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Bug#1054657: transition: r-bioc-biocgenerics

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  Bug#1054657: transition: r-bioc-biocgenerics Andreas Tille <tille@debian.org> - 2023-10-27 16:10 +0200
    Processed: transition: r-bioc-biocgenerics "Debian Bug Tracking System" <owner@bugs.debian.org> - 2023-10-27 16:10 +0200
    Bug#1054657: transition: r-bioc-biocgenerics Dirk Eddelbuettel <edd@debian.org> - 2023-10-27 16:30 +0200
      Bug#1054657: transition: r-bioc-biocgenerics Andreas Tille <andreas@an3as.eu> - 2023-10-27 16:50 +0200
        Bug#1054657: transition: r-bioc-biocgenerics Dirk Eddelbuettel <edd@debian.org> - 2023-10-27 18:40 +0200
    Processed: Re: Bug#1054657: transition: r-bioc-biocgenerics "Debian Bug Tracking System" <owner@bugs.debian.org> - 2023-10-28 19:00 +0200
    Bug#1054657: transition: r-bioc-biocgenerics Graham Inggs <ginggs@debian.org> - 2023-10-28 19:00 +0200
      Bug#1054657: transition: r-bioc-biocgenerics Andreas Tille <tille@debian.org> - 2023-10-29 06:40 +0100
        Bug#1054657: transition: r-bioc-biocgenerics Graham Inggs <ginggs@debian.org> - 2023-10-29 17:10 +0100
          Bug#1054657: transition: r-bioc-biocgenerics Andreas Tille <tille@debian.org> - 2023-10-29 18:10 +0100
            Bug#1054657: transition: r-bioc-biocgenerics Graham Inggs <ginggs@debian.org> - 2023-11-01 11:10 +0100
              Bug#1054657: transition: r-bioc-biocgenerics Andreas Tille <tille@debian.org> - 2023-11-01 11:40 +0100
                Bug#1054657: transition: r-bioc-biocgenerics Charles Plessy <plessy@debian.org> - 2023-11-03 02:10 +0100
                  Bug#1054657: transition: r-bioc-biocgenerics Andreas Tille <tille@debian.org> - 2023-11-07 06:50 +0100
                  Bug#1054657: transition: r-bioc-biocgenerics Sebastian Ramacher <sramacher@debian.org> - 2023-11-07 11:00 +0100
                    Bug#1054657: transition: r-bioc-biocgenerics Charles Plessy <plessy@debian.org> - 2023-11-07 14:10 +0100
                      Bug#1054657: transition: r-bioc-biocgenerics Dirk Eddelbuettel <edd@debian.org> - 2023-11-07 14:50 +0100
                        Bug#1054657: transition: r-bioc-biocgenerics Andreas Tille <tille@debian.org> - 2023-11-07 15:10 +0100
                          Bug#1054657: transition: r-bioc-biocgenerics Dirk Eddelbuettel <edd@debian.org> - 2023-11-07 19:40 +0100
                            Bug#1054657: transition: r-bioc-biocgenerics Andreas Tille <tille@debian.org> - 2023-11-07 21:10 +0100
                    Bug#1054657: transition: r-bioc-biocgenerics Andreas Tille <tille@debian.org> - 2023-11-07 14:40 +0100
                      Bug#1054657: transition: r-bioc-biocgenerics Sebastian Ramacher <sramacher@debian.org> - 2023-11-07 15:20 +0100
                        Bug#1054657: transition: r-bioc-biocgenerics Andreas Tille <tille@debian.org> - 2023-11-07 18:10 +0100
          Bug#1054657: transition: r-bioc-biocgenerics Charles Plessy <plessy@debian.org> - 2023-11-01 08:40 +0100
    Processed: Re: Bug#1054657: transition: r-bioc-biocgenerics "Debian Bug Tracking System" <owner@bugs.debian.org> - 2023-11-07 06:50 +0100
    Processed: Re: Bug#1054657: transition: r-bioc-biocgenerics "Debian Bug Tracking System" <owner@bugs.debian.org> - 2023-11-07 11:00 +0100
    Bug#1054657: transition: r-bioc-biocgenerics Charles Plessy <plessy@debian.org> - 2023-11-09 15:10 +0100
      Bug#1054657: transition: r-bioc-biocgenerics Charles Plessy <plessy@debian.org> - 2023-11-10 09:50 +0100
        Bug#1054657: transition: r-bioc-biocgenerics Andreas Tille <tille@debian.org> - 2023-11-10 12:10 +0100
