Re: [Bioc-devel] EXTERNAL: Re: List of Deprecated Packages Bioc 3.11
Great, thanks for the update! From: Interdonato, Kayla Sent: Thursday, February 27, 2020 2:40 PM To: Ludwig Geistlinger; bioc-devel@r-project.org Subject: Re: EXTERNAL: Re: [Bioc-devel] List of Deprecated Packages Bioc 3.11 When generating this annotation package, we believed the data we were downloading was stale which is why we chose to deprecate it. Upon seeing the deprecation list email, a user informed us of a different location where the data may be more up to date. We are currently working through our annotation pipeline with the new data to be sure we can generate all the information needed in the org.At.tair.db package. Once we have finished this pipeline and compared, we will determine if the package should in fact be deprecated and if so, what will the supplement be. Best, Kayla On 2/27/20, 1:24 PM, "Bioc-devel on behalf of Ludwig Geistlinger" wrote: Why will org.At.tair.db be deprecated and by what will it be replaced? It's the org package for Arabidopsis and thus central for gene ID mapping when working with Arabidopsis data ... Thanks, Ludwig -- Dr. Ludwig Geistlinger Department of Epidemiology and Biostatistics CUNY School of Public Health New York, NY 10027 From: Bioc-devel on behalf of Shepherd, Lori Sent: Thursday, February 27, 2020 12:32 PM To: bioc-devel@r-project.org Subject: [Bioc-devel] List of Deprecated Packages Bioc 3.11 ***ATTENTION: This email came from an external source. Do not open attachments or click on links from unknown senders or unexpected emails.*** 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 for Bioc 3.11 is as follows: Maintainer requested deprecation: Software: QUALIFIER motifRG triform CVE proteoQC affypdnn splicegear Genominator IdMappingAnalysis IdMappingRetrieval manta RefNet AnalysisPageServer scfind kimod plw Annotation: org.At.tair.db hom.At.inp.db hom.Ce.inp.db hom.Dm.inp.db hom.Dr.inp.db hom.Hs.inp.db hom.Mm.inp.db hom.Rn.inp.db hom.Sc.inp.db KEGG.db (use KEGGREST instead) Unresponsive/not-maintained packages: Software: SELEX CTDquerier MTseeker readat anamiR MEAL BiSeq CALIB cellGrowth chroGPS DEDS LVSmiRNA MANOR MCRestimate nem PAPi pcaGoPromoter pint RIPSeeker SANTA waveTiling BayesPeak RCAS bgafun lol M3D MergeMaid ExpermentData: MTseekerData RIPSeekerData The follow Annotation packages were deprecated in 3.10 and removed from 3.11 but not previously announced. MafDb.ESP6500SI.V2.SSA137.hs37d5 MafDb.EXP6500SI.V2.SSA137.GRCh38 It should be noted, we did try to reach out to these package maintainers multiple times and they were either unresponsive or had emails bounce. We encourage anyone that is familiar with a package maintainer on this list to reach out to them and notify them directly. Packages can be un-deprecated if a maintainer fixes the package to build/check cleanly before the next release and requests un-deprecation on the bioc-devel@r-project.org mailing list. We will be sending 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. Thank you 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. [[alternative HTML version deleted]] ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel ___ 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 responsibl
Re: [Bioc-devel] EXTERNAL: Re: List of Deprecated Packages Bioc 3.11
When generating this annotation package, we believed the data we were downloading was stale which is why we chose to deprecate it. Upon seeing the deprecation list email, a user informed us of a different location where the data may be more up to date. We are currently working through our annotation pipeline with the new data to be sure we can generate all the information needed in the org.At.tair.db package. Once we have finished this pipeline and compared, we will determine if the package should in fact be deprecated and if so, what will the supplement be. Best, Kayla On 2/27/20, 1:24 PM, "Bioc-devel on behalf of Ludwig Geistlinger" wrote: Why will org.At.tair.db be deprecated and by what will it be replaced? It's the org package for Arabidopsis and thus central for gene ID mapping when working with Arabidopsis data ... Thanks, Ludwig -- Dr. Ludwig Geistlinger Department of Epidemiology and Biostatistics CUNY School of Public Health New York, NY 10027 From: Bioc-devel on behalf of Shepherd, Lori Sent: Thursday, February 27, 2020 12:32 PM To: bioc-devel@r-project.org Subject: [Bioc-devel] List of Deprecated Packages Bioc 3.11 ***ATTENTION: This email came from an external source. Do not open attachments or click on links from unknown senders or unexpected emails.*** 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 for Bioc 3.11 is as follows: Maintainer requested deprecation: Software: QUALIFIER motifRG triform CVE proteoQC affypdnn splicegear Genominator IdMappingAnalysis IdMappingRetrieval manta RefNet AnalysisPageServer scfind kimod plw Annotation: org.At.tair.db hom.At.inp.db hom.Ce.inp.db hom.Dm.inp.db hom.Dr.inp.db hom.Hs.inp.db hom.Mm.inp.db hom.Rn.inp.db hom.Sc.inp.db KEGG.db (use KEGGREST instead) Unresponsive/not-maintained packages: Software: SELEX CTDquerier MTseeker readat anamiR MEAL BiSeq CALIB cellGrowth chroGPS DEDS LVSmiRNA MANOR MCRestimate nem PAPi pcaGoPromoter pint RIPSeeker SANTA waveTiling BayesPeak RCAS bgafun lol M3D MergeMaid ExpermentData: MTseekerData RIPSeekerData The follow Annotation packages were deprecated in 3.10 and removed from 3.11 but not previously announced. MafDb.ESP6500SI.V2.SSA137.hs37d5 MafDb.EXP6500SI.V2.SSA137.GRCh38 It should be noted, we did try to reach out to these package maintainers multiple times and they were either unresponsive or had emails bounce. We encourage anyone that is familiar with a package maintainer on this list to reach out to them and notify them directly. Packages can be un-deprecated if a maintainer fixes the package to build/check cleanly before the next release and requests un-deprecation on the bioc-devel@r-project.org mailing list. We will be sending 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. Thank you 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. [[alternative HTML version deleted]] ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel ___ 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, distribution, or
