Just to report that I've been able to compile affxparser on R win 64 using 1.19.6 from the devel contrib on bioconductor, using mingw64 (specifically, http://sourceforge.net/projects/mingw-w64/files/Toolchains%20targettin g%20Win64/Personal%20Builds/sezero_20100322/mingw-w64-bin_x86_64-mingw _20100322_sezero.zip/download). No idea why the 1.18 version wouldnt compile, but problem solved anyway :) Thanks, Michael On 23/03/2010 11:32 AM, Kasper Daniel Hansen wrote: > The authoritative place to look for information is the r-devel list, > particular the posts from R-core. The most recent post about this > issue is the one Martin provided a link to, which contains the > following > > "We do not anticipate any major changes to the build before 2.11.0 is > released (most likely in April), and it can now be regarded as at > 'beta' status -- users with a 64-bit Windows OS and who do not need > Bioconductor packages are encouraged to try it out." > > For specifics you should read the R-admin manual. I am not sure if > the R-devel version of that manual is available anywhere on the net, > but if you have access to a R-devel build somewhere you will see it > has a section on building for 64 bit windows. There is also a link to > a webpage with further comments. > > But you will still need to install the latest version of the mingw64 > toolchain. I assume that eventually a snapshot will be included in > Rtools, but that does not seem to be the case yet. > > Kasper > > On Tue, Mar 23, 2010 at 3:57 AM, Michael Imbeault > <michael.imbeault at="" sympatico.ca=""> wrote: > >> Hello, >> >> Sorry for the confusion about the two issues, I was under the impression >> that the build servers I linked to were the 64 bit version, my bad :) >> >> I only became aware of the affxparser on 64 bit problem yesterday, and >> stumbled upon the aroma.affymetrix group. Having not seen a post about it on >> the bioC list, I took the opportunity to post (and cc you). I'll try >> tomorrow to build 1.19.6 (I don't remember which build I tried to compile >> with mingw64). >> >> Regarding the instability of the keychain, do you happen to have a link >> where I could download the latest (semi) official version? There's a lot of >> uncertainty about this following various conversations on the web. >> >> Last, thanks for taking time to tackle this problem, and don't worry, I know >> that R 64 bit under Windows is kind of bleeding edge (and bioC running on it >> even more so) so I don't expect an overnight solution :) >> >> Cheers, >> Michael >> >> On 22/03/2010 11:20 PM, Kasper Daniel Hansen wrote: >> >>> I was not aware of the discussion on the aroma.affymetrix group. And >>> I was furthermore not aware of the fact that affxparser fails to build >>> at the moment (I thought we had automatic notification of this - >>> perhaps there is some issue with my spam filter?) For another time, >>> it is usually productive to contact the maintainer :) >>> >>> As far as I can see the Bioconductor build the OP is referring to is >>> still using mingw32, which means that the build issue should be >>> completely unrelated to 64 bit windows (or the information at >>> >>> http://bioconductor.org/checkResults/2.6/bioc-LATEST/liverpool- NodeInfo.html >>> is outdated). >>> >>> I would expect affxparser to build with mingw64. Or at least we >>> managed to build it (version 1.19.6 to be specific) under some version >>> of the toolchain (at that point the toolchain changed often I think) >>> with help from Prof. Ripley. The toolchain has now stabilized and I >>> am in the process of getting a 64bit Windows 7 up and running so I can >>> make sure affxparser (and Rgraphviz - although initial results >>> indicate that Rgraphviz will be a pain) will work on this platform. >>> >>> That leaves the issue of why affxparser does not build on the >>> Bioconductor build servers. I will look into this over the coming >>> days, but it will be much easier when I actually have a windows box to >>> test on. >>> >>> Finally, in general I suggest that people who want to use 64 bit >>> Windows arm themselves with some patience. This is a new platform and >>> it is only very recently that the R windows team settled on which >>> compiler they (probably) will use and mingw64 is still somewhat >>> experimental (as I understand). To top it off, not everyone has a 64 >>> bit windows box lying around for testing, so it will still take a >>> while for things to be "normal". >>> >>> Kasper >>> >>> On Mon, Mar 22, 2010 at 7:45 PM, Martin Morgan<mtmorgan at="" fhcrc.org=""> wrote: >>> >>> >>>> Hi Michael -- >>>> >>>> On 03/22/2010 03:59 PM, Michael Imbeault wrote: >>>> >>>> >>>>> Hi, >>>>> >>>>> A toolchain to build bioC packages from source under R win 64 bit is >>>>> available at http://download.cos.name/incoming/Rtools64.zip (see >>>>> https://stat.ethz.ch/pipermail/r-devel/2010-January/056280.html for the >>>>> original post by Gong Yu). >>>>> >>>>> >>>> but this >>>> >>>> https://stat.ethz.ch/pipermail/r-devel/2010-March/056815.html >>>> >>>> suggests that the tool chain used at CRAN is different. >>>> >>>> >>>> >>>>> However, some packages don't build/compile correctly, notably affxparser >>>>> (see the liverpool build / check for affxparser at >>>>> http://bioconductor.org/checkResults/2.6/bioc-LATEST/). >>>>> >>>>> This blocks the build of the aroma.affymetrix package under R win 64 >>>>> (among others) as it depends on it - could we find the source of this >>>>> problem (I cc'd Dr. Hansen, the maintainer of the package)? This is a >>>>> problem for many users right now >>>>> >>>>> (http://groups.google.com/group/aroma-affymetrix/browse_thread/t hread/1c01fdd3b243d3ec/5160fa633ea399a4?lnk=raot#5160fa633ea399a4). >>>>> >>>>> >>>> I don't think Zaid or others on this thread communicated with the Bioc >>>> mailing list; maybe with Kasper directly? The hard-core Windows >>>> 64-bitters can check out affxparser 1.19.0 from svn (r42686; 1.19.0 did >>>> build successfully on Windows, and is the version that Windows >>>> biocLite() retrieves for win32). Which is not to say that Kasper won't >>>> address the Windows issues... >>>> >>>> Martin >>>> >>>> >>>> >>>>> See >>>>> >>>>> http://bioconductor.org/checkResults/2.6/bioc-LATEST/affxparser /liverpool-checksrc.html >>>>> for a detailed view of the install.out log. >>>>> >>>>> Regards, >>>>> Michael >>>>> >>>>> >>>>> On 22/03/2010 5:11 PM, Martin Morgan wrote: >>>>> >>>>> >>>>>> On 03/22/2010 12:28 PM, Jin, Jp wrote: >>>>>> >>>>>> >>>>>> >>>>>>> Dear list, >>>>>>> >>>>>>> I would want to install R/bioconductor to my 64-bit machine with >>>>>>> Windows 7 installed. When are the 64-bit R build and bioconductor >>>>>>> available? will R 2.11 are Bio C 2.6 work with Windows 7? >>>>>>> >>>>>>> >>>>>>> >>>>>> Hi -- >>>>>> >>>>>> 32 bit R / Bioc installs on 64-bit windows 7. >>>>>> >>>>>> There is a 64-bit Windows R-devel; follow the 'windows64' link from a >>>>>> CRAN 'R binaries' page, e.g., at http://cran.fhcrc.org/bin/. There may >>>>>> be 64-bit Bioconductor packages in the next release but that is not >>>>>> certain. You will still be able to build your own 64-bit packages, >>>>>> although I am not exactly clear on details about the compiler required >>>>>> and availability of an appropriate Windows build tool chain. >>>>>> >>>>>> Martin >>>>>> >>>>>> >>>>>> >>>>>> >>>>>>> Thanks, >>>>>>> >>>>>>> Jp Jin >>>>>>> >>>>>>> [[alternative HTML version deleted]] >>>>>>> >>>>>>> _______________________________________________ Bioconductor mailing >>>>>>> list Bioconductor at stat.math.ethz.ch >>>>>>> https://stat.ethz.ch/mailman/listinfo/bioconductor Search the >>>>>>> archives: >>>>>>> http://news.gmane.org/gmane.science.biology.informatics.conductor >>>>>>> >>>>>>> >>>>>>> >>>>>> >>>>>> >>>> -- >>>> Martin Morgan >>>> Computational Biology / Fred Hutchinson Cancer Research Center >>>> 1100 Fairview Ave. N. >>>> PO Box 19024 Seattle, WA 98109 >>>> >>>> Location: Arnold Building M1 B861 >>>> Phone: (206) 667-2793 >>>> >>>> _______________________________________________ >>>> Bioconductor mailing list >>>> Bioconductor at stat.math.ethz.ch >>>> https://stat.ethz.ch/mailman/listinfo/bioconductor >>>> Search the archives: >>>> http://news.gmane.org/gmane.science.biology.informatics.conductor >>>> >>>> >>>> >>> >>> >> _______________________________________________ >> Bioconductor mailing list >> Bioconductor at stat.math.ethz.ch >> https://stat.ethz.ch/mailman/listinfo/bioconductor >> Search the archives: >> http://news.gmane.org/gmane.science.biology.informatics.conductor >> >> > >