[Bioc-devel] Fwd: BioC 3.12 coming soon, package a4 and a4Base need your attention!

3.11 is the current release version. Commits to the current release version were disabled yesterday.

  https://bioconductor.org/developers/release-schedule/

You want to push changes to the devel ('master') branch.

Martin

?On 10/14/20, 5:34 AM, "Bioc-devel on behalf of Laure Cougnaud" <bioc-devel-bounces at r-project.org on behalf of laure.cougnaud at openanalytics.eu> wrote:

    Dear Bioc-devel, 

    I am experiencing some issues to push changes to the release 3.11 branch of my package (a4Base) in Bioconductor, in order to fix the errors mentioned in the [ https://bioconductor.org/checkResults/3.11/bioc-LATEST/a4Base/ | build/check report for BioC 3.11 ] . 
    I could successfully push the changes in the 'master' branch to the Bioconductor repository. 

    I followed the steps in [ https://bioconductor.org/developers/how-to/git/maintain-bioc-only/ | 'Maintain a Bioconductor-only repository' ] for an existing package: 

        1. git checkout -b RELEASE_3_11 BioC/RELEASE_3_11 # (my local remote is labelled 'BioC') 
        2. make some updates 
        3. git add . 
        4. git commit -m 'commit message' 
        5. git status On branch RELEASE_3_11 Your branch is ahead of 'BioC/RELEASE_3_11' by 1 commit. (use "git push" to publish your local commits) nothing to commit, working tree clean 
        6. git push BioC RELEASE_3_11 Counting objects: 7, done. Delta compression using up to 4 threads. Compressing objects: 100% (7/7), done. Writing objects: 100% (7/7), 1.04 KiB | 1.04 MiB/s, done. Total 7 (delta 4), reused 0 (delta 0) remote: FATAL: W refs/heads/RELEASE_3_11 packages/a4Base l.cougnaud DENIED by fallthru remote: error: hook declined to update refs/heads/RELEASE_3_11 To git.bioconductor.org:packages/a4Base ! [remote rejected] RELEASE_3_11 -> RELEASE_3_11 (hook declined) error: failed to push some refs to 'git at git.bioconductor.org:packages/a4Base' 

    Would it be possible to help me out for this issue? Do I have proper permissions to push changes to the devel version of Bioconductor? 

    Many thanks in advance for the support, 

    Regards, 

    Laure Cougnaud, 
    Statistical Consultant, OpenAnalytics 

    > From: "Herv? Pag?s" <hpages.on.github at gmail.com>
    > To: "Laure Cougnaud" <laure.cougnaud at openanalytics.eu>
    > Cc: "Tobias Verbeke" <tobias.verbeke at openanalytics.eu>
    > Sent: Friday, October 9, 2020 7:34:08 PM
    > Subject: Re: BioC 3.12 coming soon, package a4 and a4Base need your attention!

    > Hi Laure,

    > On 10/9/20 08:14, Laure Cougnaud wrote:> Hi Herv?,

    >> I will investigate the issue further on Monday, I recently got some issues to
    >> pull the latest version of the a4Base package from the Bioconductor git:

    >> git pull BioC master
    >> git at git.bioconductor.org: Permission denied (publickey).
    >> fatal: Could not read from remote repository.

    >> I updated my SSH key in GitHub. If I understood correctly, it could take a few
    >> hours to have it synchronized in the Bioconductor platform, so I will test
    >> again on Monday.
    > Hopefully that will work. Please ask on the bioc-devel mailing list if
    > you keep having problems to access the Bioconductor git server. I don't
    > manage git access issues.

    > Thanks and have a nice week-end,
    > H.

