Re: [R-pkg-devel] Proper way to cleanup after build third party components?
On Mon, Jun 5, 2017 at 1:13 AM, Dirk Eddelbuettel wrote: > > On 5 June 2017 at 00:51, Konstantin Sorokin wrote: > | This third party component is a compression library for which my package > | provides bindings and I need to build this library first. Look at the > lines > | starting from > | https://github.com/thekvs/zstdr/blob/8ea428b33d986667494d940c66732d > bbc66871b3/configure.ac#L34 > > The common paradigm is to first build below src/, and to then link via > src/Makevars to the static library you just built. > > I don't have a real go-to example of a package that does this but you could > look into the BioConductor package RGBL (which builds Boost Graph first) > and/or the nloptr package (which, if need be, downloads nlopt and builds > it; > my contribution there was the other part of finding / using a libnlopt if > on > the system). > Thanks, Dirk, I'll look at nloptr package more closely. > > I wondered about this when CRANberries told me about your package. I guess > you can't assume the Zstandard library to be present? Maybe one day the > hybrid approach of nloptr may work for you. > zstandard is a young project and I think it is a bit to early to assume that zstandard library be present in the system. For example on my Ubuntu 16.04 (LTS) I have libzstd0/xenial 0.5.1-1 but the latest stable release has version 1.2. Btw, what about installing cmake on OSX and Solaris in CRAN build farm? Now it is such a ubiquitous and widely used program! -- Konstantin Sorokin [[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] Proper way to cleanup after build third party components?
Hi Konstantin, Concerning CMake, I asked a similar question here: https://stat.ethz.ch/pipermail/r-package-devel/2017q2/001600.html Essentially, I wondered if there was a way to have CMake within an R package, but obviously having a system install of CMake would work in my case too. Hopefully answers to your question will be more useful than answers to mine ;) On Mon, Jun 5, 2017 at 5:29 AM, Konstantin Sorokin wrote: > On Mon, Jun 5, 2017 at 1:13 AM, Dirk Eddelbuettel wrote: > > > > > On 5 June 2017 at 00:51, Konstantin Sorokin wrote: > > | This third party component is a compression library for which my > package > > | provides bindings and I need to build this library first. Look at the > > lines > > | starting from > > | https://github.com/thekvs/zstdr/blob/8ea428b33d986667494d940c66732d > > bbc66871b3/configure.ac#L34 > > > > The common paradigm is to first build below src/, and to then link via > > src/Makevars to the static library you just built. > > > > I don't have a real go-to example of a package that does this but you > could > > look into the BioConductor package RGBL (which builds Boost Graph first) > > and/or the nloptr package (which, if need be, downloads nlopt and builds > > it; > > my contribution there was the other part of finding / using a libnlopt if > > on > > the system). > > > > Thanks, Dirk, I'll look at nloptr package more closely. > > > > > > I wondered about this when CRANberries told me about your package. I > guess > > you can't assume the Zstandard library to be present? Maybe one day the > > hybrid approach of nloptr may work for you. > > > > zstandard is a young project and I think it is a bit to early to assume > that zstandard library be present in the system. For example on my Ubuntu > 16.04 (LTS) I have libzstd0/xenial 0.5.1-1 but the latest stable release > has version 1.2. > > Btw, what about installing cmake on OSX and Solaris in CRAN build farm? Now > it is such a ubiquitous and widely used program! > > -- > Konstantin Sorokin > > [[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] unusually slow tests on win-builder
