<html><head></head><body><div style="font-family: Verdana;font-size: 12.0px;"><div>Andreas,</div>
<div> </div>
<div>Thanks for bringing up this issue. </div>
<div> </div>
<div>I am not able to reproduce these check results when testing satellite with the latest raster version on an Ubuntu OS (sessionInfo() included below).</div>
<div>@Robert, sounds to me like this is related to what we discussed a couple of weeks ago. Maybe changes introduces to satellite with https://github.com/environmentalinformatics-marburg/satellite/commit/08837e9a04ae7bdb481d3ca0342fb3c9b81be891 weren't enough.. any ideas?</div>
<div>
<div> </div>
<div>Thanks, </div>
<div>Florian</div>
<div>
<div> </div>
<div><span style="font-family:Courier New,Courier,monospace;">sessionInfo():</span></div>
<div> </div>
<div>
<div>
<div><span style="font-family:Courier New,Courier,monospace;">R version 4.1.2 (2021-11-01)<br/>
Platform: x86_64-pc-linux-gnu (64-bit)<br/>
Running under: Ubuntu 20.04.3 LTS</span></div>
<div><span style="font-family:Courier New,Courier,monospace;">Matrix products: default<br/>
BLAS: /usr/lib/x86_64-linux-gnu/blas/libblas.so.3.9.0<br/>
LAPACK: /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.9.0</span></div>
<div><span style="font-family:Courier New,Courier,monospace;">locale:<br/>
[1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C LC_TIME=de_DE.UTF-8 <br/>
[4] LC_COLLATE=en_US.UTF-8 LC_MONETARY=de_DE.UTF-8 LC_MESSAGES=en_US.UTF-8 <br/>
[7] LC_PAPER=de_DE.UTF-8 LC_NAME=C LC_ADDRESS=C <br/>
[10] LC_TELEPHONE=C LC_MEASUREMENT=de_DE.UTF-8 LC_IDENTIFICATION=C </span></div>
<div><span style="font-family:Courier New,Courier,monospace;">attached base packages:<br/>
[1] stats graphics grDevices utils datasets methods base </span></div>
<div><span style="font-family:Courier New,Courier,monospace;">other attached packages:<br/>
[1] satellite_1.0.4 raster_3.5-2 sp_1.4-6 </span></div>
<div><span style="font-family:Courier New,Courier,monospace;">loaded via a namespace (and not attached):<br/>
[1] compiler_4.1.2 cli_3.1.0 tools_4.1.2 Rcpp_1.0.7 <br/>
[5] codetools_0.2-18 grid_4.1.2 stats4_4.1.2 prompt_1.0.1 <br/>
[9] lattice_0.20-45 terra_1.4-22 </span></div>
</div>
<div> </div>
</div>
<div name="quote" style="margin:10px 5px 5px 10px; padding: 10px 0 10px 10px; border-left:2px solid #C3D9E5; word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space;">
<div style="margin:0 0 10px 0;"><b>Gesendet:</b> Dienstag, 30. November 2021 um 09:48 Uhr<br/>
<b>Von:</b> "Andreas Tille" <andreas@fam-tille.de><br/>
<b>An:</b> 1000339@bugs.debian.org, "Robert J. Hijmans" <r.hijmans@gmail.com>, "Florian Detsch" <fdetsch@web.de><br/>
<b>Betreff:</b> Re: Bug#1000339: r-cran-raster breaks r-cran-satellite autopkgtest: unable to find an inherited method for function 'extend'</div>
<div name="quoted-content">Control: forwarded -1 Robert J. Hijmans <r.hijmans@gmail.com>, Florian Detsch <fdetsch@web.de><br/>
Control: tags -1 upstream<br/>
Control: tags -1 help<br/>
<br/>
Hi Robert and Florian,<br/>
<br/>
I'm contacting you as the maintainers or raster and satellite. As you<br/>
can see below in the Debian packaged versions of these packages some<br/>
conflict was raised in the test of satellite after the latest version of<br/>
raster was uploaded.<br/>
<br/>
I'm perfectly aware that the packages are tested on CRAN and thus I<br/>
assume that possibly some special circumstances in the Debian packaged<br/>
version might lead to the issue that is reported in the bug below. I<br/>
wonder whether you can give some hints how to solve the conflict in the<br/>
test (at the very end of this mail).<br/>
<br/>
Thanks a lot for your help<br/>
<br/>
Andreas.<br/>
<br/>
Am Sun, Nov 21, 2021 at 09:24:52PM +0100 schrieb Paul Gevers:<br/>
> Source: r-cran-raster, r-cran-satellite<br/>
> Control: found -1 r-cran-raster/3.5-2-1<br/>
> Control: found -1 r-cran-satellite/1.0.4-1<br/>
> Severity: serious<br/>
> Tags: sid bookworm<br/>
