Re: [Bioc-devel] news on tidybulk?

[stefano]

Hello,

tidybulk passed all checks now. Sorry I was waiting for a response to my
answer to a reviewer's question before sending updated versions, it was the
wrong strategy.

Please let me know if anything else is needed.

Best wishes.

*Stefano *



Stefano Mangiola | Postdoctoral fellow

Papenfuss Laboratory

The Walter Eliza Hall Institute of Medical Research

+61 (0)466452544


Il giorno mer 25 mar 2020 alle ore 12:28 stefano 
ha scritto:

> Hello,
>
> I have asked advise for a quite mysterious error in Windows and I have
> been told to wait, and I did not receive further reply. And I received a
> positive feedback
>
> dvantwisk  commented 13 days ago
> 
>
> I apologize for the wait. I've reviewed your package and found that it is
> excellently written. I really don't have much to add. My only question is
> as follows:
>
>
> And after replying I did not receive a reply. I have pushed an updated
> version. Please don't neglect this package. It is important that it will be
> included in this release of Bioconductor.
>
> Best wishes.
>
> *Stefano *
>
>
>
> Stefano Mangiola | Postdoctoral fellow
>
> Papenfuss Laboratory
>
> The Walter Eliza Hall Institute of Medical Research
>
> +61 (0)466452544
>
>
>
> Il giorno mar 24 mar 2020 alle ore 23:24 Vincent Carey <
> st...@channing.harvard.edu> ha scritto:
>
>> I think "header says it all" may be intended ... the question is whether
>> it is accepted.   since the package seems to be in error state I am not
>> sure
>> it can move forward at this time
>>
>> On Tue, Mar 24, 2020 at 8:22 AM Shepherd, Lori <
>> lori.sheph...@roswellpark.org> wrote:
>>
>>> Is there a question here? Nothing came through in the body of the email?
>>>
>>>
>>> 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
>>> Stefano Mangiola 
>>> Sent: Tuesday, March 24, 2020 7:28 AM
>>> To: bioc-devel@r-project.org 
>>> Subject: [Bioc-devel] news on tidybulk?
>>>
>>>
>>> ___
>>> 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.
>>> [[alternative HTML version deleted]]
>>>
>>> ___
>>> Bioc-devel@r-project.org mailing list
>>> https://stat.ethz.ch/mailman/listinfo/bioc-devel
>>>
>>
>> The information in this e-mail is intended only for t...{{dropped:17}}

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Re: [Bioc-devel] news on tidybulk?

[stefano]

Hello,

I have asked advise for a quite mysterious error in Windows and I have been
told to wait, and I did not receive further reply. And I received a
positive feedback

dvantwisk  commented 13 days ago


I apologize for the wait. I've reviewed your package and found that it is
excellently written. I really don't have much to add. My only question is
as follows:


And after replying I did not receive a reply. I have pushed an updated
version. Please don't neglect this package. It is important that it will be
included in this release of Bioconductor.

Best wishes.

*Stefano *



Stefano Mangiola | Postdoctoral fellow

Papenfuss Laboratory

The Walter Eliza Hall Institute of Medical Research

+61 (0)466452544



Il giorno mar 24 mar 2020 alle ore 23:24 Vincent Carey <
st...@channing.harvard.edu> ha scritto:

> I think "header says it all" may be intended ... the question is whether
> it is accepted.   since the package seems to be in error state I am not
> sure
> it can move forward at this time
>
> On Tue, Mar 24, 2020 at 8:22 AM Shepherd, Lori <
> lori.sheph...@roswellpark.org> wrote:
>
>> Is there a question here? Nothing came through in the body of the email?
>>
>>
>> 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 Stefano
>> Mangiola 
>> Sent: Tuesday, March 24, 2020 7:28 AM
>> To: bioc-devel@r-project.org 
>> Subject: [Bioc-devel] news on tidybulk?
>>
>>
>> ___
>> 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.
>> [[alternative HTML version deleted]]
>>
>> ___
>> Bioc-devel@r-project.org mailing list
>> https://stat.ethz.ch/mailman/listinfo/bioc-devel
>>
>
> The information in this e-mail is intended only for th...{{dropped:15}}

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[Bioc-devel] Problem updating Bioconductor package

[Hong Zheng]

Hi,

We followed the instruction 
(https://bioconductor.org/developers/how-to/git/maintain-bioc-only/) to update 
a Bioconductor package. All went well until the last step (git push upstream 
master).