    >> Thanks in advance for your understanding, have all a nice week-end,

    >> Regards,

    >> Laure Cougnaud,
    >> Statistical Consultant, OpenAnalytics

    >> ----- Original Message -----

    >>> From: "Laure Cougnaud" <laure.cougnaud at openanalytics.eu>
    >>> To: "Herv? Pag?s" <hpages.on.github at gmail.com>
    >>> Cc: "Tobias Verbeke" <tobias.verbeke at openanalytics.eu>
    >>> Sent: Friday, October 9, 2020 1:23:38 PM
    >>> Subject: Re: BioC 3.12 coming soon, package a4 and a4Base need your attention!
    >>> Dear Herv?,

    >>> Thanks for the reminder, I will look at the issues in the course of today.

    >>> Sorry for the later reply,

    >>> Regards,

    >>> Laure Cougnaud,
    >>> Statistical Consultant, OpenAnalytics

    >>> ----- Original Message -----

    >>>> From: "Herv? Pag?s" <hpages.on.github at gmail.com>
    >>>> To: "Tobias Verbeke" <tobias.verbeke at openanalytics.eu>, "Laure Cougnaud"
    >>>> <laure.cougnaud at openanalytics.eu>
    >>>> Sent: Friday, October 9, 2020 9:07:06 AM
    >>>> Subject: BioC 3.12 coming soon, package a4 and a4Base need your attention!
    >>>> Dear a4 and a4Base maintainers,

    >>>> The Bioconductor Build System is reporting a BUILD error on all
    >>>> platforms for the devel version of the a4 package:

    >>>> https://bioconductor.org/checkResults/3.12/bioc-LATEST/a4/

    >>>> And also a CHECK error on Windows for the devel and release versions of
    >>>> the a4Base package:

    >>>> https://bioconductor.org/checkResults/3.12/bioc-LATEST/a4Base/
    >>>> https://bioconductor.org/checkResults/3.11/bioc-LATEST/a4Base/

    >>>> Please take the time to address these issues.

    >>>> Note that the a4Base error on Windows seems to be a 32-bit specific
    >>>> error (the examples for spectralMap() fail on 32-bit Windows but not on
    >>>> 64-bit Windows). It has been reported in several past versions of
    >>>> Bioconductor:

    >>>> https://bioconductor.org/checkResults/3.10/bioc-LATEST/a4Base/
    >>>> https://bioconductor.org/checkResults/3.9/bioc-LATEST/a4Base/
    >>>> https://bioconductor.org/checkResults/3.7/bioc-LATEST/a4Base/

    >>>> If a4Base cannot be fixed on 32-bit Windows, we will mark it as
    >>>> unsupported on this platform.

    >>>> Keep in mind that the packages need to pass 'R CMD build' and 'R CMD
    >>>> check' with no error for the next Bioconductor release (BioC 3.12)
    >>>> scheduled for Wednesday October 28. See our release schedule here for
    >>>> more information:

    >>>> https://bioconductor.org/developers/release-schedule/

    >>>> Don't hesitate to ask on the bioc-devel mailing list if you have
    >>>> questions or concerns about this.

    >>>> Thanks for your contribution to Bioconductor.

    >>>> Best,
    >>>> H.

    >>>> --
    >>>> Herv? Pag?s

    >>>> Bioconductor Core Team
    >>>> hpages.on.github at gmail.com
    > --
    > Herv? Pag?s

    > Bioconductor Core Team
    > hpages.on.github at gmail.com


    _______________________________________________
    Bioc-devel at r-project.org mailing list
    https://stat.ethz.ch/mailman/listinfo/bioc-devel

Hi Martin,

Ok I miss this information.
Thanks for the information, I will push new changes to the master branch.

Thanks again for the support,

Regards, 

Laure Cougnaud, 
Statistical Consultant, OpenAnalytics

----- Original Message -----

From: "Martin Morgan" <mtmorgan.bioc at gmail.com>
To: "Laure Cougnaud" <laure.cougnaud at openanalytics.eu>, "bioc-devel" <bioc-devel at r-project.org>
Sent: Wednesday, October 14, 2020 12:33:22 PM
Subject: Re: [Bioc-devel] Fwd: BioC 3.12 coming soon, package a4 and a4Base need your attention!

