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rgentleman ★ 5.5k
@rgentleman-7725
Last seen 9.0 years ago
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Well that took less time than I thought. We have started to get subscription requests for the mailing list and we need to deal with how to handle contributed libraries. My proposal is to set up a discussion mailing list (that we all subscribe to) for Bioconductor. I don't think that we have anything to discuss yet -- which is a problem. We have had four requests to join all with .de suffixes but there will be more. Any other ideas? Next, libraries. I am hoping to have our new programmer (starting in Jan) learn how to test libraries and to handle all submissions (by doing some simple testing and then add them to a site like CRAN). Do we want to develop and start to populate the site now with the proviso that we will put in more stringent tests later? The reason for this is to gain some momentum and hopefully to find some more people who might be willing to do some of the organizational work that will be needed. Fritz/Kurt: is it feasible to set up a web page for bioconductor off of CRAN using mainly the existing structure and to populate it with unvetted software. I expect that the new programmer will be able to take this over in late January. So it would be the initial setup and population that would be required. Organization: - we need someone (volunteers please take a giant step forward) to organize some mechanism for keeping track of what we are doing and what other people are doing regarding building libraries. - it would be nice to have some place where one can see what sorts of projects are being done so that collaboration etc can go on. - perhaps a Wiki type interface? thanks robert -- +--------------------------------------------------------------------- ------+ | Robert Gentleman phone : (617) 632-5250 | | Associate Professor fax: (617) 632-2444 | | Department of Biostatistics office: M1B28 | Harvard School of Public Health email: rgentlem@jimmy.dfci.harvard.edu | +--------------------------------------------------------------------- ------+
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@vincent-j-carey-jr-4
Last seen 5 weeks ago
United States
> > My proposal is to set up a discussion mailing list (that we all > subscribe to) for Bioconductor. I don't think that we have anything to i take it that mailing to bioconductor@stat.math.ethz.ch constitutes even at this point a discussion mailing list an open question is how to structure the communications system. bioconductor-core is necessary for continuing threads like this one. bioconductor-help, bioconductor-devel also seem to make sense. > discuss yet -- which is a problem. We have had four requests to join i think we have a fair amount to discuss as core, and those who are non-core may want to describe their concerns. probably not too early to start, but a bit too early to publicize very widely > all with .de suffixes but there will be more. > Any other ideas? > > Next, libraries. I am hoping to have our new programmer (starting in > Jan) learn how to test libraries and to handle all submissions (by > doing some simple testing and then add them to a site like CRAN). > Do we want to develop and start to populate the site now with the > proviso that we will put in more stringent tests later? > The reason for this is to gain some momentum and hopefully to find > some more people who might be willing to do some of the organizational > work that will be needed. i am in favor of deployment soon. i will be working on getting test-functionality equivalent to Biobase. pointers on how to get there would be worth writing down. > > Fritz/Kurt: is it feasible to set up a web page for bioconductor off > of CRAN using mainly the existing structure and to populate it with > unvetted software. I expect that the new programmer will be able to > take this over in late January. So it would be the initial setup and > population that would be required. i hope this is possible, otherwise we need to get sourceforge or anoncvs running locally. i would put some effort into that if i knew that ad hoc security considerations would not lay that effort to waste at some arbitrary future time > > Organization: > - we need someone (volunteers please take a giant step forward) to > organize some mechanism for keeping track of what we are doing and > what other people are doing regarding building libraries. http://biowww.dfci.harvard.edu/~bioconductor/ already has a little bit in this regard. we need to distinguish between internal core-level tracking that can be used for strategizing and evaluation and public tracking that is a public service and agenda publicity i am happy to put core-generated changes into the aforementioned web page on short notice. > - it would be nice to have some place where one can see what sorts > of projects are being done so that collaboration etc can go on. > - perhaps a Wiki type interface? this depends upon security. i will install zope if i can get a publicly accessible port 8080. but perhaps that is overkill for a wiki if that is all we really want. robert's email is generated from bioconductor-admin, but i made the reply to bioconductor to reach the core. please advise if changes to my mailing strategy are desired. vince