The error message:

FATAL: W any packages/MethylMix ogevaert DENIED by fallthru
(or you mis-spelled the reponame)
fatal: Could not read from remote repository.
Please make sure you have the correct access rights
and the repository exists.

The SSH key has already been added to Bioconductor profile.

Does anyone have an idea how to solve this problem? Thanks!

Hong

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Re: [Bioc-devel] Python dependency

[Martin Morgan]

It's important to ask 'why Bioconductor?' with the answer partly involving 
interoperability with other Bioconductor packages and data representations 
(e.g., http://bioconductor.org/developers/how-to/commonMethodsAndClasses/). 
There wouldn't be much value in making something that is essentially a python 
package without connection to Bioconductor available in Bioconductor.

Martin

On 3/24/20, 11:59 AM, "Bioc-devel on behalf of Daniele Muraro" 
 wrote:

To whom it may concern,

I would like to upload onto Bioconductor a package which is currently 
developed in python.
I was wondering if Bioconductor supports python dependencies or if I should 
re-program the package in R exclusively. Is calling python from R using the 
package "reticulate" acceptable for a package submission onto Bioconductor?
Thank you for your attention.

All the best,

Daniele Muraro




--
Daniele Muraro

Computational Biologist - Staff Scientist

Wellcome Sanger Institute

Wellcome Genome Campus

Hinxton, Cambridgeshire

CB10 1SA, UK

Phone (direct) +44 (0)1223 494766

Phone (reception) +44 (0)1223 834244

e-mail: daniele.mur...@sanger.ac.uk


Sanger profile:

https://www.sanger.ac.uk/people/directory/muraro-daniele


LinkedIn profile:

https://www.linkedin.com/in/daniele-muraro-a3557630/




-- 
 The Wellcome Sanger Institute is operated by Genome Research 
 Limited, a charity registered in England with number 1021457 and a 
 company registered in England with number 2742969, whose registered 
 office is 215 Euston Road, London, NW1 2BE. 



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Re: [Bioc-devel] Python dependency

[Hervé Pagès]

Hi,

Yes Bioconductor packages can depend on Python modules. This should only 
happen behind the scene and be transparent to the end user (i.e. the end 
user is not expected to interact directly with the Python module).


You can use reticulate (from CRAN) directly or, even better, use 
basilisk (from Bioconductor):


  https://bioconductor.org/packages/basilisk

basilisk was only added to the devel version of Bioconductor recently. 
It aims at automating module installation on the end user machine and on 
the Bioconductor build machines (if you use reticulate directly, we 
would need to manually install the Python modules on the build machines).


Cheers,
H.

On 3/24/20 08:58, Daniele Muraro wrote:

To whom it may concern,

I would like to upload onto Bioconductor a package which is currently developed 
in python.
I was wondering if Bioconductor supports python dependencies or if I should re-program 
the package in R exclusively. Is calling python from R using the package 
"reticulate" acceptable for a package submission onto Bioconductor?
Thank you for your attention.

All the best,

Daniele Muraro




--
Daniele Muraro

Computational Biologist - Staff Scientist

Wellcome Sanger Institute

Wellcome Genome Campus

Hinxton, Cambridgeshire

CB10 1SA, UK

Phone (direct) +44 (0)1223 494766

Phone (reception) +44 (0)1223 834244

e-mail: daniele.mur...@sanger.ac.uk


Sanger profile:

https://urldefense.proofpoint.com/v2/url?u=https-3A__www.sanger.ac.uk_people_directory_muraro-2Ddaniele=DwICAg=eRAMFD45gAfqt84VtBcfhQ=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA=I5byLUAug01hPl-C-VbCCk-t7h7gPtd9rcxv5fK3NHk=DDLJ47WTk9au0lfoTBoXibSvAkBi1TEyL78EqjnlszE=


LinkedIn profile:

https://urldefense.proofpoint.com/v2/url?u=https-3A__www.linkedin.com_in_daniele-2Dmuraro-2Da3557630_=DwICAg=eRAMFD45gAfqt84VtBcfhQ=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA=I5byLUAug01hPl-C-VbCCk-t7h7gPtd9rcxv5fK3NHk=vL4MJYsNa8_56NxXoYbZEYYHZk9-HJku2hLUuZLDwqw=