3.11 is the current release version. Commits to the current release version were
disabled yesterday.

 https://bioconductor.org/developers/release-schedule/

You want to push changes to the devel ('master') branch.

Martin

?On 10/14/20, 5:34 AM, "Bioc-devel on behalf of Laure Cougnaud"
?<bioc-devel-bounces at r-project.org on behalf of laure.cougnaud at openanalytics.eu>
?wrote:

   Dear Bioc-devel,

   I am experiencing some issues to push changes to the release 3.11 branch of my
   package (a4Base) in Bioconductor, in order to fix the errors mentioned in the [
   https://bioconductor.org/checkResults/3.11/bioc-LATEST/a4Base/ | build/check
   report for BioC 3.11 ] .
   I could successfully push the changes in the 'master' branch to the Bioconductor
   repository.

   I followed the steps in [
   https://bioconductor.org/developers/how-to/git/maintain-bioc-only/ | 'Maintain
   a Bioconductor-only repository' ] for an existing package:

       1. git checkout -b RELEASE_3_11 BioC/RELEASE_3_11 # (my local remote is labelled
       'BioC')
       2. make some updates
       3. git add .
       4. git commit -m 'commit message'
       5. git status On branch RELEASE_3_11 Your branch is ahead of 'BioC/RELEASE_3_11'
       by 1 commit. (use "git push" to publish your local commits) nothing to commit,
       working tree clean
       6. git push BioC RELEASE_3_11 Counting objects: 7, done. Delta compression using
       up to 4 threads. Compressing objects: 100% (7/7), done. Writing objects: 100%
       (7/7), 1.04 KiB | 1.04 MiB/s, done. Total 7 (delta 4), reused 0 (delta 0)
       remote: FATAL: W refs/heads/RELEASE_3_11 packages/a4Base l.cougnaud DENIED by
       fallthru remote: error: hook declined to update refs/heads/RELEASE_3_11 To
       git.bioconductor.org:packages/a4Base ! [remote rejected] RELEASE_3_11 ->
       RELEASE_3_11 (hook declined) error: failed to push some refs to
       'git at git.bioconductor.org:packages/a4Base'

   Would it be possible to help me out for this issue? Do I have proper permissions
   to push changes to the devel version of Bioconductor?

   Many thanks in advance for the support,

   Regards,

   Laure Cougnaud,
   Statistical Consultant, OpenAnalytics

   > From: "Herv? Pag?s" <hpages.on.github at gmail.com>
   > To: "Laure Cougnaud" <laure.cougnaud at openanalytics.eu>
   > Cc: "Tobias Verbeke" <tobias.verbeke at openanalytics.eu>
   > Sent: Friday, October 9, 2020 7:34:08 PM
   > Subject: Re: BioC 3.12 coming soon, package a4 and a4Base need your attention!

   > Hi Laure,

   > On 10/9/20 08:14, Laure Cougnaud wrote:> Hi Herv?,

   >> I will investigate the issue further on Monday, I recently got some issues to
   >> pull the latest version of the a4Base package from the Bioconductor git:

   >> git pull BioC master
   >> git at git.bioconductor.org: Permission denied (publickey).
   >> fatal: Could not read from remote repository.

   >> I updated my SSH key in GitHub. If I understood correctly, it could take a few
   >> hours to have it synchronized in the Bioconductor platform, so I will test
   >> again on Monday.

   > Hopefully that will work. Please ask on the bioc-devel mailing list if
   > you keep having problems to access the Bioconductor git server. I don't
   > manage git access issues.

   > Thanks and have a nice week-end,
   > H.

   >> Thanks in advance for your understanding, have all a nice week-end,

   >> Regards,

   >> Laure Cougnaud,
   >> Statistical Consultant, OpenAnalytics

   >> ----- Original Message -----

   >>> From: "Laure Cougnaud" <laure.cougnaud at openanalytics.eu>
   >>> To: "Herv? Pag?s" <hpages.on.github at gmail.com>
   >>> Cc: "Tobias Verbeke" <tobias.verbeke at openanalytics.eu>
   >>> Sent: Friday, October 9, 2020 1:23:38 PM
   >>> Subject: Re: BioC 3.12 coming soon, package a4 and a4Base need your attention!
   >>> Dear Herv?,

   >>> Thanks for the reminder, I will look at the issues in the course of today.