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>>>>> "Vincent" == Vincent J Carey, <stvjc@channing.harvard.edu> writes: ............ Vincent> robert's email is generated from Vincent> bioconductor-admin, but i made the reply to Vincent> bioconductor to reach the core. please advise if Vincent> changes to my mailing strategy are desired. The mails from both mailman (like this) or majordomo (like the usual R lists) come with a From: <you, the="" poster=""> Sender: <listname>-admin@.... {"-admin" for mailman / "-owner" for majordomo} To: <listname> @.... (and several other headers, in particular, mailman has half a dozen of "List-*: <url>" headers.) A reply or followup of any decent MUA (mail user agent) should produce a To: <him, the="" poster=""> @ .. CC: <listname> @ .. where it may depend which is To and which (or if there) is CC. Yes, there are bad pieces of software who do reply to "admin"/"owner". Yes, they are a real pain, particularly when I am the admin/owner :-) Martin
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>>>>> "Vincent" == Vincent J Carey, <stvjc@channing.harvard.edu> writes: >> My proposal is to set up a discussion mailing list (that >> we all subscribe to) for Bioconductor. I don't think that >> we have anything to Vincent> i take it that mailing to Vincent> bioconductor@stat.math.ethz.ch constitutes even at Vincent> this point a discussion mailing list Vincent> an open question is how to structure the Vincent> communications system. bioconductor-core is Vincent> necessary for continuing threads like this one. Vincent> bioconductor-help, bioconductor-devel also seem to Vincent> make sense. I would propose to change this (current group) to "bioconductor-core" -- which I would propose to call "biocore" (the the other being too long for my taste). and make "bioconductor" a new (currently only) public list. >> discuss yet -- which is a problem. We have had four >> requests to join Vincent> i think we have a fair amount to discuss as core, Vincent> and those who are non-core may want to describe Vincent> their concerns. probably not too early to start, Vincent> but a bit too early to publicize very widely >> all with .de suffixes but there will be more. Any other >> ideas? >> Next, libraries. I am hoping to have our new programmer ^^^^^^^^^ the word is really "packages" A library is either a *.so, *.dll, *.a (etc) file or one of the [lib.loc] directories where packages are located >> (starting in Jan) learn how to test libraries and to >> handle all submissions (by doing some simple testing and >> then add them to a site like CRAN). Do we want to >> develop and start to populate the site now with the >> proviso that we will put in more stringent tests later? >> The reason for this is to gain some momentum and >> hopefully to find some more people who might be willing >> to do some of the organizational work that will be >> needed. Vincent> i am in favor of deployment soon. i will be Vincent> working on getting test-functionality equivalent to Vincent> Biobase. pointers on how to get there would be Vincent> worth writing down. >> Fritz/Kurt: is it feasible to set up a web page for >> bioconductor off of CRAN using mainly the existing >> structure and to populate it with unvetted software. I >> expect that the new programmer will be able to take this >> over in late January. So it would be the initial setup >> and population that would be required. Vincent> i hope this is possible, otherwise we need to get Vincent> sourceforge or anoncvs running locally. i would Vincent> put some effort into that if i knew that ad hoc Vincent> security considerations would not lay that effort Vincent> to waste at some arbitrary future time >> Organization: - we need someone (volunteers please take >> a giant step forward) to organize some mechanism for >> keeping track of what we are doing and what other people >> are doing regarding building packages Vincent> http://biowww.dfci.harvard.edu/~bioconductor/ Vincent> already has a little bit in this regard. we need Vincent> to distinguish between internal core-level tracking Vincent> that can be used for strategizing and evaluation Vincent> and public tracking that is a public service and Vincent> agenda publicity Vincent> i am happy to put core-generated changes into the Vincent> aforementioned web page on short notice. thank you. However, this should eventually move to www.bioconductor.org, right? <....> Martin