> X-Debbugs-CC: debian-ci@lists.debian.org<br/>
> User: debian-ci@lists.debian.org<br/>
> Usertags: breaks needs-update<br/>
><br/>
> Dear maintainer(s),<br/>
><br/>
> With a recent upload of r-cran-raster the autopkgtest of r-cran-satellite<br/>
> fails in testing when that autopkgtest is run with the binary packages of<br/>
> r-cran-raster from unstable. It passes when run with only packages from<br/>
> testing. In tabular form:<br/>
><br/>
> pass fail<br/>
> r-cran-raster from testing 3.5-2-1<br/>
> r-cran-satellite from testing 1.0.4-1<br/>
> all others from testing from testing<br/>
><br/>
> I copied some of the output at the bottom of this report.<br/>
><br/>
> Currently this regression is blocking the migration of r-cran-raster to<br/>
> testing [1]. Due to the nature of this issue, I filed this bug report<br/>
> against both packages. Can you please investigate the situation and reassign<br/>
> the bug to the right package?<br/>
><br/>
> More information about this bug and the reason for filing it can be found on<br/>
> <a href="https://wiki.debian.org/ContinuousIntegration/RegressionEmailInformation" target="_blank">https://wiki.debian.org/ContinuousIntegration/RegressionEmailInformation</a><br/>
><br/>
> Paul<br/>
><br/>
> [1] <a href="https://qa.debian.org/excuses.php?package=r-cran-raster" target="_blank">https://qa.debian.org/excuses.php?package=r-cran-raster</a><br/>
><br/>
> <a href="https://ci.debian.net/data/autopkgtest/testing/amd64/r/r-cran-satellite/16823806/log.gz" target="_blank">https://ci.debian.net/data/autopkgtest/testing/amd64/r/r-cran-satellite/16823806/log.gz</a><br/>
><br/>
> BEGIN TEST testthat.R<br/>
><br/>
> R version 4.1.2 (2021-11-01) -- "Bird Hippie"<br/>
> Copyright (C) 2021 The R Foundation for Statistical Computing<br/>
> Platform: x86_64-pc-linux-gnu (64-bit)<br/>
><br/>
> R is free software and comes with ABSOLUTELY NO WARRANTY.<br/>
> You are welcome to redistribute it under certain conditions.<br/>
> Type 'license()' or 'licence()' for distribution details.<br/>
><br/>
> R is a collaborative project with many contributors.<br/>
> Type 'contributors()' for more information and<br/>
> 'citation()' on how to cite R or R packages in publications.<br/>
><br/>
> Type 'demo()' for some demos, 'help()' for on-line help, or<br/>
> 'help.start()' for an HTML browser interface to help.<br/>
> Type 'q()' to quit R.<br/>
><br/>
> > library(testthat)<br/>
> > library(satellite)<br/>
> Loading required package: raster<br/>
> Loading required package: sp<br/>
> code for methods in class "Rcpp_SpatCategories" was not checked for<br/>
> suspicious field assignments (recommended package 'codetools' not<br/>
> available?)<br/>
> code for methods in class "Rcpp_SpatCategories" was not checked for<br/>
> suspicious field assignments (recommended package 'codetools' not<br/>
> available?)<br/>
> code for methods in class "Rcpp_SpatDataFrame" was not checked for<br/>
> suspicious field assignments (recommended package 'codetools' not<br/>
> available?)<br/>
> code for methods in class "Rcpp_SpatDataFrame" was not checked for<br/>
> suspicious field assignments (recommended package 'codetools' not<br/>
> available?)<br/>
> code for methods in class "Rcpp_SpatExtent" was not checked for suspicious<br/>
> field assignments (recommended package 'codetools' not available?)<br/>
> code for methods in class "Rcpp_SpatExtent" was not checked for suspicious<br/>
> field assignments (recommended package 'codetools' not available?)<br/>
> code for methods in class "Rcpp_SpatMessages" was not checked for suspicious<br/>
> field assignments (recommended package 'codetools' not available?)<br/>
> code for methods in class "Rcpp_SpatMessages" was not checked for suspicious<br/>
> field assignments (recommended package 'codetools' not available?)<br/>
> code for methods in class "Rcpp_SpatOptions" was not checked for suspicious<br/>
> field assignments (recommended package 'codetools' not available?)<br/>
