Hi all, I have set up both 32-bit and 64-bit versions of R.app and can run them happily at the same time. (I'll refer to them as R32.app and R64.app) However, if I install a package using the R32.app package installer, then install the same package from R64.app, the 32 bit version is removed. Is there a way to install from R64.app so that the *package*/libs/ppc64 directory is added to the already existing *package*/libs/ and the appropriate 64 bit file versions are installed into *package*/libs/ppc64 without deleting the whole library directory? (At present each R32.app or R64.app install deletes the whole package's library directory so I only end up with one architecture installed.) I've reviewed the install.packages() help and am not seeing a way to accomplish this via the command line. Did I miss something? Is there a way to add an architecture to a package's already existing libs/ directory? Steven McKinney Statistician Molecular Oncology and Breast Cancer Program British Columbia Cancer Research Centre email: smckinney +at+ bccrc +dot+ ca tel: 604-675-8000 x7561 BCCRC Molecular Oncology 675 West 10th Ave, Floor 4 Vancouver B.C. V5Z 1L3 Canada
Installing multiple architectures for a package
5 messages · Steven McKinney, Simon Urbanek, David Winsemius
On Nov 26, 2008, at 11:06 PM, Steven McKinney wrote:
Hi all, I have set up both 32-bit and 64-bit versions of R.app and can run them happily at the same time. (I'll refer to them as R32.app and R64.app) However, if I install a package using the R32.app package installer, then install the same package from R64.app, the 32 bit version is removed.
This is not about 32-bit vs. 64-bit --- this is about which build of R you use. The Tiger build supports only 32-bit, the Leopard build supports both 32 and 64-bit. It is irrelevant which architecture you use (32 ot 64-bit). You have to use the packages binaries for the correct build, but that should happen automatically.
Is there a way to install from R64.app so that the *package*/libs/ ppc64 directory is added to the already existing *package*/libs/ and the appropriate 64 bit file versions are installed into *package*/ libs/ppc64 without deleting the whole library directory? (At present each R32.app or R64.app install deletes the whole package's library directory so I only end up with one architecture installed.)
Yes, if you install from sources use R CMD INSTALL --libs-only See R for Mac FAQ "5.4 Building universal packages" However, you should only need that in rare cases (for packages with Makefile or configure script). Make sure you know what you're doing (please read the whole package installation FAQ section). Cheers, Simon
I've reviewed the install.packages() help and am not seeing a way to accomplish this via the command line. Did I miss something? Is there a way to add an architecture to a package's already existing libs/ directory? Steven McKinney Statistician Molecular Oncology and Breast Cancer Program British Columbia Cancer Research Centre email: smckinney +at+ bccrc +dot+ ca tel: 604-675-8000 x7561 BCCRC Molecular Oncology 675 West 10th Ave, Floor 4 Vancouver B.C. V5Z 1L3 Canada
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Hi Simon,
On Nov 26, 2008, at 11:06 PM, Steven McKinney wrote:
Hi all, I have set up both 32-bit and 64-bit versions of R.app and can run them happily at the same time. (I'll refer to them as R32.app and R64.app) However, if I install a package using the R32.app package installer, then install the same package from R64.app, the 32 bit version is removed.
This is not about 32-bit vs. 64-bit --- this is about which build of R you use. The Tiger build supports only 32-bit, the Leopard build supports both 32 and 64-bit. It is irrelevant which architecture you use (32 ot 64-bit). You have to use the packages binaries for the correct build, but that should happen automatically.
My apologies for 32-bit 64-bit nomenclature mangling. I have Leopard on my Mac (sessionInfo below), and 16GB RAM, and mountains of data to process. So having 64-bit capability allows me to get lots of processing done that would otherwise be painful. I use a lot of Bioconductor packages, but they are not providing ppc64 architecture with their binaries. In a recent email (Nov 6, 2008 - inserted at end of this email) you kindly offered to compile BioC packages so that ppc64 architecture would be available. Will you be able to offer this? If so, where will those binary packages containing ppc64 architecture be found - at your website or Bioconductor? If not, then I need to figure all this out. It is very convenient to install the bulk of packages via the R.app package installer, but then I have to do the ppc64 architecture additionally.