hi, i've uploaded a version of my package to the win-builder service, but it is reporting that one of my tests takes > 10 seconds to run. examining the log here: https://win-builder.r-project.org/BvR4nreDE9qP/00check.log the win-builder is taking 24 and 28 seconds to run this test. on my local machine, this same test runs in 600ms can anyone shed any light on this? why is the win-builder so slow? with thanks jonathon __ R-package-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-package-devel
Re: [R-pkg-devel] unusually slow tests on win-builder
The relevant output is below: * checking examples ... ** running examples for arch 'i386' ... [24s] NOTE Examples with CPU or elapsed time > 10s user system elapsed cfa 8.05 0.36 10.08 ** running examples for arch 'x64' ... [28s] NOTE Examples with CPU or elapsed time > 10s user system elapsed cfa 10.62 0.23 12 * checking for unstated dependencies in 'tests' ... OK * checking tests ... ** running tests for arch 'i386' ... [25s] OK Running 'testthat.R' [24s] ** running tests for arch 'x64' ... [32s] OK Running 'testthat.R' [31s] I'm not sure why you're saying it's taking too long to run your tests when the output is telling you that it's your examples that are taking too long to run. It's also not taking 24 and 28 seconds - I believe that is just a timestamp telling you that it's producing that note 24 and 28 seconds into the check but I could be wrong. Either way the relevant output for how long the examples take look like: user system elapsed cfa 8.05 0.36 10.08 That which tells you total it took 10.08 seconds to run the examples for arch 'i386'. -Dason Kurkiewicz On Mon, Jun 5, 2017 at 8:23 AM, Jonathon Love wrote: > hi, > > i've uploaded a version of my package to the win-builder service, but it is > reporting that one of my tests takes > 10 seconds to run. examining the log > here: > > https://win-builder.r-project.org/BvR4nreDE9qP/00check.log > > the win-builder is taking 24 and 28 seconds to run this test. > > on my local machine, this same test runs in 600ms > > can anyone shed any light on this? why is the win-builder so slow? > > with thanks > > jonathon > > __ > 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] unusually slow tests on win-builder
hi dason, yes, it looks like it's taking 10 seconds. 10 seconds still seems unusually long, and a lot longer than 600ms. any other suggestions as to what might be going on here? with thanks jonathon On 5/6/17 22:36, Dason Kurkiewicz wrote: The relevant output is below: * checking examples ... ** running examples for arch 'i386' ... [24s] NOTE Examples with CPU or elapsed time > 10s user system elapsed cfa 8.05 0.36 10.08 ** running examples for arch 'x64' ... [28s] NOTE Examples with CPU or elapsed time > 10s user system elapsed cfa 10.62 0.23 12 * checking for unstated dependencies in 'tests' ... OK * checking tests ... ** running tests for arch 'i386' ... [25s] OK Running 'testthat.R' [24s] ** running tests for arch 'x64' ... [32s] OK Running 'testthat.R' [31s] I'm not sure why you're saying it's taking too long to run your tests when the output is telling you that it's your examples that are taking too long to run. It's also not taking 24 and 28 seconds - I believe that is just a timestamp telling you that it's producing that note 24 and 28 seconds into the check but I could be wrong. Either way the relevant output for how long the examples take look like: user system elapsed cfa 8.05 0.36 10.08 That which tells you total it took 10.08 seconds to run the examples for arch 'i386'. -Dason Kurkiewicz On Mon, Jun 5, 2017 at 8:23 AM, Jonathon Love wrote: hi, i've uploaded a version of my package to the win-builder service, but it is reporting that one of my tests takes > 10 seconds to run. examining the log here: https://win-builder.r-project.org/BvR4nreDE9qP/00check.log the win-builder is taking 24 and 28 seconds to run this test. on my local machine, this same test runs in 600ms can anyone shed any light on this? why is the win-builder so slow? with thanks jonathon __ 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] Proper way to cleanup after build third party components?
