[Bioc-devel] request

2020-05-30 Thread Zhen Yang 
Dear Biocondcutor admins:

This is Zhen Yang from Fudan University, as the maintainer of the Bioconductor 
package of "FEM" 
(https://bioconductor.org/packages/release/bioc/html/FEM.html), I would like to 
make some update to this package. However, my last email (yangz...@picb.ac.cn) 
has been suspended, I have registered to BioC by using this new Email. I would 
like to ask if I can get the SSH key for The package by using this 
email(zheny...@fudan.edu.cn)? Now I cannot log in to the Bioconductor Git 
Credentials. Seem I need to activate my account.

Thanks a lot and best wishes!

Zhen Yang
Fudan University

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Re: [Bioc-devel] request

2020-05-30 Thread Kumar, Ashwath 


Hello all,

I am the maintainer for CSSQ 
(https://bioconductor.org/packages/release/bioc/html/CSSQ.html). I had made 
some changes  (Re authorship and email addresses) to the package last night. I 
made sure to push them to both the master and RELEASE_3_11 branches and 
confirmed the changes by checking with "git pull" that the changes were made to 
the DESCRIPTION file. Today, after the nightly build, I still don't see the 
changes reflected on the package page and the version is still 1.0.0. I had 
made sure to version number (master branch. 1.1.1 and RELEASE branch 1.0.1). 
Can someone please let me know why this is happening ? 


Thanks,
Ashwath 

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[Bioc-devel] Nightly update not updating my DESCRIPTION information

2020-05-30 Thread Kumar, Ashwath 
Hello all,

I am sorry for the duplicate email if any. I didn't realize that I had replied 
to another email instead of writing a new one.



I am the maintainer for CSSQ 
(https://bioconductor.org/packages/release/bioc/html/CSSQ.html). I had made 
some changes  (Re authorship and email addresses) to the package last night. I 
made sure to push them to both the master and RELEASE_3_11 branches and 
confirmed the changes by checking with "git pull" that the changes were made to 
the DESCRIPTION file. Today, after the nightly build, I still don't see the 
changes reflected on the package page and the version is still 1.0.0. I had 
made sure to version number (master branch. 1.1.1 and RELEASE branch 1.0.1). 
Can someone please let me know why this is happening ?





Thanks,

Ashwath


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Re: [Bioc-devel] request

2020-05-30 Thread Kumar, Ashwath 
Hi Martin,

Thanks for the reply. Thank you so much for clearing this up. I think I got 
confused by the build time and the snapshot time. I believe I was in the middle 
of editing and changing the format in the DESCRIPTION file and I think that’s 
the reason I see the errors in the devel version but not release because I 
committed to the release after the devel branch. I will follow up with the 
nightly build tomorrow which will hopefully reflect my corrected versions. 

Thanks !
Ashwath 

-Original Message-
From: Martin Morgan  
Sent: Saturday, May 30, 2020 5:12 PM
To: Kumar, Ashwath ; Bioc-devel@r-project.org
Subject: Re: [Bioc-devel] request

Please view the nightly build report

http://bioconductor.org/checkResults/devel/bioc-LATEST/CSSQ/

compare the time that your package had a 'snapshot' taken for the build to start

Snapshot Date: 2020-05-29 16:51:41 -0400 (Fri, 29 May 2020)

and commit hash and date of the last commit included in the snapshot

Last Commit: 3094509
Last Changed Date: 2020-05-29 16:58:05 -0400 (Fri, 29 May 2020)

If the commit you are concerned about is after the snapshot date, then you 
missed the start of the build. Or is the commit you are concerned about 
contributing to the build failure reported across all platforms?

Martin

On 5/30/20, 4:00 PM, "Bioc-devel on behalf of Kumar, Ashwath" 
 wrote:


Hello all,

I am the maintainer for CSSQ 
(https://bioconductor.org/packages/release/bioc/html/CSSQ.html). I had made 
some changes  (Re authorship and email addresses) to the package last night. I 
made sure to push them to both the master and RELEASE_3_11 branches and 
confirmed the changes by checking with "git pull" that the changes were made to 
the DESCRIPTION file. Today, after the nightly build, I still don't see the 
changes reflected on the package page and the version is still 1.0.0. I had 
made sure to version number (master branch. 1.1.1 and RELEASE branch 1.0.1). 
Can someone please let me know why this is happening ? 


Thanks,
Ashwath 

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[Bioc-devel] Package Submission Limbo

2020-05-30 Thread Chris Eeles 
Hello Bioconductor team and community,

My name is Christopher Eeles and I am a software developer in the Benjamin 
Haibe-Kains laboratory at Princess Margaret Cancer Research Centre in Toronto, 
Ontario, Canada.

I am concerned due to inaction on the part of my reviewer for two of my package 
submissions, and am not sure how to move forward.

Initially, I submitted three packages - CoreGx, ToxicoGx and RadioGx - on April 
4th, 2020 hoping to get included in the May Bioconductor release. It became 
apparent that approval would not be possible in time, as such I requested to 
expedite acceptance of CoreGx (on which the latter two packages depend) so it 
could be included. My reviewer obliged and I am thankful for that.

I was told to resubmit ToxicoGx and RadioGx on separate issues and that the 
review process would continue from where it was for the resubmissions. This 
occurred on April 25th, 2020. Before resubmission I had replied to a round of 
reviewer comments and was waiting for a reply before making more changes.

