Last updated on 2024-06-06 05:58:26 CEST.
| Package | ERROR | NOTE | OK |
|---|---|---|---|
| affinity | 13 | ||
| angstroms | 13 | ||
| area | 5 | 8 | |
| basf | 13 | ||
| bgmfiles | 13 | ||
| ceramic | 13 | ||
| crsmeta | 13 | ||
| decido | 13 | ||
| fasterize | 13 | ||
| geojson | 13 | ||
| ggpolypath | 13 | ||
| gibble | 13 | ||
| graticule | 13 | ||
| lazysf | 13 | ||
| ncdump | 13 | ||
| ncmeta | 13 | ||
| orsifronts | 13 | ||
| ozmaps | 1 | 12 | |
| palr | 13 | ||
| PROJ | 2 | 10 | 1 |
| quadmesh | 13 | ||
| rbgm | 13 | ||
| reproj | 13 | ||
| sfdct | 13 | ||
| silicate | 10 | 3 | |
| spbabel | 1 | 12 | |
| spex | 13 | ||
| tabularaster | 13 | ||
| tidync | 13 | ||
| traipse | 13 | ||
| trip | 13 | ||
| tripEstimation | 13 | ||
| unjoin | 13 | ||
| vapour | 6 | 5 | 2 |
Current CRAN status: OK: 13
Current CRAN status: OK: 13
Current CRAN status: NOTE: 5, OK: 8
Version: 0.2.0
Check: compiled code
Result: NOTE
File ‘area/libs/area.so’:
Found non-API calls to R: ‘SETLENGTH’, ‘SET_TRUELENGTH’
Compiled code should not call non-API entry points in R.
See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
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
Version: 0.2.0
Check: compiled code
Result: NOTE
File 'area/libs/x64/area.dll':
Found non-API calls to R: 'SETLENGTH', 'SET_TRUELENGTH'
Compiled code should not call non-API entry points in R.
See 'Writing portable packages' in the 'Writing R Extensions' manual.
Flavor: r-devel-windows-x86_64
Current CRAN status: NOTE: 13
Version: 0.2.0
Check: LazyData
Result: NOTE
'LazyData' is specified without a 'data' directory
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-devel-windows-x86_64, r-patched-linux-x86_64, r-release-linux-x86_64, r-release-macos-arm64, r-release-macos-x86_64, r-release-windows-x86_64, r-oldrel-macos-arm64, r-oldrel-macos-x86_64, r-oldrel-windows-x86_64
Current CRAN status: OK: 13
Current CRAN status: OK: 13
Current CRAN status: OK: 13
Current CRAN status: NOTE: 13
Version: 0.3.0
Check: C++ specification
Result: NOTE
Specified C++11: please drop specification unless essential
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-devel-windows-x86_64, r-patched-linux-x86_64, r-release-linux-x86_64, r-release-macos-arm64, r-release-macos-x86_64, r-release-windows-x86_64, r-oldrel-macos-arm64, r-oldrel-macos-x86_64, r-oldrel-windows-x86_64
Version: 0.3.0
Check: LazyData
Result: NOTE
'LazyData' is specified without a 'data' directory
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-devel-windows-x86_64, r-patched-linux-x86_64, r-release-linux-x86_64, r-release-macos-arm64, r-release-macos-x86_64, r-release-windows-x86_64, r-oldrel-macos-arm64, r-oldrel-macos-x86_64, r-oldrel-windows-x86_64
Current CRAN status: OK: 13
Current CRAN status: OK: 13
Current CRAN status: OK: 13
Current CRAN status: OK: 13
Current CRAN status: OK: 13
Current CRAN status: NOTE: 13
Version: 0.1.0
Check: LazyData
Result: NOTE
'LazyData' is specified without a 'data' directory
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-devel-windows-x86_64, r-patched-linux-x86_64, r-release-linux-x86_64, r-release-macos-arm64, r-release-macos-x86_64, r-release-windows-x86_64, r-oldrel-macos-arm64, r-oldrel-macos-x86_64, r-oldrel-windows-x86_64
Current CRAN status: NOTE: 13
Version: 0.0.3
Check: LazyData
Result: NOTE
'LazyData' is specified without a 'data' directory
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-devel-windows-x86_64, r-patched-linux-x86_64, r-release-linux-x86_64, r-release-macos-arm64, r-release-macos-x86_64, r-release-windows-x86_64, r-oldrel-macos-arm64, r-oldrel-macos-x86_64, r-oldrel-windows-x86_64
Current CRAN status: OK: 13
Current CRAN status: OK: 13
Current CRAN status: NOTE: 1, OK: 12
Version: 0.4.5
Check: installed package size
Result: NOTE
installed size is 5.1Mb
sub-directories of 1Mb or more:
data 4.0Mb
Flavor: r-oldrel-macos-arm64
Current CRAN status: OK: 13
Current CRAN status: ERROR: 2, NOTE: 10, OK: 1
Version: 0.4.5
Check: HTML version of manual
Result: NOTE
Found the following HTML validation problems:
proj_crs_text.html:65:1 (proj_crs_text.Rd:29): Warning: trimming empty <h3>
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-linux-x86_64, r-release-linux-x86_64
Version: 0.4.5
Check: whether package can be installed
Result: ERROR
Installation failed.
