Dear all, I've received some notice from CRAN to fix issues in geometa
pkg i'm maintaining. I've fixed some issue, and tried to upload a
package package. I've tested the package on x86_64-pc-linux-gnu (64-bit)
/ Ubuntu 14.04.5 LTS, and Windows OS. For both, R CMD check goes well.
Here results for Win.
https://win-builder.r-project.org/7ZXV14p14Spe
https://win-builder.r-project.org/RwX93ZPJuMr8
https://win-builder.r-project.org/9O8W7dYJLlOW
I've received pre-archived message here below stating that they are
still issues on Debian.
I receive 2 messages that let me suspect this is due to an issue with
XML package:
Error: package or namespace load failed for ‘XML’:
.onLoad failed in loadNamespace() for ‘XML’, details:
call: dyn.load(file, DLLpath = DLLpath, ...)
error: unable to load shared object
‘/home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/XML/libs/XML.so’:
/home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/XML/libs/XML.so:
failed to map segment from shared object
(this message also appears in this moment for XML package checks
https://cran.r-project.org/web/checks/check_results_XML.html)
and
Unknown IO errorfailed to load external entity
Would someone have any idea what could be wrong? I'm stuck on that.
Thanks in advance for your help,
Best,
Emmanuel
-------- Message transféré --------
Sujet : [CRAN-pretest-archived] CRAN submission geometa 0.4-0
Date : Sun, 16 Dec 2018 17:24:56 +0100
De : lig...@statistik.tu-dortmund.de
Répondre à : cran-submissi...@r-project.org
Pour : emmanuel.blond...@gmail.com
Copie à : cran-submissi...@r-project.org
Dear maintainer,
package geometa_0.4-0.tar.gz does not pass the incoming checks
automatically, please see the following pre-tests:
Windows:
<https://win-builder.r-project.org/incoming_pretest/geometa_0.4-0_20181216_165029/Windows/00check.log>
Status: OK
Debian:
<https://win-builder.r-project.org/incoming_pretest/geometa_0.4-0_20181216_165029/Debian/00check.log>
Status: 2 ERRORs
Last released version's CRAN status: ERROR: 10, NOTE: 1, OK: 1
See: <https://CRAN.R-project.org/web/checks/check_results_geometa.html>
CRAN Web: <https://cran.r-project.org/package=geometa>
Please fix all problems and resubmit a fixed version via the webform.
If you are not sure how to fix the problems shown, please ask for help
on the R-package-devel mailing list:
<https://stat.ethz.ch/mailman/listinfo/r-package-devel>
If you are fairly certain the rejection is a false positive, please
reply-all to this message and explain.
More details are given in the directory:
<https://win-builder.r-project.org/incoming_pretest/geometa_0.4-0_20181216_165029/>
The files will be removed after roughly 7 days.
*** Strong rev. depends ***: geonapi ows4R
Best regards,
CRAN teams' auto-check service
Flavor: r-devel-linux-x86_64-debian-gcc, r-devel-windows-ix86+x86_64
Check: CRAN incoming feasibility, Result: Note_to_CRAN_maintainers
Maintainer: 'Emmanuel Blondel <emmanuel.blond...@gmail.com>'
Flavor: r-devel-windows-ix86+x86_64
Check: Overall checktime, Result: NOTE
Overall checktime 18 min > 10 min
Flavor: r-devel-linux-x86_64-debian-gcc
Check: examples, Result: ERROR
Running examples in 'geometa-Ex.R' failed
The error most likely occurred in:
> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: GMLBaseUnit
> ### Title: GMLBaseUnit
> ### Aliases: GMLBaseUnit
> ### Keywords: GML ISO base definition unit
>
> ### ** Examples
>
> gml <- GMLBaseUnit$new()
> gml$setDescriptionReference("someref")
> gml$setIdentifier("identifier", "codespace")
> gml$addName("name1", "codespace")
[1] TRUE
> gml$addName("name2", "codespace")
----------- FAILURE REPORT --------------
--- failure: length > 1 in coercion to logical ---
--- srcref ---
:
--- package (from environment) ---
geometa
--- call from context ---
FUN(X[[i]], ...)
--- call from argument ---
(class(self[[x]]) %in% c("environment", "function")) || (x %in%
private$system_fields)
--- R stacktrace ---
where 1: FUN(X[[i]], ...)
where 2: lapply(X = X, FUN = FUN, ...)
where 3: sapply(fields, function(x) {
(class(self[[x]]) %in% c("environment", "function")) || (x %in%
private$system_fields)
})
where 4: metadataElement1$encode(addNS = TRUE, validate = FALSE,
resetSerialID = FALSE,
setSerialID = FALSE)
where 5: ISOAbstractObject$compare(x, metadataElement)
where 6: FUN(X[[i]], ...)
where 7: lapply(X = X, FUN = FUN, ...)
where 8: sapply(self[[field]], function(x) {
ISOAbstractObject$compare(x, metadataElement)
})
where 9: self$contains(field, metadataElement)
where 10: self$addListElement("name", gmlElem)
where 11: gml$addName("name2", "codespace")
--- value of length: 2 type: logical ---
[1] FALSE FALSE
--- function from context ---
function (x)
{
(class(self[[x]]) %in% c("environment", "function")) || (x %in%
private$system_fields)
}
<environment: 0x7f5131e9cce8>
--- function search by body ---
----------- END OF FAILURE REPORT --------------
Fatal error: length > 1 in coercion to logical
Flavor: r-devel-linux-x86_64-debian-gcc
Check: tests, Result: ERROR
Running 'test-all.R' [5s/20s]
Running the tests in 'tests/test-all.R' failed.