        Bug#1054657: transition: r-bioc-biocgenerics Sebastian Ramacher <sramacher@debian.org> - 2023-11-10 23:40 +0100
          Bug#1054657: transition: r-bioc-biocgenerics Charles Plessy <plessy@debian.org> - 2023-11-11 01:50 +0100
    Processed: Re: Bug#1054657: transition: r-bioc-biocgenerics "Debian Bug Tracking System" <owner@bugs.debian.org> - 2023-11-10 12:10 +0100
    Bug#1054657: transition: r-bioc-biocgenerics Andreas Tille <tille@debian.org> - 2023-11-10 23:40 +0100
      Bug#1054657: transition: r-bioc-biocgenerics Andreas Tille <tille@debian.org> - 2023-11-13 11:20 +0100
        Bug#1054657: transition: r-bioc-biocgenerics Graham Inggs <ginggs@debian.org> - 2023-11-19 16:40 +0100
        Bug#1054657: transition: r-bioc-biocgenerics Andreas Tille <andreas@an3as.eu> - 2023-11-22 21:00 +0100
          Bug#1054657: transition: r-bioc-biocgenerics Charles Plessy <plessy@debian.org> - 2023-11-28 01:30 +0100
            Bug#1054657: transition: r-bioc-biocgenerics Andreas Tille <tille@debian.org> - 2023-11-28 10:30 +0100
    Bug#1054657: r-bioc-sparsearray_1.0.12+dfsg-1_amd64.changes is NEW Andreas Tille <andreas@an3as.eu> - 2023-11-13 10:30 +0100
    Processed: Re: Bug#1054657: transition: r-bioc-biocgenerics "Debian Bug Tracking System" <owner@bugs.debian.org> - 2023-11-19 16:40 +0100
    Processed: Re: Bug#1054657: transition: r-bioc-biocgenerics "Debian Bug Tracking System" <owner@bugs.debian.org> - 2023-11-22 21:00 +0100
    Bug#1054657: transition: r-bioc-biocgenerics Andreas Tille <tille@debian.org> - 2023-11-24 22:30 +0100
    Bug#1054657: Transition issue for r-cran-rstanarm (Was: Bug#1055922: rmatrix: ABI change in Matrix 1.6-2) Andreas Tille <andreas@an3as.eu> - 2023-11-26 17:30 +0100
      Bug#1054657: Transition issue for r-cran-rstanarm (Was: Bug#1055922: rmatrix: ABI change in Matrix 1.6-2) Andreas Tille <andreas@an3as.eu> - 2023-11-28 10:20 +0100
    Bug#1054657: Transition issue for r-cran-rstanarm (Was: Bug#1055922: rmatrix: ABI change in Matrix 1.6-2) Graham Inggs <ginggs@debian.org> - 2023-11-28 11:40 +0100
      Bug#1054657: Transition issue for r-cran-rstanarm (Was: Bug#1055922: rmatrix: ABI change in Matrix 1.6-2) Andreas Tille <tille@debian.org> - 2023-11-28 16:00 +0100
        Bug#1054657: Transition issue for r-cran-rstanarm (Was: Bug#1055922: rmatrix: ABI change in Matrix 1.6-2) Graham Inggs <ginggs@debian.org> - 2023-11-29 14:40 +0100
    Processed: Re: Bug#1054657: Transition issue for r-cran-rstanarm  (Was: Bug#1055922: rmatrix: ABI change in Matrix 1.6-2) "Debian Bug Tracking System" <owner@bugs.debian.org> - 2023-11-29 14:40 +0100
    Bug#1054657: Transition seems to be blocked (Was: Bug#1054657: transition: r-bioc-biocgenerics) Andreas Tille <andreas@an3as.eu> - 2023-12-03 09:30 +0100
      Bug#1054657: Transition seems to be blocked (Was: Bug#1054657: transition: r-bioc-biocgenerics) Graham Inggs <ginggs@debian.org> - 2023-12-03 11:50 +0100
        Bug#1054657: Transition seems to be blocked (Was: Bug#1054657: transition: r-bioc-biocgenerics) Adrian Bunk <bunk@debian.org> - 2023-12-03 22:20 +0100
          Bug#1054657: Transition seems to be blocked (Was: Bug#1054657: transition: r-bioc-biocgenerics) Sebastian Ramacher <sramacher@debian.org> - 2023-12-05 15:50 +0100
      Bug#1054657: Transition seems to be blocked (Was: Bug#1054657: transition: r-bioc-biocgenerics) Graham Inggs <ginggs@debian.org> - 2023-12-07 15:40 +0100
        Bug#1054657: Transition seems to be blocked (Was: Bug#1054657: transition: r-bioc-biocgenerics) Andreas Tille <tille@debian.org> - 2023-12-07 16:20 +0100
          Bug#1054657: Transition seems to be blocked (Was: Bug#1054657: transition: r-bioc-biocgenerics) Andreas Tille <tille@debian.org> - 2023-12-07 16:40 +0100
