Re: [Bioc-devel] New Package Submission Workflow Updates!

[Martin Morgan]

Hi Lluís --

We'll try to incorporate your comments. If you can, it would be great to make 
specific pull requests on 
https://github.com/Bioconductor/Contributions/blob/master/CONTRIBUTING.md or 
https://github.com/Bioconductor/bioconductor.org, e.g., at 
https://github.com/Bioconductor/bioconductor.org/blob/master/content/developers/package-submission.md
 . There's a dockerfile for processing the Bioconductor web site in the 
repository, but having the web site build correctly is not a requirement for a 
useful pull request!

Thanks for your attention to detail; it's very valuable for the project.

Martin



On 7/8/20, 11:59 AM, "Bioc-devel on behalf of Lluís Revilla" 
 wrote:

Hi Lori and Core Team,

Hope this change will make it easier for all to submit packages to
Bioconductor (and review them).

I have a couple of comments on the documentation. I think that the
extensive documentation available can be confusing and a bit circular.
The README of github.com/Bioconductor/Contributions says: "Review the 
package
submission 
process"
While on that page under Submission it says: "Submit by opening a new issue
in the *Bioconductor* Contributions
 repository,
following the guidelines  of
the README.md file.".
Perhaps a more lineal documentation will be easier to follow and understand
for new and old contributors.

Another thing that caught my attention: on the README under "What to
expect" there is a link to the new package workflow

where it is explained how to set up the local repository to be able to
update the package for the submission. However, it isn't linked from the
package submission website and it only mentions that it is for
modifications **after moderation**. I think this is the ideal situation
(first time submitted packages pass all the check the first time), but
often new submissions must update the package so that the package passes
all the checks in order to be reviewed/moderated. I think this needs to be
mentioned too.

Best,

Lluís

On Wed, 8 Jul 2020 at 17:03, Shepherd, Lori 
wrote:

> Hello Bioconductor Development Community,
>
> The team has made a significant change to the single package builder
> process for submitting new packages to Bioconductor.
>
> Previously, when submitting a new package, the process was to submit on
> github, add a webhook for interactive building on version bump, 
acceptance,
> addition to the git.bioconductor.org repository system, and addition to
> the daily builder manifest.
>
> Now upon submission of your package to github, the preapproval process
> will involve immediately adding packages to git.bioconductor.org.
> Subsequent builds of the package during the review process will be
> triggered by a version bump and push to the upstream repository at
> g...@git.bioconductor.org:packages/. Upon acceptance your
> package will be added to the daily builder manifest for official inclusion
> in Bioconductor.
>
>
> The webhook will be deactivated and no longer trigger builds during the
> review process.
> Any package that was previously submitted (Before July 7th, 2020) will not
> have to worry about the new workflow. You can continue your new package
> review as you have been and we will deactivate your webhook once you are
> through the submission process.
> This will only affect packages newly submitted.
>
> Please ask any questions or concerns you may have.
>
> Thank you
> Lori Shepherd on behalf of the Core Team
>
>
>
> 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
>

[[alternative HTML version deleted]]

___
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Re: [Bioc-devel] New Package Submission Workflow Updates!

[Lluís Revilla]

Hi Lori and Core Team,

Hope this change will make it easier for all to submit packages to
Bioconductor (and review them).

I have a couple of comments on the documentation. I think that the
extensive documentation available can be confusing and a bit circular.
The README of github.com/Bioconductor/Contributions says: "Review the package
submission 
process"
While on that page under Submission it says: "Submit by opening a new issue
in the *Bioconductor* Contributions
 repository,
following the guidelines  of
the README.md file.".
Perhaps a more lineal documentation will be easier to follow and understand
for new and old contributors.

Another thing that caught my attention: on the README under "What to
expect" there is a link to the new package workflow

where it is explained how to set up the local repository to be able to
update the package for the submission. However, it isn't linked from the
package submission website and it only mentions that it is for
modifications **after moderation**. I think this is the ideal situation
(first time submitted packages pass all the check the first time), but
often new submissions must update the package so that the package passes
all the checks in order to be reviewed/moderated. I think this needs to be
mentioned too.

Best,

Lluís

On Wed, 8 Jul 2020 at 17:03, Shepherd, Lori 
wrote:

> Hello Bioconductor Development Community,
>
> The team has made a significant change to the single package builder
> process for submitting new packages to Bioconductor.
>
> Previously, when submitting a new package, the process was to submit on
> github, add a webhook for interactive building on version bump, acceptance,
> addition to the git.bioconductor.org repository system, and addition to
> the daily builder manifest.
>
> Now upon submission of your package to github, the preapproval process
> will involve immediately adding packages to git.bioconductor.org.
> Subsequent builds of the package during the review process will be
> triggered by a version bump and push to the upstream repository at
> g...@git.bioconductor.org:packages/. Upon acceptance your
> package will be added to the daily builder manifest for official inclusion
> in Bioconductor.
>
>
> The webhook will be deactivated and no longer trigger builds during the
> review process.
> Any package that was previously submitted (Before July 7th, 2020) will not
> have to worry about the new workflow. You can continue your new package
> review as you have been and we will deactivate your webhook once you are
> through the submission process.
> This will only affect packages newly submitted.
>
> Please ask any questions or concerns you may have.
>
> Thank you
> Lori Shepherd on behalf of the Core Team
>
>
>
> 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
>

[[alternative HTML version deleted]]

___
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Re: [Bioc-devel] New package submission : No reviewer communication.

[Shepherd, Lori]

Hi Ralf -  Martin is your reviewer and will be in touch with you shortly 
concerning your packages.



Lori Shepherd

Bioconductor Core Team

Roswell Park Comprehensive Cancer Center

Department of Biostatistics & Bioinformatics

Elm & Carlton Streets

Buffalo, New York 14263


From: Ralf Weber 
Sent: Wednesday, November 20, 2019 9:03 AM
To: Shepherd, Lori 
Cc: Neumann, Steffen ; Turaga, Nitesh 
; ashku...@gatech.edu ; 
bioc-devel@r-project.org 
Subject: Re: [Bioc-devel] New package submission : No reviewer communication.

Dear Steffen and Lori,

Steffen, many thanks for highlighting packages that are waiting review, 
including our packages.

Lori, please, let us know what input you need from us to start the reviewing 
process for the different packages (i.e. struct, structToolbox, sbcms, pmp). We 
are keen on getting our packages included in the next release.

What is the process to get involved in reviewing of other packages? We might be 
able to help out.

Many thanks,

Ralf



On Wed, 20 Nov 2019 at 12:09, lori.sheph...@roswellpark.org 
mailto:lori.sheph...@roswellpark.org>> wrote:
Those are a special set of packages that were submitted by the same author 
under a special circumstance.  We are working with that author to work through 
all the packages (which are related).

All other packages aim to have a review and response within 2-3 weeks.


