Two bioinformatics conferences in Sydney in July

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Gordon Smyth 52k

@gordon-smyth

Last seen 12 hours ago

WEHI, Melbourne, Australia

This is just a heads-up re two statistical bioinformatics related conferences in Sydney in the first and second weeks of July this year that might be of interest to users of Bioconductor software. The first is The Australian Mathematical Sciences Institute Symposium, "Recent Advances in Biostatistics, Bioinformatics and Markov Chain Monte Carlo", see http://web.maths.unsw.edu.au/~scott/symposium. The second is 20th International Workshop on Statistical Modelling "Statistical Solutions To Modern Problems", see http://www.uws.edu.au/iwsm2005 IWSM 2005 is not a specifically bioinformatics conference but has statistical genomics and gene expression as major themes this year. Abstracts are due for IWSM 2005 on January 31. There will be talks on microarray analysis at both conferences (research talks rather than tutorials). I have a vague memory that the dates may overlap with a planned R/Bioconductor workshop in Seattle, but I can't find any info on this on the www. These workshops may be of interest though to those interested in research talks who want an excuse to visit Australia. Cheers Gordon

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ADD COMMENT • link updated 19.9 years ago by James Wettenhall ▴ 1000 • written 19.9 years ago by Gordon Smyth 52k

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James Wettenhall ▴ 1000

@james-wettenhall-153

Last seen 10.2 years ago

Hi, I am a Windows/Linux user but have lots of biology clients who are Mac users. They generally don't have the Developer Tools installed, so what is the best way for me to help them to install a package like "affy" which has C source code? Does anyone provide Mac binaries for commonly used Bioconductor packages like affy upon each Release? I can ask our I.T. administrator to upgrade R and the developer tools on a shared Mac machine so I can build R packages for Mac users (which I only do occasionally), but I'm wondering if there's an easier way? Preferably not requiring admin privileges. I need affy, and would like affyPLM and gcrma also Thanks, James ---------------------------------------------------------------------- ---- James Wettenhall Tel: (+61 3) 9345 2629 Division of Genetics and Bioinformatics Fax: (+61 3) 9347 0852 The Walter & Eliza Hall Institute E-mail: wettenhall@wehi.edu.au of Medical Research, Mobile: (+61 / 0 ) 438 527 921 1G Royal Parade, Parkville, Vic 3050, Australia http://www.wehi.edu.au

ADD COMMENT • link 19.9 years ago James Wettenhall ▴ 1000

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If they're using the R GUI the Bioconductor Binary packages should be available directly from the "Package Installer..." sheet since AFAIK Stefano builds them along with the other CRAN packages. I'd check, but unfortunately my R GUI crashes (its a -devel branch version) when I try to get the list of packages. In any case, you shouldn't need to get admin rights to install packages on OS X once the Developer Tools are installed. I have all my packages (including Bioconductor) in a user-local directory (~/Library/R/library). If I had been especially clever I suppose I would have made a special Bioconductor repository and installed the BioC packages there (IIRC getBioC.R asks where you want to put them. I usually build by hand, where you can use the '-l,--library' option to specify a binary location). On Jan 18, 2005, at 5:57 PM, James Wettenhall wrote: > Hi, > > I am a Windows/Linux user but have lots of biology clients who > are Mac users. They generally don't have the Developer Tools > installed, so what is the best way for me to help them to > install a package like "affy" which has C source code? Does > anyone provide Mac binaries for commonly used Bioconductor > packages like affy upon each Release? I can ask our I.T. > administrator to upgrade R and the developer tools on a shared > Mac machine so I can build R packages for Mac users (which I > only do occasionally), but I'm wondering if there's an easier > way? Preferably not requiring admin privileges. > > I need affy, and would like affyPLM and gcrma also > > Thanks, > James > > -------------------------------------------------------------------- --- > --- > James Wettenhall Tel: (+61 3) 9345 > 2629 > Division of Genetics and Bioinformatics Fax: (+61 3) 9347 > 0852 > The Walter & Eliza Hall Institute E-mail: > wettenhall@wehi.edu.au > of Medical Research, Mobile: (+61 / 0 ) 438 527 > 921 > 1G Royal Parade, > Parkville, Vic 3050, Australia > http://www.wehi.edu.au > > _______________________________________________ > Bioconductor mailing list > Bioconductor@stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > --- Byron Ellis (ellis@stat.harvard.edu) "Oook" -- The Librarian