          Bug#1054657: Transition seems to be blocked (Was: Bug#1054657: transition: r-bioc-biocgenerics) Adrian Bunk <bunk@debian.org> - 2023-12-07 19:40 +0100
          Bug#1054657: Transition seems to be blocked (Was: Bug#1054657: transition: r-bioc-biocgenerics) Sebastian Ramacher <sramacher@debian.org> - 2023-12-11 11:40 +0100
            Bug#1054657: Transition seems to be blocked (Was: Bug#1054657: transition: r-bioc-biocgenerics) Andreas Tille <tille@debian.org> - 2023-12-11 13:40 +0100
              Bug#1054657: Transition seems to be blocked (Was: Bug#1054657: transition: r-bioc-biocgenerics) Sebastian Ramacher <sramacher@debian.org> - 2023-12-11 13:40 +0100
                Bug#1054657: Transition seems to be blocked (Was: Bug#1054657: transition: r-bioc-biocgenerics) Andreas Tille <tille@debian.org> - 2023-12-11 17:10 +0100
                  Bug#1054657: Transition seems to be blocked (Was: Bug#1054657: transition: r-bioc-biocgenerics) Sebastian Ramacher <sramacher@debian.org> - 2023-12-11 18:00 +0100
        Bug#1054657: Transition seems to be blocked (Was: Bug#1054657: transition: r-bioc-biocgenerics) Charles Plessy <plessy@debian.org> - 2023-12-08 17:10 +0100
          Bug#1054657: Transition seems to be blocked (Was: Bug#1054657: transition: r-bioc-biocgenerics) Dirk Eddelbuettel <edd@debian.org> - 2023-12-08 17:40 +0100
      Bug#1054657: Transition ready? (Was: Transition seems to be blocked (Was: Bug#1054657: transition: r-bioc-biocgenerics)) Andreas Tille <andreas@an3as.eu> - 2023-12-13 11:50 +0100
        Bug#1054657: Transition ready? (Was: Transition seems to be blocked (Was: Bug#1054657: transition: r-bioc-biocgenerics)) Adrian Bunk <bunk@debian.org> - 2023-12-13 13:30 +0100
        Bug#1054657: Transition ready? (Was: Transition seems to be blocked (Was: Bug#1054657: transition: r-bioc-biocgenerics)) Graham Inggs <ginggs@debian.org> - 2023-12-13 14:20 +0100
          Bug#1054657: Transition ready? (Was: Transition seems to be blocked (Was: Bug#1054657: transition: r-bioc-biocgenerics)) Andreas Tille <tille@debian.org> - 2023-12-13 17:10 +0100
    Bug#1054657: Transition seems to be blocked (Was: Bug#1054657: transition: r-bioc-biocgenerics) Adrian Bunk <bunk@debian.org> - 2023-12-03 22:20 +0100
      Bug#1054657: Transition seems to be blocked (Was: Bug#1054657: transition: r-bioc-biocgenerics) Andreas Tille <tille@debian.org> - 2023-12-05 14:40 +0100
    Bug#1054657: Transition seems to be blocked (Was: Bug#1054657: transition: r-bioc-biocgenerics) Andreas Tille <tille@debian.org> - 2023-12-04 06:40 +0100
    Bug#1054657: Source download of DeMixT broken Andreas Tille <andreas@an3as.eu> - 2023-12-08 16:10 +0100
      Bug#1054657: Source download of DeMixT broken Andreas Tille <andreas@fam-tille.de> - 2023-12-12 15:10 +0100
    Bug#1054657: Source archive of DSS missing Andreas Tille <andreas@fam-tille.de> - 2023-12-08 16:10 +0100
      Bug#1054657: Source archive of DSS missing Andreas Tille <andreas@fam-tille.de> - 2023-12-12 15:20 +0100
    Bug#1054657: Transition ready? (Was: Transition seems to be blocked (Was: Bug#1054657: transition: r-bioc-biocgenerics)) Andreas Tille <tille@debian.org> - 2023-12-14 09:10 +0100
    Bug#1054657: marked as done (transition: r-bioc-biocgenerics) "Debian Bug Tracking System" <owner@bugs.debian.org> - 2023-12-17 10:30 +0100
    Bug#1054657: Transition ready? (Was: Transition seems to be blocked (Was: Bug#1054657: transition: r-bioc-biocgenerics)) Graham Inggs <ginggs@debian.org> - 2023-12-17 16:20 +0100
      Bug#1054657: Transition ready? (Was: Transition seems to be blocked (Was: Bug#1054657: transition: r-bioc-biocgenerics)) Andreas Tille <tille@debian.org> - 2023-12-18 10:20 +0100