Lori Shepherd

Bioconductor Core Team

Roswell Park Comprehensive Cancer Center

Department of Biostatistics & Bioinformatics

Elm & Carlton Streets

Buffalo, New York 14263


From: Bioc-devel 
mailto:bioc-devel-boun...@r-project.org>> on 
behalf of Neumann, Steffen mailto:sneum...@ipb-halle.de>>
Sent: Wednesday, November 20, 2019 2:59 AM
To: Turaga, Nitesh ; 
ashku...@gatech.edu<mailto:ashku...@gatech.edu> 
mailto:ashku...@gatech.edu>>; 
bioc-devel@r-project.org<mailto:bioc-devel@r-project.org> 
mailto:bioc-devel@r-project.org>>
Subject: Re: [Bioc-devel] New package submission : No reviewer communication.

Hi,

I think there is quite some backlog from September
https://github.com/Bioconductor/Contributions/labels/1.%20awaiting%20moderation
Maybe the BioC team can use the momentum to assign more reviewers ?

Yours,
Steffen

On Tue, 2019-11-19 at 19:07 +, Turaga, Nitesh wrote:
> No problem at all!
>
> We are happy to help. If you have further questions feel free to ask.
>
> Best,
>
> Nitesh
>
> On 11/19/19, 1:58 PM, "Kumar, Ashwath" 
> mailto:ashku...@gatech.edu>> wrote:
>
> Hi Nitesh,
>
> Thanks a lot for the quick reply and clearing up the process.  I
> completely understand that the process is tedious and takes a lot of
> time. I just wanted to clarify with people with previous experience
> submitting packages as this is my first time.
>
> Thanks,
> Ashwath
>
> -Original Message-
> From: Turaga, Nitesh 
> Sent: Tuesday, November 19, 2019 1:56 PM
> To: Kumar, Ashwath mailto:ashku...@gatech.edu>>;
> bioc-devel@r-project.org<mailto:bioc-devel@r-project.org>
> Subject: Re: [Bioc-devel] New package submission : No reviewer
> communication.
>
> Hi,
>
> Please be patient in this regard. The reviewer will get to your
> package as soon as they can. Each package takes time to review, and
> each reviewer is reviewing multiple packages.
>
> As far as asking for support regarding your package, it is best
> to ask your questions on the "Issue" which was created for the
> package contribution.  If you have general Bioconductor questions,
> the support site can help you as well, 
> support.bioconductor.org<http://support.bioconductor.org>. If
> you are unsure, bioc-devel mailing list is the right place.
>
> Best,
>
> Nitesh
>
> On 11/19/19, 1:47 PM, "Bioc-devel on behalf of Kumar, Ashwath" <
> bioc-devel-boun...@r-project.org<mailto:bioc-devel-boun...@r-project.org> on 
> behalf of ashku...@gatech.edu<mailto:ashku...@gatech.edu>>
> wrote:
>
> Hello all,
>
> I recently submitted a package to Bioconductor and I have not
> heard back from the reviewer about any feedback or acceptance or
> otherwise. The package has indeed passed all the automated tests and
> is awaiting the revision on the next stage of review process. Is
> there a recommended period of time I wait before requesting help in
> this regard and if so, how do I go about requesting support. Thanks a
> lot !
>
> Thanks,
> Ashwath
>
>
>[[alternative HTML version deleted]]
>
> ___
> Bioc-devel@r-project.org<mailto:Bioc-devel@r-project.org>

Re: [Bioc-devel] New package submission : No reviewer communication.

[Ralf Weber]

Dear Steffen and Lori,

Steffen, many thanks for highlighting packages that are waiting review,
including our packages.

Lori, please, let us know what input you need from us to start the
reviewing process for the different packages (i.e. struct, structToolbox,
sbcms, pmp). We are keen on getting our packages included in the next
release.

What is the process to get involved in reviewing of other packages? We
might be able to help out.

Many thanks,

Ralf



On Wed, 20 Nov 2019 at 12:09, lori.sheph...@roswellpark.org <
lori.sheph...@roswellpark.org> wrote:

> Those are a special set of packages that were submitted by the same author
> under a special circumstance.  We are working with that author to work
> through all the packages (which are related).
>
> All other packages aim to have a review and response within 2-3 weeks.
>
>
> 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 Neumann,
> Steffen 
> Sent: Wednesday, November 20, 2019 2:59 AM
> To: Turaga, Nitesh ; ashku...@gatech.edu <
> ashku...@gatech.edu>; bioc-devel@r-project.org 
> Subject: Re: [Bioc-devel] New package submission : No reviewer
> communication.
>
> Hi,
>
> I think there is quite some backlog from September
>
> https://github.com/Bioconductor/Contributions/labels/1.%20awaiting%20moderation
> Maybe the BioC team can use the momentum to assign more reviewers ?
>
> Yours,
> Steffen
>
> On Tue, 2019-11-19 at 19:07 +, Turaga, Nitesh wrote:
> > No problem at all!
> >
> > We are happy to help. If you have further questions feel free to ask.
> >
> > Best,
> >
> > Nitesh
> >
> > On 11/19/19, 1:58 PM, "Kumar, Ashwath"  wrote:
> >
> > Hi Nitesh,
> >
> > Thanks a lot for the quick reply and clearing up the process.  I
> > completely understand that the process is tedious and takes a lot of
> > time. I just wanted to clarify with people with previous experience
> > submitting packages as this is my first time.
> >
> > Thanks,
> > Ashwath
> >
> > -Original Message-
> > From: Turaga, Nitesh 
> > Sent: Tuesday, November 19, 2019 1:56 PM
> > To: Kumar, Ashwath ;
> > bioc-devel@r-project.org
> > Subject: Re: [Bioc-devel] New package submission : No reviewer
> > communication.
> >
> > Hi,
> >
> > Please be patient in this regard. The reviewer will get to your
> > package as soon as they can. Each package takes time to review, and
> > each reviewer is reviewing multiple packages.
> >
> > As far as asking for support regarding your package, it is best
> > to ask your questions on the "Issue" which was created for the
> > package contribution.  If you have general Bioconductor questions,
> > the support site can help you as well, support.bioconductor.org. If
> > you are unsure, bioc-devel mailing list is the right place.
> >
> > Best,
> >
> > Nitesh
> >
> > On 11/19/19, 1:47 PM, "Bioc-devel on behalf of Kumar, Ashwath" <
> > bioc-devel-boun...@r-project.org on behalf of ashku...@gatech.edu>
> > wrote:
> >
> > Hello all,
> >
> > I recently submitted a package to Bioconductor and I have not
> > heard back from the reviewer about any feedback or acceptance or
> > otherwise. The package has indeed passed all the automated tests and
> > is awaiting the revision on the next stage of review process. Is
> > there a recommended period of time I wait before requesting help in
> > this regard and if so, how do I go about requesting support. Thanks a
> > lot !
> >
> > Thanks,
> > Ashwath
> >
> >
> >[[alternative HTML version deleted]]
> >
> > ___
> > Bioc-devel@r-project.org mailing list
> > https://stat.ethz.ch/mailman/listinfo/bioc-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 

Re: [Bioc-devel] New package submission : No reviewer communication.