Flavors: r-devel-windows-x86_64, r-release-windows-x86_64
Version: 0.4.5
Check: installed package size
Result: NOTE
installed size is 17.8Mb
sub-directories of 1Mb or more:
libs 17.5Mb
Flavors: r-release-macos-arm64, r-release-macos-x86_64, r-oldrel-macos-arm64, r-oldrel-windows-x86_64
Current CRAN status: OK: 13
Current CRAN status: OK: 13
Current CRAN status: OK: 13
Current CRAN status: OK: 13
Current CRAN status: NOTE: 10, OK: 3
Version: 0.7.1
Check: Rd files
Result: NOTE
checkRd: (-1) inlandwaters.Rd:14: Lost braces in \itemize; meant \describe ?
checkRd: (-1) inlandwaters.Rd:15: Lost braces in \itemize; meant \describe ?
checkRd: (-1) inlandwaters.Rd:16: Lost braces in \itemize; meant \describe ?
checkRd: (-1) inlandwaters.Rd:17: Lost braces in \itemize; meant \describe ?
checkRd: (-1) inlandwaters.Rd:18: Lost braces in \itemize; meant \describe ?
checkRd: (-1) inlandwaters.Rd:19: Lost braces in \itemize; meant \describe ?
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-devel-windows-x86_64, r-patched-linux-x86_64, r-release-linux-x86_64, r-release-macos-arm64, r-release-macos-x86_64, r-release-windows-x86_64
Current CRAN status: NOTE: 1, OK: 12
Version: 0.6.0
Check: Rd cross-references
Result: NOTE
Undeclared package ‘vctrs’ in Rd xrefs
Flavor: r-devel-linux-x86_64-fedora-clang
Current CRAN status: OK: 13
Current CRAN status: OK: 13
Current CRAN status: OK: 13
Current CRAN status: OK: 13
Current CRAN status: OK: 13
Current CRAN status: OK: 13
Current CRAN status: NOTE: 13
Version: 0.1.0
Check: LazyData
Result: NOTE
'LazyData' is specified without a 'data' directory
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-devel-windows-x86_64, r-patched-linux-x86_64, r-release-linux-x86_64, r-release-macos-arm64, r-release-macos-x86_64, r-release-windows-x86_64, r-oldrel-macos-arm64, r-oldrel-macos-x86_64, r-oldrel-windows-x86_64
Current CRAN status: ERROR: 6, NOTE: 5, OK: 2
clang-UBSAN gcc-UBSAN valgrind
Version: 0.9.5
Check: examples
Result: ERROR
Running examples in ‘vapour-Ex.R’ failed
The error most likely occurred in:
> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: gdal_raster_data
> ### Title: General raster read and convert
> ### Aliases: gdal_raster_data gdal_raster_dsn gdal_raster_image
>
> ### ** Examples
>
> dsn <- system.file("extdata/sst.tif", package = "vapour")
> par(mfrow = c(2, 2))
> ## do nothing, get native
> X <- gdal_raster_data(dsn)
*** caught segfault ***
address 0x1, cause 'memory not mapped'
Traceback:
1: warp_general_cpp(dsn, target_crs, as.numeric(target_ext), as.integer(target_dim), as.numeric(target_res), bands = as.integer(bands), resample = resample, silent = FALSE, band_output_type = band_output_type, options = options, dsn_outname = "")
2: gdal_raster_data(dsn)
An irrecoverable exception occurred. R is aborting now ...