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#121467 — Bug#1054657: Transition seems to be blocked (Was: Bug#1054657: transition: r-bioc-biocgenerics)

On 2023-12-11 16:57:34 +0100, Andreas Tille wrote:
> Am Mon, Dec 11, 2023 at 01:36:38PM +0100 schrieb Sebastian Ramacher:
> > > OK, but what is your suggestion?  Reverting and have broken tests due to
> > > the pandoc issue?
> > 
> > pandoc is fixed in unstable.
> 
> Really?  Salsa CI[1] says:
> 
>    pandoc : Depends: pandoc-data (>= 3.0.1+ds) but 3.0.1-3 is to be installed
> 
> I uploaded anyway and hope this will be cured somehow.

This issue was fixed in 3.0.1+ds-3 which was uploaded today.

Cheers
-- 
Sebastian Ramacher

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#121373 — Bug#1054657: Transition seems to be blocked (Was: Bug#1054657: transition: r-bioc-biocgenerics)

Hi Graham and Andreas,

Le Thu, Dec 07, 2023 at 01:37:02PM -0100, Graham Inggs a écrit :
> 
> Also, why do r-bioc-netsam and r-bioc-org.hs.eg.db not even appear on
> the tracker?

I do not know for r-bioc-netsam, but for r-bioc-org.hs.eg.db and similar
packages, it is because it is an "annotation package" made of data and
therefore not managed the same way as the other Bioconductor packages.

This is why it DESCRIPTION file does not mention its Bioconductor Git
branch.  This is also why its version number matches the Bioconductor
release number.  Also, its homepage resolves to
https://bioconductor.org/packages/release/data/annotation/html/org.Hs.eg.db.html
while for regular packages there is no data/annotation/html in the URL.

I think that it does not have to depend on the bioc api pseudo-package.

I hope it helps,

Charles

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#121374 — Bug#1054657: Transition seems to be blocked (Was: Bug#1054657: transition: r-bioc-biocgenerics)

On 9 December 2023 at 01:06, Charles Plessy wrote:
| I do not know for r-bioc-netsam, but for r-bioc-org.hs.eg.db and similar
| packages, it is because it is an "annotation package" made of data and
| therefore not managed the same way as the other Bioconductor packages.
| 
| This is why it DESCRIPTION file does not mention its Bioconductor Git
| branch.  This is also why its version number matches the Bioconductor
| release number.  Also, its homepage resolves to
| https://bioconductor.org/packages/release/data/annotation/html/org.Hs.eg.db.html
| while for regular packages there is no data/annotation/html in the URL.
| 
| I think that it does not have to depend on the bioc api pseudo-package.

When r2u builds all of CRAN plus the ~ 200 BioC that are implied plus ~ 200
more that either in Debian or high on BioC's own 'karma' list, I query all
four repositories as one must.  That is basically what the BioC installer
helpers always did for twenty-some years.  My code (quicker for me to find)
is

            ## cf  contrib.url(BiocManager::repositories())
            ##     [1] "https://bioconductor.org/packages/3.14/bioc/src/contrib"
            ##     [2] "https://bioconductor.org/packages/3.14/data/annotation/src/contrib"
            ##     [3] "https://bioconductor.org/packages/3.14/data/experiment/src/contrib"
            biocrepo <- paste0("https://bioconductor.org/packages/", .getConfig("bioc_version"), "/bioc")
            apBIOC <- data.table(ap="Bioc", as.data.frame(available.packages(repos=biocrepo)))
            biocdataannrepo <- paste0("https://bioconductor.org/packages/", .getConfig("bioc_version"), "/data/annotation")
            apBIOCdataann <- data.table(ap="Bioc", as.data.frame(available.packages(repos=biocdataannrepo)))
            apBIOC <- merge(apBIOC, apBIOCdataann, all=TRUE)
            biocdataexprepo <- paste0("https://bioconductor.org/packages/", .getConfig("bioc_version"), "/data/experiment")
            apBIOCdataexp <- data.table(ap="Bioc", as.data.frame(available.packages(repos=biocdataexprepo)))
            apBIOC <- merge(apBIOC, apBIOCdataexp, all=TRUE)

Ah, and younger Dirk left a message for current Dirk that this does indeed
show it too:

    > contrib.url(BiocManager::repositories())
    'getOption("repos")' replaces Bioconductor standard repositories, see
    'help("repositories", package = "BiocManager")' for details.
    Replacement repositories:
        CRAN: https://cloud.r-project.org
    [1] "https://bioconductor.org/packages/3.18/bioc/src/contrib"           
    [2] "https://bioconductor.org/packages/3.18/data/annotation/src/contrib"
    [3] "https://bioconductor.org/packages/3.18/data/experiment/src/contrib"
    [4] "https://bioconductor.org/packages/3.18/workflows/src/contrib"      
    [5] "https://bioconductor.org/packages/3.18/books/src/contrib"          
    [6] "https://cloud.r-project.org/src/contrib"                           
    > 

And when I bulk-updated the BioC packages for my 20.04 and 22.04 build in
r2u, I did notice that some of the 'non-R-package packages' in annotations
and experiment did not update.  One could always ask BioC which of these are
/ are not considered release dependent.  Their slack is open and pretty
friendly, I hang there too.