[Shepherd, Lori]

Those are a special set of packages that were submitted by the same author 
under a special circumstance.  We are working with that author to work through 
all the packages (which are related).

All other packages aim to have a review and response within 2-3 weeks.


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 Neumann, 
Steffen 
Sent: Wednesday, November 20, 2019 2:59 AM
To: Turaga, Nitesh ; ashku...@gatech.edu 
; bioc-devel@r-project.org 
Subject: Re: [Bioc-devel] New package submission : No reviewer communication.

Hi,

I think there is quite some backlog from September
https://github.com/Bioconductor/Contributions/labels/1.%20awaiting%20moderation
Maybe the BioC team can use the momentum to assign more reviewers ?

Yours,
Steffen

On Tue, 2019-11-19 at 19:07 +, Turaga, Nitesh wrote:
> No problem at all!
>
> We are happy to help. If you have further questions feel free to ask.
>
> Best,
>
> Nitesh
>
> On 11/19/19, 1:58 PM, "Kumar, Ashwath"  wrote:
>
> Hi Nitesh,
>
> Thanks a lot for the quick reply and clearing up the process.  I
> completely understand that the process is tedious and takes a lot of
> time. I just wanted to clarify with people with previous experience
> submitting packages as this is my first time.
>
> Thanks,
> Ashwath
>
> -Original Message-
> From: Turaga, Nitesh 
> Sent: Tuesday, November 19, 2019 1:56 PM
> To: Kumar, Ashwath ;
> bioc-devel@r-project.org
> Subject: Re: [Bioc-devel] New package submission : No reviewer
> communication.
>
> Hi,
>
> Please be patient in this regard. The reviewer will get to your
> package as soon as they can. Each package takes time to review, and
> each reviewer is reviewing multiple packages.
>
> As far as asking for support regarding your package, it is best
> to ask your questions on the "Issue" which was created for the
> package contribution.  If you have general Bioconductor questions,
> the support site can help you as well, support.bioconductor.org. If
> you are unsure, bioc-devel mailing list is the right place.
>
> Best,
>
> Nitesh
>
> On 11/19/19, 1:47 PM, "Bioc-devel on behalf of Kumar, Ashwath" <
> bioc-devel-boun...@r-project.org on behalf of ashku...@gatech.edu>
> wrote:
>
> Hello all,
>
> I recently submitted a package to Bioconductor and I have not
> heard back from the reviewer about any feedback or acceptance or
> otherwise. The package has indeed passed all the automated tests and
> is awaiting the revision on the next stage of review process. Is
> there a recommended period of time I wait before requesting help in
> this regard and if so, how do I go about requesting support. Thanks a
> lot !
>
> Thanks,
> Ashwath
>
>
>[[alternative HTML version deleted]]
>
> ___
> Bioc-devel@r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/bioc-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.
>
>
>
>
> 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.
> ___
> Bioc-devel@r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/bioc-devel
--

Current bits of interest:

* Advances in Plant and Food Metabolomics
  10./11. and 12.12.2019 Workshop & Symposium
  
https://www.wur.nl/en/activity/Advances-in-Plant-and-Food-Metabolomics-workshop.htm

* European RFMF-Metabomeeting 2020
  Toulouse, France, January 22-24 2020
  https://rfmf-mpf-2020.sciencesconf.org

* HUPO P

Re: [Bioc-devel] New package submission : No reviewer communication.

[Neumann, Steffen]

Hi,

I think there is quite some backlog from September 
https://github.com/Bioconductor/Contributions/labels/1.%20awaiting%20moderation
Maybe the BioC team can use the momentum to assign more reviewers ? 

Yours,
Steffen

On Tue, 2019-11-19 at 19:07 +, Turaga, Nitesh wrote:
> No problem at all! 
> 
> We are happy to help. If you have further questions feel free to ask.
> 
> Best,
> 
> Nitesh 
> 
> On 11/19/19, 1:58 PM, "Kumar, Ashwath"  wrote:
> 
> Hi Nitesh,
> 
> Thanks a lot for the quick reply and clearing up the process.  I
> completely understand that the process is tedious and takes a lot of
> time. I just wanted to clarify with people with previous experience
> submitting packages as this is my first time. 
> 
> Thanks,
> Ashwath 
> 
> -Original Message-
> From: Turaga, Nitesh  
> Sent: Tuesday, November 19, 2019 1:56 PM
>     To: Kumar, Ashwath ; 
> bioc-devel@r-project.org
> Subject: Re: [Bioc-devel] New package submission : No reviewer
> communication.
> 
> Hi,
> 
> Please be patient in this regard. The reviewer will get to your
> package as soon as they can. Each package takes time to review, and
> each reviewer is reviewing multiple packages. 
> 
> As far as asking for support regarding your package, it is best
> to ask your questions on the "Issue" which was created for the
> package contribution.  If you have general Bioconductor questions,
> the support site can help you as well, support.bioconductor.org. If
> you are unsure, bioc-devel mailing list is the right place. 
> 
> Best,
> 
> Nitesh 
> 
> On 11/19/19, 1:47 PM, "Bioc-devel on behalf of Kumar, Ashwath" <
> bioc-devel-boun...@r-project.org on behalf of ashku...@gatech.edu>
> wrote:
> 
> Hello all,
> 
> I recently submitted a package to Bioconductor and I have not
> heard back from the reviewer about any feedback or acceptance or
> otherwise. The package has indeed passed all the automated tests and
> is awaiting the revision on the next stage of review process. Is
> there a recommended period of time I wait before requesting help in
> this regard and if so, how do I go about requesting support. Thanks a
> lot !
> 
> Thanks,
> Ashwath
> 
> 
>   [[alternative HTML version deleted]]
> 
> ___
> Bioc-devel@r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/bioc-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.
> 
> 
> 
> 
> 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.
> ___
> Bioc-devel@r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/bioc-devel
-- 

Current bits of interest:

* Advances in Plant and Food Metabolomics 
  10./11. and 12.12.2019 Workshop & Symposium
  
https://www.wur.nl/en/activity/Advances-in-Plant-and-Food-Metabolomics-workshop.htm

* European RFMF-Metabomeeting 2020
  Toulouse, France, January 22-24 2020
  https://rfmf-mpf-2020.sciencesconf.org

* HUPO PSI spring meeting, 23.-25.03.2020, San Diego, CA
  Watch out: http://www.psidev.info/events

---
IPB HalleAG Massenspektrometrie & Bioinformatik
Dr. Steffen Neumann  http://www.IPB-Halle.DE
Weinberg 3   Tel. +49 (0) 345 5582 - 1470
06120 Halle   +49 (0) 345 5582 - 0
sneumann(at)IPB-Halle.DE Fax. +49 (0) 345 5582 - 1409
___
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https://stat.ethz.ch/mailman/listinfo/bioc-devel

Re: [Bioc-devel] New package submission : No reviewer communication.