Is there a way to install from R64.app so that the *package*/libs/ ppc64 directory is added to the already existing *package*/libs/ and the appropriate 64 bit file versions are installed into *package*/ libs/ppc64 without deleting the whole library directory? (At present each R32.app or R64.app install deletes the whole package's library directory so I only end up with one architecture installed.)
Yes, if you install from sources use R CMD INSTALL --libs-only See R for Mac FAQ "5.4 Building universal packages" However, you should only need that in rare cases (for packages with Makefile or configure script). Make sure you know what you're doing (please read the whole package installation FAQ section).
Since I use many Bioconductor packages, this is not rare, unfortunately, since they do not offer ppc64 binaries. Not all CRAN binaries include ppc64 either. It appears that if I install binaries from R32.app, then I have to add the ppc64 versions via command line R --arch=ppc64 CMD INSTALL --libs-only packagename.tar.gz Would it be possible to add a --libs-only option to the R.app package installer to help automate this? Thanks for your guidance Steve M
Cheers, Simon
I've reviewed the install.packages() help and am not seeing a way to accomplish this via the command line. Did I miss something? Is there a way to add an architecture to a package's already existing libs/ directory? Steven McKinney Statistician Molecular Oncology and Breast Cancer Program British Columbia Cancer Research Centre email: smckinney +at+ bccrc +dot+ ca tel: 604-675-8000 x7561 BCCRC Molecular Oncology 675 West 10th Ave, Floor 4 Vancouver B.C. V5Z 1L3 Canada
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On Nov 6, 2008, at 7:24 PM, Patrick Aboyoun wrote:
Steve and Steve, While this is slightly off topic, I would just like to offer a brief aside since Bioconductor has been brought up on this mailing list. The Bioconductor project doesn't support ppc64 at this time and that is why I was silent on it in my e-mail to the Bioconductor community. We currently have only one Mac OS X 10.5 (Leopard) build machine and it uses Intel technology. The reason why some of the BioC 2.3 packages have ppc64 binaries and some don't is because some packages with external source code let R fully control the compiler flags (like the one specifying the architecture) and others don't (e.g. because they include a make framework). For the ones that R has complete compiler flag control over, the BioC 2.3 Mac OS X Leopard packages contain all four architectures since we use Simon Urbanek's R binaries that contain quad-architecture support as well as the compilers he recommends. When R doesn't have full control over the compilation flags, we use a standard R-based compilation method to create the libraries that are appropriate for ppc, i386, x86_64. If there are others out there who are in the same boat as Steve McKinney and would like to use BioC 2.3 on a ppc64 and are having trouble doing so, let me know so I can pass that information on to the BioC core team.
This is slightly off-topic, but I could offer my ppc64 machine to build libraries for BioC binaries with configure script if that is desirable. According to the Mac survey there are very few ppc64 machines with enough memory to warrant 64-bit R for ppc64, so it's still a questionable endeavor, but possible. (In fact I'm still not quite convinced that it's worth maintaining ppc64 binaries since G5 is now obsolete and next OS X reportedly won't support it anyway, but as long as I have a G5 in my office I'm simply keeping it in the chain). Cheers, Simon
sessionInfo()
R version 2.8.0 Patched (2008-11-06 r46845) powerpc-apple-darwin9.5.0 locale: en_CA.UTF-8/en_CA.UTF-8/C/C/en_CA.UTF-8/en_CA.UTF-8 attached base packages: [1] splines grid tools stats graphics grDevices utils datasets methods base other attached packages: [1] oligo_1.6.0 affxparser_1.14.0 VanillaICE_1.4.0 SNPchip_1.6.0 [5] oligoClasses_1.4.0 beadarraySNP_1.8.0 quantsmooth_1.8.0 lodplot_1.1 [9] quantreg_4.23 SparseM_0.78 beadarray_1.10.0 sma_0.5.15 [13] hwriter_0.93 geneplotter_1.20.0 lattice_0.17-15 limma_2.16.3 [17] illuminaHumanv3.db_1.1.2 lumi_1.8.3 RSQLite_0.7-1 DBI_0.2-4 [21] preprocessCore_1.4.0 mgcv_1.4-1 affy_1.20.0 annotate_1.20.1 [25] xtable_1.5-4 AnnotationDbi_1.4.1 Biobase_2.2.1 loaded via a namespace (and not attached): [1] KernSmooth_2.22-22 RColorBrewer_1.0-2 affyio_1.10.1
On Nov 27, 2008, at 12:22 AM, Steven McKinney wrote:
I have Leopard on my Mac (sessionInfo below), and 16GB RAM, and mountains of data to process. So having 64-bit capability allows me to get lots of processing done that would otherwise be painful. I use a lot of Bioconductor packages, but they are not providing ppc64 architecture with their binaries.