Cheers, Dirk

-- 
dirk.eddelbuettel.com | @eddelbuettel | edd@debian.org

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#121493 — Bug#1054657: Transition ready? (Was: Transition seems to be blocked (Was: Bug#1054657: transition: r-bioc-biocgenerics))

Hi,

as you might have noticed the upstream source for r-bioc-dss and
r-bioc-demixt are missing and upstream did not answered two mails about
this.  Since the transition looks clean for me so far[1] after I fixed
two autopkgtest issues yesterday I (naively) think we could remove
r-bioc-dss and r-bioc-demixt from testing and all other packages can
migrate to finish the transition from r-bioc perspective.

I'm wondering what I can do in some cases that are caused by the pandoc
issue like shortread[2] which should be solved in principle.  I'm worried
about issues in r-rcan-rmarkdown[3] and r-cran-flextable[4] which are
caused by pandoc errors on ppc64el architecture *only*.  That's really
strange and might mean that pandoc on this architecture is broken?

Regarding pandoc I've just uploaded a fix for pypandoc (fixing bugs
#1057946 and #1058153)

I have neither any clue nor any time to check nbconvert.

Kind regards
      Andreas.


[1] https://tracker.debian.org/pkg/r-bioc-biocgenerics
[2] https://tracker.debian.org/pkg/r-bioc-shortread
[3] https://ci.debian.net/packages/r/r-cran-rmarkdown/testing/ppc64el/40945637/
[4] https://ci.debian.net/packages/r/r-cran-flextable/testing/ppc64el/40945625/

-- 
http://fam-tille.de

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#121496 — Bug#1054657: Transition ready? (Was: Transition seems to be blocked (Was: Bug#1054657: transition: r-bioc-biocgenerics))

On Wed, Dec 13, 2023 at 11:43:56AM +0100, Andreas Tille wrote:
>...
> I'm worried
> about issues in r-rcan-rmarkdown[3] and r-cran-flextable[4] which are
> caused by pandoc errors on ppc64el architecture *only*.  That's really
> strange and might mean that pandoc on this architecture is broken?
>...

ppc64el has Lua support disabled[1] due to [2] (#1057857),
AFAIK that's the last non-trivial issue of the Haskell transition.

I haven't confirmed that this is related, but that would be my first 
guess for the ppc64el-only [3] in pandoc.

> Kind regards
>       Andreas.
>...

cu
Adrian

[1] https://tracker.debian.org/media/packages/p/pandoc/control-3.0.1ds-3
[2] https://buildd.debian.org/status/package.php?p=haskell-lua
[3] https://tracker.debian.org/pkg/pandoc

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#121497 — Bug#1054657: Transition ready? (Was: Transition seems to be blocked (Was: Bug#1054657: transition: r-bioc-biocgenerics))

Hi Andreas

On Wed, 13 Dec 2023 at 09:45, Andreas Tille <andreas@an3as.eu> wrote:
> as you might have noticed the upstream source for r-bioc-dss and
> r-bioc-demixt are missing and upstream did not answered two mails about
> this.  Since the transition looks clean for me so far[1] after I fixed
> two autopkgtest issues yesterday I (naively) think we could remove
> r-bioc-dss and r-bioc-demixt from testing and all other packages can
> migrate to finish the transition from r-bioc perspective.

I've added removal hints for r-bioc-dss and r-bioc-demixt.  Please
file an RC bug for r-bioc-dss to prevent it from migrating straight
back (r-bioc-demixt already has #1058278).

One problem I see at [1]:

Not built on buildd: arch all binaries uploaded by tille, a new
source-only upload is needed to allow migration

Remember, all r-bioc-* packages need to migrate together, so all of
your uploads need to be ready before r-bioc-biocgenerics can migrate.
I checked only the first few "Migrates after" links from [1], and
found at least these packages still show autopkgtest regressions
[2][3][4][5][6].

Regards
Graham


> [1] https://tracker.debian.org/pkg/r-bioc-biocgenerics

[2] https://tracker.debian.org/pkg/r-bioc-beachmat
[3] https://tracker.debian.org/pkg/r-bioc-biobase
[4] https://tracker.debian.org/pkg/r-bioc-biocbaseutils
[5] https://tracker.debian.org/pkg/r-bioc-biocio
[6] https://tracker.debian.org/pkg/r-bioc-biostrings

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#121501 — Bug#1054657: Transition ready? (Was: Transition seems to be blocked (Was: Bug#1054657: transition: r-bioc-biocgenerics))

Hi Graham,

Am Wed, Dec 13, 2023 at 12:13:54PM -0100 schrieb Graham Inggs:
> I've added removal hints for r-bioc-dss and r-bioc-demixt.  Please
> file an RC bug for r-bioc-dss to prevent it from migrating straight
> back (r-bioc-demixt already has #1058278).

