[R-pkg-team] Bug#1000339: r-cran-raster breaks r-cran-satellite autopkgtest: unable to find an inherited method for function 'extend'
Paul Gevers
elbrus at debian.org
Sun Nov 21 20:24:52 GMT 2021
Source: r-cran-raster, r-cran-satellite
Control: found -1 r-cran-raster/3.5-2-1
Control: found -1 r-cran-satellite/1.0.4-1
Severity: serious
Tags: sid bookworm
X-Debbugs-CC: debian-ci at lists.debian.org
User: debian-ci at lists.debian.org
Usertags: breaks needs-update
Dear maintainer(s),
With a recent upload of r-cran-raster the autopkgtest of
r-cran-satellite fails in testing when that autopkgtest is run with the
binary packages of r-cran-raster from unstable. It passes when run with
only packages from testing. In tabular form:
pass fail
r-cran-raster from testing 3.5-2-1
r-cran-satellite from testing 1.0.4-1
all others from testing from testing
I copied some of the output at the bottom of this report.
Currently this regression is blocking the migration of r-cran-raster to
testing [1]. Due to the nature of this issue, I filed this bug report
against both packages. Can you please investigate the situation and
reassign the bug to the right package?
More information about this bug and the reason for filing it can be found on
https://wiki.debian.org/ContinuousIntegration/RegressionEmailInformation
Paul
[1] https://qa.debian.org/excuses.php?package=r-cran-raster
https://ci.debian.net/data/autopkgtest/testing/amd64/r/r-cran-satellite/16823806/log.gz
BEGIN TEST testthat.R
R version 4.1.2 (2021-11-01) -- "Bird Hippie"
Copyright (C) 2021 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.
R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.
Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.
> library(testthat)
> library(satellite)
Loading required package: raster
Loading required package: sp
code for methods in class "Rcpp_SpatCategories" was not checked for
suspicious field assignments (recommended package 'codetools' not
available?)
code for methods in class "Rcpp_SpatCategories" was not checked for
suspicious field assignments (recommended package 'codetools' not
available?)
code for methods in class "Rcpp_SpatDataFrame" was not checked for
suspicious field assignments (recommended package 'codetools' not
available?)
code for methods in class "Rcpp_SpatDataFrame" was not checked for
suspicious field assignments (recommended package 'codetools' not
available?)
code for methods in class "Rcpp_SpatExtent" was not checked for
suspicious field assignments (recommended package 'codetools' not
available?)
code for methods in class "Rcpp_SpatExtent" was not checked for
suspicious field assignments (recommended package 'codetools' not
available?)
code for methods in class "Rcpp_SpatMessages" was not checked for
suspicious field assignments (recommended package 'codetools' not
available?)
code for methods in class "Rcpp_SpatMessages" was not checked for
suspicious field assignments (recommended package 'codetools' not
available?)
code for methods in class "Rcpp_SpatOptions" was not checked for
suspicious field assignments (recommended package 'codetools' not
available?)
code for methods in class "Rcpp_SpatOptions" was not checked for
suspicious field assignments (recommended package 'codetools' not
available?)
code for methods in class "Rcpp_SpatRaster" was not checked for
suspicious field assignments (recommended package 'codetools' not
available?)
code for methods in class "Rcpp_SpatRaster" was not checked for
suspicious field assignments (recommended package 'codetools' not
available?)
code for methods in class "Rcpp_SpatRasterCollection" was not checked
for suspicious field assignments (recommended package 'codetools' not
available?)
code for methods in class "Rcpp_SpatRasterCollection" was not checked
for suspicious field assignments (recommended package 'codetools' not
available?)
code for methods in class "Rcpp_SpatRasterStack" was not checked for
suspicious field assignments (recommended package 'codetools' not
available?)
code for methods in class "Rcpp_SpatRasterStack" was not checked for
suspicious field assignments (recommended package 'codetools' not
available?)
code for methods in class "Rcpp_SpatSRS" was not checked for suspicious
field assignments (recommended package 'codetools' not available?)
code for methods in class "Rcpp_SpatSRS" was not checked for suspicious
field assignments (recommended package 'codetools' not available?)
code for methods in class "Rcpp_SpatVector" was not checked for
suspicious field assignments (recommended package 'codetools' not
available?)
code for methods in class "Rcpp_SpatVector" was not checked for
suspicious field assignments (recommended package 'codetools' not
available?)
code for methods in class "Rcpp_SpatVectorCollection" was not checked
for suspicious field assignments (recommended package 'codetools' not
available?)
code for methods in class "Rcpp_SpatVectorCollection" was not checked
for suspicious field assignments (recommended package 'codetools' not
available?)
code for methods in class "Rcpp_SpExtent" was not checked for suspicious
field assignments (recommended package 'codetools' not available?)
code for methods in class "Rcpp_SpExtent" was not checked for suspicious
field assignments (recommended package 'codetools' not available?)
code for methods in class "Rcpp_SpPoly" was not checked for suspicious
field assignments (recommended package 'codetools' not available?)
code for methods in class "Rcpp_SpPoly" was not checked for suspicious
field assignments (recommended package 'codetools' not available?)
code for methods in class "Rcpp_SpPolyPart" was not checked for
suspicious field assignments (recommended package 'codetools' not
available?)
code for methods in class "Rcpp_SpPolyPart" was not checked for
suspicious field assignments (recommended package 'codetools' not
available?)
code for methods in class "Rcpp_SpPolygons" was not checked for
suspicious field assignments (recommended package 'codetools' not
available?)
code for methods in class "Rcpp_SpPolygons" was not checked for
suspicious field assignments (recommended package 'codetools' not
available?)
