[Bioc-devel] Updated Deprecated Package List for Bioc 3.7

Mon Mar 26 15:49:24 CEST 2018

Hi Lori,

I have worked through the ToPASeq package.

1. The package implements an extended range of operations for the 'Pathway' class (defined in the graphite package).

I am currently in contact with the author of the graphite package, Gabriele Sales, whether these operations are generally useful for the class and could be accordingly moved to the graphite package.

2. The implementations of the pathway enrichment methods SPIA, DEGraph, and TopologyGSA are redundant with existing functionality in Bioconductor and will be accordingly delegated to corresponding implementations in the graphite and EnrichmentBrowser package. The core of the package that I will maintain further are the implementations of the pathway enrichment methods PRS, PWEA and TAPPA, which seem to be unique to the package.

3. Parallel computation will be reworked to be based on BiocParallel, thereby resolving the package's current platform dependence (linux-only).

I have  required access rights, have set up a github repo under lgeistlinger/ToPASeq, and I am optimistic to have a working version ready in devel in agreement with the respective deadline of the release schedule (Wed, April 25,

Deadline for packages passing ��R CMD build�� and ��R CMD check�� without errors or warnings).

Best,

Ludwig

--
Dr. Ludwig Geistlinger
CUNY School of Public Health
________________________________
From: Shepherd, Lori <Lori.Shepherd at RoswellPark.org>
Sent: Monday, March 26, 2018 8:07 AM
To: Ludwig Geistlinger
Subject: Re: [Bioc-devel] Updated Deprecated Package List for Bioc 3.7

Hi Ludwig,

I just wanted to touch base and make sure you had the access rights to ToPASeq.  The release is scheduled

for next month http://bioconductor.org/developers/release-schedule/<https://urldefense.proofpoint.com/v2/url?u=http-3A__bioconductor.org_developers_release-2Dschedule_&d=DwMFAg&c=mRWFL96tuqj9V0Jjj4h40ddo0XsmttALwKjAEOCyUjY&r=OdfcI7SrMMnS3DAUJULIgzR9ZFOeXSyzUMNqMKXj4yE&m=A6USjX0wMQjoU6_viKxatj3j6gq2X7SCNrkkK-6gGRA&s=aaqpSz33LI5XkpuV6t-9hktb7ikL64-9vt9lybZgr60&e=>  and I was curious as to your estimated time frame for looking at fixing the ERRORs in the package?

Cheers,

Lori Shepherd

Bioconductor Core Team

Roswell Park Cancer Institute

Department of Biostatistics & Bioinformatics

Elm & Carlton Streets

Buffalo, New York 14263

________________________________
From: Ludwig Geistlinger <Ludwig.Geistlinger at sph.cuny.edu>
Sent: Saturday, March 3, 2018 5:51:10 PM
To: Shepherd, Lori; Martin Morgan
Subject: Re: [Bioc-devel] Updated Deprecated Package List for Bioc 3.7

Hi Lori,

Yes I would take over maintenance.

Anything particular that I need to take care of?

Otherwise I would just follow:

https://bioconductor.org/developers/how-to/git/maintain-github-bioc/<https://urldefense.proofpoint.com/v2/url?u=https-3A__bioconductor.org_developers_how-2Dto_git_maintain-2Dgithub-2Dbioc_&d=DwMFAg&c=mRWFL96tuqj9V0Jjj4h40ddo0XsmttALwKjAEOCyUjY&r=OdfcI7SrMMnS3DAUJULIgzR9ZFOeXSyzUMNqMKXj4yE&m=A6USjX0wMQjoU6_viKxatj3j6gq2X7SCNrkkK-6gGRA&s=5Fgho__A-8_HMECEdkVGInWgNTMX6sweJl1aUrtpPGo&e=>

to accordingly set this up.

Thanks,

Ludwig

--
Dr. Ludwig Geistlinger
CUNY School of Public Health
________________________________
From: Shepherd, Lori <Lori.Shepherd at RoswellPark.org>
Sent: Saturday, March 3, 2018 5:14 PM
To: Ludwig Geistlinger; Martin Morgan
Subject: Re: [Bioc-devel] Updated Deprecated Package List for Bioc 3.7

Hi Ludwig,

Were you still interested in taking over maintainership of ToPaSeq?  We have switched permission and you should have access now.  If you are no longer interested please let us know.

Lori Shepherd

Bioconductor Core Team

Roswell Park Cancer Institute

Department of Biostatistics & Bioinformatics

Elm & Carlton Streets

Buffalo, New York 14263

________________________________
From: Ludwig Geistlinger <Ludwig.Geistlinger at sph.cuny.edu>
Sent: Friday, December 15, 2017 1:05:16 PM
To: Shepherd, Lori; Martin Morgan
Subject: Re: [Bioc-devel] Updated Deprecated Package List for Bioc 3.7

Hi Lori,

I would be willing to take over maintenance of

ToPASeq

in case maintainers remain unresponsive.

Best,
Ludwig

--
Dr. Ludwig Geistlinger
CUNY School of Public Health

________________________________________
From: Bioc-devel <bioc-devel-bounces at r-project.org> on behalf of Shepherd, Lori <Lori.Shepherd at RoswellPark.org>
Sent: Friday, December 15, 2017 9:29 AM
To: Martin Morgan
Subject: [Bioc-devel] Updated Deprecated Package List for Bioc 3.7

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 list will be updated monthly.

The current list of deprecated packages is as follows:

Maintainer requested deprecation:

Software Package:
ontoCAT

Experiment Data Package:
RnaSeqTutorial
cheung2010

Unresponsive/not-maintained packages:

Software:
GMRP
MBttest
OperaMate
ToPASeq

Lori Shepherd

Bioconductor Core Team

Roswell Park Cancer Institute

Department of Biostatistics & Bioinformatics

Elm & Carlton Streets

Buffalo, New York 14263

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