Re: [Bioc-devel] plotMotifLogo function of motifStack package generates an empty plot

[Shin, Sunyoung]

Hello,

I got it. Thank you. I pushed changes made to atSNP Bioconductor.

I am fixing the graphic error in creating vignettes with plotMotifMatch 
function. This graphic function uses plotMotifLogo function from motifStack 
package. The issue seemed to be linked to that plotMotifLogo produces an empty 
plot by itself. I added graphics.off() after using plotMotifLogo based on the 
suggestion of Jianhong, the motifStack developer. This could fix the problem on 
windows machine, but did not work on linux machine. What else should I modify 
to fix the error on linux machine?

FYI, I added BUILD reports of atSNP Bioconductor:
http://bioconductor.org/checkResults/3.10/bioc-LATEST/atSNP/malbec1-buildsrc.html
 and 
http://bioconductor.org/checkResults/devel/bioc-LATEST/atSNP/malbec2-checksrc.html


Best,
Sunyoung

On Feb 17, 2020, at 1:59 AM, Neumann, Steffen 
mailto:sneum...@ipb-halle.de>> wrote:

Hi,

the source package on 3.11/bioc/html/atSNP.html
will only be updated with a new one if all checks succeed.
This prevents that you download a broken package.

Nowadays one would call that a continuous integration pipeline,
but the BioC team already does that since, um, more than a decade ;-)

Yours,
Steffen


On Mon, 2020-02-17 at 07:44 +, Shin, Sunyoung wrote:
Hello Steffen,

Thank you for the response. You are right, and I also recognized it.
However, I don’t see the updates from the source package I downloaded
from the package webpage at
https://nam02.safelinks.protection.outlook.com/?url=http%3A%2F%2Fbioconductor.org%2Fpackages%2F3.11%2Fbioc%2Fhtml%2FatSNP.htmldata=02%7C01%7CSunyoung.Shin%40utdallas.edu%7C07c7b31c220b40962c4b08d7b37f4ad4%7C8d281d1d9c4d4bf7b16e032d15de9f6c%7C0%7C0%7C637175231610633533sdata=fCnYXHnxM%2BJTDxYeXTGdpw5H6o4DObbwEGhVC81KVfY%3Dreserved=0.
 I updated
both DESCRIPTION and graphic.R, but neither were updated.


Best,
Sunyoung

On Feb 17, 2020, at 1:38 AM, Neumann, Steffen <
sneum...@ipb-halle.de> wrote:

Hi,

please have a look at the build report first:

https://nam02.safelinks.protection.outlook.com/?url=http%3A%2F%2Fbioconductor.org%2FcheckResults%2Fdevel%2Fbioc-LATEST%2FatSNP%2Fdata=02%7C01%7CSunyoung.Shin%40utdallas.edu%7C07c7b31c220b40962c4b08d7b37f4ad4%7C8d281d1d9c4d4bf7b16e032d15de9f6c%7C0%7C0%7C637175231610633533sdata=ni0I8fqdIf2j8grnIAAR8eS5HdBxs7g2IZRGwntSnhc%3Dreserved=0

where your commit 2020-02-12 has been picked up.
The check has an ERROR, most likely in the examples
to plotMotifMatch().

Also, I guess the version 1.3.0 was the version number
bumped after the last BioC release, so consider
to bump atSNP to 1.3.1 with you next commit.

Hope that helped,

Yours,
Steffen


On Mon, 2020-02-17 at 05:10 +, Shin, Sunyoung wrote:
Dear all,

I used "git push upstream master” to commit changes for atSNP
package
to Bioconductor 4 days ago. But, Bioconductor does not take the
updated version, but sticks with the old version of the package,
which I committed in October. Does someone have an idea about how
to
fix it? Thanks.