--
Hervé Pagès

Program in Computational Biology
Division of Public Health Sciences
Fred Hutchinson Cancer Research Center
1100 Fairview Ave. N, M1-B514
P.O. Box 19024
Seattle, WA 98109-1024

E-mail: hpa...@fredhutch.org
Phone:  (206) 667-5791
Fax:(206) 667-1319

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Re: [Bioc-devel] Trouble accessing packages

[Shepherd, Lori]

If you added your github id to the credentials app (which would provide access 
keys)  you should try to access the git.bioconductor.org repository for your 
package.
See the git help pages for linking to bioconductor git repository
http://bioconductor.org/developers/how-to/git/



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 Enio Gjerga 

Sent: Tuesday, March 24, 2020 12:39 PM
To: bioc-devel@r-project.org 
Subject: Re: [Bioc-devel] Trouble accessing packages

P.S. I have submitted my GitHub id to Bioconductor (enio23) but not sure
how to proceed any further with this.

Thanks again.

On Tue, 24 Mar 2020 at 17:38, Enio Gjerga  wrote:

> Hello,
>
> I am Enio Gjerga and I have recently been assigned the maintenance of the
> CNORfeeder and CNORode packages. I have recently got the news that
> CNORfeeder have been having troubles which I intend to fix. Also I intend
> to update both of the packages with a few new features.
>
> However, I am having a major issue: I am not sure where I can access the
> codes where these packages are stored in Bioconductor and how can I fix the
> issues of CNORfeeder and update the two packages. Is there any easy way
> where I can find the codes for these two packages and push my updates?
>
> Any help/instruction would be much appreciated as I am very new to this.
>
> Cheers,
> Enio Gjerga
> --
> Enio GJERGA
> PhD student
> JRC-COMBINE RWTH Aachen
> Tel : +4917685132057
>


--
Enio GJERGA
PhD student
JRC-COMBINE RWTH Aachen
Tel : +4917685132057

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recipient(s), you are hereby notified that any disclosure, copying, 
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[Bioc-devel] Trouble accessing packages

[Enio Gjerga]

Hello,

I am Enio Gjerga and I have recently been assigned the maintenance of the
CNORfeeder and CNORode packages. I have recently got the news that
CNORfeeder have been having troubles which I intend to fix. Also I intend
to update both of the packages with a few new features.

However, I am having a major issue: I am not sure where I can access the
codes where these packages are stored in Bioconductor and how can I fix the
issues of CNORfeeder and update the two packages. Is there any easy way
where I can find the codes for these two packages and push my updates?

Any help/instruction would be much appreciated as I am very new to this.

Cheers,
Enio Gjerga
-- 
Enio GJERGA
PhD student
JRC-COMBINE RWTH Aachen
Tel : +4917685132057

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Re: [Bioc-devel] Trouble accessing packages

[Enio Gjerga]

P.S. I have submitted my GitHub id to Bioconductor (enio23) but not sure
how to proceed any further with this.

Thanks again.

On Tue, 24 Mar 2020 at 17:38, Enio Gjerga  wrote:

> Hello,
>
> I am Enio Gjerga and I have recently been assigned the maintenance of the
> CNORfeeder and CNORode packages. I have recently got the news that
> CNORfeeder have been having troubles which I intend to fix. Also I intend
> to update both of the packages with a few new features.
>
> However, I am having a major issue: I am not sure where I can access the
> codes where these packages are stored in Bioconductor and how can I fix the
> issues of CNORfeeder and update the two packages. Is there any easy way
> where I can find the codes for these two packages and push my updates?
>
> Any help/instruction would be much appreciated as I am very new to this.
>
> Cheers,
> Enio Gjerga
> --
> Enio GJERGA
> PhD student
> JRC-COMBINE RWTH Aachen
> Tel : +4917685132057
>


-- 
Enio GJERGA
PhD student
JRC-COMBINE RWTH Aachen
Tel : +4917685132057

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Re: [Bioc-devel] Help needed on BioC Git credential for package maintainer

[Turaga, Nitesh]

Hi 

I've created the account for you. I'll send you your login details in a private 
email.

