<div dir="ltr">Andreas, <br class="gmail-Apple-interchange-newline"><div><br>The background of this problem is the change in dependency between "raster" and "terra". "terra" was dependent on "raster"; now it is the other way around. This change was made in terra 1.4-07, 1.4-09 and 1.4-11 that were released between 2021-10-05 and 2021-10-11, and in raster 3.5-2 (2021-10-11).<br></div><div><br></div><div>In the attachment I show the behavior of `library(satellite)` with the raster package prior to 2021-10-11, with the current versions, and for possible intermediate steps. It shows that you can get the warnings you see if you have current versions of terra/raster but an old version of satellite. </div><div><br></div><div>>From what I can tell from this log:</div><div><a href="https://ci.debian.net/data/autopkgtest/testing/amd64/r/r-cran-satellite/16823806/log.gz">https://ci.debian.net/data/autopkgtest/testing/amd64/r/r-cran-satellite/16823806/log.gz</a><br></div><div>you are using satellite_1.0.4 and raster_3.5-2 (current versions), and terra_1.4-11 (the current version is 1.4-22; but 1.4-11 should be OK). </div><div><br></div><div>Is it possible that your session is actually loading satellite_1.0.2?</div><div><br></div><div>Hope this helps, </div><div>Robert</div><div><br></div></div><br><div class="gmail_quote"><div dir="ltr" class="gmail_attr">On Tue, Nov 30, 2021 at 12:48 AM Andreas Tille <<a href="mailto:andreas@fam-tille.de">andreas@fam-tille.de</a>> wrote:<br></div><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex">Control: forwarded -1 Robert J. Hijmans <<a href="mailto:r.hijmans@gmail.com" target="_blank">r.hijmans@gmail.com</a>>, Florian Detsch <<a href="mailto:fdetsch@web.de" target="_blank">fdetsch@web.de</a>><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: <a href="mailto:debian-ci@lists.debian.org" target="_blank">debian-ci@lists.debian.org</a><br>
> User: <a href="mailto:debian-ci@lists.debian.org" target="_blank">debian-ci@lists.debian.org</a><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" rel="noreferrer" 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" rel="noreferrer" 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" rel="noreferrer" 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>
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> <a href="mailto:R-pkg-team@alioth-lists.debian.net" target="_blank">R-pkg-team@alioth-lists.debian.net</a><br>
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<br>
<br>
-- <br>
<a href="http://fam-tille.de" rel="noreferrer" target="_blank">http://fam-tille.de</a><br>
</blockquote></div>