Segmentation fault
Flavors: r-devel-linux-x86_64-debian-clang, r-devel-linux-x86_64-debian-gcc
Version: 0.9.5
Check: tests
Result: ERROR
Running ‘spelling.R’ [0s/1s]
Running ‘testthat.R’ [2s/2s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
> library(testthat)
> library(vapour)
>
> test_check("vapour")
*** caught segfault ***
address 0x55, cause 'memory not mapped'
Traceback:
1: raster_gdalinfo_app_cpp(x, options)
2: gdalinfo_internal(x[1L], json = TRUE, stats = min_max, sd = sd, ...)
3: vapour_raster_info(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(), default_reporter = local_interactive_reporter())
15: test_that("with with no source crs works", { f <- system.file("extdata/volcano.png", package = "vapour", mustWork = TRUE) info <- vapour_raster_info(f) ok <- vapour_warp_raster(f, dimension = info$dimension, extent = c(0, 1, 0, 1), transformation_options = c("SRC_METHOD=NO_GEOTRANSFORM")) if (dir.exists("/rdsi/PUBLIC/raad/data/www.ncei.noaa.gov")) { sds <- "NETCDF:/rdsi/PUBLIC/raad/data/www.ncei.noaa.gov/data/sea-surface-temperature-optimum-interpolation/v2.1/access/avhrr/198109/oisst-avhrr-v02r01.19810901.nc:sst" expect_silent(vapour_warp_raster(sds, extent = c(0, 1, 0, 1), dimension = c(4, 4))) expect_silent(vapour_warp_raster(sds, extent = c(0, 1, 0, 1), dimension = c(4, 4), source_projection = "+proj=laea")) expect_warning(vapour_warp_raster(sds, extent = c(0, 1, 0, 1), dimension = c(4, 4), projection = "OGC:CRS84")) } badnc <- system.file("extdata/gdal", "bad_netcdf_geoloc_arrays.nc", package = "vapour") sds <- vapour_sds_names(badnc) lcc <- "+proj=lcc +lat_0=-30 +lon_0=134.33 +lat_1=-50 +lat_2=-10 +R=6378137" ex <- c(-3077504, 3968504, -2763621, 3472383) vrt <- vapour_vrt(sds[3], geolocation = sds[2:1], bands = 1) info <- vapour_raster_info(vrt) expect_warning(im <- vapour_warp_raster_dbl(vrt, extent = ex, dimension = info$dimension, projection = lcc, transformation_options = c("SRC_METHOD=NO_GEOTRANSFORM"))) ex <- c(-180, 180, -90, 90) dm <- c(512, 1024) vrt <- vapour_vrt(sds[3], geolocation = sds[2:1], bands = 1) vapour::vapour_set_config("GDAL_NETCDF_BOTTOMUP", "NO") expect_warning(im <- vapour_warp_raster_dbl(vrt, extent = ex, dimension = dm, projection = "OGC:CRS84", transformation_options = c("SRC_METHOD=GEOLOC_ARRAY")))})
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(test = NULL, code = exprs, env = env, default_reporter = StopReporter$new())
27: source_file(path, env = env(env), desc = desc, error_call = error_call)
28: FUN(X[[i]], ...)
29: lapply(test_paths, test_one_file, env = env, desc = desc, error_call = error_call)
30: doTryCatch(return(expr), name, parentenv, handler)
31: tryCatchOne(expr, names, parentenv, handlers[[1L]])
32: tryCatchList(expr, classes, parentenv, handlers)
33: tryCatch(code, testthat_abort_reporter = function(cnd) { cat(conditionMessage(cnd), "\n") NULL})
34: with_reporter(reporters$multi, lapply(test_paths, test_one_file, env = env, desc = desc, error_call = error_call))
35: test_files_serial(test_dir = test_dir, test_package = test_package, test_paths = test_paths, load_helpers = load_helpers, reporter = reporter, env = env, stop_on_failure = stop_on_failure, stop_on_warning = stop_on_warning, desc = desc, load_package = load_package, error_call = error_call)
36: test_files(test_dir = path, test_paths = test_paths, test_package = package, reporter = reporter, load_helpers = load_helpers, env = env, stop_on_failure = stop_on_failure, stop_on_warning = stop_on_warning, load_package = load_package, parallel = parallel)
37: test_dir("testthat", package = package, reporter = reporter, ..., load_package = "installed")
38: test_check("vapour")
An irrecoverable exception occurred. R is aborting now ...