Nitesh 

> On Mar 24, 2020, at 12:20 PM, Huang, Lei [CRI]  
> wrote:
> 
> Dear Bioconductor team,
> 
> I am one of the maintainers of BioC packages Lumi 
> (https://bioconductor.org/packages/release/bioc/html/lumi.html) and 
> methyAnalysis 
> (https://bioconductor.org/packages/release/bioc/html/methyAnalysis.html); and 
> would like to sync the bug-fix with the bioc-devel repository. Since BioC 
> allows only one maintainer per package, I was wondering if you could help 
> create BioC Git credential for me as the sole maintainer?
> 
> Thanks,
> Lei
> 
> Lei Huang, Ph.D.
> Senior Bioinformatician
> Center for Research Informatics
> University of Chicago
> Email: lhuang at bsd.uchicago.edu
> 
> 
> On Mar 23, 2020, at 3:44 PM, Huang, Lei [CRI] 
> mailto:lhu...@bsd.uchicago.edu>> wrote:
> 
> Dear Bioconductor team,
> 
> We are the maintainers of Bioconductor packages Lumi 
> (https://bioconductor.org/packages/release/bioc/html/lumi.html) and 
> methyAnalysis 
> (https://bioconductor.org/packages/release/bioc/html/methyAnalysis.html). We 
> were trying to obtain Bioconductor Git credentials by activating the account 
> associated to those packages at 
> https://git.bioconductor.org/BiocCredentials/account_activation/ but got the 
> following error message instead.
> 
> 
> "lhu...@bsd.uchicago.edu is not associated 
> with a maintainer of a Bioconductor package. Please check the spelling or 
> contact bioc-devel@r-project.org for help."
> 
> Would you please help us on this?
> 
> Best,
> Lei
> 
> 
> Lei Huang, Ph.D.
> Senior Bioinformatician
> Center for Research Informatics
> University of Chicago
> Email: lhuang at bsd.uchicago.edu
> 
> 
> 
> 
> 
>   [[alternative HTML version deleted]]
> 
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[Bioc-devel] Help needed on BioC Git credential for package maintainer

[Huang, Lei [CRI]]

Dear Bioconductor team,

I am one of the maintainers of BioC packages Lumi 
(https://bioconductor.org/packages/release/bioc/html/lumi.html) and 
methyAnalysis 
(https://bioconductor.org/packages/release/bioc/html/methyAnalysis.html); and 
would like to sync the bug-fix with the bioc-devel repository. Since BioC 
allows only one maintainer per package, I was wondering if you could help 
create BioC Git credential for me as the sole maintainer?

Thanks,
Lei

Lei Huang, Ph.D.
Senior Bioinformatician
Center for Research Informatics
University of Chicago
Email: lhuang at bsd.uchicago.edu


On Mar 23, 2020, at 3:44 PM, Huang, Lei [CRI] 
mailto:lhu...@bsd.uchicago.edu>> wrote:

Dear Bioconductor team,

We are the maintainers of Bioconductor packages Lumi 
(https://bioconductor.org/packages/release/bioc/html/lumi.html) and 
methyAnalysis 
(https://bioconductor.org/packages/release/bioc/html/methyAnalysis.html). We 
were trying to obtain Bioconductor Git credentials by activating the account 
associated to those packages at 
https://git.bioconductor.org/BiocCredentials/account_activation/ but got the 
following error message instead.


"lhu...@bsd.uchicago.edu is not associated with 
a maintainer of a Bioconductor package. Please check the spelling or contact 
bioc-devel@r-project.org for help."

Would you please help us on this?

Best,
Lei


Lei Huang, Ph.D.
Senior Bioinformatician
Center for Research Informatics
University of Chicago
Email: lhuang at bsd.uchicago.edu





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[Bioc-devel] Python dependency

[Daniele Muraro]

To whom it may concern,

I would like to upload onto Bioconductor a package which is currently developed 
in python.
I was wondering if Bioconductor supports python dependencies or if I should 
re-program the package in R exclusively. Is calling python from R using the 
package "reticulate" acceptable for a package submission onto Bioconductor?
Thank you for your attention.

