last = i == length(out), use_try = stop_on_error != 2L, keep_warning = keep_warning, keep_message = keep_message, log_echo = log_echo, log_warning = log_warning, output_handler = output_handler, include_timing = include_timing)
11: evaluate::evaluate(...)
12: evaluate(code, envir = env, new_device = FALSE, keep_warning = if (is.numeric(options$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))
13: in_dir(input_dir(), expr)
14: 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$render, options)))
15: eng_r(options)
16: block_exec(params)
17: call_block(x)
18: process_group.block(group)
19: process_group(group)
20: withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), error = function(e) if (xfun::pkg_available("rlang", "1.0.0")) rlang::entrace(e))
21: withCallingHandlers(expr, error = function(e) { loc = paste0(current_lines(), label, sprintf(" (%s)", knit_concord$get("infile"))) message(one_string(handler(e, loc)))})
22: 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(e, loc) { setwd(wd) write_utf8(res, output %n% stdout()) paste0("\nQuitting from lines ", loc) }, if (labels[i] != "") sprintf(" [%s]", labels[i]))
23: process_file(text, output)
24: knitr::knit(knit_input, knit_output, envir = envir, quiet = quiet)
25: rmarkdown::render(file, encoding = encoding, quiet = quiet, envir = globalenv(), output_dir = getwd(), ...)
26: vweave_rmarkdown(...)
27: engine$weave(file, quiet = quiet, encoding = enc)
28: doTryCatch(return(expr), name, parentenv, handler)
29: tryCatchOne(expr, names, parentenv, handlers[[1L]])
30: tryCatchList(expr, classes, parentenv, handlers)
31: tryCatch({ engine$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)))})
32: tools::buildVignettes(dir = "/home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/GenomeAdapt.Rcheck/vign_test/GenomeAdapt", skip = TRUE, ser_elibs = "/tmp/RtmpEQrCE1/file3946d11008f48c.rds")
An irrecoverable exception occurred. R is aborting now ...
Segmentation fault
Flavor: r-devel-linux-x86_64-debian-clang
Version: 1.0.0
Check: re-building of vignette outputs
Result: ERROR
Error(s) in re-building vignettes:
...
--- re-building ‘GenomeAdapt_introduction.Rmd’ using rmarkdown
*** caught segfault ***
address 0x7fbac082a990, cause 'memory not mapped'
Traceback:
1: SNPRelate::snpgdsGRM(genf, sample.id = sample.id, snp.id = snp.id, autosome.only = autosome.only, remove.monosnp = remove.monosnp, maf = maf, missing.rate = missing.rate, method = method, num.thread = num.thread, out.fn = out.fn, out.prec = out.prec, out.compress = out.compress, with.id = with.id, verbose = verbose)
2: GenomeAdapt.gds(genfile = SNPRelate::snpgdsExampleFileName(), method = "EIGMIX", num.thread = 6, autosome.only = TRUE, remove.monosnp = TRUE, maf = 0.01, missing.rate = 0.1)
3: eval(expr, envir, enclos)
4: eval(expr, envir, enclos)
5: eval_with_user_handlers(expr, envir, enclos, user_handlers)
6: withVisible(eval_with_user_handlers(expr, envir, enclos, user_handlers))
7: withCallingHandlers(withVisible(eval_with_user_handlers(expr, envir, enclos, user_handlers)), warning = wHandler, error = eHandler, message = mHandler)
8: handle(ev <- withCallingHandlers(withVisible(eval_with_user_handlers(expr, envir, enclos, user_handlers)), warning = wHandler, error = eHandler, message = mHandler))
9: timing_fn(handle(ev <- withCallingHandlers(withVisible(eval_with_user_handlers(expr, envir, enclos, user_handlers)), warning = wHandler, error = eHandler, message = mHandler)))
10: evaluate_call(expr, parsed$src[[i]], envir = envir, enclos = enclos, debug = debug, last = i == length(out), use_try = stop_on_error != 2L, keep_warning = keep_warning, keep_message = keep_message, log_echo = log_echo, log_warning = log_warning, output_handler = output_handler, include_timing = include_timing)
11: evaluate::evaluate(...)