Segmentation fault
Flavor: r-devel-linux-x86_64-debian-clang
Version: 0.9.5
Check: re-building of vignette outputs
Result: ERROR
Error(s) in re-building vignettes:
...
--- re-building ‘feature-access.Rmd’ using rmarkdown
--- finished re-building ‘feature-access.Rmd’
--- re-building ‘vapour.Rmd’ using rmarkdown
*** caught segfault ***
address 0x51, cause 'memory not mapped'
Traceback:
1: raster_gdalinfo_app_cpp(x, options)
2: gdalinfo_internal(x[1L], json = TRUE, stats = min_max, sd = sd, ...)
3: vapour_raster_info(f)
4: eval(expr, envir, enclos)
5: eval(expr, envir, enclos)
6: eval_with_user_handlers(expr, envir, enclos, user_handlers)
7: withVisible(eval_with_user_handlers(expr, envir, enclos, user_handlers))
8: withCallingHandlers(withVisible(eval_with_user_handlers(expr, envir, enclos, user_handlers)), warning = wHandler, error = eHandler, message = mHandler)
9: handle(ev <- withCallingHandlers(withVisible(eval_with_user_handlers(expr, envir, enclos, user_handlers)), warning = wHandler, error = eHandler, message = mHandler))
10: timing_fn(handle(ev <- withCallingHandlers(withVisible(eval_with_user_handlers(expr, envir, enclos, user_handlers)), warning = wHandler, error = eHandler, message = mHandler)))
11: evaluate_call(expr, parsed$src[[i]], envir = envir, enclos = enclos, debug = debug, last = i == length(out), use_try = stop_on_error != 2L, keep_warning = keep_warning, keep_message = keep_message, log_echo = log_echo, log_warning = log_warning, output_handler = output_handler, include_timing = include_timing)
12: evaluate::evaluate(...)
13: evaluate(code, envir = env, new_device = FALSE, keep_warning = if (is.numeric(options$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))
14: in_dir(input_dir(), expr)
15: 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$render, options)))
16: eng_r(options)
17: block_exec(params)
18: call_block(x)
19: process_group(group)
20: withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), error = function(e) if (xfun::pkg_available("rlang", "1.0.0")) rlang::entrace(e))
21: xfun:::handle_error(withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), error = function(e) if (xfun::pkg_available("rlang", "1.0.0")) rlang::entrace(e)), function(loc) { setwd(wd) write_utf8(res, output %n% stdout()) paste0("\nQuitting from lines ", loc) }, if (labels[i] != "") sprintf(" [%s]", labels[i]), get_loc)
22: process_file(text, output)
23: knitr::knit(knit_input, knit_output, envir = envir, quiet = quiet)
24: rmarkdown::render(file, encoding = encoding, quiet = quiet, envir = globalenv(), output_dir = getwd(), ...)
25: vweave_rmarkdown(...)
26: engine$weave(file, quiet = quiet, encoding = enc)
27: doTryCatch(return(expr), name, parentenv, handler)
28: tryCatchOne(expr, names, parentenv, handlers[[1L]])
29: tryCatchList(expr, classes, parentenv, handlers)
30: 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)))})
31: tools:::.buildOneVignette("vapour.Rmd", "/home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/vapour.Rcheck/vign_test/vapour", TRUE, FALSE, "vapour", "UTF-8", "/tmp/RtmpZ1yHvv/file295e12ca9082c.rds")
An irrecoverable exception occurred. R is aborting now ...
Segmentation fault
SUMMARY: processing the following file failed:
‘vapour.Rmd’
Error: Vignette re-building failed.
