[Bioc-devel] New ExperimentHub resource and some related questions

2018-12-19 Thread Lu, Dongyi (Lambda) 
Hi everyone,

I’m writing a package (biocViews SinigleCell) that converts files of the BUS 
format (standing for Barcode, UMI, Set, see 
https://www.biorxiv.org/content/early/2018/11/21/472571) into a sparse matrix 
in R that can be used in Seurat and SingleCellExperiment. In order to write the 
examples and the vignette, I’m also putting the data itself into a package for 
ExperimentHub. The data used here are some mixed human and mouse cells from 
10x. Here are my questions:


  1.  In the documentation for `ExperimentHubData::makeExperimentHubMetadata`, 
the fields `RDataClass` and `DispatchClass` are required. However, this 
accompanying dataset package is meant to download text files (generated by 
command line tools outside R) to disk rather than into the R session, and it’s 
the job of the SingleCell package to converts the text files into a sparse 
matrix. There is a website documenting how the command line tools were used to 
generate the text files. So is this dataset still appropriate for ExperimentHub?
  2.  If it is appropriate, then what shall I put in `RDataClass` and 
`DispatchClass`?

Thanks,
Lambda

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Re: [Bioc-devel] Additional developer

2018-12-19 Thread Daniela Cassol 
Hi Nitesh,
Thank you very much.
I already have access to both packages.

Best,
Daniela

On Wed, Dec 19, 2018 at 8:55 AM Thomas Girke  wrote:

> Thanks a lot!
>
> On Wed, Dec 19, 2018 at 7:10 AM Turaga, Nitesh <
> nitesh.tur...@roswellpark.org> wrote:
>
> > Hi Thomas,
> >
> > Your group member should have access to the repo now.
> >
> > Hi Daniela,
> >
> > Please check the email danicas...@gmail.com, for details on how to log
> in
> > to BiocCredentials and activate your account.
> >
> > Best,
> >
> > Nitesh
> >
> > > On Dec 17, 2018, at 9:53 PM, Thomas Girke 
> wrote:
> > >
> > > Dear Nitesh,
> > >
> > > Could you please add a new developer to my BioC packages systemPipeR
> and
> > > systemPipeRdata to provide commit/push access for the corresponding git
> > > repositories on git.bioconductor.org. The person's name is Daniela
> > Cassol
> > > (new postdoc in my group) and her email is danicas...@gmail.com.
> > >
> > > Please let me know if you require anything else for this change.
> > >
> > > Thanks in advance for your help!
> > >
> > > Best,
> > >
> > > Thomas
> > >
> > >   [[alternative HTML version deleted]]
> > >
> > > ___
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> >
> >
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> or
> > agent responsible for the delivery of this message to the intended
> > recipient(s), you are hereby notified that any disclosure, copying,
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Re: [Bioc-devel] Additional developer

2018-12-19 Thread Thomas Girke 
Thanks a lot!

On Wed, Dec 19, 2018 at 7:10 AM Turaga, Nitesh <
nitesh.tur...@roswellpark.org> wrote:

> Hi Thomas,
>
> Your group member should have access to the repo now.
>
> Hi Daniela,
>
> Please check the email danicas...@gmail.com, for details on how to log in
> to BiocCredentials and activate your account.
>
> Best,
>
> Nitesh
>
> > On Dec 17, 2018, at 9:53 PM, Thomas Girke  wrote:
> >
> > Dear Nitesh,
> >
> > Could you please add a new developer to my BioC packages systemPipeR and
> > systemPipeRdata to provide commit/push access for the corresponding git
> > repositories on git.bioconductor.org. The person's name is Daniela
> Cassol
> > (new postdoc in my group) and her email is danicas...@gmail.com.
> >
> > Please let me know if you require anything else for this change.
> >
> > Thanks in advance for your help!
> >
> > Best,
> >
> > Thomas
> >
> >   [[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,
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>

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Re: [Bioc-devel] Additional developer

2018-12-19 Thread Turaga, Nitesh 
Hi Thomas,

Your group member should have access to the repo now. 

