Re: [Bioc-devel] Help needed: Rdisop on Windows "File format not recognized"
Hi, thanks everyone for the input, I now have a few more leads to follow. It would be great to have a general single package builder even for existing packages to check if one has no direct access to the failing architecture. https://win-builder.r-project.org/ is discouraging BioC package upload, and might have a different build environment. Let's see if we get a working Rdisop for easter. A nice weekend everyone, yours, Steffen On Thu, 2019-04-18 at 13:25 +, Martin Morgan wrote: > I second the idea of reproducing with the Windows build commands, > which have to do more than 'just' build for a particular > architecture. One might test the hypothesis that it is staged install > that is causing the problem with > > StagedInstalll: no > > in the DESCRIPTION file. -- IPB HalleAG Massenspektrometrie & Bioinformatik Dr. Steffen Neumann http://www.IPB-Halle.DE Weinberg 3 Tel. +49 (0) 345 5582 - 1470 06120 Halle +49 (0) 345 5582 - 0 sneumann(at)IPB-Halle.DE Fax. +49 (0) 345 5582 - 1409 ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
Re: [Bioc-devel] Help needed: Rdisop on Windows "File format not recognized"
I second the idea of reproducing with the Windows build commands, which have to do more than 'just' build for a particular architecture. One might test the hypothesis that it is staged install that is causing the problem with StagedInstalll: no in the DESCRIPTION file. Makevars is evaluated on Windows, unless there's a Makevars.win. cleanup is not, but cleanup.win is. Martin On 4/18/19, 8:38 AM, "Bioc-devel on behalf of Mike Smith" wrote: I can reproduce the error using R-3.6.0beta and running the following two steps to replicate the Bioc builder commands: R CMD build --keep-empty-dirs --no-resave-data Rdisop rm -rf Rdisop.buildbin-libdir && mkdir Rdisop.buildbin-libdir && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=Rdisop.buildbin-libdir Rdisop_1.43.4.tar.gz Bit of a guess, and I don't know why this would have changed, but the Rdisop_1.43.4.tar.gz produced by step one contains the *.o files referenced in the error. If these were produced for 64-bit architecture then they'll fail when the build process tries to use them for the 32-bit binary. Perhaps your Rcpp edits removed some cleanup code that was there before? I note there's no Makevars.win or cleanup.win but my memory is a bit fuzzy on whether only versions with *.win will be run on Windows or if that's just a way to provide alternative code if needed. On Thu, 18 Apr 2019 at 11:35, Neumann, Steffen wrote: > Hi, > > with the next release coming up, I am out of wits regarding the failure at > > http://bioconductor.org/checkResults/devel/bioc-LATEST/Rdisop/tokay2-buildbin.html > which exists since before April this year, when we committed > some changes to get rid of the RcppClassic dependency. > > Max Helf succeeded to build locally on windows without problem. > > So it seems that Rdisop has issues with the BioC windows build > environment, but I totally fail to see the reason. > > Could it be the new staged installation ? > But I wouldn't know why that'd affect the compile/linking. > > The issue is tracked at > https://github.com/sneumann/Rdisop/issues/13 > > Any help/pointers appreciated. > > Yours, > Steffen > > -- > > IPB HalleAG Massenspektrometrie & Bioinformatik > Dr. Steffen Neumann http://www.IPB-Halle.DE > Weinberg 3 Tel. +49 (0) 345 5582 - 1470 > 06120 Halle +49 (0) 345 5582 - 0 > sneumann(at)IPB-Halle.DE Fax. +49 (0) 345 5582 - 1409 > ___ > Bioc-devel@r-project.org mailing list > https://stat.ethz.ch/mailman/listinfo/bioc-devel > [[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
Re: [Bioc-devel] Help needed: Rdisop on Windows "File format not recognized"
I can reproduce the error using R-3.6.0beta and running the following two steps to replicate the Bioc builder commands: R CMD build --keep-empty-dirs --no-resave-data Rdisop rm -rf Rdisop.buildbin-libdir && mkdir Rdisop.buildbin-libdir && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=Rdisop.buildbin-libdir Rdisop_1.43.4.tar.gz Bit of a guess, and I don't know why this would have changed, but the Rdisop_1.43.4.tar.gz produced by step one contains the *.o files referenced in the error. If these were produced for 64-bit architecture then they'll fail when the build process tries to use them for the 32-bit binary. Perhaps your Rcpp edits removed some cleanup code that was there before? I note there's no Makevars.win or cleanup.win but my memory is a bit fuzzy on whether only versions with *.win will be run on Windows or if that's just a way to provide alternative code if needed. On Thu, 18 Apr 2019 at 11:35, Neumann, Steffen wrote: > Hi, > > with the next release coming up, I am out of wits regarding the failure at > > http://bioconductor.org/checkResults/devel/bioc-LATEST/Rdisop/tokay2-buildbin.html > which exists since before April this year, when we committed > some changes to get rid of the RcppClassic dependency. > > Max Helf succeeded to build locally on windows without problem. > > So it seems that Rdisop has issues with the BioC windows build > environment, but I totally fail to see the reason. > > Could it be the new staged installation ? > But I wouldn't know why that'd affect the compile/linking. > > The issue is tracked at > https://github.com/sneumann/Rdisop/issues/13 > > Any help/pointers appreciated. > > Yours, > Steffen > > -- > > IPB HalleAG Massenspektrometrie & Bioinformatik > Dr. Steffen Neumann http://www.IPB-Halle.DE > Weinberg 3 Tel. +49 (0) 345 5582 - 1470 > 06120 Halle +49 (0) 345 5582 - 0 > sneumann(at)IPB-Halle.DE Fax. +49 (0) 345 5582 - 1409 > ___ > Bioc-devel@r-project.org mailing list > https://stat.ethz.ch/mailman/listinfo/bioc-devel > [[alternative HTML version deleted]] ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
[Bioc-devel] Help needed: Rdisop on Windows "File format not recognized"
Hi, with the next release coming up, I am out of wits regarding the failure at http://bioconductor.org/checkResults/devel/bioc-LATEST/Rdisop/tokay2-buildbin.html which exists since before April this year, when we committed some changes to get rid of the RcppClassic dependency. Max Helf succeeded to build locally on windows without problem. So it seems that Rdisop has issues with the BioC windows build environment, but I totally fail to see the reason. Could it be the new staged installation ? But I wouldn't know why that'd affect the compile/linking. The issue is tracked at https://github.com/sneumann/Rdisop/issues/13 Any help/pointers appreciated. Yours, Steffen -- IPB HalleAG Massenspektrometrie & Bioinformatik Dr. Steffen Neumann http://www.IPB-Halle.DE Weinberg 3 Tel. +49 (0) 345 5582 - 1470 06120 Halle +49 (0) 345 5582 - 0 sneumann(at)IPB-Halle.DE Fax. +49 (0) 345 5582 - 1409 ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