Execution halted
Flavor: r-devel-linux-x86_64-debian-clang
Version: 0.9.5
Check: tests
Result: ERROR
Running ‘spelling.R’ [0s/1s]
Running ‘testthat.R’ [1s/2s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
> library(testthat)
> library(vapour)
>
> test_check("vapour")
*** caught segfault ***
address 0x53, cause 'memory not mapped'
Traceback:
1: raster_gdalinfo_app_cpp(x, options)
2: gdalinfo_internal(x[1L], json = TRUE, stats = min_max, sd = sd, ...)
3: vapour_raster_info(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(), default_reporter = local_interactive_reporter())
15: test_that("with with no source crs works", { f <- system.file("extdata/volcano.png", package = "vapour", mustWork = TRUE) info <- vapour_raster_info(f) ok <- vapour_warp_raster(f, dimension = info$dimension, extent = c(0, 1, 0, 1), transformation_options = c("SRC_METHOD=NO_GEOTRANSFORM")) if (dir.exists("/rdsi/PUBLIC/raad/data/www.ncei.noaa.gov")) { sds <- "NETCDF:/rdsi/PUBLIC/raad/data/www.ncei.noaa.gov/data/sea-surface-temperature-optimum-interpolation/v2.1/access/avhrr/198109/oisst-avhrr-v02r01.19810901.nc:sst" expect_silent(vapour_warp_raster(sds, extent = c(0, 1, 0, 1), dimension = c(4, 4))) expect_silent(vapour_warp_raster(sds, extent = c(0, 1, 0, 1), dimension = c(4, 4), source_projection = "+proj=laea")) expect_warning(vapour_warp_raster(sds, extent = c(0, 1, 0, 1), dimension = c(4, 4), projection = "OGC:CRS84")) } badnc <- system.file("extdata/gdal", "bad_netcdf_geoloc_arrays.nc", package = "vapour") sds <- vapour_sds_names(badnc) lcc <- "+proj=lcc +lat_0=-30 +lon_0=134.33 +lat_1=-50 +lat_2=-10 +R=6378137" ex <- c(-3077504, 3968504, -2763621, 3472383) vrt <- vapour_vrt(sds[3], geolocation = sds[2:1], bands = 1) info <- vapour_raster_info(vrt) expect_warning(im <- vapour_warp_raster_dbl(vrt, extent = ex, dimension = info$dimension, projection = lcc, transformation_options = c("SRC_METHOD=NO_GEOTRANSFORM"))) ex <- c(-180, 180, -90, 90) dm <- c(512, 1024) vrt <- vapour_vrt(sds[3], geolocation = sds[2:1], bands = 1) vapour::vapour_set_config("GDAL_NETCDF_BOTTOMUP", "NO") expect_warning(im <- vapour_warp_raster_dbl(vrt, extent = ex, dimension = dm, projection = "OGC:CRS84", transformation_options = c("SRC_METHOD=GEOLOC_ARRAY")))})
16: eval(code, test_env)
17: eval(code, test_env)
18: withCallingHandlers({ eval(code, test_env) if (!handled && !is.null(test)) { skip_empty() }}, expectation = handle_expectation, skip = handle_skip, warning = handle_warning, message = handle_message, error = handle_error)
19: doTryCatch(return(expr), name, parentenv, handler)
20: tryCatchOne(expr, names, parentenv, handlers[[1L]])
21: tryCatchList(expr, names[-nh], parentenv, handlers[-nh])
22: doTryCatch(return(expr), name, parentenv, handler)
23: tryCatchOne(tryCatchList(expr, names[-nh], parentenv, handlers[-nh]), names[nh], parentenv, handlers[[nh]])
24: tryCatchList(expr, classes, parentenv, handlers)
25: tryCatch(withCallingHandlers({ eval(code, test_env) if (!handled && !is.null(test)) { skip_empty() }}, expectation = handle_expectation, skip = handle_skip, warning = handle_warning, message = handle_message, error = handle_error), error = handle_fatal, skip = function(e) { })
26: test_code(test = NULL, code = exprs, env = env, default_reporter = StopReporter$new())
27: source_file(path, env = env(env), desc = desc, error_call = error_call)
28: FUN(X[[i]], ...)