All the best,

Daniele Muraro




--
Daniele Muraro

Computational Biologist - Staff Scientist

Wellcome Sanger Institute

Wellcome Genome Campus

Hinxton, Cambridgeshire

CB10 1SA, UK

Phone (direct) +44 (0)1223 494766

Phone (reception) +44 (0)1223 834244

e-mail: daniele.mur...@sanger.ac.uk


Sanger profile:

https://www.sanger.ac.uk/people/directory/muraro-daniele


LinkedIn profile:

https://www.linkedin.com/in/daniele-muraro-a3557630/




-- 
 The Wellcome Sanger Institute is operated by Genome Research 
 Limited, a charity registered in England with number 1021457 and a 
 company registered in England with number 2742969, whose registered 
 office is 215 Euston Road, London, NW1 2BE. 



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Re: [Bioc-devel] Issue Reproducing BioC 3.11 COHCAP Error Message

[Charles Warden]

Hi Lori,

Thank you very much for your help!

Sincerely,
Charles

From: Shepherd, Lori 
Sent: Tuesday, March 24, 2020 5:39 AM
To: Charles Warden ; 'Martin Morgan' 
; 'Alexey Sergushichev' 
Cc: 'bioc-devel@r-project.org' 
Subject: Re: [Bioc-devel] Issue Reproducing BioC 3.11 COHCAP Error Message

Thank you for your contributions to Bioconductor.  We appreciate you fixing 
COHCAP.

I will begin the deprecation process for sRAP;  there is no further action 
needed.

Cheers,


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 Charles Warden mailto:cwar...@coh.org>>
Sent: Monday, March 23, 2020 3:53 PM
To: 'Martin Morgan' mailto:mtmorgan.b...@gmail.com>>; 
'Alexey Sergushichev' mailto:alserg...@gmail.com>>
Cc: 'bioc-devel@r-project.org' 
mailto:bioc-devel@r-project.org>>
Subject: Re: [Bioc-devel] Issue Reproducing BioC 3.11 COHCAP Error Message

Hi Everybody,

Thank you again for your help!

I think the issue for the COHCAP devel package has now been resolved:

http://bioconductor.org/checkResults/release/bioc-LATEST/COHCAP/

I had somewhat similar error messages for sRAP (which is different than 
COHCAP), but I am OK with sRAP being removed from the next version of 
Bioconductor (since it is no longer being maintained).  If you can please let 
me know if there is a contact that I should e-mail (beyond this mailing list, 
or not fixing the error), then I would appreciate that.

Thanks Again,
Charles

-Original Message-
From: Charles Warden
Sent: Friday, March 20, 2020 1:40 PM
To: Martin Morgan mailto:mtmorgan.b...@gmail.com>>; 
Alexey Sergushichev mailto:alserg...@gmail.com>>
Cc: bioc-devel@r-project.org
Subject: RE: [Bioc-devel] Issue Reproducing BioC 3.11 COHCAP Error Message

Hi Martin,

That is probably what happened.

Thank you again for your help!

Sincerely,
Charles

-Original Message-
From: Martin Morgan mailto:mtmorgan.b...@gmail.com>>
Sent: Friday, March 20, 2020 1:38 PM
To: Charles Warden mailto:cwar...@coh.org>>; Alexey 
Sergushichev mailto:alserg...@gmail.com>>
Cc: bioc-devel@r-project.org
Subject: Re: [Bioc-devel] Issue Reproducing BioC 3.11 COHCAP Error Message

yes, use 1.33.1. Maybe you had a space between the '.' and the '1' or similar, 
'1.33. 1' ? This generates an error

** using staged installation
Error : Invalid DESCRIPTION file

Malformed package version.

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.

ERROR: installing package DESCRIPTION failed for package ...

Martin


On 3/20/20, 4:28 PM, "Charles Warden" 
mailto:cwar...@coh.org>> wrote:

Hi Martin,

I am currently having difficulty reproducing my earlier error (which I 
think didn’t even get to the step of testing the demo code).  So, I think the 
short answer is that I should just use version 1.33.1.

In my search history, I can tell that I Googled "R Malformed package 
version," so I think that was part of the earlier message that I got.

For what is worth, I think this is what gave me the idea to change the 
version numbering system:


https://urldefense.com/v3/__https://cran.r-project.org/doc/manuals/r-release/R-exts.html*The-DESCRIPTION-file__;Iw!!Fou38LsQmgU!54yJgFhe0LVN6Sfb91X3m3HjH3zyeO6TroDujXtNKpwV4g0kwCruJ9yJaP_S$

However, if I am not currently getting an error message, then I won't worry 
about it.

Thank you very much for your help!