   >>> Sorry for the later reply,

   >>> Regards,

   >>> Laure Cougnaud,
   >>> Statistical Consultant, OpenAnalytics

   >>> ----- Original Message -----

   >>>> From: "Herv? Pag?s" <hpages.on.github at gmail.com>
   >>>> To: "Tobias Verbeke" <tobias.verbeke at openanalytics.eu>, "Laure Cougnaud"
   >>>> <laure.cougnaud at openanalytics.eu>
   >>>> Sent: Friday, October 9, 2020 9:07:06 AM
   >>>> Subject: BioC 3.12 coming soon, package a4 and a4Base need your attention!
   >>>> Dear a4 and a4Base maintainers,

   >>>> The Bioconductor Build System is reporting a BUILD error on all
   >>>> platforms for the devel version of the a4 package:

   >>>> https://bioconductor.org/checkResults/3.12/bioc-LATEST/a4/

   >>>> And also a CHECK error on Windows for the devel and release versions of
   >>>> the a4Base package:

   >>>> https://bioconductor.org/checkResults/3.12/bioc-LATEST/a4Base/
   >>>> https://bioconductor.org/checkResults/3.11/bioc-LATEST/a4Base/

   >>>> Please take the time to address these issues.

   >>>> Note that the a4Base error on Windows seems to be a 32-bit specific
   >>>> error (the examples for spectralMap() fail on 32-bit Windows but not on
   >>>> 64-bit Windows). It has been reported in several past versions of
   >>>> Bioconductor:

   >>>> https://bioconductor.org/checkResults/3.10/bioc-LATEST/a4Base/
   >>>> https://bioconductor.org/checkResults/3.9/bioc-LATEST/a4Base/
   >>>> https://bioconductor.org/checkResults/3.7/bioc-LATEST/a4Base/

   >>>> If a4Base cannot be fixed on 32-bit Windows, we will mark it as
   >>>> unsupported on this platform.

   >>>> Keep in mind that the packages need to pass 'R CMD build' and 'R CMD
   >>>> check' with no error for the next Bioconductor release (BioC 3.12)
   >>>> scheduled for Wednesday October 28. See our release schedule here for
   >>>> more information:

   >>>> https://bioconductor.org/developers/release-schedule/

   >>>> Don't hesitate to ask on the bioc-devel mailing list if you have
   >>>> questions or concerns about this.

   >>>> Thanks for your contribution to Bioconductor.

   >>>> Best,
   >>>> H.

   >>>> --
   >>>> Herv? Pag?s

   >>>> Bioconductor Core Team
   >>>> hpages.on.github at gmail.com

   > --
   > Herv? Pag?s

   > Bioconductor Core Team
   > hpages.on.github at gmail.com

   	[[alternative HTML version deleted]]

   _______________________________________________
   Bioc-devel at r-project.org mailing list
    https://stat.ethz.ch/mailman/listinfo/bioc-devel

Dear bioc team,

I am getting the following warning
<http://bioconductor.org/checkResults/devel/bioc-LATEST/artMS/> that I do
not understand and cannot reproduce locally (and my search online didn't
help):

* checking whether package ?artMS? can be installed ... WARNING
Found the following significant warnings:
  Warning: replacing previous import ?ComplexHeatmap::pheatmap? by
?pheatmap::pheatmap? when loading ?artMS?
See ?/home/biocbuild/bbs-3.12-bioc/meat/artMS.Rcheck/00install.out? for details.

What does this mean? How could I get rid of the warning?

Thanks a lot!
David


Found the following significant warnings:
  Warning: replacing previous import ?ComplexHeatmap::pheatmap? by
?pheatmap::pheatmap? when loading

Your NAMESPACE has

import(ComplexHeatmap)
...
import(pheatmap)

and both packages have a function pheatmap -- the import from ComplexHeatmap is being replaced by the import from pheatmap.