Done for r-bioc-dss.
 
> One problem I see at [1]:
> 
> Not built on buildd: arch all binaries uploaded by tille, a new
> source-only upload is needed to allow migration

I do not understand this line.  What exact package needs a source-only
upload?

> Remember, all r-bioc-* packages need to migrate together, so all of
> your uploads need to be ready before r-bioc-biocgenerics can migrate.
> I checked only the first few "Migrates after" links from [1], and
> found at least these packages still show autopkgtest regressions
> [2][3][4][5][6].

Thank you for these links.  Could you please explain how I can obtain
these myself?  Is there any page I could look at for some kind of
summary?

Now to these links:
 
> > [1] https://tracker.debian.org/pkg/r-bioc-biocgenerics

OK, no idea what source-only upload is needed (see above).

> [2] https://tracker.debian.org/pkg/r-bioc-beachmat

This shows:
  autopkgtest for r-bioc-biocsingular/1.16.0+ds-1: amd64: Regression or new test...
but that version of r-bioc-biocsingular is in testing and bound
to fail.  Version 1.18.0+ds matches to BioC API 3.18.
Autopkgtest in Salsa CI works as expected.  When looking
in debci (https://ci.debian.net/packages/r/r-bioc-biocsingular/unstable/amd64/40579344/)
the test suite error is caused by pandoc.

> [3] https://tracker.debian.org/pkg/r-bioc-biobase

Same here:
  autopkgtest for r-bioc-degreport/1.36.0+dfsg-1: amd64: Regression or new test...
we have r-bioc-degreport 1.38.3+dfsg-1 in unstable matching BioC API
3.18.  Failures with any former version is bound to fail.

Similarly:
  autopkgtest for r-bioc-multiassayexperiment/1.26.0+dfsg-1: amd64: Regression or new test...
version in testing not unstable

> [4] https://tracker.debian.org/pkg/r-bioc-biocbaseutils

See above
  autopkgtest for r-bioc-multiassayexperiment/1.26.0+dfsg-1: amd64: Regression or new test...

> [5] https://tracker.debian.org/pkg/r-bioc-biocio
> [6] https://tracker.debian.org/pkg/r-bioc-biostrings

Same problem as above
  autopkgtest for r-bioc-bsgenome/1.68.0-1: amd64: Regression or new test...
in both cases.

I admit I have no idea what to do.  If the migration issues are
caused by running tests against versions in testing which can't
pass something is broken.  As you wrote above

> Remember, all r-bioc-* packages need to migrate together,

... yes, that's why running debci tests is not needed - at least as far
as I understood the purpose of a transition.  Please let me know if I
can do something to fix the situation, but for the moment I have no idea
what to do.

Sorry if I'm a bit slow to catch on.

Kind regards
   Andreas.

-- 
http://fam-tille.de

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#121306 — Bug#1054657: Transition seems to be blocked (Was: Bug#1054657: transition: r-bioc-biocgenerics)

On Sun, Dec 03, 2023 at 09:51:38PM +0100, Paul Gevers wrote:
>...
> And it also means that r-bioc-biocgenerics is now blocked on the haskell
> transition. Lovely. Good thing that pandoc is supposed to be the last piece
> in that several months long transition.

It's only blocked by the pandoc part of the Haskell transition, 
it shouldn't be blocked by the other remaining parts of the
transition or by getting the transition into testing.

> Paul

cu
Adrian

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#121335 — Bug#1054657: Transition seems to be blocked (Was: Bug#1054657: transition: r-bioc-biocgenerics)

Hi Adrian,

Am Sun, Dec 03, 2023 at 11:15:49PM +0200 schrieb Adrian Bunk:
> > And it also means that r-bioc-biocgenerics is now blocked on the haskell
> > transition. Lovely. Good thing that pandoc is supposed to be the last piece
> > in that several months long transition.
> 
> It's only blocked by the pandoc part of the Haskell transition, 
> it shouldn't be blocked by the other remaining parts of the
> transition or by getting the transition into testing.

Is there any chance to upload a working pandoc to unstable?

Nearly all r-* package tests I tried in upgrades are broken and I'd like
to know when it makes sense again to touch those packages.

Kind regards
   Andreas.