> code for methods in class "Rcpp_SpatOptions" was not checked for suspicious<br/>
> field assignments (recommended package 'codetools' not available?)<br/>
> code for methods in class "Rcpp_SpatRaster" was not checked for suspicious<br/>
> field assignments (recommended package 'codetools' not available?)<br/>
> code for methods in class "Rcpp_SpatRaster" was not checked for suspicious<br/>
> field assignments (recommended package 'codetools' not available?)<br/>
> code for methods in class "Rcpp_SpatRasterCollection" was not checked for<br/>
> suspicious field assignments (recommended package 'codetools' not<br/>
> available?)<br/>
> code for methods in class "Rcpp_SpatRasterCollection" was not checked for<br/>
> suspicious field assignments (recommended package 'codetools' not<br/>
> available?)<br/>
> code for methods in class "Rcpp_SpatRasterStack" was not checked for<br/>
> suspicious field assignments (recommended package 'codetools' not<br/>
> available?)<br/>
> code for methods in class "Rcpp_SpatRasterStack" was not checked for<br/>
> suspicious field assignments (recommended package 'codetools' not<br/>
> available?)<br/>
> code for methods in class "Rcpp_SpatSRS" was not checked for suspicious<br/>
> field assignments (recommended package 'codetools' not available?)<br/>
> code for methods in class "Rcpp_SpatSRS" was not checked for suspicious<br/>
> field assignments (recommended package 'codetools' not available?)<br/>
> code for methods in class "Rcpp_SpatVector" was not checked for suspicious<br/>
> field assignments (recommended package 'codetools' not available?)<br/>
> code for methods in class "Rcpp_SpatVector" was not checked for suspicious<br/>
> field assignments (recommended package 'codetools' not available?)<br/>
> code for methods in class "Rcpp_SpatVectorCollection" was not checked for<br/>
> suspicious field assignments (recommended package 'codetools' not<br/>
> available?)<br/>
> code for methods in class "Rcpp_SpatVectorCollection" was not checked for<br/>
> suspicious field assignments (recommended package 'codetools' not<br/>
> available?)<br/>
> code for methods in class "Rcpp_SpExtent" was not checked for suspicious<br/>
> field assignments (recommended package 'codetools' not available?)<br/>
> code for methods in class "Rcpp_SpExtent" was not checked for suspicious<br/>
> field assignments (recommended package 'codetools' not available?)<br/>
> code for methods in class "Rcpp_SpPoly" was not checked for suspicious field<br/>
> assignments (recommended package 'codetools' not available?)<br/>
> code for methods in class "Rcpp_SpPoly" was not checked for suspicious field<br/>
> assignments (recommended package 'codetools' not available?)<br/>
> code for methods in class "Rcpp_SpPolyPart" was not checked for suspicious<br/>
> field assignments (recommended package 'codetools' not available?)<br/>
> code for methods in class "Rcpp_SpPolyPart" was not checked for suspicious<br/>
> field assignments (recommended package 'codetools' not available?)<br/>
> code for methods in class "Rcpp_SpPolygons" was not checked for suspicious<br/>
> field assignments (recommended package 'codetools' not available?)<br/>
> code for methods in class "Rcpp_SpPolygons" was not checked for suspicious<br/>
> field assignments (recommended package 'codetools' not available?)<br/>
> Warning messages:<br/>
> 1: multiple methods tables found for 'crop' 2: multiple methods tables found<br/>
> for 'extend' > > > ### functions to create test data sets -----<br/>
> ><br/>
> > ### Utility functions to quickly create test data sets for various sensors<br/>
> > ### Florian Detsch, last modified on 2017-07-24<br/>
> ><br/>
> > tst_obj <- function(type = c("LC08", "LC8", "LE07", "LE7", "LT05")) {<br/>
> + if (type[1] == "LC08")<br/>
> + tst_obj_lc08()<br/>
> + else if (type[1] == "LC8")<br/>
> + tst_obj_lc8()<br/>
> + else if (type[1] == "LE07")<br/>
> + tst_obj_le07()<br/>
> + else if (type[1] == "LE7")<br/>