Complete output:
> library(testthat)
> library(geometa)
Loading ISO 19139 XML schemas...
Loading ISO 19115 codelists...
> test_check("geometa")
----------- FAILURE REPORT --------------
--- failure: length > 1 in coercion to logical ---
--- srcref ---
:
--- package (from environment) ---
geometa
--- call from context ---
FUN(X[[i]], ...)
--- call from argument ---
(class(self[[x]]) %in% c("environment", "function")) || (x %in%
private$system_fields)
--- R stacktrace ---
where 1: FUN(X[[i]], ...)
where 2: lapply(X = X, FUN = FUN, ...)
where 3: sapply(fields, function(x) {
(class(self[[x]]) %in% c("environment", "function")) || (x %in%
private$system_fields)
})
where 4: metadataElement1$encode(addNS = TRUE, validate = FALSE,
resetSerialID = FALSE,
setSerialID = FALSE)
where 5: ISOAbstractObject$compare(x, metadataElement)
where 6: FUN(X[[i]], ...)
where 7: lapply(X = X, FUN = FUN, ...)
where 8: sapply(self[[field]], function(x) {
ISOAbstractObject$compare(x, metadataElement)
})
where 9: self$contains(field, metadataElement)
where 10: self$addListElement("name", gmlElem)
where 11 at testthat/test_GMLParameterValue.R#44: op$addName("name2",
"codespace")
where 12: eval(code, test_env)
where 13: eval(code, test_env)
where 14: 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)
where 15: doTryCatch(return(expr), name, parentenv, handler)
where 16: tryCatchOne(expr, names, parentenv, handlers[[1L]])
where 17: tryCatchList(expr, names[-nh], parentenv, handlers[-nh])
where 18: doTryCatch(return(expr), name, parentenv, handler)
where 19: tryCatchOne(tryCatchList(expr, names[-nh], parentenv,
handlers[-nh]),
names[nh], parentenv, handlers[[nh]])
where 20: tryCatchList(expr, classes, parentenv, handlers)
where 21: 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) {
})
where 22: test_code(desc, code, env = parent.frame())
where 23 at testthat/test_GMLParameterValue.R#36: test_that("encoding -
stringValue", {
gml <- GMLParameterValue$new()
gml$setStringValue("test")
op <- GMLOperationParameter$new()
op$setDescriptionReference("someref")
op$setIdentifier("identifier", "codespace")
op$addName("name1", "codespace")
op$addName("name2", "codespace")
op$setMinimumOccurs(2L)
gml$setOperationParameter(op)
xml <- gml$encode()
expect_is(xml, "XMLInternalNode")
gml2 <- GMLParameterValue$new(xml = xml)
xml2 <- gml2$encode()
expect_true(ISOAbstractObject$compare(gml, gml2))
})
where 24: eval(code, test_env)
where 25: eval(code, test_env)
where 26: withCallingHandlers({
eval(code, test_env)
if (!handled && !is.null(test)) {
skip_empty()
}
}, expectation = handle_expectation, skip = handle_skip, warning =
handle_warning,
message = handle_message, error = handle_error)
where 27: doTryCatch(return(expr), name, parentenv, handler)
where 28: tryCatchOne(expr, names, parentenv, handlers[[1L]])
where 29: tryCatchList(expr, names[-nh], parentenv, handlers[-nh])
where 30: doTryCatch(return(expr), name, parentenv, handler)
where 31: tryCatchOne(tryCatchList(expr, names[-nh], parentenv,
handlers[-nh]),
names[nh], parentenv, handlers[[nh]])
where 32: tryCatchList(expr, classes, parentenv, handlers)
where 33: tryCatch(withCallingHandlers({
eval(code, test_env)
if (!handled && !is.null(test)) {
skip_empty()
}
}, expectation = handle_expectation, skip = handle_skip, warning =
handle_warning,
message = handle_message, error = handle_error), error = handle_fatal,
skip = function(e) {
})
where 34: test_code(NULL, exprs, env)
where 35: source_file(path, new.env(parent = env), chdir = TRUE, wrap =
wrap)
where 36: force(code)
where 37: with_reporter(reporter = reporter, start_end_reporter =
start_end_reporter,
{
lister$start_file(basename(path))
source_file(path, new.env(parent = env), chdir = TRUE,
wrap = wrap)
end_context()
})
where 38: FUN(X[[i]], ...)
where 39: lapply(paths, test_file, env = env, reporter = current_reporter,
start_end_reporter = FALSE, load_helpers = FALSE, wrap = wrap)
where 40: force(code)
where 41: with_reporter(reporter = current_reporter, results <-
lapply(paths,
test_file, env = env, reporter = current_reporter, start_end_reporter =
FALSE,
load_helpers = FALSE, wrap = wrap))
where 42: test_files(paths, reporter = reporter, env = env, stop_on_failure
= stop_on_failure,
stop_on_warning = stop_on_warning, wrap = wrap)
where 43: 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)
where 44: 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)
where 45: test_check("geometa")
--- value of length: 2 type: logical ---
[1] FALSE FALSE
--- function from context ---
function (x)
{
(class(self[[x]]) %in% c("environment", "function")) || (x %in%
private$system_fields)
}
<environment: 0x7fbe6ddd9dc8>
--- function search by body ---
----------- END OF FAILURE REPORT --------------
Fatal error: length > 1 in coercion to logical
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