Bug#1000339: r-cran-raster breaks r-cran-satellite autopkgtest: unable to find an inherited method for function 'extend'
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 wrote: > Control: forwarded -1 Robert J. Hijmans , Florian > Detsch > 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: > > > >passfail > > r-cran-raster from testing3.5-2-1 > > r-cran-satellite from testing1.0.4-1 > > all others from testingfrom 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 (recomm
Bug#1000339: r-cran-raster breaks r-cran-satellite autopkgtest: unable to find an inherited method for function 'extend'
On Tue, Nov 30, 2021 at 10:46 PM Andreas Tille wrote: > Dear Robert, > > Am Tue, Nov 30, 2021 at 09:18:18PM -0800 schrieb Robert J. Hijmans: > > Dear Andreas, > > > > raster 3-5.2 depends on terra; but it does not specify which version of > > terra. I believe it needs to be terra 1.4-11 to not get this error. > > Is it *exactly* this version or >= 1.4-11? We had once packaged terra > just for raster startung with 1.4-11 and than moved on upgrading it to > the current version 1.4-22. > Sorry about being not very precise, I should have said >= 1.4-11 1.4-22 is even better I now wonder whether it is the order of installation. Can you install raster *after* installing terra? That might help in getting the namespaces work as they should. If not, I will try to make some dockers to see if I can reproduce this. > > From what you sent I cannot see which version of terra is installed, but > I > > am guessing it is an earlier version. Is that something you can check? > > There was never any earlier version than 1.4-11 in Debian. The Debian > bug report links to a full log of the test[1] which installs > > ... > Get:117 http://deb.debian.org/debian testing/main amd64 r-cran-terra > amd64 1.4-11-2 [2,358 kB] > Get:118 http://deb.debian.org/debian unstable/main amd64 r-cran-raster > amd64 3.5-2-1 [3,063 kB] > ... > > > I can dig a bit more if needed, please let me know. > > Your help would be really appreciated > > Andreas. > > > [1] > https://ci.debian.net/data/autopkgtest/testing/amd64/r/r-cran-satellite/16823806/log.gz > > -- > http://fam-tille.de >
Bug#1000339: r-cran-raster breaks r-cran-satellite autopkgtest: unable to find an inherited method for function 'extend'
Dear Andreas, raster 3-5.2 depends on terra; but it does not specify which version of terra. I believe it needs to be terra 1.4-11 to not get this error. >From what you sent I cannot see which version of terra is installed, but I am guessing it is an earlier version. Is that something you can check? I can dig a bit more if needed, please let me know. Robert On Tue, Nov 30, 2021 at 12:48 AM Andreas Tille wrote: > Control: forwarded -1 Robert J. Hijmans , Florian > Detsch > 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: > > > >passfail > > r-cran-raster from testing3.5-2-1 > > r-cran-satellite from testing1.0.4-1 > > all others from testingfrom 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_SpatExt