Have you tried installing what you need? I was asked offlist whether there would be any point in installing the 64 bit version by someone who was using selected portions of the bioconductor suite. The entire biocLite superpackage installed from binaries under my 64bit GUI installation without complaint and ran a brief test suite. I still am not having that same error free installation with Harrell's Design and Hmisc combo however. If someone on the list has had a go at figuring out what is stopping the Design and Hmisc packages from compiling, I would be interested.
David Winsemius > > > In a recent email (Nov 6, 2008 - inserted at end of this > email) you kindly offered to compile BioC packages > so that ppc64 architecture would be available. Will > you be able to offer this? If so, where will those > binary packages containing ppc64 architecture be > found - at your website or Bioconductor? > > If not, then I need to figure all this out. > It is very convenient to install the bulk of > packages via the R.app package installer, but > then I have to do the ppc64 architecture additionally. >
Hi David, What platform are you running on? Yes, I figured out how to get it all done yesterday, and now have a great R installation with ppc and ppc64 architectures running well. I spent the day cranking through HMM modeling of bunches of Illumina chip data, which I just could not do with limited memory or 32 bit software. There's no need to install 64 bit stuff if you don't have much memory or large data sets. I'm not seeing ppc64 architecture when I install bioconductor packages. When you say the biocLite stuff installed, are you saying you have 64 bit architecture versions available? I only see i386 and ppc architectures install when I install from Bioconductor binaries. Hmisc and Design are working fine for me, so it can be done. What error messages are you seeing when you try to install from source? Best Steve M -----Original Message----- From: David Winsemius [mailto:dwinsemius at comcast.net] Sent: Thu 11/27/2008 6:19 AM To: Steven McKinney Cc: Simon Urbanek; R-SIG-Mac at stat.math.ethz.ch Subject: Re: [R-SIG-Mac] Installing multiple architectures for a package
On Nov 27, 2008, at 12:22 AM, Steven McKinney wrote:
I have Leopard on my Mac (sessionInfo below), and 16GB RAM, and mountains of data to process. So having 64-bit capability allows me to get lots of processing done that would otherwise be painful. I use a lot of Bioconductor packages, but they are not providing ppc64 architecture with their binaries.
Have you tried installing what you need? I was asked offlist whether there would be any point in installing the 64 bit version by someone who was using selected portions of the bioconductor suite. The entire biocLite superpackage installed from binaries under my 64bit GUI installation without complaint and ran a brief test suite. I still am not having that same error free installation with Harrell's Design and Hmisc combo however. If someone on the list has had a go at figuring out what is stopping the Design and Hmisc packages from compiling, I would be interested.
David Winsemius > > > In a recent email (Nov 6, 2008 - inserted at end of this > email) you kindly offered to compile BioC packages > so that ppc64 architecture would be available. Will > you be able to offer this? If so, where will those > binary packages containing ppc64 architecture be > found - at your website or Bioconductor? > > If not, then I need to figure all this out. > It is very convenient to install the bulk of > packages via the R.app package installer, but > then I have to do the ppc64 architecture additionally. >