Your message dated Wed, 29 Sep 2021 16:44:36 -0500
with message-id <24916.56900.432114.333...@rob.eddelbuettel.com>
and subject line Re: Bug#980809: rmatrix: breaks autopkgtest of r-cran-glmmtmb
on s390x
has caused the Debian Bug report #980809,
regarding rmatrix: breaks autopkgtest of r-cran-glmmtmb on s390x
to be marked as done.
This means that you claim that the problem has been dealt with.
If this is not the case it is now your responsibility to reopen the
Bug report if necessary, and/or fix the problem forthwith.
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--
980809: https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=980809
Debian Bug Tracking System
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--- Begin Message ---
Source: rmatrix, r-cran-glmmtmb
Control: found -1 rmatrix/1.3-0-1
Control: found -1 r-cran-glmmtmb/1.0.2.1-1
Severity: serious
Tags: sid bullseye
X-Debbugs-CC: debian...@lists.debian.org
User: debian...@lists.debian.org
Usertags: breaks needs-update
Hi Maintainers
The upload of rmatrix/1.3-0-1 caused the autopkgtest of r-cran-glmmtmb
on s390x to fail.
Unfortunately, gating of autopkgtest failures was not yet enabled on
s390x at the time, and this failure has now made it into testing [2].
I've copied what I hope is the relevant part of the log below.
More information about this bug and the reason for filing it can be found on
https://wiki.debian.org/ContinuousIntegration/RegressionEmailInformation
Regards
Graham
[1] https://ci.debian.net/packages/r/r-cran-glmmtmb/unstable/s390x/
[2] https://ci.debian.net/packages/r/r-cran-glmmtmb/testing/s390x/
== Failed ======================================================================
-- 1. Error (test-VarCorr.R:11:1): (code run outside of `test_that()`) ---------
Error: gradient function must return a numeric vector of length 6
Backtrace:
1. glmmTMB::glmmTMB(distance ~ age + (age | Subject), data =
Orthodont) test-VarCorr.R:11:0
2. glmmTMB::fitTMB(TMBStruc)
4. glmmTMB:::optfun()
6. base::with.default(...)
7. [ base::eval(...) ] with 1 more call
-- 2. Error (test-basics.R:29:1): (code run outside of `test_that()`) ----------
Error: gradient function must return a numeric vector of length 3
Backtrace:
1. glmmTMB::glmmTMB(Reaction ~ 1 + (1 | Subject), sleepstudy)
test-basics.R:29:0
2. glmmTMB::fitTMB(TMBStruc)
4. glmmTMB:::optfun()
6. base::with.default(...)
7. [ base::eval(...) ] with 1 more call
-- 3. Error (test-bootMer.R:11:5): Bernoulli responses -------------------------
Error: gradient function must return a numeric vector of length 3
Backtrace:
1. glmmTMB::glmmTMB(...) test-bootMer.R:11:4
2. glmmTMB::fitTMB(TMBStruc)
4. glmmTMB:::optfun()
6. base::with.default(...)
7. [ base::eval(...) ] with 1 more call
-- 4. Error (test-bootMer.R:19:5): Bernoulli responses -------------------------
Error: gradient function must return a numeric vector of length 3
Backtrace:
1. glmmTMB::glmmTMB(...) test-bootMer.R:19:4
2. glmmTMB::fitTMB(TMBStruc)
4. glmmTMB:::optfun()
6. base::with.default(...)
7. [ base::eval(...) ] with 1 more call
-- 5. Error (test-control.R:26:5): profile method ------------------------------
Error: gradient function must return a numeric vector of length 15
Backtrace:
1. glmmTMB:::myfit(profile = FALSE) test-control.R:26:4
2. glmmTMB::glmmTMB(...) test-control.R:20:8
3. glmmTMB::fitTMB(TMBStruc)
5. glmmTMB:::optfun()
7. base::with.default(...)