[Turaga, Nitesh]

No problem at all! 

We are happy to help. If you have further questions feel free to ask.

Best,

Nitesh 

On 11/19/19, 1:58 PM, "Kumar, Ashwath"  wrote:

Hi Nitesh,

Thanks a lot for the quick reply and clearing up the process.  I completely 
understand that the process is tedious and takes a lot of time. I just wanted 
to clarify with people with previous experience submitting packages as this is 
my first time. 

Thanks,
Ashwath 

-Original Message-
From: Turaga, Nitesh  
Sent: Tuesday, November 19, 2019 1:56 PM
To: Kumar, Ashwath ; bioc-devel@r-project.org
    Subject: Re: [Bioc-devel] New package submission : No reviewer 
communication.

Hi,

Please be patient in this regard. The reviewer will get to your package as 
soon as they can. Each package takes time to review, and each reviewer is 
reviewing multiple packages. 

As far as asking for support regarding your package, it is best to ask your 
questions on the "Issue" which was created for the package contribution.  If 
you have general Bioconductor questions, the support site can help you as well, 
support.bioconductor.org. If you are unsure, bioc-devel mailing list is the 
right place. 

Best,

Nitesh 

On 11/19/19, 1:47 PM, "Bioc-devel on behalf of Kumar, Ashwath" 
 wrote:

Hello all,

I recently submitted a package to Bioconductor and I have not heard 
back from the reviewer about any feedback or acceptance or otherwise. The 
package has indeed passed all the automated tests and is awaiting the revision 
on the next stage of review process. Is there a recommended period of time I 
wait before requesting help in this regard and if so, how do I go about 
requesting support. Thanks a lot !

Thanks,
Ashwath


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Re: [Bioc-devel] New package submission : No reviewer communication.

[Kumar, Ashwath]

Hi Nitesh,

Thanks a lot for the quick reply and clearing up the process.  I completely 
understand that the process is tedious and takes a lot of time. I just wanted 
to clarify with people with previous experience submitting packages as this is 
my first time. 

Thanks,
Ashwath 

-Original Message-
From: Turaga, Nitesh  
Sent: Tuesday, November 19, 2019 1:56 PM
To: Kumar, Ashwath ; bioc-devel@r-project.org
Subject: Re: [Bioc-devel] New package submission : No reviewer communication.

Hi,

Please be patient in this regard. The reviewer will get to your package as soon 
as they can. Each package takes time to review, and each reviewer is reviewing 
multiple packages. 

As far as asking for support regarding your package, it is best to ask your 
questions on the "Issue" which was created for the package contribution.  If 
you have general Bioconductor questions, the support site can help you as well, 
support.bioconductor.org. If you are unsure, bioc-devel mailing list is the 
right place. 

Best,

Nitesh 

On 11/19/19, 1:47 PM, "Bioc-devel on behalf of Kumar, Ashwath" 
 wrote:

Hello all,

I recently submitted a package to Bioconductor and I have not heard back 
from the reviewer about any feedback or acceptance or otherwise. The package 
has indeed passed all the automated tests and is awaiting the revision on the 
next stage of review process. Is there a recommended period of time I wait 
before requesting help in this regard and if so, how do I go about requesting 
support. Thanks a lot !

Thanks,
Ashwath


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Re: [Bioc-devel] New package submission : No reviewer communication.

[Turaga, Nitesh]

Hi,

Please be patient in this regard. The reviewer will get to your package as soon 
as they can. Each package takes time to review, and each reviewer is reviewing 
multiple packages. 

As far as asking for support regarding your package, it is best to ask your 
questions on the "Issue" which was created for the package contribution.  If 
you have general Bioconductor questions, the support site can help you as well, 
support.bioconductor.org. If you are unsure, bioc-devel mailing list is the 
right place. 

Best,

Nitesh 

On 11/19/19, 1:47 PM, "Bioc-devel on behalf of Kumar, Ashwath" 
 wrote:

Hello all,

I recently submitted a package to Bioconductor and I have not heard back 
from the reviewer about any feedback or acceptance or otherwise. The package 
has indeed passed all the automated tests and is awaiting the revision on the 
next stage of review process. Is there a recommended period of time I wait 
before requesting help in this regard and if so, how do I go about requesting 
support. Thanks a lot !

Thanks,
Ashwath


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Re: [Bioc-devel] New package submission failing only in devel due to dependent package errors

[Pages, Herve]

Hi Daniel,

The 'invalid class "VCFHeader" object' error on Windows has been fixed 
in Rhtslib 1.15.6.

Cheers,

H.

On 4/11/19 04:04, Daniel Cameron wrote:
> The package adds structural variant functionality on top of
> VariantAnnotation. It's been pretty stable for the last 18 months and
> getting more users so I thought it was time to bit the bullet and get it
> into BioConductor. install_github() isn't the ideal distribution mechanism
> for a package with so many BioConductor dependencies.
>
> https://urldefense.proofpoint.com/v2/url?u=https-3A__github.com_Bioconductor_Contributions_issues_1079&d=DwICAg&c=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=5aEeNhD9UdwqFxQXOsQFfaNMAzzX3-PhISQsEMXm-Kg&s=Q4Uek0PObHV1TC1upYL6ddQ6B1mJYdmnRWbZiu9Xk2M&e=
> https://urldefense.proofpoint.com/v2/url?u=http-3A__bioconductor.org_spb-5Freports_StructuralVariantAnnotation-5Fbuildreport-5F20190411011937.html&d=DwICAg&c=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=5aEeNhD9UdwqFxQXOsQFfaNMAzzX3-PhISQsEMXm-Kg&s=-gAUBmCTCkhHFFtG8VTHK3TcNePZ2TpClbWqf25xkn8&e=
>
>
> No errors in the linux/mac builds although I did just add a warning from a
> commit addressing review feedback.
>
> On Wed, Apr 10, 2019 at 12:00 AM Shepherd, Lori <
> lori.sheph...@roswellpark.org> wrote:
>
>> We are aware of the issue in VariantAnnotation and hopefully will have a
>> fix soon.  We have been seeing this ERROR on tokay2 (windows)  but not on
>> the other two platforms.  Is this the case for your package?  What is the
>> name/package issue number of the submitted package?If so,  we would
>> accept your package conditionally since the ERROR is not with your package
>> directly as long as it is building on the other two platforms without
>> ERROR.
>>
>>
>> Lori Shepherd
>>
>> Bioconductor Core Team
>>
>> Roswell Park Cancer Institute
>>
>> Department of Biostatistics & Bioinformatics
>>
>> Elm & Carlton Streets
>>
>> Buffalo, New York 14263
>> --
>> *From:* Bioc-devel  on behalf of Daniel
>> Cameron 
>> *Sent:* Tuesday, April 9, 2019 7:21:54 AM
>> *To:* bioc-devel@r-project.org
>> *Subject:* [Bioc-devel] New package submission failing only in devel due
>> to dependent package errors
>>
>> Hello,
>>
>> I am attempting to submit a new package, and everything builds correctly
>> against R 3.5 and release bioconductor, but the package build is failing in
>> devel due to a dependent package. The build error is:
>>
>> Quitting from lines 52-56 (vignettes.Rmd)
>> Error: processing vignette 'vignettes.Rmd' failed with diagnostics:
>> invalid class "VCFHeader" object: 'info(VCFHeader)' must be a 3 column
>> DataFrame with names Number, Type, Description
>> --- failed re-building 'vignettes.Rmd'
>>
>> Which I can reproduce locally when building against devel but I'm not sure
>> what do you as the offending line is:
>> vcf <- VariantAnnotation::readVcf(vcf.file, "hg19")The VCF itself is valid
>> (in that it complies with the VCF specifications), and has been parsing
>> just fine in my unit tests since May 2016, it's just failing in devel.
>>
>> Presumably this is a blocker for package acceptance but I'm not sure
>> exactly how to proceed given the change is not in my package. Should I be
>> raising an issue against VariantAnnotation and hoping it gets resolved fast
>> enough for my package to go in this round, or should I also be doing
>> something else?
>>
>> Thanks
>> Daniel
>>
>>  [[alternative HTML version deleted]]
>>
>> ___
>> Bioc-devel@r-project.org mailing list
>> https://urldefense.proofpoint.com/v2/url?u=https-3A__stat.ethz.ch_mailman_listinfo_bioc-2Ddevel&d=DwICAg&c=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=5aEeNhD9UdwqFxQXOsQFfaNMAzzX3-PhISQsEMXm-Kg&s=m6HdfwMZhlzMOUf37A7tCI7r0js2hvbf_UxPDs8JfJ0&e=
>>
>> 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://urldefense.proofpoint.com/v2/url?u=https-3A__stat.ethz.ch_mailman_listinfo_bioc-2Ddevel&d=DwICAg&c=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=5aEeNhD9UdwqFxQXOsQFfaNMAzzX3-PhISQsEMXm-Kg&s=m6HdfwMZhlzMOUf37A7tCI7r0js2hvbf_UxPDs8JfJ0&e=