-- 
http://fam-tille.de

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#121315 — Bug#1054657: Transition seems to be blocked (Was: Bug#1054657: transition: r-bioc-biocgenerics)

Hi,

Am Sun, Dec 03, 2023 at 09:51:38PM +0100 schrieb Paul Gevers:
> 
> And it also means that r-bioc-biocgenerics is now blocked on the haskell
> transition. Lovely. Good thing that pandoc is supposed to be the last piece
> in that several months long transition.

... which on the other hand shows, that new packages have never been the
main blocker in r-bioc-* transitions (even if I confirm I'm happy that
you convinced us to get rid of this reason).

Kind regards
    Andreas.

-- 
http://fam-tille.de

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#121371 — Bug#1054657: Source download of DeMixT broken

Hi,

when looking at

    https://bioconductor.org/packages/release/bioc/html/DeMixT.html

and following the link "Source Archive" at bottom of the page linking
to
    https://bioconductor.org/packages/3.18/bioc/src/contrib/Archive/DeMixT/

I can only see

   Page Not Found
   The page you were looking for was not found. 

I'm trying to upgrade the Debian package of DeMixT to its latest version
and would need the source tarball which can be usually downloaded from
the "Source Archive" link.

Kind regards
    Andreas.

-- 
http://fam-tille.de

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#121471 — Bug#1054657: Source download of DeMixT broken

Hi again,

could someone please have a look at the source download?

Thank you
    Andreas.

Am Fri, Dec 08, 2023 at 04:01:17PM +0100 schrieb Andreas Tille:
> Hi,
> 
> when looking at
> 
>     https://bioconductor.org/packages/release/bioc/html/DeMixT.html
> 
> and following the link "Source Archive" at bottom of the page linking
> to
>     https://bioconductor.org/packages/3.18/bioc/src/contrib/Archive/DeMixT/
> 
> I can only see
> 
>    Page Not Found
>    The page you were looking for was not found. 
> 
> I'm trying to upgrade the Debian package of DeMixT to its latest version
> and would need the source tarball which can be usually downloaded from
> the "Source Archive" link.
> 
> Kind regards
>     Andreas.
> 
> -- 
> http://fam-tille.de

-- 
http://fam-tille.de

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#121372 — Bug#1054657: Source archive of DSS missing

Hi,

when looking at

    https://bioconductor.org/packages/release/bioc/html/DSS.html

and following the link "Source Archive" at bottom of the page linking
to
    https://bioconductor.org/packages/3.18/bioc/src/contrib/Archive/DSS/

I can only see

   Page Not Found
   The page you were looking for was not found. 

I'm trying to upgrade the Debian package of DSS to its latest version
and would need the source tarball which can be usually downloaded from
the "Source Archive" link.

Kind regards
    Andreas.

-- 
http://fam-tille.de

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#121472 — Bug#1054657: Source archive of DSS missing

Hi,

could someone please have a look at the source download?

Thank you
   Andreas.

Am Fri, Dec 08, 2023 at 04:04:27PM +0100 schrieb Andreas Tille:
> Hi,
> 
> when looking at
> 
>     https://bioconductor.org/packages/release/bioc/html/DSS.html
> 
> and following the link "Source Archive" at bottom of the page linking
> to
>     https://bioconductor.org/packages/3.18/bioc/src/contrib/Archive/DSS/
> 
> I can only see
> 
>    Page Not Found
>    The page you were looking for was not found. 
> 
> I'm trying to upgrade the Debian package of DSS to its latest version
> and would need the source tarball which can be usually downloaded from
> the "Source Archive" link.
> 
> Kind regards
>     Andreas.
> 
> -- 
> http://fam-tille.de

-- 
http://fam-tille.de

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#121513 — Bug#1054657: Transition ready? (Was: Transition seems to be blocked (Was: Bug#1054657: transition: r-bioc-biocgenerics))

Hi Paul,

Am Wed, Dec 13, 2023 at 09:56:14PM +0100 schrieb Paul Gevers:
> > > Not built on buildd: arch all binaries uploaded by tille, a new
> > > source-only upload is needed to allow migration
> > 
> > I do not understand this line.  What exact package needs a source-only
> > upload?
> 
> You uploaded binaries together with the source. Because this is an arch:all
> binary we can't binNMU in a meaningful way and we don't accept uploader
> built binaries in testing anymore. Currently the only way to solve this is
> by doing a source-only (so, no binaries) upload (of r-bioc-biocgenerics).

This must have been by pure accident since I never do so except for
packages targeting new.  I did a source-only upload for
r-bioc-biocgenerics.
 
> > Please let me know if I
> > can do something to fix the situation, but for the moment I have no idea
> > what to do.
> 
> Patches for britney2 please ;).

I'm using this chance to thank you for all your work in the release team
and patchinbg britney2 at least to the current state.
 
