Re: [Bioc-devel] How to proper write documentation (Rd) file for setReplaceMethod

2021-04-15 Thread Jianhong Ou, Ph.D. 
Thank you Lori for the information.

Best!

Your sincerely,

Jianhong Ou

On Apr 15, 2021, at 8:38 AM, Kern, Lori  wrote:


Please see this related post

https://stat.ethz.ch/pipermail/bioc-devel/2021-January/017587.html

I believe you can ignore the window warnings for now as it is a product of the 
way we are building/checking the packages.


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 Jianhong Ou, 
Ph.D. 
Sent: Wednesday, April 14, 2021 3:11 PM
To: bioc-devel@r-project.org 
Subject: [Bioc-devel] How to proper write documentation (Rd) file for 
setReplaceMethod

Hi All,

I got warning message in windows building like:


Rd warning: cannot open file 
'D:/biocbuild/bbs-3.13-bioc/meat/trackViewer.buildbin-libdir/00LOCK-trackViewer/00new/trackViewer/help/$<-,track-method.html':
 Invalid argument

I used RoxygenNote to create the Rd file and the note I wrote like this:

#' Method $<-
#' @rdname trackStyle-class
#' @exportMethod $<-
#' @aliases $<-,track-method

Any help will be appreciated. Thanks in advance.


Yours Sincerely,

Jianhong Ou

Email: jianhong...@duke.edu
Bioinformatician II
Department of Cell Biology
Duke University School of Medicine
Durham, NC, 27710

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Re: [Bioc-devel] How to proper write documentation (Rd) file for setReplaceMethod

2021-04-15 Thread Kern, Lori 
Please see this related post

https://stat.ethz.ch/pipermail/bioc-devel/2021-January/017587.html

I believe you can ignore the window warnings for now as it is a product of the 
way we are building/checking the packages.


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 Jianhong Ou, 
Ph.D. 
Sent: Wednesday, April 14, 2021 3:11 PM
To: bioc-devel@r-project.org 
Subject: [Bioc-devel] How to proper write documentation (Rd) file for 
setReplaceMethod

Hi All,

I got warning message in windows building like:


Rd warning: cannot open file 
'D:/biocbuild/bbs-3.13-bioc/meat/trackViewer.buildbin-libdir/00LOCK-trackViewer/00new/trackViewer/help/$<-,track-method.html':
 Invalid argument

I used RoxygenNote to create the Rd file and the note I wrote like this:

#' Method $<-
#' @rdname trackStyle-class
#' @exportMethod $<-
#' @aliases $<-,track-method

Any help will be appreciated. Thanks in advance.


Yours Sincerely,

Jianhong Ou

Email: jianhong...@duke.edu
Bioinformatician II
Department of Cell Biology
Duke University School of Medicine
Durham, NC, 27710

Confidentiality Notice:\ This e-mail message, including ...{{dropped:23}}

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Re: [Bioc-devel] Bioconductor package InterMineR

2021-04-15 Thread Nitesh Turaga 
Hi,

Going back in time like this will cause major breaks in the way Bioconductor 
does releases and also just in general for users of the InterMineR package.

I think a better way is to just copy the changes from your earlier version 
during �Release 3.10� and apply them to your �devel� branch as a simple commit.

Also, I�d like you to think if making such a drastic change is needed for a 
�release� version. �Release 3.12� or any release is meant to fix high priority 
bugs only, and with Release 3.13 coming in about one month, is it worth it? 
Please think about this.

Best,

Nitesh

From: Kern, Lori 
Date: Thursday, April 15, 2021 at 8:27 AM
To: rac...@intermine.org , Nitesh Turaga 

Subject: Re: Bioconductor package InterMineR
Looping one of our better git experts in for an opinion on this.

Nitesh, advise on reverting to previous version that won't cause conflicting 
issues?




Lori Shepherd

Bioconductor Core Team

Roswell Park Comprehensive Cancer Center

Department of Biostatistics & Bioinformatics

Elm & Carlton Streets

Buffalo, New York 14263


From: rac...@intermine.org 
Sent: Thursday, April 15, 2021 6:40 AM
To: Kern, Lori 
Subject: Re: Bioconductor package InterMineR

Hi Lori,

Apologies for this.  I thought I had fixed a minor issue only to
introduce some more major errors.  I think I will need to go back to our
release 3.10 version so that we can then work on the errors now in the
3_12 version.  We had student work on this package but it seems we need
to fix a few things before we can submit their updates.

I have a question though - if I submit our 3.10 version to the
Bioconductor 3.12 release, should I sync with Bioconductor first? Or
would this re-introduce our current errors into our 3_10 version?

Many thanks,

Rachel.



On 2021-04-12 15:47, Kern, Lori wrote:
> The package has been failing since January. The package continues to
> fail.  This needs to be resolved to avoid deprecation.
>
> Lori Shepherd
>
> Bioconductor Core Team
>
> Roswell Park Comprehensive Cancer Center
>
> Department of Biostatistics & Bioinformatics
>
> Elm & Carlton Streets
>
> Buffalo, New York 14263
>
> -
>
> FROM: rac...@intermine.org 
> SENT: Friday, February 26, 2021 7:20 AM
> TO: Kern, Lori 
> SUBJECT: Re: Bioconductor package InterMineR
>
> Hi Lori,
>
> Apologies, this is taking a little longer than I anticipated to sort
> out
> - but please be assured that we are working towards fixing the problem
>
> and hope to have it resolved by the end of next week,
>
> Best wishes,
>
> Rachel.
>
> On 2021-02-08 16:16, Kern, Lori wrote:
>> We would like to bring to your attention that your package is
> failing
>> to build
>> or check on our release and devel build machines:
>>
>> Devel:
>> bioconductor.org/checkResults/devel/bioc-LATEST/InterMineR
>>
>> Release:
>> bioconductor.org/checkResults/release/bioc-LATEST/InterMineR
>>
>> Would you mind taking a look at this? Don't hesitate to ask on the
>> bioc-devel mailing list if you have any question or need help.
>>
>>  This is very problematic.   If no action is taken over the next few
>> weeks we will begin the deprecation process for your package.  Thank
>> you for your time and effort
>>
>> 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
>> 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.

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 
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