-- 
Hervé Pagès

Program in Computational Biology
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Fred Hutchinson Cancer Research Center
1100 Fairview Ave. N, M1-B514
P.O. Box 19024
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Re: [Bioc-devel] New package submission failing only in devel due to dependent package errors

[Daniel Cameron]

The package adds structural variant functionality on top of
VariantAnnotation. It's been pretty stable for the last 18 months and
getting more users so I thought it was time to bit the bullet and get it
into BioConductor. install_github() isn't the ideal distribution mechanism
for a package with so many BioConductor dependencies.

https://github.com/Bioconductor/Contributions/issues/1079
http://bioconductor.org/spb_reports/StructuralVariantAnnotation_buildreport_20190411011937.html


No errors in the linux/mac builds although I did just add a warning from a
commit addressing review feedback.

On Wed, Apr 10, 2019 at 12:00 AM Shepherd, Lori <
lori.sheph...@roswellpark.org> wrote:

> We are aware of the issue in VariantAnnotation and hopefully will have a
> fix soon.  We have been seeing this ERROR on tokay2 (windows)  but not on
> the other two platforms.  Is this the case for your package?  What is the
> name/package issue number of the submitted package?If so,  we would
> accept your package conditionally since the ERROR is not with your package
> directly as long as it is building on the other two platforms without
> ERROR.
>
>
> Lori Shepherd
>
> Bioconductor Core Team
>
> Roswell Park Cancer Institute
>
> Department of Biostatistics & Bioinformatics
>
> Elm & Carlton Streets
>
> Buffalo, New York 14263
> --
> *From:* Bioc-devel  on behalf of Daniel
> Cameron 
> *Sent:* Tuesday, April 9, 2019 7:21:54 AM
> *To:* bioc-devel@r-project.org
> *Subject:* [Bioc-devel] New package submission failing only in devel due
> to dependent package errors
>
> Hello,
>
> I am attempting to submit a new package, and everything builds correctly
> against R 3.5 and release bioconductor, but the package build is failing in
> devel due to a dependent package. The build error is:
>
> Quitting from lines 52-56 (vignettes.Rmd)
> Error: processing vignette 'vignettes.Rmd' failed with diagnostics:
> invalid class "VCFHeader" object: 'info(VCFHeader)' must be a 3 column
> DataFrame with names Number, Type, Description
> --- failed re-building 'vignettes.Rmd'
>
> Which I can reproduce locally when building against devel but I'm not sure
> what do you as the offending line is:
> vcf <- VariantAnnotation::readVcf(vcf.file, "hg19")The VCF itself is valid
> (in that it complies with the VCF specifications), and has been parsing
> just fine in my unit tests since May 2016, it's just failing in devel.
>
> Presumably this is a blocker for package acceptance but I'm not sure
> exactly how to proceed given the change is not in my package. Should I be
> raising an issue against VariantAnnotation and hoping it gets resolved fast
> enough for my package to go in this round, or should I also be doing
> something else?
>
> Thanks
> Daniel
>
> [[alternative HTML version deleted]]
>
> ___
> Bioc-devel@r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/bioc-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.

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Re: [Bioc-devel] New package submission failing only in devel due to dependent package errors

[Shepherd, Lori]

We are aware of the issue in VariantAnnotation and hopefully will have a fix 
soon.  We have been seeing this ERROR on tokay2 (windows)  but not on the other 
two platforms.  Is this the case for your package?  What is the name/package 
issue number of the submitted package?If so,  we would accept your package 
conditionally since the ERROR is not with your package directly as long as it 
is building on the other two platforms without ERROR.


Lori Shepherd

Bioconductor Core Team

Roswell Park Cancer Institute

Department of Biostatistics & Bioinformatics

Elm & Carlton Streets

Buffalo, New York 14263


From: Bioc-devel  on behalf of Daniel Cameron 

Sent: Tuesday, April 9, 2019 7:21:54 AM
To: bioc-devel@r-project.org
Subject: [Bioc-devel] New package submission failing only in devel due to 
dependent package errors

Hello,

I am attempting to submit a new package, and everything builds correctly
against R 3.5 and release bioconductor, but the package build is failing in
devel due to a dependent package. The build error is:

Quitting from lines 52-56 (vignettes.Rmd)
Error: processing vignette 'vignettes.Rmd' failed with diagnostics:
invalid class "VCFHeader" object: 'info(VCFHeader)' must be a 3 column
DataFrame with names Number, Type, Description
--- failed re-building 'vignettes.Rmd'

Which I can reproduce locally when building against devel but I'm not sure
what do you as the offending line is:
vcf <- VariantAnnotation::readVcf(vcf.file, "hg19")The VCF itself is valid
(in that it complies with the VCF specifications), and has been parsing
just fine in my unit tests since May 2016, it's just failing in devel.

Presumably this is a blocker for package acceptance but I'm not sure
exactly how to proceed given the change is not in my package. Should I be
raising an issue against VariantAnnotation and hoping it gets resolved fast
enough for my package to go in this round, or should I also be doing
something else?