29: lapply(test_paths, test_one_file, env = env, desc = desc, error_call = error_call)
30: doTryCatch(return(expr), name, parentenv, handler)
31: tryCatchOne(expr, names, parentenv, handlers[[1L]])
32: tryCatchList(expr, classes, parentenv, handlers)
33: tryCatch(code, testthat_abort_reporter = function(cnd) { cat(conditionMessage(cnd), "\n") NULL})
34: with_reporter(reporters$multi, lapply(test_paths, test_one_file, env = env, desc = desc, error_call = error_call))
35: test_files_serial(test_dir = test_dir, test_package = test_package, test_paths = test_paths, load_helpers = load_helpers, reporter = reporter, env = env, stop_on_failure = stop_on_failure, stop_on_warning = stop_on_warning, desc = desc, load_package = load_package, error_call = error_call)
36: test_files(test_dir = path, test_paths = test_paths, test_package = package, reporter = reporter, load_helpers = load_helpers, env = env, stop_on_failure = stop_on_failure, stop_on_warning = stop_on_warning, load_package = load_package, parallel = parallel)
37: test_dir("testthat", package = package, reporter = reporter, ..., load_package = "installed")
38: test_check("vapour")
An irrecoverable exception occurred. R is aborting now ...
Segmentation fault
Flavor: r-devel-linux-x86_64-debian-gcc
Version: 0.9.5
Check: re-building of vignette outputs
Result: ERROR
Error(s) in re-building vignettes:
...
--- re-building ‘feature-access.Rmd’ using rmarkdown
--- finished re-building ‘feature-access.Rmd’
--- re-building ‘vapour.Rmd’ using rmarkdown
*** caught segfault ***
address 0x4f, cause 'memory not mapped'
Traceback:
1: raster_gdalinfo_app_cpp(x, options)
2: gdalinfo_internal(x[1L], json = TRUE, stats = min_max, sd = sd, ...)
3: vapour_raster_info(f)
4: eval(expr, envir, enclos)
5: eval(expr, envir, enclos)
6: eval_with_user_handlers(expr, envir, enclos, user_handlers)
7: withVisible(eval_with_user_handlers(expr, envir, enclos, user_handlers))
8: withCallingHandlers(withVisible(eval_with_user_handlers(expr, envir, enclos, user_handlers)), warning = wHandler, error = eHandler, message = mHandler)
9: handle(ev <- withCallingHandlers(withVisible(eval_with_user_handlers(expr, envir, enclos, user_handlers)), warning = wHandler, error = eHandler, message = mHandler))
10: timing_fn(handle(ev <- withCallingHandlers(withVisible(eval_with_user_handlers(expr, envir, enclos, user_handlers)), warning = wHandler, error = eHandler, message = mHandler)))
11: 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)
12: evaluate::evaluate(...)
13: 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$render, options))
14: in_dir(input_dir(), expr)
15: in_input_dir(evaluate(code, envir = env, new_device = FALSE, keep_warning = if (is.numeric(options$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)))
16: eng_r(options)
17: block_exec(params)
18: call_block(x)
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: 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)
22: process_file(text, output)
23: knitr::knit(knit_input, knit_output, envir = envir, quiet = quiet)
24: rmarkdown::render(file, encoding = encoding, quiet = quiet, envir = globalenv(), output_dir = getwd(), ...)
25: vweave_rmarkdown(...)
26: engine$weave(file, quiet = quiet, encoding = enc)
27: doTryCatch(return(expr), name, parentenv, handler)
28: tryCatchOne(expr, names, parentenv, handlers[[1L]])
29: tryCatchList(expr, classes, parentenv, handlers)
30: tryCatch({ engine$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)))})
31: tools:::.buildOneVignette("vapour.Rmd", "/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/vapour.Rcheck/vign_test/vapour", TRUE, FALSE, "vapour", "UTF-8", "/home/hornik/tmp/scratch/RtmpOYUknz/file1527e97ada862e.rds")
An irrecoverable exception occurred. R is aborting now ...
Segmentation fault
SUMMARY: processing the following file failed:
‘vapour.Rmd’
Error: Vignette re-building failed.
