Re: [R-pkg-devel] Running tests on 32-bit and 64-bit
On 17/08/2015 5:03 AM, Thierry Onkelinx wrote: Dear all, Is there an easy way to run the tests of a package on both a 32-bit and 64-bit version? Ideally it should work when using R CMD check --as-cran on all OS's. Although I expect that multi architecture versions are only available on windows. So a Windows only solution will be fine as well. The origin of the problem is that I calculate some SHA1 hashed on objects containing floating point numbers. The floating points have different precision on 32-bit and 64-bit, and thus different hashes. I'm trying to work around that problem. And thus need an easy way to run tests on both 32-bit and 64-bit. I'm not sure I see the problem. If you install both the 32 and 64 bit versions, then you can run whichever one you want. To run both, just give the full path to the R.exe executables when you run the tests. Duncan Murdoch Best regards, ir. Thierry Onkelinx Instituut voor natuur- en bosonderzoek / Research Institute for Nature and Forest team Biometrie Kwaliteitszorg / team Biometrics Quality Assurance Kliniekstraat 25 1070 Anderlecht Belgium To call in the statistician after the experiment is done may be no more than asking him to perform a post-mortem examination: he may be able to say what the experiment died of. ~ Sir Ronald Aylmer Fisher The plural of anecdote is not data. ~ Roger Brinner The combination of some data and an aching desire for an answer does not ensure that a reasonable answer can be extracted from a given body of data. ~ John Tukey [[alternative HTML version deleted]] __ R-package-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-package-devel __ R-package-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-package-devel
Re: [R-pkg-devel] Running tests on 32-bit and 64-bit
Use winbuilder, it runs 32-bit and 64-bit R tests on a Windows 64-bit platform. Not sure how you implemented the different precisions, but just go ahead and try on winbiulder. Best, Uwe Ligges On 17.08.2015 11:03, Thierry Onkelinx wrote: Dear all, Is there an easy way to run the tests of a package on both a 32-bit and 64-bit version? Ideally it should work when using R CMD check --as-cran on all OS's. Although I expect that multi architecture versions are only available on windows. So a Windows only solution will be fine as well. The origin of the problem is that I calculate some SHA1 hashed on objects containing floating point numbers. The floating points have different precision on 32-bit and 64-bit, and thus different hashes. I'm trying to work around that problem. And thus need an easy way to run tests on both 32-bit and 64-bit. Best regards, ir. Thierry Onkelinx Instituut voor natuur- en bosonderzoek / Research Institute for Nature and Forest team Biometrie Kwaliteitszorg / team Biometrics Quality Assurance Kliniekstraat 25 1070 Anderlecht Belgium To call in the statistician after the experiment is done may be no more than asking him to perform a post-mortem examination: he may be able to say what the experiment died of. ~ Sir Ronald Aylmer Fisher The plural of anecdote is not data. ~ Roger Brinner The combination of some data and an aching desire for an answer does not ensure that a reasonable answer can be extracted from a given body of data. ~ John Tukey [[alternative HTML version deleted]] __ R-package-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-package-devel __ R-package-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-package-devel
Re: [R-pkg-devel] Running tests on 32-bit and 64-bit
Perhaps related: in the Bioconductor minfi package I do some checking on somewhat large matrices (450,000 times n). To save space, I compute a hash of the correct result using the digest package. As you, I ran into obvious issues with precision across platforms. To solve this, I take the matrix and run it through sprintf() with (my choice) 6 digits and then I hash the resulting character matrix. It works pretty nice for my purpose. You find minfi on github. Code is in inst/unitTests/test_preprocess.R (testing using Runit) inst/testData/testData/testData_preprocessQuantile.R (creating the reference correct matrix - this is only intended to be re-run when the algorithm change) R/utils.R for the two convenience functions .digestMatrix and .digestVector Best, Kasper On Mon, Aug 17, 2015 at 5:03 AM, Thierry Onkelinx thierry.onkel...