Thanks
Daniel

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Re: [Bioc-devel] New package submission - how to add a webhook?

[Kenneth Condon]

Oh lord, rookie mistakei was in the main settings instead of the
repository settings haha

Thank you Martin!

On Fri, Aug 17, 2018 at 6:07 PM, Kenneth Condon 
wrote:

> Hi all,
>
> I have just submitted a new package for inclusion in the next bioconductor
> release.
>
> According to the instructions
> ,
> after adding a new issue I must now add a webhook.
>
> How do I add a webhook since the deprecation of "Webhooks & services" in
> github settings?
>
> Regards,
> Kenneth
>

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Re: [Bioc-devel] New package submission - how to add a webhook?

[Martin Morgan]

See under Settings -> Webhooks rather than Settings -> Integrations & 
services, and the instructions at



https://github.com/Bioconductor/Contributions/blob/master/CONTRIBUTING.md#adding-a-web-hook

We use plain-old-webhooks, rather than GitHub Services.

On 08/17/2018 01:07 PM, Kenneth Condon wrote:

Hi all,

I have just submitted a new package for inclusion in the next bioconductor
release.

According to the instructions
,
after adding a new issue I must now add a webhook.

How do I add a webhook since the deprecation of "Webhooks & services" in
github settings?

Regards,
Kenneth

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Re: [Bioc-devel] New Package Submission Tracker

[Shepherd, Lori]

Sorry for the delay.  The single package builder was down for updates last week 
and it slipped through undetected.  We have remedied the situation and you 
should be assigned a reviewer shortly.


Lori Shepherd

Bioconductor Core Team

Roswell Park Cancer Institute

Department of Biostatistics & Bioinformatics

Elm & Carlton Streets

Buffalo, New York 14263


From: Hien To 
Sent: Tuesday, June 19, 2018 11:05:00 PM
To: Shepherd, Lori; bioc-devel@r-project.org
Subject: Re: [Bioc-devel] New Package Submission Tracker


Hi


I've submitted a new package (issues #774) on that day (14/06) and it still 
doesn't have any label such as  1. awaiting moderation. Just wondering if it 
was this problem, or something I've done wrong with the submission. Thanks for 
your help.


Hien



From: Bioc-devel  on behalf of Shepherd, Lori 

Sent: Thursday, 14 June 2018 10:17:56 PM
To: bioc-devel@r-project.org
Subject: [Bioc-devel] New Package Submission Tracker

The Single Package Builder for new package submissions is experience some 
intermittent connectivity issues.  We are working on the issue and hope to have 
it resolved soon.


Lori Shepherd

Bioconductor Core Team

Roswell Park Cancer Institute

Department of Biostatistics & Bioinformatics

Elm & Carlton Streets

Buffalo, New York 14263


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 
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Re: [Bioc-devel] New Package Submission Tracker

[Hien To]

Hi


I've submitted a new package (issues #774) on that day (14/06) and it still 
doesn't have any label such as  1. awaiting moderation. Just wondering if it 
was this problem, or something I've done wrong with the submission. Thanks for 
your help.


Hien



From: Bioc-devel  on behalf of Shepherd, Lori 

Sent: Thursday, 14 June 2018 10:17:56 PM
To: bioc-devel@r-project.org
Subject: [Bioc-devel] New Package Submission Tracker

The Single Package Builder for new package submissions is experience some 
intermittent connectivity issues.  We are working on the issue and hope to have 
it resolved soon.


Lori Shepherd

Bioconductor Core Team

Roswell Park Cancer Institute

Department of Biostatistics & Bioinformatics

Elm & Carlton Streets

Buffalo, New York 14263


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 
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Re: [Bioc-devel] New package submission

[Martin Morgan]

Hi Divy --

Please don't be shy about providing specifics, like the package name or 
issue!


The additional information is posted as a comment on your contribution 
issue ('by email' is no longer inaccurate, it'll be updated).


  https://github.com/Bioconductor/Contributions/issues/592

https://github.com/Bioconductor/Contributions/issues/592#issuecomment-366364083

Martin

On 02/22/2018 03:37 PM, Kangeyan, Divy wrote:

Hi,
 The package I submitted was accepted about a week ago and the message
from the *bioc-issue-bot* in github said that I will receive additional
information via email. I haven't received any email yet. So I am wondering
when I will receive it and how to proceed.

Thank you,
Divy

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Re: [Bioc-devel] new package submission (pcxn) Abnormal build result

[Sokratis Kariotis]

Thanks for the reply!

For now I have commented out the problematic lines (# network <-
pcxn.network(df) , in man files and vignette) and the package builds OK.

Cheers,
Sokratis

On 5 October 2017 at 12:56, Shepherd, Lori 
wrote:

> Yes, this seems to be a problem on our side. We are looking into it. For
> now you can ignore this ERROR.
>
> There was a similar post here:
>
> https://stat.ethz.ch/pipermail/bioc-devel/2017-September/011773.html
>
>
> Lori Shepherd
>
> Bioconductor Core Team
>
> Roswell Park Cancer Institute
>
> Department of Biostatistics & Bioinformatics
>
> Elm & Carlton Streets
>
> Buffalo, New York 14263
> --
> *From:* Bioc-devel  on behalf of
> Sokratis Kariotis 
> *Sent:* Monday, October 2, 2017 8:07:12 AM
> *To:* Bioc-devel@r-project.org
> *Subject:* [Bioc-devel] new package submission (pcxn) Abnormal build
> result
>
> Hi all,
>
> Today I submitted a new package called "pcxn" in bioconductor and I got the
> following Abnormal built result:
>
> Warning in fun(libname, pkgname) :
>   no display name and no $DISPLAY environment variable
>
> Error: processing vignette 'usingPCxNdb.Rnw' failed with diagnostics:
>  chunk 4 (label = pcxn.network)
> Error in structure(.External(.C_dotTclObjv, objv), class = "tclObj") :
>   [tcl] invalid command name "font".
>
> The pcxn.network function uses igraph::tkplot to return a network, which
> works every time on several local machines. After searching for a while it
> seems that whenever this problem arises its because of the igraph package
> installation. How can I deal with this? Thanks in advance.
>
> With Regards,
> Sokratis
> --
> Sokratis Kariotis
> Scientific Programmer
> Hidelab
> Sheffield Institute for Translational Neuroscience
> 385a Glossop Rd, Sheffield, S10 2HQ
> 
>
> [[alternative HTML version deleted]]
>
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>
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> information. If you are not the intended recipient(s), or the employee or
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> 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.




-- 
Sokratis Kariotis
Scientific Programmer
Hidelab
Sheffield Institute for Translational Neuroscience
385a Glossop Rd, Sheffield, S10 2HQ

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Re: [Bioc-devel] new package submission (pcxn) Abnormal build result

[Shepherd, Lori]

Yes, this seems to be a problem on our side. We are looking into it. For now 
you can ignore this ERROR.

