Re: [Bioc-devel] EXTERNAL: Re: Bad description file

[matine rb]

Thank you all for the help. I corrected the DESCRIPTION file and bump the
version.

Thank you,
Matineh Rahmatbakhsh

On Tue, Apr 4, 2023 at 1:50 PM Ramos Perez, Marcel <
marcel.ramospe...@roswellpark.org> wrote:

> Thank you Martin for providing the link.
>
> I misread the changes on the release branch.
> It looks like the DESCRIPTION file should be modified by removing the
> merge commit tag and
> following the bug fix instructions here:
>
>
> https://contributions.bioconductor.org/git-version-control.html?q=bug#bug-fix-in-release-and-devel
>
> Marcel
>
> On 4/4/23 3:34 PM, Martin Morgan wrote:
>
> The release version DESCRIPTION file is malformed, because it contains a
> (partial) merge commit tag
>
> https://code.bioconductor.org/browse/HPiP/blob/RELEASE_3_16/DESCRIPTION#L69
>
> Martin
>
> From: Bioc-devel  bioc-devel-boun...@r-project.org> on behalf of matine rb <
> matinerb...@gmail.com><mailto:matinerb...@gmail.com>
> Date: Tuesday, April 4, 2023 at 3:00 PM
> To: bioc-devel@r-project.org<mailto:bioc-devel@r-project.org> <
> bioc-devel@r-project.org><mailto:bioc-devel@r-project.org>
> Subject: [Bioc-devel] Bad description file
> Dear Bioc team
>
> I am the maintainer of the HPiP package which is currently showing unknown
> on the build report on the landing page.
>
> I would appreciate it if you could please help with this matter.
>
> Thank you,
> Matineh Rahmatbakhsh
>
> [[alternative HTML version deleted]]
>
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>
> ---
> Marcel Ramos
> Bioconductor Core Team
> Roswell Park Comprehensive Cancer Center
> Dept. of Biostatistics & Bioinformatics
> Elm St. & Carlton St.
> Buffalo, New York 14263
>
>
> This email message may contain legally privileged and/or confidential
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[Bioc-devel] Bad description file

[matine rb]

Dear Bioc team

I am the maintainer of the HPiP package which is currently showing unknown
on the build report on the landing page.

I would appreciate it if you could please help with this matter.

Thank you,
Matineh Rahmatbakhsh

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Re: [Bioc-devel] Push changes to release branch

[matine rb]

Hi Jennifer,

Thank you for the help,

Best wishes,
Matine

On Mon, Mar 27, 2023 at 2:20 PM Jennifer Wokaty <
jennifer.wok...@sph.cuny.edu> wrote:

> Yes, you should make changes on release as well. You can read more about
> how to do this at
> https://contributions.bioconductor.org/git-version-control.html#bug-fix-in-release-and-devel.
>
> Chapter 21 Git Version Control | Bioconductor Packages: Development,
> Maintenance, and Peer Review
> <https://contributions.bioconductor.org/git-version-control.html#bug-fix-in-release-and-devel>
> The Bioconductor project is maintained in a Git source control system.
> Package maintainers update their packages by pushing changes to their git
> repositories. This chapter contains several...
> contributions.bioconductor.org
>
>
> Jennifer Wokaty (they/them)
>
> Waldron Lab at CUNY SPH
> Bioconductor Core Team
> ----------
> *From:* Bioc-devel  on behalf of matine
> rb 
> *Sent:* Monday, March 27, 2023 4:09 PM
> *To:* bioc-devel@r-project.org 
> *Subject:* [Bioc-devel] Push changes to release branch
>
> ***ATTENTION: This email came from an external source. Do not open
> attachments or click on links from unknown senders or unexpected emails.***
>
>
> Hi Bioc-team,
>
> I am the maintainer of the HPiP package. The package showed a problem last
> couple of weeks and I have already committed changes to the devel branch.
> The package is fine now without any errors or warnings in the devel branch.
> My question is do I need to commit those changes to the release branch as
> well?
>
> Thank you,
> Matineh Rahmatbakhsh
>
> [[alternative HTML version deleted]]
>
> ___
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> https://urldefense.proofpoint.com/v2/url?u=https-3A__stat.ethz.ch_mailman_listinfo_bioc-2Ddevel=DwICAg=mRWFL96tuqj9V0Jjj4h40ddo0XsmttALwKjAEOCyUjY=FKSqKXkUOES-D4VQb2jSn9QK7Vz5lE18rLcyn73CPhA=D2WeHerUr5ukjRs0NRwlI4HrTjcP3vJxAWQfMelwQVFoYANfTcOqxGnVBNeyEDZa=AHzZRZ8bAXjrSnFmX0IKwCo1F26mp2TcctP3G7MawxU=
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[Bioc-devel] Push changes to release branch