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>>>>> "MM" == Martin Maechler <maechler@stat.math.ethz.ch> writes: >>>>> "Vincent" == Vincent J Carey, <stvjc@channing.harvard.edu> writes: >>> My proposal is to set up a discussion mailing list (that >>> we all subscribe to) for Bioconductor. I don't think >>> that we have anything to Vincent> i take it that mailing to Vincent> bioconductor@stat.math.ethz.ch constitutes even at Vincent> this point a discussion mailing list Vincent> an open question is how to structure the Vincent> communications system. bioconductor-core is Vincent> necessary for continuing threads like this one. Vincent> bioconductor-help, bioconductor-devel also seem to Vincent> make sense. MM> I would propose to change this (current group) to MM> "bioconductor-core" -- which I would propose to call MM> "biocore" (the the other being too long for my taste). MM> and make "bioconductor" a new (currently only) public MM> list. which -- after nodding from Robert -- I'm about to implement. Bioconductor := Public Mailing List for Discussion about the Bioconductor Project and its pieces of Software. Biocore := "Bioconductor Core Development Group" So, actually, I'd appreciate if you guys could stop posting for a while to both "bioconductor" and "biocore", and later post to "biocore" only for `internal discussion'. I'll have you all subscribed to both biocore and bioconductor and will add the other interested people to bioconductor only. I'll also move the archives which is a bit tricky, and that's why I'd appreciate a two hour (or so) complete silence break. (Next time think more in advance, Martin!) Martin Martin Maechler <maechler@stat.math.ethz.ch> http://stat.ethz.ch/~maechler/ Seminar fuer Statistik, ETH-Zentrum LEO C16 Leonhardstr. 27 ETH (Federal Inst. Technology) 8092 Zurich SWITZERLAND phone: x-41-1-632-3408 fax: ...-1228 <><
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We now have have two mailing lists for the bioconductor project (which is ``in construction''). The bioconductor project has been `opened' by two nice guys from Harvard, Robert Gentleman and Vincent Carey, and also runs under the heading Bioconductor : R-based software for bioinformatics I currently am just the person who helped setting up the mailing lists. There's currently a very innofficial website with notes from Vincent at http://biowww.dfci.harvard.edu/~bioconductor/ Whereas the mailing list for the "BioC. core developer group" was formed 2 days ago, we (I) only later realized that we should have created a public list for the same project simultaneously which I now have done. Bioconductor := Public Mailing List for Discussion about the Bioconductor Project and its pieces of Software. Biocore := "Bioconductor Core Development Group" However, since things are too much in a state of construction, please do not yet advertize any of these two groups but rather postpone this for a few weeks! Both Robert and I have full ``List Admin'' priviledges. Note however that for the public "Bioconductor" List, users can do everything themselves (by the passwords that you all should have received in an automatic welcome message), and the archives are completely open to the world -- both of which is *not* the case for the `private-only' biocore list. Yours, list administrator, Martin Maechler <maechler@stat.math.ethz.ch> http://stat.ethz.ch/~maechler/ Seminar fuer Statistik, ETH-Zentrum LEO C16 Leonhardstr. 27 ETH (Federal Inst. Technology) 8092 Zurich SWITZERLAND phone: x-41-1-632-3408 fax: ...-1228 <><
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@friedrichleischcituwienacat-7
Last seen 9.6 years ago
>>>>> On Tue, 27 Nov 2001 09:24:21 -0500, >>>>> Robert Gentleman (RG) wrote: > Well that took less time than I thought. > We have started to get subscription requests for the mailing list and > we need to deal with how to handle contributed libraries. > My proposal is to set up a discussion mailing list (that we all > subscribe to) for Bioconductor. I don't think that we have anything to > discuss yet -- which is a problem. We have had four requests to join > all with .de suffixes but there will be more. > Any other ideas? > Next, libraries. I am hoping to have our new programmer (starting in > Jan) learn how to test libraries and to handle all submissions (by > doing some simple testing and then add them to a site like CRAN). > Do we want to develop and start to populate the site now with the > proviso that we will put in more stringent tests later? > The reason for this is to gain some momentum and hopefully to find > some more people who might be willing to do some of the organizational > work that will be needed. > Fritz/Kurt: is it feasible to set up a web page for bioconductor off > of CRAN using mainly the existing structure and to populate it with > unvetted software. I expect that the new programmer will be able to > take this over in late January. So it would be the initial setup and > population that would be required. Is OK, but I'll probably not find time within the next 2 weeks for that. christmas break (for students) starts on dec. 17, then I'll have more time. best, fritz

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