[Bioc-devel] Updated Deprecated Package List for Bioc 3.7
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
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 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 at r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel<https://urldefense.proofpoint.com/v2/url?u=https-3A__stat.ethz.ch_mailman_listinfo_bioc-2Ddevel&d=DwMFAg&c=mRWFL96tuqj9V0Jjj4h40ddo0XsmttALwKjAEOCyUjY&r=OdfcI7SrMMnS3DAUJULIgzR9ZFOeXSyzUMNqMKXj4yE&m=U_m_leinYsy4QmdwhzgtnqkLI0Nyqx3hADyGLrc9Qs0&s=MI8Wx4E5bER4kpsrf72qXRTElrE8aW8eFJl5WkhqkxY&e=> 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.