Bug#1000339: Aw: Re: Bug#1000339: r-cran-raster breaks r-cran-satellite autopkgtest: unable to find an inherited method for function 'extend'
I can only agree. Thanks for the effort, you guys! Florian Gesendet: Sonntag, 12. Dezember 2021 um 10:54 Uhr Von: "Nilesh Patra" An: "Andreas Tille" Cc: "Robert J. Hijmans" , "Debian R" , "Florian Detsch" , 1000...@bugs.debian.org Betreff: Re: Bug#1000339: r-cran-raster breaks r-cran-satellite autopkgtest: unable to find an inherited method for function 'extend' On 11 December 2021 8:53:04 pm IST, Andreas Tille wrote: >Am Sat, Dec 11, 2021 at 02:33:40PM +0530 schrieb Nilesh Patra: >> On 12/11/21 12:14 PM, Nilesh Patra wrote: >> > Tests are still failing, see here[1]. It is not a problem of terra version, as it seems, it is installed in the >> > way pretty much every other package is. I face the same stuff locally as well now. >> > Would you have some other fix in mind? >> >> When I try running tests as root, the error vanishes. I have no idea what's up :( > >Well, root has write permissions to /usr. I'd suggest to check the md5 sum >of the files of the package after running the test as root. I am pretty sure it is unrelated to the '/usr' thingy. I had uploaded r-cran-satellite with minimal changes, and it passes debci now. I guess a headache that took care of itself. The excuses for raster are now green. https://qa.debian.org/excuses.php?package=r-cran-raster Thanks a lot, Robert for taking out the time to help us and fix the problems with cran-satellite. Regards, Nilesh
Bug#1000339: r-cran-raster breaks r-cran-satellite autopkgtest: unable to find an inherited method for function 'extend'
On 11 December 2021 8:53:04 pm IST, Andreas Tille wrote: >Am Sat, Dec 11, 2021 at 02:33:40PM +0530 schrieb Nilesh Patra: >> On 12/11/21 12:14 PM, Nilesh Patra wrote: >> > Tests are still failing, see here[1]. It is not a problem of terra >> > version, as it seems, it is installed in the >> > way pretty much every other package is. I face the same stuff locally as >> > well now. >> > Would you have some other fix in mind? >> >> When I try running tests as root, the error vanishes. I have no idea what's >> up :( > >Well, root has write permissions to /usr. I'd suggest to check the md5 sum >of the files of the package after running the test as root. I am pretty sure it is unrelated to the '/usr' thingy. I had uploaded r-cran-satellite with minimal changes, and it passes debci now. I guess a headache that took care of itself. The excuses for raster are now green. https://qa.debian.org/excuses.php?package=r-cran-raster Thanks a lot, Robert for taking out the time to help us and fix the problems with cran-satellite. Regards, Nilesh
Bug#1000339: r-cran-raster breaks r-cran-satellite autopkgtest: unable to find an inherited method for function 'extend'
Am Sat, Dec 11, 2021 at 02:33:40PM +0530 schrieb Nilesh Patra: > On 12/11/21 12:14 PM, Nilesh Patra wrote: > > Tests are still failing, see here[1]. It is not a problem of terra version, > > as it seems, it is installed in the > > way pretty much every other package is. I face the same stuff locally as > > well now. > > Would you have some other fix in mind? > > When I try running tests as root, the error vanishes. I have no idea what's > up :( Well, root has write permissions to /usr. I'd suggest to check the md5 sum of the files of the package after running the test as root. Kind regards Andreas. -- http://fam-tille.de
Bug#1000339: r-cran-raster breaks r-cran-satellite autopkgtest: unable to find an inherited method for function 'extend'
On 12/11/21 12:14 PM, Nilesh Patra wrote:
control: notfixed -1 r-cran-raster/3.5-9-1
Hi Robert,
On 12/11/21 12:10 AM, Nilesh Patra wrote:
On 12/10/21 11:43 PM, Robert J. Hijmans wrote:
The new release of raster should first update terra if indeed it finds an older
version. So let's hope I am right.
I just uploaded the new version (3.5-9) and it seems to fix the problem
locally. We will see if it works on the debci
infrastructure as well. I will report whatever it says. Thanks a lot for the
help.
Tests are still failing, see here[1]. It is not a problem of terra version, as
it seems, it is installed in the
way pretty much every other package is. I face the same stuff locally as well
now.
Would you have some other fix in mind?