Execution halted
Flavor: r-devel-linux-x86_64-debian-gcc
Version: 0.9.5
Check: examples
Result: ERROR
Running examples in ‘vapour-Ex.R’ failed
The error most likely occurred in:
> ### Name: gdal_raster_data
> ### Title: General raster read and convert
> ### Aliases: gdal_raster_data gdal_raster_dsn gdal_raster_image
>
> ### ** Examples
>
> dsn <- system.file("extdata/sst.tif", package = "vapour")
> par(mfrow = c(2, 2))
> ## do nothing, get native
> X <- gdal_raster_data(dsn)
*** caught segfault ***
address 0x1, cause 'memory not mapped'
Traceback:
1: warp_general_cpp(dsn, target_crs, as.numeric(target_ext), as.integer(target_dim), as.numeric(target_res), bands = as.integer(bands), resample = resample, silent = FALSE, band_output_type = band_output_type, options = options, dsn_outname = "")
2: gdal_raster_data(dsn)
An irrecoverable exception occurred. R is aborting now ...
Flavors: r-devel-linux-x86_64-fedora-clang, r-devel-linux-x86_64-fedora-gcc
Version: 0.9.5
Check: tests
Result: ERROR
Running ‘spelling.R’
Running ‘testthat.R’
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
> library(testthat)
> library(vapour)
>
> test_check("vapour")
*** caught segfault ***
address 0x1, cause 'memory not mapped'
Traceback:
1: warp_in_memory_gdal_cpp(x, source_WKT = source_projection, target_WKT = projection, target_extent = as.numeric(extent), target_dim = as.integer(dimension), bands = as.integer(bands), source_extent = as.numeric(source_extent), resample = resample, silent = silent, band_output_type = band_output_type, options = options, nomd = nomd, overview)
2: vapour_warp_raster(f, dimension = info$dimension, extent = c(0, 1, 0, 1), transformation_options = c("SRC_METHOD=NO_GEOTRANSFORM"))
3: eval(code, test_env)
4: eval(code, test_env)
5: withCallingHandlers({ eval(code, test_env) if (!handled && !is.null(test)) { skip_empty() }}, expectation = handle_expectation, skip = handle_skip, warning = handle_warning, message = handle_message, error = handle_error)
6: doTryCatch(return(expr), name, parentenv, handler)
7: tryCatchOne(expr, names, parentenv, handlers[[1L]])
8: tryCatchList(expr, names[-nh], parentenv, handlers[-nh])
9: doTryCatch(return(expr), name, parentenv, handler)
10: tryCatchOne(tryCatchList(expr, names[-nh], parentenv, handlers[-nh]), names[nh], parentenv, handlers[[nh]])
11: tryCatchList(expr, classes, parentenv, handlers)
12: tryCatch(withCallingHandlers({ eval(code, test_env) if (!handled && !is.null(test)) { skip_empty() }}, expectation = handle_expectation, skip = handle_skip, warning = handle_warning, message = handle_message, error = handle_error), error = handle_fatal, skip = function(e) { })
13: test_code(desc, code, env = parent.frame(), default_reporter = local_interactive_reporter())
14: test_that("with with no source crs works", { f <- system.file("extdata/volcano.png", package = "vapour", mustWork = TRUE) info <- vapour_raster_info(f) ok <- vapour_warp_raster(f, dimension = info$dimension, extent = c(0, 1, 0, 1), transformation_options = c("SRC_METHOD=NO_GEOTRANSFORM")) if (dir.exists("/rdsi/PUBLIC/raad/data/www.ncei.noaa.gov")) { sds <- "NETCDF:/rdsi/PUBLIC/raad/data/www.ncei.noaa.gov/data/sea-surface-temperature-optimum-interpolation/v2.1/access/avhrr/198109/oisst-avhrr-v02r01.19810901.nc:sst" expect_silent(vapour_warp_raster(sds, extent = c(0, 1, 0, 1), dimension = c(4, 4))) expect_silent(vapour_warp_raster(sds, extent = c(0, 1, 0, 1), dimension = c(4, 4), source_projection = "+proj=laea")) expect_warning(vapour_warp_raster(sds, extent = c(0, 1, 0, 1), dimension = c(4, 4), projection = "OGC:CRS84")) } badnc <- system.file("extdata/gdal", "bad_netcdf_geoloc_arrays.nc", package = "vapour") sds <- vapour_sds_names(badnc) lcc <- "+proj=lcc +lat_0=-30 +lon_0=134.33 +lat_1=-50 +lat_2=-10 +R=6378137" ex <- c(-3077504, 3968504, -2763621, 3472383) vrt <- vapour_vrt(sds[3], geolocation = sds[2:1], bands = 1) info <- vapour_raster_info(vrt) expect_warning(im <- vapour_warp_raster_dbl(vrt, extent = ex, dimension = info$dimension, projection = lcc, transformation_options = c("SRC_METHOD=NO_GEOTRANSFORM"))) ex <- c(-180, 180, -90, 90) dm <- c(512, 1024) vrt <- vapour_vrt(sds[3], geolocation = sds[2:1], bands = 1) vapour::vapour_set_config("GDAL_NETCDF_BOTTOMUP", "NO") expect_warning(im <- vapour_warp_raster_dbl(vrt, extent = ex, dimension = dm, projection = "OGC:CRS84", transformation_options = c("SRC_METHOD=GEOLOC_ARRAY")))})
15: eval(code, test_env)
16: eval(code, test_env)
17: withCallingHandlers({ eval(code, test_env) if (!handled && !is.null(test)) { skip_empty() }}, expectation = handle_expectation, skip = handle_skip, warning = handle_warning, message = handle_message, error = handle_error)
18: doTryCatch(return(expr), name, parentenv, handler)
19: tryCatchOne(expr, names, parentenv, handlers[[1L]])
20: tryCatchList(expr, names[-nh], parentenv, handlers[-nh])
21: doTryCatch(return(expr), name, parentenv, handler)
22: tryCatchOne(tryCatchList(expr, names[-nh], parentenv, handlers[-nh]), names[nh], parentenv, handlers[[nh]])
23: tryCatchList(expr, classes, parentenv, handlers)
24: tryCatch(withCallingHandlers({ eval(code, test_env) if (!handled && !is.null(test)) { skip_empty() }}, expectation = handle_expectation, skip = handle_skip, warning = handle_warning, message = handle_message, error = handle_error), error = handle_fatal, skip = function(e) { })
25: test_code(test = NULL, code = exprs, env = env, default_reporter = StopReporter$new())
26: source_file(path, env = env(env), desc = desc, error_call = error_call)
27: FUN(X[[i]], ...)
28: lapply(test_paths, test_one_file, env = env, desc = desc, error_call = error_call)
29: doTryCatch(return(expr), name, parentenv, handler)
30: tryCatchOne(expr, names, parentenv, handlers[[1L]])
31: tryCatchList(expr, classes, parentenv, handlers)
32: tryCatch(code, testthat_abort_reporter = function(cnd) { cat(conditionMessage(cnd), "\n") NULL})
33: with_reporter(reporters$multi, lapply(test_paths, test_one_file, env = env, desc = desc, error_call = error_call))
34: test_files_serial(test_dir = test_dir, test_package = test_package, test_paths = test_paths, load_helpers = load_helpers, reporter = reporter, env = env, stop_on_failure = stop_on_failure, stop_on_warning = stop_on_warning, desc = desc, load_package = load_package, error_call = error_call)
35: test_files(test_dir = path, test_paths = test_paths, test_package = package, reporter = reporter, load_helpers = load_helpers, env = env, stop_on_failure = stop_on_failure, stop_on_warning = stop_on_warning, load_package = load_package, parallel = parallel)
36: test_dir("testthat", package = package, reporter = reporter, ..., load_package = "installed")
37: test_check("vapour")
An irrecoverable exception occurred. R is aborting now ...
Flavors: r-devel-linux-x86_64-fedora-clang, r-devel-linux-x86_64-fedora-gcc
Version: 0.9.5
Check: whether package can be installed
Result: ERROR
Installation failed.
Flavors: r-devel-windows-x86_64, r-release-windows-x86_64
Version: 0.9.5
Check: installed package size
Result: NOTE
installed size is 250.7Mb
sub-directories of 1Mb or more:
extdata 2.8Mb
libs 246.5Mb
Flavors: r-release-macos-arm64, r-release-macos-x86_64, r-oldrel-macos-arm64, r-oldrel-macos-x86_64, r-oldrel-windows-x86_64