Sincerely,
Charles

-Original Message-
From: Martin Morgan 
mailto:mtmorgan.b...@gmail.com>>
Sent: Friday, March 20, 2020 1:09 PM
To: Charles Warden mailto:cwar...@coh.org>>; Alexey 
Sergushichev mailto:alserg...@gmail.com>>
Cc: bioc-devel@r-project.org
Subject: Re: [Bioc-devel] Issue Reproducing BioC 3.11 COHCAP Error Message

Can you be precise about the concern about 1.33.1 as a version number (what 
precise note / error / warning you received)? This scheme is very standard for 
package versions, and as you see enforced (for many years!) by Bioconductor.

Martin

On 3/20/20, 4:03 PM, "Bioc-devel on behalf of Charles Warden" 
mailto:bioc-devel-boun...@r-project.org%20on%20behalf%20of%20cwar...@coh.org>>
 wrote:

Hi Everybody,

I think changing that read.table() parameter fixed the main issue.

However, when I tested my code, R used a different way to note 

Re: [Bioc-devel] Issue Reproducing BioC 3.11 COHCAP Error Message

[Shepherd, Lori]

Thank you for your contributions to Bioconductor.  We appreciate you fixing 
COHCAP.

I will begin the deprecation process for sRAP;  there is no further action 
needed.

Cheers,


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 Charles Warden 

Sent: Monday, March 23, 2020 3:53 PM
To: 'Martin Morgan' ; 'Alexey Sergushichev' 

Cc: 'bioc-devel@r-project.org' 
Subject: Re: [Bioc-devel] Issue Reproducing BioC 3.11 COHCAP Error Message

Hi Everybody,

Thank you again for your help!

I think the issue for the COHCAP devel package has now been resolved:

http://bioconductor.org/checkResults/release/bioc-LATEST/COHCAP/

I had somewhat similar error messages for sRAP (which is different than 
COHCAP), but I am OK with sRAP being removed from the next version of 
Bioconductor (since it is no longer being maintained).  If you can please let 
me know if there is a contact that I should e-mail (beyond this mailing list, 
or not fixing the error), then I would appreciate that.

Thanks Again,
Charles

-Original Message-
From: Charles Warden
Sent: Friday, March 20, 2020 1:40 PM
To: Martin Morgan ; Alexey Sergushichev 

Cc: bioc-devel@r-project.org
Subject: RE: [Bioc-devel] Issue Reproducing BioC 3.11 COHCAP Error Message

Hi Martin,

That is probably what happened.

Thank you again for your help!

Sincerely,
Charles

-Original Message-
From: Martin Morgan 
Sent: Friday, March 20, 2020 1:38 PM
To: Charles Warden ; Alexey Sergushichev 
Cc: bioc-devel@r-project.org
Subject: Re: [Bioc-devel] Issue Reproducing BioC 3.11 COHCAP Error Message

yes, use 1.33.1. Maybe you had a space between the '.' and the '1' or similar, 
'1.33. 1' ? This generates an error

** using staged installation
Error : Invalid DESCRIPTION file

Malformed package version.

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.

ERROR: installing package DESCRIPTION failed for package ...

Martin


On 3/20/20, 4:28 PM, "Charles Warden"  wrote:

Hi Martin,

I am currently having difficulty reproducing my earlier error (which I 
think didn’t even get to the step of testing the demo code).  So, I think the 
short answer is that I should just use version 1.33.1.

In my search history, I can tell that I Googled "R Malformed package 
version," so I think that was part of the earlier message that I got.

For what is worth, I think this is what gave me the idea to change the 
version numbering system:


https://urldefense.com/v3/__https://cran.r-project.org/doc/manuals/r-release/R-exts.html*The-DESCRIPTION-file__;Iw!!Fou38LsQmgU!54yJgFhe0LVN6Sfb91X3m3HjH3zyeO6TroDujXtNKpwV4g0kwCruJ9yJaP_S$

However, if I am not currently getting an error message, then I won't worry 
about it.

Thank you very much for your help!

Sincerely,
Charles

-Original Message-
From: Martin Morgan 
Sent: Friday, March 20, 2020 1:09 PM
To: Charles Warden ; Alexey Sergushichev 

Cc: bioc-devel@r-project.org
Subject: Re: [Bioc-devel] Issue Reproducing BioC 3.11 COHCAP Error Message

Can you be precise about the concern about 1.33.1 as a version number (what 
precise note / error / warning you received)? This scheme is very standard for 
package versions, and as you see enforced (for many years!) by Bioconductor.

