Re: [Bioc-devel] Final List of Deprecated Packages for Bioc3.10

[Ludwig Geistlinger]

Thanks Nitesh.

I ported the fix and the package builds fine - besides the deprecation warning:

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

Best,
Ludwig


From: Turaga, Nitesh 
Sent: Thursday, December 19, 2019 2:12 PM
To: Shepherd, Lori
Cc: Ludwig Geistlinger; bioc-devel@r-project.org
Subject: Re: [Bioc-devel] Final List of Deprecated Packages for Bioc3.10

Hi Ludwig,

Thank you for volunteering to take over as maintainer for PathNet and 
PathNetData.

You should now have access to both packages as the maintainer. They should show 
up on the build machine tomorrow.

You should port your fix(s) to the build machine for the PathNet package when 
you can and see if it is fixed on the devel builder.


Best regards,

 Nitesh

> On Dec 4, 2019, at 1:54 PM, Shepherd, Lori  
> wrote:
>
> We will start the process and be in touch off the bioc mailing list.
>
> We would require you officially take over as maintainer as all bioconductor 
> packages require an active maintainer.  PathNet was failing and we reached 
> out (several times) and deemed the package orphaned as we never heard back 
> from the currently listed maintainer.
>
> Cheers,
>
>
> Lori Shepherd
>
> Bioconductor Core Team
>
> Roswell Park Comprehensive Cancer Center
>
> Department of Biostatistics & Bioinformatics
>
> Elm & Carlton Streets
>
> Buffalo, New York 14263
>
> 
> From: Ludwig Geistlinger 
> Sent: Wednesday, December 4, 2019 1:32 PM
> To: Shepherd, Lori ; bioc-devel@r-project.org 
> 
> Subject: Re: Final List of Deprecated Packages for Bioc3.10
>
>
> Yes, I could do that if needed.
>
> 
> From: Shepherd, Lori 
> Sent: Wednesday, December 4, 2019 1:28 PM
> To: Ludwig Geistlinger; bioc-devel@r-project.org
> Subject: Re: Final List of Deprecated Packages for Bioc3.10
>
> ***ATTENTION: This email came from an external source. Do not open 
> attachments or click on links from unknown senders or unexpected emails.***
>
> Are you volunteering to permanently take over as maintainer of this package?
>
>
>
> Lori Shepherd
>
> Bioconductor Core Team
>
> Roswell Park Comprehensive Cancer Center
>
> Department of Biostatistics & Bioinformatics
>
> Elm & Carlton Streets
>
> Buffalo, New York 14263
>
> 
> From: Ludwig Geistlinger 
> Sent: Wednesday, December 4, 2019 1:22 PM
> To: Shepherd, Lori ; bioc-devel@r-project.org 
> 
> Subject: Re: Final List of Deprecated Packages for Bioc3.10
>
> Hi Lori,
>
> Is it possible to undeprecate the "PathNet" package?
> I just checked, the problem is a failing unit test, causing the otherwise 
> well working package to fail R CMD check.
>
> I fixed this here on a local clone of 
> https://git.bioconductor.org/packages/PathNet
>  and could push these minor changes if granted access.
>
> The PathNet package implements a solid network-based enrichment method and 
> the corresponding paper has some 50 citations - it would thus be unfortunate 
> to see it gone.
>
> Thanks,
> Ludwig
>
>
> 
> From: Bioc-devel  on behalf of Shepherd, 
> Lori 
> Sent: Monday, October 7, 2019 9:41 AM
> To: bioc-devel@r-project.org
> Subject: [Bioc-devel] Final List of Deprecated Packages for Bioc3.10
>
> The Bioconductor Team is continuing to identify packages that will be 
> deprecated in the next release to allow for the Bioconductor community to 
> respond accordingly.
>
> The final list for the 3.10 release is as follows:
>
> Maintainer requested deprecation:
>
> Software:
>
> SNPchip
> GenomeGraphs
> HTSanalyzeR
> Rchemcpp
> charm
> Pbase
>
>
> Experiment Data Package:
>
> charmData
>
>
>
> Unresponsive/not-maintained packages:
>
> Software:
>
> dSimer
> flipflop
> exomePeak
> CNPBayes
> brainImageR
> plateCore
> rHVDM
> SEPA
> condcomp
> PathNet
> scone
> birte
> mlm4omics
> RnaSeqSampleSize
>
>
> Experiment Data Package:
>
> facopy.annot
> allenpvc
>
>
> Renaming The package CAMTHC is marked for deprecation. This package has been 
> renamed to debCAM
>
>
>
> The following Annotation Packages have been user requested deprecated:
>
> MafDb.gnomADex.r2.0.1.GRCh38
> MafDb.gnomAD.r2.0.1.GRCh38
> MafDb.gnomADex.r2.0.1.hs37d5
> MafDb.gnomAD.r2.0.1.hs37d5
> They are replaced with
>
> MafDb.gnomADex.r2.1.GRCh38
> MafDb.gnomAD.r2.1.GRCh38
> MafDb.gnomADex.r2.1.hs37d5
> MafDb.gnomAD.r2.1.hs37d5
>
>
> The Bioconductor team will continue to send emails out to packages that have 
> been broken across all platforms for an extended period of time as those are 
> packages that are up for immediate deprecation if not corrected in a timely 
> fashion. Packages that are ERRORing and not fixed 

[Bioc-devel] bsapply and vcountPattern: sapply -> bplapply

[Bhagwat, Aditya]

Dear Herve & co,

Wish you a happy new year :-).

I am optimizing code that calls BSgenome::vcountPDict.
BSgenome::vcountPDict calls bsapply, which calls sapply.

Could this sapply be replaced by a bplapply instead - that would turn all the 
vcount, vmatch, etc operations into parallellized operations, by just a minimal 
intervention (sapply -> bplapply).

Or is there a reason why this was not done, or perhaps is there an alternative 
paradigm which you use for speeding up things?

Aditya

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