ADD REPLY • link 19.9 years ago Byron Ellis ▴ 60

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Hi Byron and others, > If they're using the R GUI the Bioconductor Binary packages should be > available directly from the "Package Installer..." sheet since AFAIK > Stefano builds them along with the other CRAN packages. I'd check, but > unfortunately my R GUI crashes (its a -devel branch version) when I try > to get the list of packages. That sounds perfect. Can anyone confirm this? The reason I questioned whether Mac binaries existed is that if you click on "Release 1.5 Packages" link from the main Bioconductor website, you only get Win32 and Source. > In any case, you shouldn't need to get admin rights to install packages > on OS X once the Developer Tools are installed. My users are probably not interested in the Developer Tools unless they are absolutely necessary. I've heard they take a while to install. The reason I mentioned admin privileges is because I seem to remember that at one stage, there was a massive R installer for Mac which installed lots of CRAN and Bioconductor packages. As my biologist client already has R installed, I would prefer not to have to ask their I.T. adminstrator to reinstall R (in order to get a few missing packages). I can easily install R packages for them (in a suitable directory) without admin privileges, as long as binaries are available somewhere. Thanks, James

ADD REPLY • link 19.9 years ago James Wettenhall ▴ 1000

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Well, let me shed some light on this. There is one "official" binary version of R for Mac OS X which is available only on CRAN under /bin/macos This comes with an installer that only install R itself, base+recommended packages and a GUI front end to R. Call this version 1. There is also Jan de Leeuw build of R for Mac OS X which (which is prefectly ok) that installs R+almost all CRAN packages and all BioC packages (I'm not sure about all BioC). Call this version 2. On CRAN there is also a set of prebuilt CRAN packages for Mac OS X. These are guarantee to work with 1., and they are all packages which pass all the checks previewed by R tools to assess the quality of a binary build (this is platform dependent) Most of the BioC 1.5 packages are also distributed in binary form on the BioC web site (http://www.bioconductor.org/bin/macosx/2.0/ ). Both kind of binary packages are accessible for download and install via the GUI front-end distributed with 1. Specifically to BioC: with 1. also comes the installer of the X11/TclTk libraries. You need to install this to use tcltk widgets, which are widly used in BioC. There is NO NEED to install developer tools to use 1. + the prebuilt packages. Developer tools, which means C compiler and other things, ARE NEEDED only if one wants to build packages from source (this could happen for some packages that can be built on Mac OS X but are not distributed as binary by us, as they don't pass all the test) The installation of 1. needs admin priviledges, but after that packages can be installed locally on a per user basis. BTW: please always use the latest R official release. There is also a "R for Mac OS X FAQ" available that explains several of these aspects. stefano On Jan 20, 2005, at 3:13 AM, James Wettenhall wrote: > Hi Byron and others, > >> If they're using the R GUI the Bioconductor Binary packages should be >> available directly from the "Package Installer..." sheet since AFAIK >> Stefano builds them along with the other CRAN packages. I'd check, but >> unfortunately my R GUI crashes (its a -devel branch version) when I >> try >> to get the list of packages. > > That sounds perfect. Can anyone confirm this? The reason I questioned > whether Mac binaries existed is that if you click on "Release 1.5 > Packages" link from the main Bioconductor website, you only get Win32 > and > Source. > >> In any case, you shouldn't need to get admin rights to install >> packages >> on OS X once the Developer Tools are installed. > > My users are probably not interested in the Developer Tools unless they > are absolutely necessary. I've heard they take a while to install. > > The reason I mentioned admin privileges is because I seem to remember > that > at one stage, there was a massive R installer for Mac which installed > lots > of CRAN and Bioconductor packages. As my biologist client already has > R > installed, I would prefer not to have to ask their I.T. adminstrator to > reinstall R (in order to get a few missing packages). I can easily > install R packages for them (in a suitable directory) without admin > privileges, as long as binaries are available somewhere. > > Thanks, > James > > _______________________________________________ > Bioconductor mailing list > Bioconductor@stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor >

ADD REPLY • link 19.9 years ago stefano iacus ▴ 430

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At 12.57pm +1100 19/1/05, James Wettenhall wrote: >Hi, > >I am a Windows/Linux user but have lots of biology clients who >are Mac users. They generally don't have the Developer Tools >installed, so what is the best way for me to help them to >install a package like "affy" which has C source code? Does >anyone provide Mac binaries for commonly used Bioconductor >packages like affy upon each Release? I can ask our I.T. >administrator to upgrade R and the developer tools on a shared >Mac machine so I can build R packages for Mac users (which I >only do occasionally), but I'm wondering if there's an easier >way? Preferably not requiring admin privileges. > >I need affy, and would like affyPLM and gcrma also You can get the developer tools for free by joining ADC at : <https: connect.apple.com="" cgi-="" bin="" webobjects="" membersite.woa="" 106="" wo="" ar6peqmkw3id277qbjj1iqq8dr4="" 0.0=""> They also came with the most recent OS release (10.3). I haven't bought a mac in a while so I do not know if they come with new Macs. Simon

ADD REPLY • link 19.9 years ago Simon Kidd ▴ 180

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