Best,
Sunyoung
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Current bits of interest:

* Computational Metabolomics PhD Position @ IPB


https://nam02.safelinks.protection.outlook.com/?url=https%3A%2F%2Fwww.ipb-halle.de%2Fen%2Fcareer%2Fjob-vacancies%2Fjoboffer-detail%2Fwissenschaftlichen-mitarbeiterin-doktorandin-bioinformatikmetabolomics-mwd%2Fdata=02%7C01%7CSunyoung.Shin%40utdallas.edu%7C07c7b31c220b40962c4b08d7b37f4ad4%7C8d281d1d9c4d4bf7b16e032d15de9f6c%7C0%7C0%7C637175231610633533sdata=dCsMhmj07FHhrDA6%2BkTSmDgCl3LZ%2F%2Fi1R6uFecNalcs%3Dreserved=0


* Leibniz Plant Biochemistry Symposium, 14./15.05.2020, Halle

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* HUPO PSI spring meeting, 23.-25.03.2020, San Diego, CA

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---
IPB HalleAG Massenspektrometrie & Bioinformatik
Dr. Steffen Neumann

Re: [Bioc-devel] Question about passphrase for SSH key

[Xu Ren]

Sorry, please ignore my previous email. I remember my passphrase and pushed
the updates successfully.

On Tue, Feb 18, 2020 at 12:02 PM Xu Ren  wrote:

> Hi,
>
> I'm the package maintainer of Bioconductor package methylGSA
> https://bioconductor.org/packages/devel/bioc/html/methylGSA.html. I have
> some issues when updating the package, and I'd appreciate it if someone
> could help.
>
> When I was trying to update the package, I followed the guideline here:
> https://bioconductor.org/developers/how-to/git/sync-existing-repositories/
> However, when I do
> git fetch --all
> Fetching origin
> Fetching upstream
> Enter passphrase for key '/Users/renxu/.ssh/id_rsa':
>
> It asked for the passphrase for the SSH key. I'm using macbook so I was
> trying to enter the password stored in the "Keychain Access".
> Unfortunately, it didn't work. I'm quite sure that I haven't changed my
> Github account and I was using the same laptop as before. Could someone
> help me with this? Thanks!
>
> Sincerely,
> Xu Ren
>

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[Bioc-devel] Bioc2020 - Deadline for workshops/talk/poster proposals in two weeks!

[Shepherd, Lori]

Reminder: Two weeks left to submit proposals for Bioc2020 
workshops/talks/posters as well as travel scholarships! See the Bioc2020 
website for more details.

http://bioc2020.bioconductor.org/




Lori Shepherd

Bioconductor Core Team

Roswell Park Comprehensive Cancer Center

Department of Biostatistics & Bioinformatics

Elm & Carlton Streets

Buffalo, New York 14263


This email message may contain legally privileged and/or confidential 
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Re: [Bioc-devel] Changing the name of your package while it has been submitted

[Krutik Patel (PGR)]

Thank you for the instructions, will do so soon.

Best Wishes,
Krutik

From: Shepherd, Lori 
Sent: 18 February 2020 14:28
To: Krutik Patel (PGR) ; bioc-devel@r-project.org 

Subject: Re: Changing the name of your package while it has been submitted

Excellent - much easier process than trying to change the name of a package 
already in Bioconductor -

Change the name of the issue
Change the link for the repository in the first comment  
https://github.com/Bioconductor/Contributions/issues/1337#issue-549669447
Change the name in the DESCRIPTION of the package

We will also have to change the github link in our database for the version 
bump to trigger a new build -  so once you  have done the above please comment 
in the issue you are ready for us to change the database and tag @lshep  (also 
I would double check that the webhooks stayed initialized)

Cheers,


Lori Shepherd

Bioconductor Core Team

Roswell Park Comprehensive Cancer Center

Department of Biostatistics & Bioinformatics

Elm & Carlton Streets

Buffalo, New York 14263


From: Krutik Patel (PGR) 
Sent: Tuesday, February 18, 2020 9:22 AM
To: Shepherd, Lori ; bioc-devel@r-project.org 

Subject: Re: Changing the name of your package while it has been submitted

Hi Lori,

The name of my package is smiRk, issue #1337. The package is still in the 
review process.