In other places your NAMESPACE has lines like

import(seqinr, except = c(zscore, count, a))

so you'd like to do the same for one or the other of ComplexHeatmap / pheatmap. It looks like the roxygen for this is

#' @rawNamespace import(ComplexHeatmap, except = c(pheatmap))

...but I wonder whether you really want to import both packages?? Does your package really need functionality from each? I see from

  https://bioconductor.org/packages/artMS

that your package has 200 dependencies, which is a lot and means that changes in any of those could break your package -- it sounds like a quite fragile situation.

Martin



?On 10/22/20, 2:13 AM, "Bioc-devel on behalf of David Jimenez-Morales" <bioc-devel-bounces at r-project.org on behalf of biodavidjm at gmail.com> wrote:

    Dear bioc team,

    I am getting the following warning
    <http://bioconductor.org/checkResults/devel/bioc-LATEST/artMS/> that I do
    not understand and cannot reproduce locally (and my search online didn't
    help):

    * checking whether package ?artMS? can be installed ... WARNING
    Found the following significant warnings:
      Warning: replacing previous import ?ComplexHeatmap::pheatmap? by
    ?pheatmap::pheatmap? when loading ?artMS?
    See ?/home/biocbuild/bbs-3.12-bioc/meat/artMS.Rcheck/00install.out? for details.

    What does this mean? How could I get rid of the warning?

    Thanks a lot!
    David


    Found the following significant warnings:
      Warning: replacing previous import ?ComplexHeatmap::pheatmap? by
    ?pheatmap::pheatmap? when loading


    _______________________________________________
    Bioc-devel at r-project.org mailing list
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Thanks a lot, Martin,

I'll take care of that. I guess that's a new function in that package
(because it always worked before)

And yes, I am planning to start removing dependencies. artMS has one
function that tries to help the very inexperienced R users by doing a lot
of things for them out of the box.

Thank you very much!
David

On Thu, Oct 22, 2020 at 12:25 AM Martin Morgan <mtmorgan.bioc at gmail.com>
wrote:

Your NAMESPACE has

import(ComplexHeatmap)
...
import(pheatmap)

and both packages have a function pheatmap -- the import from
ComplexHeatmap is being replaced by the import from pheatmap.

In other places your NAMESPACE has lines like

import(seqinr, except = c(zscore, count, a))

so you'd like to do the same for one or the other of ComplexHeatmap /
pheatmap. It looks like the roxygen for this is

#' @rawNamespace import(ComplexHeatmap, except = c(pheatmap))

...but I wonder whether you really want to import both packages?? Does
your package really need functionality from each? I see from

  https://bioconductor.org/packages/artMS

that your package has 200 dependencies, which is a lot and means that
changes in any of those could break your package -- it sounds like a quite
fragile situation.

Martin



?On 10/22/20, 2:13 AM, "Bioc-devel on behalf of David Jimenez-Morales" <
bioc-devel-bounces at r-project.org on behalf of biodavidjm at gmail.com> wrote:

    Dear bioc team,

    I am getting the following warning
    <http://bioconductor.org/checkResults/devel/bioc-LATEST/artMS/> that
I do
    not understand and cannot reproduce locally (and my search online
didn't
    help):

    * checking whether package ?artMS? can be installed ... WARNING
    Found the following significant warnings:
      Warning: replacing previous import ?ComplexHeatmap::pheatmap? by
    ?pheatmap::pheatmap? when loading ?artMS?
    See ?/home/biocbuild/bbs-3.12-bioc/meat/artMS.Rcheck/00install.out?
for details.

    What does this mean? How could I get rid of the warning?

    Thanks a lot!
    David


    Found the following significant warnings:
      Warning: replacing previous import ?ComplexHeatmap::pheatmap? by
    ?pheatmap::pheatmap? when loading

        [[alternative HTML version deleted]]

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