Andreas, 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).
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. >From what I can tell from this log: https://ci.debian.net/data/autopkgtest/testing/amd64/r/r-cran-satellite/16823806/log.gz 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). Is it possible that your session is actually loading satellite_1.0.2? Hope this helps, Robert On Tue, Nov 30, 2021 at 12:48 AM Andreas Tille <andr...@fam-tille.de> wrote: > Control: forwarded -1 Robert J. Hijmans <r.hijm...@gmail.com>, Florian > Detsch <fdet...@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...@lists.debian.org > > User: debian...@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@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 > > > > > > > > > > _______________________________________________ > > R-pkg-team mailing list > > r-pkg-t...@alioth-lists.debian.net > > https://alioth-lists.debian.net/cgi-bin/mailman/listinfo/r-pkg-team > > > -- > http://fam-tille.de >
debian_problem_satellite.R
Description: Binary data