> + tst_obj_le7()<br/>
> + else if (type[1] == "LT05")<br/>
> + tst_obj_lt05()<br/>
> + else + stop("Sensor test data not available, yet.\n")<br/>
> + }<br/>
> ><br/>
> ><br/>
> > ### collection 1 level-1 -----<br/>
> ><br/>
> > ## landsat 8<br/>
> > tst_obj_lc08 <- function() {<br/>
> + path <- system.file("extdata", package = "satellite")<br/>
> + files <- list.files(path, pattern = glob2rx("LC08*.TIF"), full.names =<br/>
> TRUE)<br/>
> + satellite(files)<br/>
> + }<br/>
> ><br/>
> > ## landsat 7<br/>
> > tst_obj_le07 <- function() {<br/>
> + path <- system.file("extdata", package = "satellite")<br/>
> + files <- list.files(path, pattern = glob2rx("LE07*.TIF"), full.names =<br/>
> TRUE)<br/>
> + satellite(files)<br/>
> + }<br/>
> ><br/>
> > ## landsat 5<br/>
> > tst_obj_lt05 <- function() {<br/>
> + path <- system.file("testdata/LT05", package = "satellite")<br/>
> + files <- list.files(path, pattern = glob2rx("LT05*.TIF"), full.names =<br/>
> TRUE)<br/>
> + satellite(files)<br/>
> + }<br/>
> ><br/>
> ><br/>
> > ### precollection level-1 -----<br/>
> ><br/>
> > ## landsat 8<br/>
> > tst_obj_lc8 <- function() {<br/>
> + path <- system.file("testdata/LC8", package = "satellite")<br/>
> + files <- list.files(path, pattern = glob2rx("LC8*.TIF"), full.names =<br/>
> TRUE)<br/>
> + satellite(files)<br/>
> + }<br/>
> ><br/>
> > ## landsat 7<br/>
> > tst_obj_le7 <- function() {<br/>
> + path <- system.file("testdata/LE7", package = "satellite")<br/>
> + files <- list.files(path, pattern = glob2rx("LE7*.TIF"), full.names =<br/>
> TRUE)<br/>
> + satellite(files)<br/>
> + }<br/>
> ><br/>
> ><br/>
> > ### perform tests -----<br/>
> ><br/>
> > test_check("satellite")<br/>
> == Skipped tests<br/>
> ===============================================================<br/>
> * empty test (12)<br/>
><br/>
> == Failed tests<br/>
> ================================================================<br/>
> -- Error (test-extend.R:9:1): (code run outside of `test_that()`)<br/>
> --------------<br/>
> Error in `(function (classes, fdef, mtable) {<br/>
> methods <- .findInheritedMethods(classes, fdef, mtable)<br/>
> if (length(methods) == 1L) return(methods[[1L]])<br/>
> else if (length(methods) == 0L) {<br/>
> cnames <- paste0("\"", vapply(classes, as.character, ""), "\"",<br/>
> collapse = ", ")<br/>
> stop(gettextf("unable to find an inherited method for function %s<br/>
> for signature %s", sQuote(fdef@generic), sQuote(cnames)), domain<br/>
> = NA)<br/>
> }<br/>
> else stop("Internal error in finding inherited methods; didn't return a<br/>
> unique method", domain = NA)<br/>
> })(list(structure("Satellite", package = "satellite")),<br/>
> new("standardGeneric", .Data = function (x, y, ...)<br/>
> standardGeneric("extend"), generic = structure("extend", package = "terra"),<br/>
> package = "terra", group = list(), valueClass = character(0), signature<br/>
> = c("x", "y"), default = NULL, skeleton = (function (x, y, ...)<br/>
> stop("invalid call in method dispatch to 'extend' (no default method)",<br/>
> domain = NA))(x, y, ...)), <environment>)`: unable to find an inherited<br/>
> method for function 'extend' for signature '"Satellite"'<br/>
> Backtrace:<br/>
> x<br/>
> 1. \-terra::extend(sat, ext_ggs) test-extend.R:9:0<br/>
> 2. \-(function (classes, fdef, mtable) ...<br/>
><br/>
> [ FAIL 1 | WARN 0 | SKIP 12 | PASS 139 ]<br/>
> Error: Test failures<br/>
> Execution halted<br/>
> autopkgtest [20:13:13]: test run-unit-test<br/>
><br/>
><br/>
<br/>
<br/>
<br/>
<br/>
> _______________________________________________<br/>
> R-pkg-team mailing list<br/>
> R-pkg-team@alioth-lists.debian.net<br/>
> <a href="https://alioth-lists.debian.net/cgi-bin/mailman/listinfo/r-pkg-team" target="_blank">https://alioth-lists.debian.net/cgi-bin/mailman/listinfo/r-pkg-team</a><br/>
<br/>
<br/>
--<br/>
<a href="http://fam-tille.de" target="_blank">http://fam-tille.de</a></div>
</div>
</div>
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