[matine rb]

Hi Bioc-team,

I am the maintainer of the HPiP package. The package showed a problem last
couple of weeks and I have already committed changes to the devel branch.
The package is fine now without any errors or warnings in the devel branch.
My question is do I need to commit those changes to the release branch as
well?

Thank you,
Matineh Rahmatbakhsh

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Re: [Bioc-devel] version bump

[matine rb]

Hi Hervé, 

Thank alot for the help. It works now 

Matine

Sent from my iPhone

> On Nov 30, 2021, at 1:33 PM, Hervé Pagès  wrote:
> 
> Hervé

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[Bioc-devel] version bump

[matine rb]

Dear Bioconductor community members,

I have pushed some changes to the HPiP package, but I
mistakenly  changed the version bump from 0.99.19 to 1.99.1, and therefore
I am getting the following error:
(Illegal version bump from '1.99.1' to '0.99.19')

May you please help me with this issue? I really want the changes to appear
in both the devel and release versions.

thank you,
Matineh

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Re: [Bioc-devel] Updating the vignette in the published package

[matine rb]

Hi Hervé,

Thank you a lot for the help, It is already updated.

Matine

On Tue, Oct 26, 2021 at 1:04 PM Hervé Pagès 
wrote:

> Hi Matine,
>
> You bumped the version to 0.99.18 on Sunday evening so it was too late
> to be reflected on yesterday's (Monday) build report.
>
> The new version is reflected on today's report:
>
>https://bioconductor.org/checkResults/3.14/bioc-LATEST/HPiP/
>
> and the package landing page on the website will automatically refresh
> in a few minutes. After the refresh, it should have a link to the new
> vignette. Let us know if it doesn't. Thanks!
>
> Cheers,
> H.
>
>
> On 26/10/2021 11:22, matine rb wrote:
> > Hi Lori,
> >
> > Thank you for the help, I have updated the version bump on Saturday.
> >
> > thank you,
> > Matine
> >
> > On Fri, Oct 22, 2021 at 11:29 AM Kern, Lori <
> lori.sheph...@roswellpark.org>
> > wrote:
> >
> >> The changes to the vignette did not include a valid version bump.  Could
> >> you please trying bumping the version of your description.  Regardless
> of
> >> if this is needed to update the website, it would be needed to propagate
> >> and have the correct version available from within R using the
> vignette()
> >> function.
> >> If the issue persists after the version bump, please let us know and we
> >> can investigate further.
> >>
> >>
> >> Lori Shepherd
> >>
> >> Bioconductor Core Team
> >>
> >> Roswell Park Comprehensive Cancer Center
> >>
> >> Department of Biostatistics & Bioinformatics
> >>
> >> Elm & Carlton Streets
> >>
> >> Buffalo, New York 14263
> >> --
> >> *From:* Bioc-devel  on behalf of
> matine
> >> rb 
> >> *Sent:* Friday, October 22, 2021 1:17 PM
> >> *To:* bioc-devel@r-project.org 
> >> *Subject:* [Bioc-devel] Updating the vignette in the published package
> >>
> >> Dear Bioconductor community members,
> >>
> >> I am wondering how to update the vignette after the package is available
> >> from the Bioconductor website? As I have noticed, the available vignette
> >> for my package (*https://bioconductor.org/packages/HPiP/
> >> <https://bioconductor.org/packages/HPiP/>*) includes two
> introductions. I
> >> have already pushed the changes, but I think the vignette can not be
> >> updated once the package is available online.
> >>
> >> I would appreciate it if you help me with this matter.
> >>
> >> with thanks,
> >> Matineh
> >>
> >>  [[alternative HTML version deleted]]
> >>
> >> ___
> >> Bioc-devel@r-project.org mailing list
> >>
> >>
> https://secure-web.cisco.com/1PumdJEebo5gsSjq7pNXKugQ_8YHiPPxHwcj9EZP-K0A3yfGWhn4RA-tSQdK1k5SP_BelEaIITVq6GLyRwfY5nkhmLN2dVKre9B6UPH1ZEN6AfQV4Bt3Bsx-ZT1fTzxcU-kV2cuCLrv65ZMOZ_DPYLionk4CmNDOnyYaGRSyI3BdTrPQKhUm_ZpuMGwVv5ptoQxi0JoDGYfEWjYO91lM2rIptudVwdZ7hMdjZgjScQws_rMDKYcReo-zOhFcUUONkFx4lV1OxpSAb_8qJwX3mV9jhnkTIogHNmaRbbC0dWK_R6zGvKIZw4bGENSbcDW90/https%3A%2F%2Fstat.ethz.ch%2Fmailman%2Flistinfo%2Fbioc-devel
> >>
> >>
> >> This email message may contain legally privileged and/or confidential
> >> information. If you are not the intended recipient(s), or the employee
> or
> >> agent responsible for the delivery of this message to the intended
> >> recipient(s), you are hereby notified that any disclosure, copying,
> >> distribution, or use of this email message is prohibited. If you have
> >> received this message in error, please notify the sender immediately by
> >> e-mail and delete this email message from your computer. Thank you.
> >
> >   [[alternative HTML version deleted]]
> >
> > ___
> > Bioc-devel@r-project.org mailing list
> > https://stat.ethz.ch/mailman/listinfo/bioc-devel
> >
>
> --
> Hervé Pagès
>
> Bioconductor Core Team
> hpages.on.git...@gmail.com
>