There was a similar post here:

https://stat.ethz.ch/pipermail/bioc-devel/2017-September/011773.html


Lori Shepherd

Bioconductor Core Team

Roswell Park Cancer Institute

Department of Biostatistics & Bioinformatics

Elm & Carlton Streets

Buffalo, New York 14263


From: Bioc-devel  on behalf of Sokratis 
Kariotis 
Sent: Monday, October 2, 2017 8:07:12 AM
To: Bioc-devel@r-project.org
Subject: [Bioc-devel] new package submission (pcxn) Abnormal build result

Hi all,

Today I submitted a new package called "pcxn" in bioconductor and I got the
following Abnormal built result:

Warning in fun(libname, pkgname) :
  no display name and no $DISPLAY environment variable

Error: processing vignette 'usingPCxNdb.Rnw' failed with diagnostics:
 chunk 4 (label = pcxn.network)
Error in structure(.External(.C_dotTclObjv, objv), class = "tclObj") :
  [tcl] invalid command name "font".

The pcxn.network function uses igraph::tkplot to return a network, which
works every time on several local machines. After searching for a while it
seems that whenever this problem arises its because of the igraph package
installation. How can I deal with this? Thanks in advance.

With Regards,
Sokratis
--
Sokratis Kariotis
Scientific Programmer
Hidelab
Sheffield Institute for Translational Neuroscience
385a Glossop Rd, Sheffield, S10 2HQ

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Re: [Bioc-devel] New Package submission request to Bioconductor Project

[Jurat Shayidin]

Dear Lori :

Thanks for your prompt response. Yes, I did follow new package submission
guideline from Bioconductor site, package contribution page helped me how
to create new issue, Now I opened the issue for new package submission.
Thanks again for Bioconductor team on kind evaluation of my packages.

Best regards :

Jurat

On Tue, Dec 20, 2016 at 1:01 PM, Shepherd, Lori <
lori.sheph...@roswellpark.org> wrote:

> We Thank you for taking the time and diligence to try and have a clean R
> CMD check and BiocCheck before submission.  If these are your only issues
> and you feel the package is ready to be reviewed please submit
> http://bioconductor.org/developers/package-submission/  and your assigned
> reviewer can assist you further.
>
>
> Lori Shepherd
>
> Bioconductor Core Team
>
> Roswell Park Cancer Institute
>
> Department of Biostatistics & Bioinformatics
>
> Elm & Carlton Streets
>
> Buffalo, New York 14263
> --
> *From:* Bioc-devel  on behalf of Jurat
> Shayidin 
> *Sent:* Tuesday, December 20, 2016 6:35:52 AM
> *To:* bioc-devel@r-project.org
> *Subject:* [Bioc-devel] New Package submission request to Bioconductor
> Project
>
> Dear BiocDevel, Bioconductor Team :
>
> I've read Bioconductor contribution repository, and new package submission
> with full instruction, and make sure I am ready to submit my packages --
> MSPC -- to Bioconductor projects. However, my package both succeed with R
> CMD check, R CMD BiocCheck without any error, warning. However, R CMD
> BiocCheck alarmed me 2 NOTES about indentation issue on my code, and adding
> NEWS file. I did add NEWS files where specify list of function in current
> version of MSPC packages, but R CMD BiocCheck always gave me same NOTE.
> Plus, I fixed code indentation with 4 space tab, but R CMD BiocCheck still
> alarmed me that 3% of code needs to re-indent. May be Bioconductor team
> guide me how to fix this small issue. To be short, I'll open issue on my
> project repository if this mail is sufficient to inform my request. Thanks
> a lot.
>
> Best regards :
>
> Jurat
>
> --
> Jurat Shahidin
>
> Dipartimento di Elettronica, Informazione e Bioingegneria
> Politecnico di Milano
> Piazza Leonardo da Vinci 32 - 20133 Milano, Italy
> Mobile : +39 3279366608 <+39%20327%20936%206608> <+39%20327%20936%206608>
>
> [[alternative HTML version deleted]]
>
> ___
> Bioc-devel@r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/bioc-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.




-- 
Jurat Shahidin

Dipartimento di Elettronica, Informazione e Bioingegneria
Politecnico di Milano
Piazza Leonardo da Vinci 32 - 20133 Milano, Italy
Mobile : +39 3279366608 <+39%20327%20936%206608>

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Re: [Bioc-devel] New Package submission request to Bioconductor Project

[Shepherd, Lori]

We Thank you for taking the time and diligence to try and have a clean R CMD 
check and BiocCheck before submission.  If these are your only issues and you 
feel the package is ready to be reviewed please submit 
http://bioconductor.org/developers/package-submission/  and your assigned 
reviewer can assist you further.



Lori Shepherd

Bioconductor Core Team

Roswell Park Cancer Institute

Department of Biostatistics & Bioinformatics

Elm & Carlton Streets

Buffalo, New York 14263


From: Bioc-devel  on behalf of Jurat Shayidin 

Sent: Tuesday, December 20, 2016 6:35:52 AM
To: bioc-devel@r-project.org
Subject: [Bioc-devel] New Package submission request to Bioconductor Project

Dear BiocDevel, Bioconductor Team :

I've read Bioconductor contribution repository, and new package submission
with full instruction, and make sure I am ready to submit my packages --
MSPC -- to Bioconductor projects. However, my package both succeed with R
CMD check, R CMD BiocCheck without any error, warning. However, R CMD
BiocCheck alarmed me 2 NOTES about indentation issue on my code, and adding
NEWS file. I did add NEWS files where specify list of function in current
version of MSPC packages, but R CMD BiocCheck always gave me same NOTE.
Plus, I fixed code indentation with 4 space tab, but R CMD BiocCheck still
alarmed me that 3% of code needs to re-indent. May be Bioconductor team
guide me how to fix this small issue. To be short, I'll open issue on my
project repository if this mail is sufficient to inform my request. Thanks
a lot.

Best regards :

Jurat

--
Jurat Shahidin

Dipartimento di Elettronica, Informazione e Bioingegneria
Politecnico di Milano
Piazza Leonardo da Vinci 32 - 20133 Milano, Italy
Mobile : +39 3279366608 <+39%20327%20936%206608>

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Re: [Bioc-devel] New Package Submission Process

[Dan Tenenbaum]

I put the wrong link in my announcement--the instructions for submitting a new 
package are at:

https://github.com/Bioconductor/Contributions

Dan



- Original Message -
> From: "Dan Tenenbaum" 
> To: "bioc-devel" 
> Sent: Monday, June 6, 2016 10:52:05 AM
> Subject: Re: [Bioc-devel] New Package Submission Process