8. [ base::eval(...) ] with 1 more call
-- 6. Error (test-control.R:71:3): parallel regions ----------------------------
Error: gradient function must return a numeric vector of length 15
Backtrace:
1. glmmTMB:::capture_time_model(parallel = 1) test-control.R:71:2
2. glmmTMB:::myfit(...) test-control.R:64:4
3. glmmTMB::glmmTMB(...) test-control.R:54:4
4. glmmTMB::fitTMB(TMBStruc)
6. glmmTMB:::optfun()
8. base::with.default(...)
9. [ base::eval(...) ] with 1 more call
-- 7. Error (test-disp.R:33:1): (code run outside of `test_that()`) ------------
Error: gradient function must return a numeric vector of length 5
Backtrace:
1. glmmTMB::glmmTMB(x ~ disp + (1 | fac), dispformula = ~disp, dat)
test-disp.R:33:0
2. glmmTMB::fitTMB(TMBStruc)
4. glmmTMB:::optfun()
6. base::with.default(...)
7. [ base::eval(...) ] with 1 more call
-- 8. Error (test-edgecases.R:9:5): profiling failure --------------------------
Error: gradient function must return a numeric vector of length 3
Backtrace:
1. testthat::expect_warning(...) test-edgecases.R:9:4
6. glmmTMB::glmmTMB(...)
7. glmmTMB::fitTMB(TMBStruc)
9. glmmTMB:::optfun()
11. base::with.default(...)
12. [ base::eval(...) ] with 1 more call
-- 9. Error (test-env.R:18:5): basic example #1 --------------------------------
Error: gradient function must return a numeric vector of length 4
Backtrace:
1. glmmTMB::glmmTMB(Reaction ~ Days + (1 | Subject), data =
sleepstudy) test-env.R:18:4
2. glmmTMB::fitTMB(TMBStruc)
4. glmmTMB:::optfun()
6. base::with.default(...)
7. [ base::eval(...) ] with 1 more call
-- 10. Error (test-env.R:34:5): paranoia ---------------------------------------
Error: gradient function must return a numeric vector of length 4
Backtrace:
1. glmmTMB::glmmTMB(Reaction ~ Days + (1 | Subject), data =
sleepstudy) test-env.R:34:4
2. glmmTMB::fitTMB(TMBStruc)
4. glmmTMB:::optfun()
6. base::with.default(...)
7. [ base::eval(...) ] with 1 more call
... and 20 more
Maximum number of 10 failures reached, some test results may be missing.
--- End Message ---
--- Begin Message ---
Hi Nilesh,
On 30 September 2021 at 02:45, Nilesh Patra wrote:
| Hi Dirk, all,
|
| On Fri, 9 Apr 2021 15:20:37 -0500 Dirk Eddelbuettel <e...@debian.org> wrote:
| > On 9 April 2021 at 10:43, Graham Inggs wrote:
| > | Control: tags -1 + fixed-upstream
| > |
| > | Fixed in Matrix upstream svn rev 3376 [1].
| > |
| > |
| > | [1]
https://r-forge.r-project.org/scm/viewvc.php?view=rev&root=matrix&revision=3376
| >
| > Even better.
| >
| > Big BIG Thank You for persistently chasing that to the end. Thank you!
|
| I see all changes from that diff in version 1.3-4-2 version currently in
| unstable. So I suppose this is fixed already, right?
I think so. This was a really tricky issue, but Graham was right on it -- and
it was fixed in Matrix (aka our rmatrix) many moons ago (Jan? Feb?) but then
release happened, and then r-base-core was stalled, ... I actually had the
tab with the build status open in my browser 'forever'.
| If that's the case, please close this bug since it stalls rmatrix
| migration to testing, and many packages need the latest version.
Thanks so much for the heads-up. I was unaware of the blockage.
Per https://buildd.debian.org/status/package.php?p=r-cran-glmmtmb it looks
good so closing this. It was always an upstream issue anyway...
| I just fixed the last standing blocker for rmatrix (r-cran-seurat) and
| this bug is the last thing that prevents it from going to testing.
What was the issue? (I am just curious as I interface Seurat outside of
Debian too for $work.)
Dirk
--
https://dirk.eddelbuettel.com | @eddelbuettel | e...@debian.org
--- End Message ---