12: evaluate(code, envir = env, new_device = FALSE, keep_warning = if (is.numeric(options$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))
13: in_dir(input_dir(), expr)
14: 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$render, options)))
15: eng_r(options)
16: block_exec(params)
17: call_block(x)
18: process_group.block(group)
19: process_group(group)
20: withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), error = function(e) if (xfun::pkg_available("rlang", "1.0.0")) rlang::entrace(e))
21: withCallingHandlers(expr, error = function(e) { loc = paste0(current_lines(), label, sprintf(" (%s)", knit_concord$get("infile"))) message(one_string(handler(e, loc)))})
22: 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(e, loc) { setwd(wd) write_utf8(res, output %n% stdout()) paste0("\nQuitting from lines ", loc) }, if (labels[i] != "") sprintf(" [%s]", labels[i]))
23: process_file(text, output)
24: knitr::knit(knit_input, knit_output, envir = envir, quiet = quiet)
25: rmarkdown::render(file, encoding = encoding, quiet = quiet, envir = globalenv(), output_dir = getwd(), ...)
26: vweave_rmarkdown(...)
27: engine$weave(file, quiet = quiet, encoding = enc)
28: doTryCatch(return(expr), name, parentenv, handler)
29: tryCatchOne(expr, names, parentenv, handlers[[1L]])
30: tryCatchList(expr, classes, parentenv, handlers)
31: tryCatch({ engine$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)))})
32: tools::buildVignettes(dir = "/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/GenomeAdapt.Rcheck/vign_test/GenomeAdapt", skip = TRUE, ser_elibs = "/home/hornik/tmp/scratch/RtmpEOmG8a/file249e383bff92c7.rds")
An irrecoverable exception occurred. R is aborting now ...
Segmentation fault
Flavor: r-devel-linux-x86_64-debian-gcc
Version: 1.0.0
Check: re-building of vignette outputs
Result: ERROR
Error(s) in re-building vignettes:
--- re-building ‘GenomeAdapt_introduction.Rmd’ using rmarkdown
*** caught segfault ***
address 0x7fed39b42910, cause 'memory not mapped'
Traceback:
1: SNPRelate::snpgdsGRM(genf, sample.id = sample.id, snp.id = snp.id, autosome.only = autosome.only, remove.monosnp = remove.monosnp, maf = maf, missing.rate = missing.rate, method = method, num.thread = num.thread, out.fn = out.fn, out.prec = out.prec, out.compress = out.compress, with.id = with.id, verbose = verbose)
2: GenomeAdapt.gds(genfile = SNPRelate::snpgdsExampleFileName(), method = "EIGMIX", num.thread = 6, autosome.only = TRUE, remove.monosnp = TRUE, maf = 0.01, missing.rate = 0.1)
3: eval(expr, envir, enclos)
4: eval(expr, envir, enclos)
5: eval_with_user_handlers(expr, envir, enclos, user_handlers)
6: withVisible(eval_with_user_handlers(expr, envir, enclos, user_handlers))
7: withCallingHandlers(withVisible(eval_with_user_handlers(expr, envir, enclos, user_handlers)), warning = wHandler, error = eHandler, message = mHandler)
8: handle(ev <- withCallingHandlers(withVisible(eval_with_user_handlers(expr, envir, enclos, user_handlers)), warning = wHandler, error = eHandler, message = mHandler))
9: timing_fn(handle(ev <- withCallingHandlers(withVisible(eval_with_user_handlers(expr, envir, enclos, user_handlers)), warning = wHandler, error = eHandler, message = mHandler)))
10: evaluate_call(expr, parsed$src[[i]], envir = envir, enclos = enclos, debug = debug, last = i == length(out), use_try = stop_on_error != 2L, keep_warning = keep_warning, keep_message = keep_message, log_echo = log_echo, log_warning = log_warning, output_handler = output_handler, include_timing = include_timing)
11: evaluate::evaluate(...)
12: evaluate(code, envir = env, new_device = FALSE, keep_warning = if (is.numeric(options$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))
13: in_dir(input_dir(), expr)
14: 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$render, options)))
15: eng_r(options)
16: block_exec(params)
17: call_block(x)
18: process_group.block(group)
19: process_group(group)
20: withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), error = function(e) if (xfun::pkg_available("rlang", "1.0.0")) rlang::entrace(e))
21: withCallingHandlers(expr, error = function(e) { loc = paste0(current_lines(), label, sprintf(" (%s)", knit_concord$get("infile"))) message(one_string(handler(e, loc)))})
22: 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(e, loc) { setwd(wd) write_utf8(res, output %n% stdout()) paste0("\nQuitting from lines ", loc) }, if (labels[i] != "") sprintf(" [%s]", labels[i]))
23: process_file(text, output)
24: knitr::knit(knit_input, knit_output, envir = envir, quiet = quiet)
25: rmarkdown::render(file, encoding = encoding, quiet = quiet, envir = globalenv(), output_dir = getwd(), ...)