> The new GitHub-based new package contribution system is up and running.
> 
> To contribute a Bioconductor package, file a new issue at
> 
> https://github.com/Bioconductor/Contributions/issues/new
> 
> 
> Read the full instructions here:
> 
> https://github.com/Bioconductor/Contributions/issues/new
> 
> as well as the updated package submission page:
> 
> http://bioconductor.org/developers/package-submission/
> 
> The old issue/package tracker is still up, but adding new packages is 
> disabled.
> 
> Please post questions/issues to bioc-devel.
> 
> Dan
> 
> 
> 
> - Original Message -
>> From: "Valerie Obenchain" 
>> To: "bioc-devel" 
>> Sent: Tuesday, May 31, 2016 5:43:41 AM
>> Subject: [Bioc-devel] New Package Submission Process
> 
>> Package developers,
>> 
>> On June 6 we will transition to our new 'package tracker' on github. The
>> new system will enable a more public review process where community
>> members (not just the assigned reviewer) can give technical and
>> scientific input during the review.  More background in this post:
>> 
>>https://support.bioconductor.org/p/76472
>> 
>> Over the next week, we'll post instructions for the new submission
>> process on the web site and announce when access to the old tracker is
>> shut off. Reviews that are in-progress in the old tracker will continue
>> there and not be transferred to the new system.
>> 
>> Valerie
>> 
>> 
>> 
>> 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.
>> ___
>> Bioc-devel@r-project.org mailing list
>> https://stat.ethz.ch/mailman/listinfo/bioc-devel
> 
> ___
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Re: [Bioc-devel] New Package Submission Process

[Dan Tenenbaum]

The new GitHub-based new package contribution system is up and running.

To contribute a Bioconductor package, file a new issue at

https://github.com/Bioconductor/Contributions/issues/new


Read the full instructions here:

https://github.com/Bioconductor/Contributions/issues/new

as well as the updated package submission page:

http://bioconductor.org/developers/package-submission/

The old issue/package tracker is still up, but adding new packages is disabled.

Please post questions/issues to bioc-devel.

Dan



- Original Message -
> From: "Valerie Obenchain" 
> To: "bioc-devel" 
> Sent: Tuesday, May 31, 2016 5:43:41 AM
> Subject: [Bioc-devel] New Package Submission Process

> Package developers,
> 
> On June 6 we will transition to our new 'package tracker' on github. The
> new system will enable a more public review process where community
> members (not just the assigned reviewer) can give technical and
> scientific input during the review.  More background in this post:
> 
>https://support.bioconductor.org/p/76472
> 
> Over the next week, we'll post instructions for the new submission
> process on the web site and announce when access to the old tracker is
> shut off. Reviews that are in-progress in the old tracker will continue
> there and not be transferred to the new system.
> 
> Valerie
> 
> 
> 
> 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.
> ___
> Bioc-devel@r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/bioc-devel

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Re: [Bioc-devel] New package submission warning

[Dario Strbenac]

Hello,

I doubt that a dataset package such as GSE64985 is suitable for inclusion in 
Bioconductor. It creates unnecessary duplication of what can already be 
obtained easily with GEOquery. Have you considered using

library(GEOquery)
humanDataset <- getGEO("GSE64985")

? If everyone converted their GEO or ArrayExpress dataset into a Bioconductor 
package, Bioconductor would quickly become cluttered.

--
Dario Strbenac
PhD Student
University of Sydney
Camperdown NSW 2050
Australia
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Re: [Bioc-devel] New package submission warning

[Dan Tenenbaum]

You can ignore these warnings. Those build machines need to be updated to the 
devel version of Bioconductor but there are several other things that need to 
happen before we can do that.

Dan


- Original Message -
> From: "Brad Nelms" 
> To: "bioc-devel" 
> Sent: Friday, May 20, 2016 1:11:38 PM
> Subject: [Bioc-devel] New package submission warning

> Hi,
> I'm trying to submit two packages to Bioconductor ('GSE64985' and
> 'E.MTAB.62'), but am receiving this warning from BiocCheck:
> 
> * Checking version number validity...
>* RECOMMENDED: y of x.y.z version should be even in release
> 
> The version number of my packages are 0.99.x, which is required for new
> packages. I have been unable to find any information about why I am
> receiving this error, perhaps there is something I need to change so that
> BiocCheck recognizes the submission as a devel package rather than a
> release package? Is there a mistake in how I am submitting my packages?
> 
> Thanks,
> Brad
> 
>   [[alternative HTML version deleted]]
> 
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Re: [Bioc-devel] New package submission process

[xiaobei]

Many thanks to Dan and Kieran O'Neill!
I will adjust my plan according to the estimated timeline.
Xiaobei

On 6/26/2014 5:19 PM, Kieran O'Neill wrote:
> After the initial response, the package will be sent on to a reviewer, 
> who will usually respond within a week or two, but could take longer. 
> Typically there will be a few rounds of corrections with the reviewer, 
> after which the package is accepted into the current development 
> branch (making it shareable on the website for e.g. reviewers), and 
> gets queued for inclusion in the next release.
>
> All in all, it takes about a month or so to get a package accepted, 
> and a few more months before it's in the main branch of Bioconductor.
>
> More details about the process are here: 
> http://www.bioconductor.org/developers/package-submission/
>
>
> On 26 June 2014 07:46, Dan Tenenbaum  > wrote:
>
>
>
> - Original Message -
> > From: "Xiaobei Zhao"  >
> > To: bioc-devel@r-project.org 
> > Sent: Thursday, June 26, 2014 5:20:31 AM
> > Subject: [Bioc-devel] New package submission process
> >
> > Hi everyone,
> >
> > I am about to submit a new package at Bioconductor. I have followed
> > the
> > instructions linked below to prepare my package,
> > http://master.bioconductor.org/developers/package-guidelines/
> >
> > Early this week, I sent an initial request according to the contact
> > information listed at
> > http://master.bioconductor.org/developers/package-submission/
> >
> > While waiting for response, please can you share your experience
> > about
> > how long it would take before I will be guided to make a submission?
> > For
> > good estimation, could you outline the submission process? I would
> > appreciate that!
> >
>
> Normally it would just be a couple of days. However, the main
> person who responds to
> new package submissions is currently away, and will return
> tomorrow. You should expect
> a response soon.
>
> Dan
>


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Re: [Bioc-devel] New package submission process

[Dan Tenenbaum]

- Original Message -
> From: "Xiaobei Zhao" 
> To: bioc-devel@r-project.org
> Sent: Thursday, June 26, 2014 5:20:31 AM
> Subject: [Bioc-devel] New package submission process
> 
> Hi everyone,
> 
> I am about to submit a new package at Bioconductor. I have followed
> the
> instructions linked below to prepare my package,
> http://master.bioconductor.org/developers/package-guidelines/
> 
> Early this week, I sent an initial request according to the contact
> information listed at
> http://master.bioconductor.org/developers/package-submission/
> 
> While waiting for response, please can you share your experience
> about
> how long it would take before I will be guided to make a submission?
> For
> good estimation, could you outline the submission process? I would
> appreciate that!
> 

Normally it would just be a couple of days. However, the main person who 
responds to
new package submissions is currently away, and will return tomorrow. You should 
expect
a response soon.

Dan


> Xiaobei
> 
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