Hi Daniela,

Please check the email danicas...@gmail.com, for details on how to log in to 
BiocCredentials and activate your account.

Best,

Nitesh 

> On Dec 17, 2018, at 9:53 PM, Thomas Girke  wrote:
> 
> Dear Nitesh,
> 
> Could you please add a new developer to my BioC packages systemPipeR and
> systemPipeRdata to provide commit/push access for the corresponding git
> repositories on git.bioconductor.org. The person's name is Daniela Cassol
> (new postdoc in my group) and her email is danicas...@gmail.com.
> 
> Please let me know if you require anything else for this change.
> 
> Thanks in advance for your help!
> 
> Best,
> 
> Thomas
> 
>   [[alternative HTML version deleted]]
> 
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Re: [Bioc-devel] NEWS not updated on devel site

2018-12-19 Thread Obenchain, Valerie 
Kristoffer,

Thanks for the report. This has been fixed.

Valerie


On 12/14/18 4:09 AM, Shepherd, Lori wrote:
> We will look into the issue.  Thank you for making us aware.
> 
> 
> 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 Kristoffer 
> Vitting-Seerup 
> Sent: Friday, December 14, 2018 5:23:26 AM
> To: bioc-devel@r-project.org
> Subject: [Bioc-devel] NEWS not updated on devel site
> 
> I just noticed that on the devel site for my package
> 
> the NEWS file linked to in the "Documentation" tab (linking to this
> )
> is outdated. The current version of the package in devel is 1.5.3 but the
> NEWS tab refers to an older version (1.5.1). I checked by downloading the
> source files and the NEWS file there contain info about 1.5.3. Are the NEWS
> files parsed slower?
> 
> Kindest Regard
> Kristoffer
> 
>  [[alternative HTML version deleted]]
> 
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> This email message may contain legally privileged and/or confidential 
> information.  If you are not the intended recipient(s), or the employee or 
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Re: [Bioc-devel] Aliasing `]` breaks BiocCheck::BiocCheck() version 1.18.0

2018-12-19 Thread Tierney, Luke 
codetools already checks only closures in checkUsageENv and hande
checkUsagePackage, so this is anissue on the Bioc side.

Best,

luke

On Tue, 18 Dec 2018, Tierney, Luke wrote:

> Codetools should probably be ignoring those. Will have a look
>
> Sent from my iPhone
>
>> On Dec 18, 2018, at 6:54 AM, Shepherd, Lori  
>> wrote:
>>
>> Can you please open an issue for this so we don't lose track of it -
>>
>> https://github.com/Bioconductor/BiocCheck/issues
>>
>>
>>
>> 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 Shian Su 
>> 
>> Sent: Monday, December 17, 2018 8:34:10 PM
>> To: bioc-devel
>> Subject: [Bioc-devel] Aliasing `]` breaks BiocCheck::BiocCheck() version 
>> 1.18.0
>>
>> Hi all,
>>
>> If you put
>>
>> foo <- `[`
>>
>> Somewhere in a package, it will trigger
>>
>> Error in makeUsageCollector(fun, ...) : only works for closures
>>
>> In BiocCheck::BiocCheck() (version 1.18.0). This comes from
>>
>> if (typeof(fun) != "closure")
>>stop("only works for closures")
>>
>> In codetools::makeUsageCollector(), but
>>
>>> typeof(`[`)
>> ## "special"
>>
>> Not that it matters for my use-case because I had discovered magrittr???s 
>> extract alias, but it might be an edge case worth covering, especially since 
>> the error message is so cryptic.
>>
>> Kind regards,
>> Shian Su
>>
>> ___
>>
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-- 
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Ralph E. Wareham Professor of Mathematical Sciences
University of Iowa  Phone: 319-335-3386
Department of Statistics andFax:   319-335-3017
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