> I'll try to do some manual triggering of tests tonight/tomorrow, but after a
> quick glance, that might be too much to handle manually.
> 
> Paul
> 
> [1] https://tracker.debian.org/pkg/r-bioc-biocgenerics
> [tracker] https://tracker.debian.org/teams/r-pkg-team/ the piece below
> Packages with test failures: if it goes from passing in testing to fail in
> unstable there is potentially a problem

This tracker page was new to me and is extremely helpful!  Thanks to
whoever this thanks deserves.  Very helpful also for other teams I'm
working in.

> [excuses] https://release.debian.org/britney/update_excuses.html
> [yaml] https://release.debian.org/britney/excuses.yaml.gz

Well, it also points to several pandoc related issues which I can't
do anything about.

> [britney2] https://salsa.debian.org/release-team/britney2/-/blob/master/britney2/policies/autopkgtest.py#L622
> until line 743

Please let me know when I (realistically) can do more than just that
source-only upload mentioned above.

Kind regards
   Andreas.
-- 
http://fam-tille.de

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#121547 — Bug#1054657: marked as done (transition: r-bioc-biocgenerics)

[Multipart message — attachments visible in raw view] — view raw

Your message dated Sun, 17 Dec 2023 10:19:26 +0100
with message-id <3bcff6da-fe14-40e7-bf90-0d476ff1f73d@debian.org>
and subject line Re: Bug#1054657: Transition ready? (Was: Transition seems to be blocked (Was: Bug#1054657: transition: r-bioc-biocgenerics))
has caused the Debian Bug report #1054657,
regarding transition: r-bioc-biocgenerics
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.

(NB: If you are a system administrator and have no idea what this
message is talking about, this may indicate a serious mail system
misconfiguration somewhere. Please contact owner@bugs.debian.org
immediately.)


-- 
1054657: https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=1054657
Debian Bug Tracking System
Contact owner@bugs.debian.org with problems

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#121550 — Bug#1054657: Transition ready? (Was: Transition seems to be blocked (Was: Bug#1054657: transition: r-bioc-biocgenerics))

Hi Andreas

There are some packages that have still not migrated since the
previous r-api-bioc-3.17 transition in July 2023.

Links to their tracker pages, which should tell you what is needed, follow:

https://tracker.debian.org/pkg/r-bioc-cner
https://tracker.debian.org/pkg/r-bioc-dada2
https://tracker.debian.org/pkg/r-bioc-edaseq
https://tracker.debian.org/pkg/r-bioc-ioniser
https://tracker.debian.org/pkg/r-bioc-megadepth
https://tracker.debian.org/pkg/r-bioc-scater
https://tracker.debian.org/pkg/r-bioc-shortread
https://tracker.debian.org/pkg/r-bioc-tcgabiolinks
https://tracker.debian.org/pkg/r-bioc-tfbstools

As a bonus, here's another, not related to the transition, but from a
similar time:
https://tracker.debian.org/pkg/r-cran-dials

Regards
Graham

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#121554 — Bug#1054657: Transition ready? (Was: Transition seems to be blocked (Was: Bug#1054657: transition: r-bioc-biocgenerics))

Hi Graham,

Am Sun, Dec 17, 2023 at 02:11:47PM -0100 schrieb Graham Inggs:
> There are some packages that have still not migrated since the
> previous r-api-bioc-3.17 transition in July 2023.
> 
> Links to their tracker pages, which should tell you what is needed, follow:
> 
> https://tracker.debian.org/pkg/r-bioc-cner

Fixed.

> https://tracker.debian.org/pkg/r-bioc-dada2
> https://tracker.debian.org/pkg/r-bioc-edaseq
> https://tracker.debian.org/pkg/r-bioc-ioniser

Due to shortread.

> https://tracker.debian.org/pkg/r-bioc-megadepth

d/tests/control has

   Architecture: !s390x

Why is it considered failing on s390x anyway?

> https://tracker.debian.org/pkg/r-bioc-scater

While this is an Architecture:all package it Depends from r-bioc-densvis
which exists only on amd64 and arm64 due to the Build-Depends:
r-bioc-basiklisk.  Thus tests on other architectures are failing since
r-bioc-densvis is not installable.  What solution do you suggest in this
case?

> https://tracker.debian.org/pkg/r-bioc-shortread

Fixed.

> https://tracker.debian.org/pkg/r-bioc-tcgabiolinks

Reported upstream ( https://github.com/BioinformaticsFMRP/TCGAbiolinks/issues/612 )

> https://tracker.debian.org/pkg/r-bioc-tfbstools

Due to cner which is fixed.
 
> As a bonus, here's another, not related to the transition, but from a
> similar time:
> https://tracker.debian.org/pkg/r-cran-dials

Forgot source-only upload - done.

Thanks a lot for the links

   Andreas.

-- 
http://fam-tille.de

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