26: vweave_rmarkdown(...)
27: engine$weave(file, quiet = quiet, encoding = enc)
28: doTryCatch(return(expr), name, parentenv, handler)
29: tryCatchOne(expr, names, parentenv, handlers[[1L]])
30: tryCatchList(expr, classes, parentenv, handlers)
31: tryCatch({ engine$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)))})
32: tools::buildVignettes(dir = "/data/gannet/ripley/R/packages/tests-clang/GenomeAdapt.Rcheck/vign_test/GenomeAdapt", skip = TRUE, ser_elibs = "/tmp/RtmpoC6Egv/file29f49ca1b730a.rds")
An irrecoverable exception occurred. R is aborting now ...
Flavor: r-devel-linux-x86_64-fedora-clang
Version: 1.0.0
Check: re-building of vignette outputs
Result: ERROR
Error(s) in re-building vignettes:
...
--- re-building ‘GenomeAdapt_introduction.Rmd’ using rmarkdown
*** caught segfault ***
address 0x7f1cfadcc990, cause 'memory not mapped'
Traceback:
1: SNPRelate::snpgdsGRM(genf, sample.id = sample.id, snp.id = snp.id, autosome.only = autosome.only, remove.monosnp = remove.monosnp, maf = maf, missing.rate = missing.rate, method = method, num.thread = num.thread, out.fn = out.fn, out.prec = out.prec, out.compress = out.compress, with.id = with.id, verbose = verbose)
2: GenomeAdapt.gds(genfile = SNPRelate::snpgdsExampleFileName(), method = "EIGMIX", num.thread = 6, autosome.only = TRUE, remove.monosnp = TRUE, maf = 0.01, missing.rate = 0.1)
3: eval(expr, envir, enclos)
4: eval(expr, envir, enclos)
5: eval_with_user_handlers(expr, envir, enclos, user_handlers)
6: withVisible(eval_with_user_handlers(expr, envir, enclos, user_handlers))
7: withCallingHandlers(withVisible(eval_with_user_handlers(expr, envir, enclos, user_handlers)), warning = wHandler, error = eHandler, message = mHandler)
8: handle(ev <- withCallingHandlers(withVisible(eval_with_user_handlers(expr, envir, enclos, user_handlers)), warning = wHandler, error = eHandler, message = mHandler))
9: timing_fn(handle(ev <- withCallingHandlers(withVisible(eval_with_user_handlers(expr, envir, enclos, user_handlers)), warning = wHandler, error = eHandler, message = mHandler)))
10: evaluate_call(expr, parsed$src[[i]], envir = envir, enclos = enclos, debug = debug, last = i == length(out), use_try = stop_on_error != 2L, keep_warning = keep_warning, keep_message = keep_message, log_echo = log_echo, log_warning = log_warning, output_handler = output_handler, include_timing = include_timing)
11: evaluate::evaluate(...)
12: evaluate(code, envir = env, new_device = FALSE, keep_warning = if (is.numeric(options$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))
13: in_dir(input_dir(), expr)
14: 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$render, options)))
15: eng_r(options)
16: block_exec(params)
17: call_block(x)
18: process_group.block(group)
19: process_group(group)
20: withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), error = function(e) if (xfun::pkg_available("rlang", "1.0.0")) rlang::entrace(e))
21: withCallingHandlers(expr, error = function(e) { loc = paste0(current_lines(), label, sprintf(" (%s)", knit_concord$get("infile"))) message(one_string(handler(e, loc)))})
22: 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(e, loc) { setwd(wd) write_utf8(res, output %n% stdout()) paste0("\nQuitting from lines ", loc) }, if (labels[i] != "") sprintf(" [%s]", labels[i]))
23: process_file(text, output)
24: knitr::knit(knit_input, knit_output, envir = envir, quiet = quiet)
25: rmarkdown::render(file, encoding = encoding, quiet = quiet, envir = globalenv(), output_dir = getwd(), ...)
26: vweave_rmarkdown(...)