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Re: [Bioc-devel] Updating the vignette in the published package

[matine rb]

Hi Lori,

Thank you for the help, I have updated the version bump on Saturday.

thank you,
Matine

On Fri, Oct 22, 2021 at 11:29 AM Kern, Lori 
wrote:

> The changes to the vignette did not include a valid version bump.  Could
> you please trying bumping the version of your description.  Regardless of
> if this is needed to update the website, it would be needed to propagate
> and have the correct version available from within R using the vignette()
> function.
> If the issue persists after the version bump, please let us know and we
> can investigate further.
>
>
> Lori Shepherd
>
> Bioconductor Core Team
>
> Roswell Park Comprehensive Cancer Center
>
> Department of Biostatistics & Bioinformatics
>
> Elm & Carlton Streets
>
> Buffalo, New York 14263
> ------
> *From:* Bioc-devel  on behalf of matine
> rb 
> *Sent:* Friday, October 22, 2021 1:17 PM
> *To:* bioc-devel@r-project.org 
> *Subject:* [Bioc-devel] Updating the vignette in the published package
>
> Dear Bioconductor community members,
>
> I am wondering how to update the vignette after the package is available
> from the Bioconductor website? As I have noticed, the available vignette
> for my package (*https://bioconductor.org/packages/HPiP/
> <https://bioconductor.org/packages/HPiP/>*) includes two introductions. I
> have already pushed the changes, but I think the vignette can not be
> updated once the package is available online.
>
> I would appreciate it if you help me with this matter.
>
> with thanks,
> Matineh
>
> [[alternative HTML version deleted]]
>
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> recipient(s), you are hereby notified that any disclosure, copying,
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> received this message in error, please notify the sender immediately by
> e-mail and delete this email message from your computer. Thank you.

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[Bioc-devel] Updating the vignette in the published package

[matine rb]

Dear Bioconductor community members,

I am wondering how to update the vignette after the package is available
from the Bioconductor website? As I have noticed, the available vignette
for my package (*https://bioconductor.org/packages/HPiP/
*) includes two introductions. I
have already pushed the changes, but I think the vignette can not be
updated once the package is available online.