Warning messages:
1: multiple methods tables found for 'crop' 2: multiple methods tables
found for 'extend' > > > ### functions to create test data sets -----
>
> ### Utility functions to quickly create test data sets for various sensors
> ### Florian Detsch, last modified on 2017-07-24
>
> tst_obj <- function(type = c("LC08", "LC8", "LE07", "LE7", "LT05")) {
+ if (type[1] == "LC08")
+ tst_obj_lc08()
+ else if (type[1] == "LC8")
+ tst_obj_lc8()
+ else if (type[1] == "LE07")
+ tst_obj_le07()
+ else if (type[1] == "LE7")
+ tst_obj_le7()
+ else if (type[1] == "LT05")
+ tst_obj_lt05()
+ else + stop("Sensor test data not available, yet.\n")
+ }
>
>
> ### collection 1 level-1 -----
>
> ## landsat 8
> tst_obj_lc08 <- function() {
+ path <- system.file("extdata", package = "satellite")
+ files <- list.files(path, pattern = glob2rx("LC08*.TIF"), full.names
= TRUE)
+ satellite(files)
+ }
>
> ## landsat 7
> tst_obj_le07 <- function() {
+ path <- system.file("extdata", package = "satellite")
+ files <- list.files(path, pattern = glob2rx("LE07*.TIF"), full.names
= TRUE)
+ satellite(files)
+ }
>
> ## landsat 5
> tst_obj_lt05 <- function() {
+ path <- system.file("testdata/LT05", package = "satellite")
+ files <- list.files(path, pattern = glob2rx("LT05*.TIF"), full.names
= TRUE)
+ satellite(files)
+ }
>
>
> ### precollection level-1 -----
>
> ## landsat 8
> tst_obj_lc8 <- function() {
+ path <- system.file("testdata/LC8", package = "satellite")
+ files <- list.files(path, pattern = glob2rx("LC8*.TIF"), full.names
= TRUE)
+ satellite(files)
+ }
>
> ## landsat 7
> tst_obj_le7 <- function() {
+ path <- system.file("testdata/LE7", package = "satellite")
+ files <- list.files(path, pattern = glob2rx("LE7*.TIF"), full.names
= TRUE)
+ satellite(files)
+ }
>
>
> ### perform tests -----
>
> test_check("satellite")
== Skipped tests
===============================================================
* empty test (12)
== Failed tests
================================================================
-- Error (test-extend.R:9:1): (code run outside of `test_that()`)
--------------
Error in `(function (classes, fdef, mtable) {
methods <- .findInheritedMethods(classes, fdef, mtable)
if (length(methods) == 1L) return(methods[[1L]])
else if (length(methods) == 0L) {
cnames <- paste0("\"", vapply(classes, as.character,
""), "\"", collapse = ", ")
stop(gettextf("unable to find an inherited method for function
%s for signature %s", sQuote(fdef at generic), sQuote(cnames)),
domain = NA)
}
else stop("Internal error in finding inherited methods; didn't
return a unique method", domain = NA)
})(list(structure("Satellite", package = "satellite")),
new("standardGeneric", .Data = function (x, y, ...)
standardGeneric("extend"), generic = structure("extend", package =
"terra"), package = "terra", group = list(), valueClass =
character(0), signature = c("x", "y"), default = NULL, skeleton =
(function (x, y, ...) stop("invalid call in method dispatch
to 'extend' (no default method)", domain = NA))(x, y, ...)),
<environment>)`: unable to find an inherited method for function
'extend' for signature '"Satellite"'
Backtrace:
x
1. \-terra::extend(sat, ext_ggs) test-extend.R:9:0
2. \-(function (classes, fdef, mtable) ...
[ FAIL 1 | WARN 0 | SKIP 12 | PASS 139 ]
Error: Test failures
Execution halted
autopkgtest [20:13:13]: test run-unit-test
-------------- next part --------------
A non-text attachment was scrubbed...
Name: OpenPGP_signature
Type: application/pgp-signature
Size: 495 bytes
Desc: OpenPGP digital signature
URL: <http://alioth-lists.debian.net/pipermail/r-pkg-team/attachments/20211121/6c99b2bf/attachment.sig>
More information about the R-pkg-team
mailing list