Martin

On 3/20/20, 4:03 PM, "Bioc-devel on behalf of Charles Warden" 
 wrote:

Hi Everybody,

I think changing that read.table() parameter fixed the main issue.

However, when I tested my code, R used a different way to note versions 
in R-v.4.0.0.

For example, in order to clear a message from “R CMD check” or “R CMD 
build”, I had to say the version was 1.33-1 (instead of 1.33.1).

I uploaded those changes to GitHub and tested an R-3.6 installation, 
and that was OK.

However, when I am working on merging the GitHub and Bioconductor 
branches, I get the following error message:

“Remote: Error: Illegal version bump from ‘1.33.0’ to ‘1.33-1’“

Is this going to be changed in Bioconductor, or should I see if this is 
only a NOTE or WARNING (and submit the package as version 1.33.1)?

Thank You,
Charles

From: Alexey Sergushichev 
Sent: Thursday, March 19, 2020 3:00 PM
To: Charles Warden 
Cc: Shepherd, Lori ; 
bioc-devel@r-project.org
Subject: Re: [Bioc-devel] Issue Reproducing BioC 3.11 COHCAP Error 
Message

I think one of the major changes recently is setting stringsAsFactors 
option to FALSE by default.

Best,
Alexey

On Fri, Mar 20, 2020 at 12:48 AM Charles Warden 
mailto:cwar...@coh.org>> wrote:
Hi Lori,

Thank you very much.

If I use R-4.0 (instead of R-3.6), then I can reproduce the error 
message.

  

Re: [Bioc-devel] issue 1333 tscR package accepted

[Shepherd, Lori]

Sorry for the delay.  We will look at moving accepted packages into the 
official Bioconductor repository over the next few days.


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 Fernando P�rez 

Sent: Tuesday, March 24, 2020 5:11 AM
To: bioc-devel@r-project.org 
Subject: [Bioc-devel] issue 1333 tscR package accepted


Dear Bioconductor team

The package "tscR" was accepted 12 days ago. I would like to know how
long it takes
to send additional information as indicated in the issue (Bioconductor
github issue 1333).


Thank you so much.


best,

Fernando

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Re: [Bioc-devel] news on tidybulk?

[Vincent Carey]

I think "header says it all" may be intended ... the question is whether
it is accepted.   since the package seems to be in error state I am not sure
it can move forward at this time

On Tue, Mar 24, 2020 at 8:22 AM Shepherd, Lori <
lori.sheph...@roswellpark.org> wrote:

> Is there a question here? Nothing came through in the body of the email?
>
>
> 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 Stefano
> Mangiola 
> Sent: Tuesday, March 24, 2020 7:28 AM
> To: bioc-devel@r-project.org 
> Subject: [Bioc-devel] news on tidybulk?
>
>
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Re: [Bioc-devel] news on tidybulk?

[Vincent Carey]

I am weak on finding logs, but at
https://github.com/Bioconductor/Contributions/issues?q=is%3Aissue+is%3Aopen+tidybulk
I see the package is in an error state.  Can you fix that?

On Tue, Mar 24, 2020 at 7:31 AM Stefano Mangiola 
wrote:

>
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Re: [Bioc-devel] news on tidybulk?

[Shepherd, Lori]

Is there a question here? Nothing came through in the body of the email?


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 Stefano 
Mangiola 
Sent: Tuesday, March 24, 2020 7:28 AM
To: bioc-devel@r-project.org 
Subject: [Bioc-devel] news on tidybulk?


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[Bioc-devel] news on tidybulk?

[Stefano Mangiola]

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[Bioc-devel] issue 1333 tscR package accepted

[Fernando Pérez]

Dear Bioconductor team

The package "tscR" was accepted 12 days ago. I would like to know how 
long it takes
to send additional information as indicated in the issue (Bioconductor 
github issue 1333).



Thank you so much.


best,

Fernando

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[Bioc-devel] issue 1333 tscR package accepted

[Fernando Pérez]

Dear Bioconductor team

The package "tscR" was accepted 12 days ago. I would like to know how 
long it takes
to send additional information as indicated in the issue (Bioconductor 
github issue 1333).



Thank you so much.


best,

Fernando

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