I would appreciate it if you help me with this matter.

with thanks,
Matineh

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[Bioc-devel] Reset package

[matine rb]

Dear Bioconductor community,

My package HPiP (https://bioconductor.org/packages/devel/bioc/html/HPiP.html)
has been cleaned for large files, May you please reset the repository on
Bioconductor?

Matineh Rahmatbakhsh

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Re: [Bioc-devel] Error when building a package

[matine rb]

Thanks a lot for the help, I found the issue.

On Mon, Oct 4, 2021 at 9:40 PM Hervé Pagès 
wrote:

> Let's keep this conversation on the bioc-devel list where it started.
>
> On 04/10/2021 20:28, matine rb wrote:
> > Hi Hervé,
> >
> > yes, I am using R CMD build *--keep-empty-dirs -- no-resave-data* and
> > getting no error. I still don't know what is causing the problem.
>
> Again, make sure to read what's in the rectangular box on the following
> page:
>
>http://bioconductor.org/checkResults/devel/bioc-LATEST/HPiP/
>
> It's not about using --keep-empty-dirs or --no-resave-data when you run
> 'R CMD build'. It's about... well, just read it! (and follow the
> provided link).
>
> Best,
> H.
>
>
> >
> >
> >
> > On Mon, Oct 4, 2021 at 4:21 PM Hervé Pagès  > <mailto:hpages.on.git...@gmail.com>> wrote:
> >
> > Hi,
> >
> > Are you using the same settings as the build machines as explained in
> > the rectangular box on the following page?
> >
> > http://bioconductor.org/checkResults/devel/bioc-LATEST/HPiP/
> > <http://bioconductor.org/checkResults/devel/bioc-LATEST/HPiP/>
> >
> > Best,
> > H.
> >
> >
> > On 04/10/2021 13:50, matine rb wrote:
> >  > Dear Bioconductor community members,
> >  >
> >  > I have submitted the package 'HPiP' and the package has been
> > accepted (link
> >  > :
> >  > http://bioconductor.org/packages/3.14/bioc/html/HPiP.html
> > <http://bioconductor.org/packages/3.14/bioc/html/HPiP.html>).
> > However, the
> >  > package has the following problem :
> >  >
> >  > package or namespace load failed for 'kableExtra':
> >  >   .onLoad failed in loadNamespace() for 'kableExtra', details:
> >  >
> >  > but, when I try to build and check the package locally, I got no
> > error
> >  > message.
> >  >
> >  > May please someone advise me regarding this issue?
> >  >
> >  > With thanks,
> >  > Matineh
> >  >
> >  >   [[alternative HTML version deleted]]
> >  >
> >  > ___
> >  > Bioc-devel@r-project.org <mailto:Bioc-devel@r-project.org>
> > mailing list
> >  > https://stat.ethz.ch/mailman/listinfo/bioc-devel
> > <https://stat.ethz.ch/mailman/listinfo/bioc-devel>
> >  >
> >
> > --
> > Hervé Pagès
> >
> > Bioconductor Core Team
> > hpages.on.git...@gmail.com <mailto:hpages.on.git...@gmail.com>
> >
>
> --
> Hervé Pagès
>
> Bioconductor Core Team
> hpages.on.git...@gmail.com
>

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[Bioc-devel] Error when building a package

[matine rb]

Dear Bioconductor community members,

I have submitted the package 'HPiP' and the package has been accepted (link
:
http://bioconductor.org/packages/3.14/bioc/html/HPiP.html). However, the
package has the following problem :

package or namespace load failed for 'kableExtra':
 .onLoad failed in loadNamespace() for 'kableExtra', details:

but, when I try to build and check the package locally, I got no error
message.

May please someone advise me regarding this issue?

With thanks,
Matineh

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[Bioc-devel] Package submission status: 'under review'

[matine rb]

Dear Bioconductor community members,

I submitted a package 'HPiP' ten days ago (submission link:
https://github.com/Bioconductor/Contributions/issues/2230), and the
submission status is 'under review'. However, still, there is no one
assigned to review my package. So, I would like to know if there is
anything that I missed during the package submission or I just need to wait
longer.

with thanks,
Matineh

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