@inbo.be wrote: Dear all, Is there an easy way to run the tests of a package on both a 32-bit and 64-bit version? Ideally it should work when using R CMD check --as-cran on all OS's. Although I expect that multi architecture versions are only available on windows. So a Windows only solution will be fine as well. The origin of the problem is that I calculate some SHA1 hashed on objects containing floating point numbers. The floating points have different precision on 32-bit and 64-bit, and thus different hashes. I'm trying to work around that problem. And thus need an easy way to run tests on both 32-bit and 64-bit. Best regards, ir. Thierry Onkelinx Instituut voor natuur- en bosonderzoek / Research Institute for Nature and Forest team Biometrie Kwaliteitszorg / team Biometrics Quality Assurance Kliniekstraat 25 1070 Anderlecht Belgium To call in the statistician after the experiment is done may be no more than asking him to perform a post-mortem examination: he may be able to say what the experiment died of. ~ Sir Ronald Aylmer Fisher The plural of anecdote is not data. ~ Roger Brinner The combination of some data and an aching desire for an answer does not ensure that a reasonable answer can be extracted from a given body of data. ~ John Tukey [[alternative HTML version deleted]] __ R-package-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-package-devel [[alternative HTML version deleted]] __ R-package-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-package-devel
[R-pkg-devel] Running tests on 32-bit and 64-bit
Dear all, Is there an easy way to run the tests of a package on both a 32-bit and 64-bit version? Ideally it should work when using R CMD check --as-cran on all OS's. Although I expect that multi architecture versions are only available on windows. So a Windows only solution will be fine as well. The origin of the problem is that I calculate some SHA1 hashed on objects containing floating point numbers. The floating points have different precision on 32-bit and 64-bit, and thus different hashes. I'm trying to work around that problem. And thus need an easy way to run tests on both 32-bit and 64-bit. Best regards, ir. Thierry Onkelinx Instituut voor natuur- en bosonderzoek / Research Institute for Nature and Forest team Biometrie Kwaliteitszorg / team Biometrics Quality Assurance Kliniekstraat 25 1070 Anderlecht Belgium To call in the statistician after the experiment is done may be no more than asking him to perform a post-mortem examination: he may be able to say what the experiment died of. ~ Sir Ronald Aylmer Fisher The plural of anecdote is not data. ~ Roger Brinner The combination of some data and an aching desire for an answer does not ensure that a reasonable answer can be extracted from a given body of data. ~ John Tukey [[alternative HTML version deleted]] __ R-package-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-package-devel
Re: [R-pkg-devel] how to make r-release-osx-x86_64-mavericks machine support rgl 3D plots
| Check DetailsVersion: 1.8.3 | Check: tests | Result: ERROR | Running the tests in ‘tests/stdUsage.R’ failed. | Last 13 lines of output: | plot(ffTest42,col=Col,plot_GOF=TRUE,speed=T) | [1] compute goodness-of-fit with leave-one-out k-nearest neighbor(guassian kernel), kknn package | | #if ever needed, k-nearest neighbor parameters for goodness-of-fit can be access through convolute_ff | #a new fit will be calculated and added to forstFloor object as ffTest42$FCfit | ffTest42 = convolute_ff(ffTest42,userArgs.kknn=alist(kernel=epanechnikov,kmax=5)) | plot(ffTest42,col=Col,plot_GOF=TRUE) | | #in 3D the interaction between X3 and X reveals itself completely | show3d(ffTest42,3:4,col=Col,plot.rgl=list(size=5),sortByImportance=FALSE) | Error in rgl.open(useNULL) : rgl.open failed | Calls: show3d ... plot3d.default - next3d - .check3d - open3d - rgl.open | Execution halted | Flavor: r-release-osx-x86_64-mavericks Yes, I see lots of that on Linux too as the tests run 'headless' without a controlling terminal. A while ago I added support in rgl to run on headless machines. Set the environment variable RGL_USE_NULL=TRUE before loading rgl, and should never try to call X11 (or whatever graphics system you're using). (It's also possible to use options(rgl.useNULL = TRUE) within R. That's no help to you, but is useful when embedding rgl plots in knitr documents.) Oh that's great! I have a related problem to Dirk - except I run R CMD check on my local machine, so while the checks are running, RGL windows randomly pop up over the course of hours. Hadley -- http://had.co.nz/ __ R-package-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-package-devel
