Bug#771154: plink: New major upstream version of plink
Hi Andreas, 2014-12-16 15:35 GMT+01:00 Andreas Tille andr...@an3as.eu: For this actual case I wonder whether plink2 would be a drop in replacement we can provide instead of the old pling (which means the interface is compatible and the test suite if there is any creates the same results) or whether you think plink and plink2 should be provided in parallel. I recommend to provide both versions of plink for the moment as the first version is always widely used and the interface is not completely compatible, some flags are not supported by the new version. The upstream recommends to use the old plink for these flags. Moreover, the new version is a major update (i.e. many algorithms changes) which could be problematic for replicate some previous results for those using old plink. I will push the new plink on git.debian. Best regards, Dylan
Bug#771154: plink: New major upstream version of plink
Hi Dylan, On Mon, Dec 22, 2014 at 09:51:06AM +0100, Dylan wrote: I recommend to provide both versions of plink for the moment as the first version is always widely used and the interface is not completely compatible, some flags are not supported by the new version. The upstream recommends to use the old plink for these flags. Moreover, the new version is a major update (i.e. many algorithms changes) which could be problematic for replicate some previous results for those using old plink. I will push the new plink on git.debian. Fine. Just post on the list once it is ready for sponsering. Please keep on with your good work to package software for Debian Med Andreas. -- http://fam-tille.de -- To UNSUBSCRIBE, email to debian-bugs-dist-requ...@lists.debian.org with a subject of unsubscribe. Trouble? Contact listmas...@lists.debian.org
Bug#771154: [Debian-med-packaging] Bug#771154: plink: New major upstream version of plink
Much in support of Dylan, please also think about the binary filename of the executable. We had the unfortunate p-link for Version 1 to avoid a clash with one of the putty tools. This was a mistake at the time imho. Shall we correct for that? Or is upstream already defaulting to plink2? This would then give us p-link and plink2 as executables. Hurts. Cheers, Steffen -- Sent from my Android phone with GMX Mail. Please excuse my brevity.Dylan bob.dyb...@gmail.com wrote: Hi Andreas, 2014-12-16 15:35 GMT+01:00 Andreas Tille andr...@an3as.eu: For this actual case I wonder whether plink2 would be a drop in replacement we can provide instead of the old pling (which means the interface is compatible and the test suite if there is any creates the same results) or whether you think plink and plink2 should be provided in parallel. I recommend to provide both versions of plink for the moment as the first version is always widely used and the interface is not completely compatible, some flags are not supported by the new version. The upstream recommends to use the old plink for these flags. Moreover, the new version is a major update (i.e. many algorithms changes) which could be problematic for replicate some previous results for those using old plink. I will push the new plink on git.debian. Best regards, Dylan ___ Debian-med-packaging mailing list debian-med-packag...@lists.alioth.debian.org http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-packaging -- To UNSUBSCRIBE, email to debian-bugs-dist-requ...@lists.debian.org with a subject of "unsubscribe". Trouble? Contact listmas...@lists.debian.org
Bug#771154: [Debian-med-packaging] Bug#771154: plink: New major upstream version of plink
Hi Steffen, 2014-12-22 10:22 GMT+01:00 Steffen Möller steffen_moel...@gmx.de: Much in support of Dylan, please also think about the binary filename of the executable. We had the unfortunate p-link for Version 1 to avoid a clash with one of the putty tools. This was a mistake at the time imho. Shall we correct for that? Or is upstream already defaulting to plink2? This would then give us p-link and plink2 as executables. Hurts. The upstream devs always name the new binary plink but they recommend to rename it to plink2 and the old plink to plink1 to avoid the name conflict. So, I rename the binary plink2 for the new version and maybe we can also rename the first plink from p-link to plink1 with a symbolic link to p-link to avoid problem for our users which already use the name p-link. What do you think? Best regards, Dylan
Bug#771154: Plink2 (Was: Bug#771154: plink: New major upstream version of plink)
Hi, On Mon, Dec 22, 2014 at 10:45:12AM +0100, Dylan wrote: Hi Steffen, 2014-12-22 10:22 GMT+01:00 Steffen Möller steffen_moel...@gmx.de: Much in support of Dylan, please also think about the binary filename of the executable. We had the unfortunate p-link for Version 1 to avoid a clash with one of the putty tools. This was a mistake at the time imho. Shall we correct for that? Or is upstream already defaulting to plink2? This would then give us p-link and plink2 as executables. Hurts. The upstream devs always name the new binary plink but they recommend to rename it to plink2 and the old plink to plink1 to avoid the name conflict. So, I rename the binary plink2 for the new version and maybe we can also rename the first plink from p-link to plink1 with a symbolic link to p-link to avoid problem for our users which already use the name p-link. What do you think? Sounds good. In addition I would recommend to teach upstream again about the name clash with putty tools. Kind regards Andreas. -- http://fam-tille.de -- To UNSUBSCRIBE, email to debian-bugs-dist-requ...@lists.debian.org with a subject of unsubscribe. Trouble? Contact listmas...@lists.debian.org
Bug#771154: plink: New major upstream version of plink
Hi Bob On Thu, Nov 27, 2014 at 08:31:29AM +0100, Bob Dybian wrote: Package: plink Severity: wishlist Dear Maintainer, Plink2 [1] was just presented at the annual meeting of the American Society of Human Genetics 2014 [2]. Plink2 is a comprehensive update of plink with new algorithms and new methods, faster and less memory consumer than the first plink. As it was not totally compatible with first plink [1], I propose to create a new package to permit the cohabitation of these two versions (like for bowtie and bowtie2). If you agree, I will submit it [3] on Alioth. In case you might wait for a confirmation and wondering why nobody is sending one: Usually there is no reason at all to stop anybody from working so you can simply enject your packaging without asking. Just ping the list if you need a sponsor. For this actual case I wonder whether plink2 would be a drop in replacement we can provide instead of the old pling (which means the interface is compatible and the test suite if there is any creates the same results) or whether you think plink and plink2 should be provided in parallel. Kind regards and thanks for your work on this Andreas. -- http://fam-tille.de -- To UNSUBSCRIBE, email to debian-bugs-dist-requ...@lists.debian.org with a subject of unsubscribe. Trouble? Contact listmas...@lists.debian.org
Bug#771154: plink: New major upstream version of plink
Package: plink Severity: wishlist Dear Maintainer, Plink2 [1] was just presented at the annual meeting of the American Society of Human Genetics 2014 [2]. Plink2 is a comprehensive update of plink with new algorithms and new methods, faster and less memory consumer than the first plink. As it was not totally compatible with first plink [1], I propose to create a new package to permit the cohabitation of these two versions (like for bowtie and bowtie2). If you agree, I will submit it [3] on Alioth. Best regards, Dylan [1] https://www.cog-genomics.org/plink2/ [2] https://www.cog-genomics.org/static/pdf/plink2-ashg.pdf [3] https://bitbucket.org/Dybian/package-debian-plink2 -- System Information: Debian Release: 7.7 APT prefers stable-updates APT policy: (500, 'stable-updates'), (500, 'stable') Architecture: amd64 (x86_64) Kernel: Linux 3.2.0-4-amd64 (SMP w/2 CPU cores) Locale: LANG=fr_FR.utf8, LC_CTYPE=fr_FR.utf8 (charmap=UTF-8) Shell: /bin/sh linked to /bin/dash -- To UNSUBSCRIBE, email to debian-bugs-dist-requ...@lists.debian.org with a subject of unsubscribe. Trouble? Contact listmas...@lists.debian.org