However, since resubmission I have received no further reviewer comments and no 
reply to my code updates since the last review. RadioGx will be a part of a 
workshop our lab is putting together for Bioconductor conference in July, but 
without acceptance of the package it will have to be installed from GitHub.

Additionally, ToxicoGx is the package that was used to curate data for our web 
application, ToxicoDB, which has been accepted to the NAR web server edition. 
We had assumed that the package would be accepted by now and have had criticism 
from our NAR reviewers about it's lack of availability. Both of these packages 
were available on CRAN before our submission to Bioconductor.

My question is, how do I move forward? Without response from my reviewer I do 
not know which conditions I need to meet for package acceptance? I am available 
to respond to criticism.

Initial submission of these packages occurred almost 2 months ago, and it has 
been over a month since the resubmissions. Is this normal? Are there 
extenuating circumstances of which I am unaware?

Our lab put a lot of time and effort into these packages and wish to share them 
with the Bioconductor community. Does anyone have advice on what I can do to 
get the ball rolling again?

Thanks for your assistance.

Best,
---
Christopher Eeles
Software Developer
BHK Laboratory
Princess Margaret Cancer Centre
University Health Network




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Re: [Bioc-devel] request

2020-05-30 Thread Martin Morgan 
Please view the nightly build report

http://bioconductor.org/checkResults/devel/bioc-LATEST/CSSQ/

compare the time that your package had a 'snapshot' taken for the build to start

Snapshot Date: 2020-05-29 16:51:41 -0400 (Fri, 29 May 2020)

and commit hash and date of the last commit included in the snapshot

Last Commit: 3094509
Last Changed Date: 2020-05-29 16:58:05 -0400 (Fri, 29 May 2020)

If the commit you are concerned about is after the snapshot date, then you 
missed the start of the build. Or is the commit you are concerned about 
contributing to the build failure reported across all platforms?

Martin

On 5/30/20, 4:00 PM, "Bioc-devel on behalf of Kumar, Ashwath" 
 wrote:


Hello all,

I am the maintainer for CSSQ 
(https://bioconductor.org/packages/release/bioc/html/CSSQ.html). I had made 
some changes  (Re authorship and email addresses) to the package last night. I 
made sure to push them to both the master and RELEASE_3_11 branches and 
confirmed the changes by checking with "git pull" that the changes were made to 
the DESCRIPTION file. Today, after the nightly build, I still don't see the 
changes reflected on the package page and the version is still 1.0.0. I had 
made sure to version number (master branch. 1.1.1 and RELEASE branch 1.0.1). 
Can someone please let me know why this is happening ? 


Thanks,
Ashwath 

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Re: [Bioc-devel] Package Submission Limbo

2020-05-30 Thread Martin Morgan 
Sorry that your packages have not been reviewed more promptly.

We try to have an initial review in two weeks, how long a full review takes 
depends on many factors, including complexity of the review process. Your own 
packages were I believe handled relatively efficiently initially. The release 
at the end of April) is a major activity for us, and necessarily slows the 
overall process down.

We are exploring processes to reduce the reviewer burden so that packages like 
yours are added to Bioconductor more promptly; a major concern is to do so in a 
manner that does not compromise the overall quality of accepted packages.

Martin

On 5/30/20, 4:52 PM, "Bioc-devel on behalf of Chris Eeles" 
 
wrote:

Hello Bioconductor team and community,

My name is Christopher Eeles and I am a software developer in the Benjamin 
Haibe-Kains laboratory at Princess Margaret Cancer Research Centre in Toronto, 
Ontario, Canada.

I am concerned due to inaction on the part of my reviewer for two of my 
package submissions, and am not sure how to move forward.

Initially, I submitted three packages - CoreGx, ToxicoGx and RadioGx - on 
April 4th, 2020 hoping to get included in the May Bioconductor release. It 
became apparent that approval would not be possible in time, as such I 
requested to expedite acceptance of CoreGx (on which the latter two packages 
depend) so it could be included. My reviewer obliged and I am thankful for that.

I was told to resubmit ToxicoGx and RadioGx on separate issues and that the 
review process would continue from where it was for the resubmissions. This 
occurred on April 25th, 2020. Before resubmission I had replied to a round of 
reviewer comments and was waiting for a reply before making more changes.

However, since resubmission I have received no further reviewer comments 
and no reply to my code updates since the last review. RadioGx will be a part 
of a workshop our lab is putting together for Bioconductor conference in July, 
but without acceptance of the package it will have to be installed from GitHub.

Additionally, ToxicoGx is the package that was used to curate data for our 
web application, ToxicoDB, which has been accepted to the NAR web server 
edition. We had assumed that the package would be accepted by now and have had 
criticism from our NAR reviewers about it's lack of availability. Both of these 
packages were available on CRAN before our submission to Bioconductor.

My question is, how do I move forward? Without response from my reviewer I 
do not know which conditions I need to meet for package acceptance? I am 
available to respond to criticism.

Initial submission of these packages occurred almost 2 months ago, and it 
has been over a month since the resubmissions. Is this normal? Are there 
extenuating circumstances of which I am unaware?

Our lab put a lot of time and effort into these packages and wish to share 
them with the Bioconductor community. Does anyone have advice on what I can do 
to get the ball rolling again?

Thanks for your assistance.

Best,
---
Christopher Eeles
Software Developer
BHK Laboratory
Princess Margaret Cancer Centre
University Health Network




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