27: engine$weave(file, quiet = quiet, encoding = enc)
28: doTryCatch(return(expr), name, parentenv, handler)
29: tryCatchOne(expr, names, parentenv, handlers[[1L]])
30: tryCatchList(expr, classes, parentenv, handlers)
31: tryCatch({ engine$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)))})
32: tools::buildVignettes(dir = "/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/GenomeAdapt.Rcheck/vign_test/GenomeAdapt", skip = TRUE, ser_elibs = "/tmp/Rtmp2aE2P7/file3133c77e367c6d.rds")
An irrecoverable exception occurred. R is aborting now ...
Segmentation fault
Flavor: r-patched-linux-x86_64
Version: 1.0.0
Check: re-building of vignette outputs
Result: ERROR
Error(s) in re-building vignettes:
...
--- re-building ‘GenomeAdapt_introduction.Rmd’ using rmarkdown
*** caught segfault ***
address 0x7fc53c7cc990, cause 'memory not mapped'
Traceback:
1: SNPRelate::snpgdsGRM(genf, sample.id = sample.id, snp.id = snp.id, autosome.only = autosome.only, remove.monosnp = remove.monosnp, maf = maf, missing.rate = missing.rate, method = method, num.thread = num.thread, out.fn = out.fn, out.prec = out.prec, out.compress = out.compress, with.id = with.id, verbose = verbose)
2: GenomeAdapt.gds(genfile = SNPRelate::snpgdsExampleFileName(), method = "EIGMIX", num.thread = 6, autosome.only = TRUE, remove.monosnp = TRUE, maf = 0.01, missing.rate = 0.1)
3: eval(expr, envir, enclos)
4: eval(expr, envir, enclos)
5: eval_with_user_handlers(expr, envir, enclos, user_handlers)
6: withVisible(eval_with_user_handlers(expr, envir, enclos, user_handlers))
7: withCallingHandlers(withVisible(eval_with_user_handlers(expr, envir, enclos, user_handlers)), warning = wHandler, error = eHandler, message = mHandler)
8: handle(ev <- withCallingHandlers(withVisible(eval_with_user_handlers(expr, envir, enclos, user_handlers)), warning = wHandler, error = eHandler, message = mHandler))
9: timing_fn(handle(ev <- withCallingHandlers(withVisible(eval_with_user_handlers(expr, envir, enclos, user_handlers)), warning = wHandler, error = eHandler, message = mHandler)))
10: evaluate_call(expr, parsed$src[[i]], envir = envir, enclos = enclos, debug = debug, last = i == length(out), use_try = stop_on_error != 2L, keep_warning = keep_warning, keep_message = keep_message, log_echo = log_echo, log_warning = log_warning, output_handler = output_handler, include_timing = include_timing)
11: evaluate::evaluate(...)
12: evaluate(code, envir = env, new_device = FALSE, keep_warning = if (is.numeric(options$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))
13: in_dir(input_dir(), expr)
14: 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$render, options)))
15: eng_r(options)
16: block_exec(params)
17: call_block(x)
18: process_group.block(group)
19: process_group(group)
20: withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), error = function(e) if (xfun::pkg_available("rlang", "1.0.0")) rlang::entrace(e))
21: withCallingHandlers(expr, error = function(e) { loc = paste0(current_lines(), label, sprintf(" (%s)", knit_concord$get("infile"))) message(one_string(handler(e, loc)))})
22: 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(e, loc) { setwd(wd) write_utf8(res, output %n% stdout()) paste0("\nQuitting from lines ", loc) }, if (labels[i] != "") sprintf(" [%s]", labels[i]))
23: process_file(text, output)
24: knitr::knit(knit_input, knit_output, envir = envir, quiet = quiet)
25: rmarkdown::render(file, encoding = encoding, quiet = quiet, envir = globalenv(), output_dir = getwd(), ...)
26: vweave_rmarkdown(...)
27: engine$weave(file, quiet = quiet, encoding = enc)
28: doTryCatch(return(expr), name, parentenv, handler)
29: tryCatchOne(expr, names, parentenv, handlers[[1L]])
30: tryCatchList(expr, classes, parentenv, handlers)
31: tryCatch({ engine$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)))})
32: tools::buildVignettes(dir = "/home/hornik/tmp/R.check/r-release-gcc/Work/PKGS/GenomeAdapt.Rcheck/vign_test/GenomeAdapt", skip = TRUE, ser_elibs = "/tmp/Rtmp6qZm8F/file2088142bac9539.rds")
An irrecoverable exception occurred. R is aborting now ...
Segmentation fault
Flavor: r-release-linux-x86_64