When I try running tests as root, the error vanishes. I have no idea what's up
:(
== ROOT =
# bash ./debian/tests/run-unit-test
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
### 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)
[ FAIL 0 | WARN 0 | SKIP 12 | PASS 145 ]
NORMAL USER =
$ bash ./debian/tests/run-unit-test
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
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()
+
Bug#1000339: r-cran-raster breaks r-cran-satellite autopkgtest: unable to find an inherited method for function 'extend'
control: notfixed -1 r-cran-raster/3.5-9-1 Hi Robert, On 12/11/21 12:10 AM, Nilesh Patra wrote: On 12/10/21 11:43 PM, Robert J. Hijmans wrote: The new release of raster should first update terra if indeed it finds an older version. So let's hope I am right. I just uploaded the new version (3.5-9) and it seems to fix the problem locally. We will see if it works on the debci infrastructure as well. I will report whatever it says. Thanks a lot for the help. Tests are still failing, see here[1]. It is not a problem of terra version, as it seems, it is installed in the way pretty much every other package is. I face the same stuff locally as well now. Would you have some other fix in mind? [1]: https://qa.debian.org/excuses.php?package=r-cran-raster Regards, Nilesh OpenPGP_signature Description: OpenPGP digital signature
Bug#1000339: r-cran-raster breaks r-cran-satellite autopkgtest: unable to find an inherited method for function 'extend'
control: notfound -1 r-cran-satellite/1.0.4-1 control: fixed -1 r-cran-raster/3.5-9-1 The new release fixes things for me locally, I will check debci and close the bug when debci runs the tests. Please hold on until then. Regards, Nilesh signature.asc Description: PGP signature
Bug#1000339: r-cran-raster breaks r-cran-satellite autopkgtest: unable to find an inherited method for function 'extend'
Hi Robert, thanks a lot for your analysis. Am Fri, Dec 03, 2021 at 03:36:40PM -0800 schrieb Robert J. Hijmans: > 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? I do not think so since you see: Get:1 http://deb.debian.org/debian testing/main r-cran-satellite 1.0.4-1 (dsc) [2,198 B] so this is the version that is testet. Kind regards Andreas. > 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 > > >
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 (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
Bug#1000339: r-cran-raster breaks r-cran-satellite autopkgtest: unable to find an inherited method for function 'extend'
Hi Robert, Am Wed, Dec 01, 2021 at 10:59:45PM -0800 schrieb Robert J. Hijmans: > On Tue, Nov 30, 2021 at 10:46 PM Andreas Tille wrote: > > > > 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 OK. > 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. The Debian autopkgtest procedure is to install *all* needed dependencies but in a random order (so there is no way I'm aware of to specify one package before others are installed). Could you please be more verbose in how far you consider the sequence in which the R code is installed is relevant for the test? I mean after installing all the R packages the files and directories are equal in any case since the files in /usr are identical to the content inside the packages no matter in what sequence the code was installed. > If not, I will try to make some dockers to see if I can reproduce this. This would be really helpful. Kind regards Andreas. > > > 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 > > > ___ > 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
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 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. > 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_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
Bug#1000339: Aw: Re: Bug#1000339: r-cran-raster breaks r-cran-satellite autopkgtest: unable to find an inherited method for function 'extend'
Andreas, Thanks for bringing up this issue. I am not able to reproduce these check results when testing satellite with the latest raster version on an Ubuntu OS (sessionInfo() included below). @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? Thanks, Florian sessionInfo(): R version 4.1.2 (2021-11-01) Platform: x86_64-pc-linux-gnu (64-bit) Running under: Ubuntu 20.04.3 LTS Matrix products: default BLAS: /usr/lib/x86_64-linux-gnu/blas/libblas.so.3.9.0 LAPACK: /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.9.0 locale: [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C LC_TIME=de_DE.UTF-8 [4] LC_COLLATE=en_US.UTF-8 LC_MONETARY=de_DE.UTF-8 LC_MESSAGES=en_US.UTF-8 [7] LC_PAPER=de_DE.UTF-8 LC_NAME=C LC_ADDRESS=C [10] LC_TELEPHONE=C LC_MEASUREMENT=de_DE.UTF-8 LC_IDENTIFICATION=C attached base packages: [1] stats graphics grDevices utils datasets methods base other attached packages: [1] satellite_1.0.4 raster_3.5-2 sp_1.4-6 loaded via a namespace (and not attached): [1] compiler_4.1.2 cli_3.1.0 tools_4.1.2 Rcpp_1.0.7 [5] codetools_0.2-18 grid_4.1.2 stats4_4.1.2 prompt_1.0.1 [9] lattice_0.20-45 terra_1.4-22 Gesendet: Dienstag, 30. November 2021 um 09:48 Uhr Von: "Andreas Tille" An: 1000...@bugs.debian.org, "Robert J. Hijmans" , "Florian Detsch" Betreff: Re: Bug#1000339: r-cran-raster breaks r-cran-satellite autopkgtest: unable to find an inherited method for function 'extend' 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: > > 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'
Bug#1000339: r-cran-raster breaks r-cran-satellite autopkgtest: unable to find an inherited method for function 'extend'
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_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
Bug#1000339: r-cran-raster breaks r-cran-satellite autopkgtest: unable to find an inherited method for function 'extend'
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_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