Best
Krutik



From: Shepherd, Lori 
Sent: 18 February 2020 13:00
To: Krutik Patel (PGR) ; bioc-devel@r-project.org 

Subject: Re: Changing the name of your package while it has been submitted

A few clarification points:

What is the name of your package?
Has your package already been accepted into Bioconductor or is it still in the 
review process?




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 Krutik Patel 
(PGR) 
Sent: Monday, February 17, 2020 4:34 AM
To: bioc-devel@r-project.org 
Subject: [Bioc-devel] Changing the name of your package while it has been 
submitted

Hello,

I am planning to push some updates on my package, including a name change. My 
question is what is the cleanest way of changing the name of an already 
submitted package which is the process of review?

Is it OK to just manually edit the name of the package on the issue page?

Best,
Krutik

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Re: [Bioc-devel] Integrating python into an R package

[Turaga, Nitesh]

Take a look at BiocSklearn. 

Nitesh

> On Feb 18, 2020, at 8:11 AM, Zhang, David  wrote:
> 
> Dear all, 
> 
> I’m a bioinformatics PhD student at UCL who’s recently been trying to develop 
> an R package that has some python dependencies. Specifically, areas of my 
> current pipeline are written in python for speed and any ML has been 
> implemented through sklearn. I was wondering what you would advise as the 
> best practice of integrating python code into Bioconductor/R p
> packages? E.g. R to python interfaces (such as reticulate) or advising 
> package users to call python scripts independently or re-writing python code 
> in R? 
> 
> Any advice would be much appreciated. 
> 
> Many thanks in advance, 
> 
> David 
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[Bioc-devel] Integrating python into an R package

[Zhang, David]

Dear all, 

I’m a bioinformatics PhD student at UCL who’s recently been trying to develop 
an R package that has some python dependencies. Specifically, areas of my 
current pipeline are written in python for speed and any ML has been 
implemented through sklearn. I was wondering what you would advise as the best 
practice of integrating python code into Bioconductor/R p
packages? E.g. R to python interfaces (such as reticulate) or advising package 
users to call python scripts independently or re-writing python code in R? 

Any advice would be much appreciated. 

Many thanks in advance, 

David 
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Re: [Bioc-devel] Changing the maintanor of IMMAN package

[Turaga, Nitesh]

Hi,

The error you are showing in your feed is currently saying, you are NOT in a 
repository which is hosted by github. 

Also, your remotes should be the set to look like Step #2 
(http://bioconductor.org/developers/how-to/git/push-to-github-bioc/). If that 
is set up, your GitHub name should have NO effect on pushing to Bioconductor. 

If you'd like to change your Github username, you can log into the 
BiocCredentials application, and change your Github username on your account. 

Best,

Nitesh 

> On Feb 18, 2020, at 8:51 AM, minoo ashtiani  wrote:
> 
> Hi to all,
> 
> This is Minoo Ashtiani the maintainer of "IMMAN" software package. My
> git-hub account is changed from "Minoo-Ashtiani" to "Minoo-ASTY". Now I
> want to update the package using my new account however I cant. When I want
> push to the origin I faced this errors:
> 
> git push origin master
>fatal: 'LINK' does not appear to be a git repository
> fatal: Could not read from remote repository.
> 
> 
> What should I do? Any help would be appreciated.
> P.S. I am the only maintainer of this package.
> -- 
> Minoo Ashtiani,
> 
> Research Assistant @ Russell Lab, Heidelberg University
> +491605667176 Germany
> minoo.ashti...@bioquant.uni-heidelberg.de
> 
> for accessing papers:
> https://scholar.google.com/citations?user=nnCwxpEJ=en
> 
>   [[alternative HTML version deleted]]
> 
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Re: [Bioc-devel] Changing the name of your package while it has been submitted

[Shepherd, Lori]

Excellent - much easier process than trying to change the name of a package 
already in Bioconductor -

Change the name of the issue
Change the link for the repository in the first comment  
https://github.com/Bioconductor/Contributions/issues/1337#issue-549669447
Change the name in the DESCRIPTION of the package

We will also have to change the github link in our database for the version 
bump to trigger a new build -  so once you  have done the above please comment 
in the issue you are ready for us to change the database and tag @lshep  (also 
I would double check that the webhooks stayed initialized)

Cheers,


Lori Shepherd

Bioconductor Core Team

Roswell Park Comprehensive Cancer Center

Department of Biostatistics & Bioinformatics

Elm & Carlton Streets

Buffalo, New York 14263


From: Krutik Patel (PGR) 
Sent: Tuesday, February 18, 2020 9:22 AM
To: Shepherd, Lori ; bioc-devel@r-project.org 

Subject: Re: Changing the name of your package while it has been submitted

Hi Lori,

The name of my package is smiRk, issue #1337. The package is still in the 
review process.

