[R-pkg-team] Bug#1000339: r-cran-raster breaks r-cran-satellite autopkgtest: unable to find an inherited method for function 'extend'
Andreas Tille
andreas at fam-tille.de
Tue Nov 30 08:48:52 GMT 2021
Control: forwarded -1 Robert J. Hijmans <r.hijmans at gmail.com>, Florian Detsch <fdetsch at web.de>
Control: tags -1 upstream
Control: tags -1 help
Hi Robert and Florian,
I'm contacting you as the maintainers or raster and satellite. As you
can see below in the Debian packaged versions of these packages some
conflict was raised in the test of satellite after the latest version of
raster was uploaded.
I'm perfectly aware that the packages are tested on CRAN and thus I
assume that possibly some special circumstances in the Debian packaged
version might lead to the issue that is reported in the bug below. I
wonder whether you can give some hints how to solve the conflict in the
test (at the very end of this mail).
Thanks a lot for your help
Andreas.
Am Sun, Nov 21, 2021 at 09:24:52PM +0100 schrieb Paul Gevers:
> 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
>
>
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