Best
Krutik



From: Shepherd, Lori 
Sent: 18 February 2020 13:00
To: Krutik Patel (PGR) ; bioc-devel@r-project.org 

Subject: Re: Changing the name of your package while it has been submitted

A few clarification points:

What is the name of your package?
Has your package already been accepted into Bioconductor or is it still in the 
review process?




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 Krutik Patel 
(PGR) 
Sent: Monday, February 17, 2020 4:34 AM
To: bioc-devel@r-project.org 
Subject: [Bioc-devel] Changing the name of your package while it has been 
submitted

Hello,

I am planning to push some updates on my package, including a name change. My 
question is what is the cleanest way of changing the name of an already 
submitted package which is the process of review?

Is it OK to just manually edit the name of the package on the issue page?

Best,
Krutik

[[alternative HTML version deleted]]

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Re: [Bioc-devel] Changing the name of your package while it has been submitted

[Krutik Patel (PGR)]

Hi Lori,

The name of my package is smiRk, issue #1337. The package is still in the 
review process.

Best
Krutik



From: Shepherd, Lori 
Sent: 18 February 2020 13:00
To: Krutik Patel (PGR) ; bioc-devel@r-project.org 

Subject: Re: Changing the name of your package while it has been submitted

A few clarification points:

What is the name of your package?
Has your package already been accepted into Bioconductor or is it still in the 
review process?




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 Krutik Patel 
(PGR) 
Sent: Monday, February 17, 2020 4:34 AM
To: bioc-devel@r-project.org 
Subject: [Bioc-devel] Changing the name of your package while it has been 
submitted

Hello,

I am planning to push some updates on my package, including a name change. My 
question is what is the cleanest way of changing the name of an already 
submitted package which is the process of review?

Is it OK to just manually edit the name of the package on the issue page?

Best,
Krutik

[[alternative HTML version deleted]]

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[Bioc-devel] Changing the maintanor of IMMAN package

[minoo ashtiani]

Hi to all,

This is Minoo Ashtiani the maintainer of "IMMAN" software package. My
git-hub account is changed from "Minoo-Ashtiani" to "Minoo-ASTY". Now I
want to update the package using my new account however I cant. When I want
push to the origin I faced this errors:

 git push origin master
fatal: 'LINK' does not appear to be a git repository
 fatal: Could not read from remote repository.


What should I do? Any help would be appreciated.
P.S. I am the only maintainer of this package.
-- 
Minoo Ashtiani,

Research Assistant @ Russell Lab, Heidelberg University
+491605667176 Germany
minoo.ashti...@bioquant.uni-heidelberg.de

for accessing papers:
https://scholar.google.com/citations?user=nnCwxpEJ=en

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Re: [Bioc-devel] Changing the name of your package while it has been submitted

[Shepherd, Lori]

A few clarification points:

What is the name of your package?
Has your package already been accepted into Bioconductor or is it still in the 
review process?




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 Krutik Patel 
(PGR) 
Sent: Monday, February 17, 2020 4:34 AM
To: bioc-devel@r-project.org 
Subject: [Bioc-devel] Changing the name of your package while it has been 
submitted

Hello,

I am planning to push some updates on my package, including a name change. My 
question is what is the cleanest way of changing the name of an already 
submitted package which is the process of review?

Is it OK to just manually edit the name of the package on the issue page?

Best,
Krutik

[[alternative HTML version deleted]]

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recipient(s), you are hereby notified that any disclosure, copying, 
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