On 5 June 2017 at 12:29, Konstantin Sorokin wrote: | zstandard is a young project and I think it is a bit to early to assume that | zstandard library be present in the system. For example on my Ubuntu 16.04 | (LTS) I have libzstd0/xenial 0.5.1-1 but the latest stable release has version | 1.2. I use the PPA service on launchpad.net to great effect for that. Take most recent (packaged !!) version from Debian, adjust debian/control and debian/changelog ever so slightly, upload to launchpad and use the thusly generated version on older Ubuntu and e.g. Travis. I need to blog about that... | Btw, what about installing cmake on OSX and Solaris in CRAN build farm? Now it | is such a ubiquitous and widely used program! As far as I know, some packages already use cmake. See e.g. this query among the GitHub-mirrored CRAN packages: https://github.com/search?q=user%3Acran+CMakeLists.txt&type=Code Dirk -- http://dirk.eddelbuettel.com | @eddelbuettel | e...@debian.org __ R-package-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-package-devel
Re: [R-pkg-devel] unusually slow tests on win-builder
On 05.06.2017 14:48, Jonathon Love wrote: hi dason, yes, it looks like it's taking 10 seconds. 10 seconds still seems unusually long, and a lot longer than 600ms. So your windows installation of R-3.4.0 can solve this in 600ms? Or is yoiur another OS? For winbuilder, it could be it was heavily loaded, but even then it should never take more than twice as long as on an idling machine. Then winbuilder has server CPUs with lots of cores hence operates at a lower frequency, altogether not more than 3-4 times the the time you got can be expected. Best, Uwe Ligges any other suggestions as to what might be going on here? with thanks jonathon On 5/6/17 22:36, Dason Kurkiewicz wrote: The relevant output is below: * checking examples ... ** running examples for arch 'i386' ... [24s] NOTE Examples with CPU or elapsed time > 10s user system elapsed cfa 8.05 0.36 10.08 ** running examples for arch 'x64' ... [28s] NOTE Examples with CPU or elapsed time > 10s user system elapsed cfa 10.62 0.23 12 * checking for unstated dependencies in 'tests' ... OK * checking tests ... ** running tests for arch 'i386' ... [25s] OK Running 'testthat.R' [24s] ** running tests for arch 'x64' ... [32s] OK Running 'testthat.R' [31s] I'm not sure why you're saying it's taking too long to run your tests when the output is telling you that it's your examples that are taking too long to run. It's also not taking 24 and 28 seconds - I believe that is just a timestamp telling you that it's producing that note 24 and 28 seconds into the check but I could be wrong. Either way the relevant output for how long the examples take look like: user system elapsed cfa 8.05 0.36 10.08 That which tells you total it took 10.08 seconds to run the examples for arch 'i386'. -Dason Kurkiewicz On Mon, Jun 5, 2017 at 8:23 AM, Jonathon Love wrote: hi, i've uploaded a version of my package to the win-builder service, but it is reporting that one of my tests takes > 10 seconds to run. examining the log here: https://win-builder.r-project.org/BvR4nreDE9qP/00check.log the win-builder is taking 24 and 28 seconds to run this test. on my local machine, this same test runs in 600ms can anyone shed any light on this? why is the win-builder so slow? with thanks jonathon __ 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 __ R-package-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-package-devel
Re: [R-pkg-devel] unusually slow tests on win-builder
So your windows installation of R-3.4.0 can solve this in 600ms? Or is yoiur another OS? ah, yes, another OS. it turns out on windows this takes 6 seconds. the issue is that we only load imports on demand (not in our NAMESPACE), there's a behemoth dependency chain that that analysis invokes, and package loading appears to be *quite a bit* slower on windows than macOS/linux. with thanks jonathon For winbuilder, it could be it was heavily loaded, but even then it should never take more than twice as long as on an idling machine. Then winbuilder has server CPUs with lots of cores hence operates at a lower frequency, altogether not more than 3-4 times the the time you got can be expected. Best, Uwe Ligges any other suggestions as to what might be going on here? with thanks jonathon On 5/6/17 22:36, Dason Kurkiewicz wrote: The relevant output is below: * checking examples ... ** running examples for arch 'i386' ... [24s] NOTE Examples with CPU or elapsed time > 10s user system elapsed cfa 8.05 0.36 10.08 ** running examples for arch 'x64' ... [28s] NOTE Examples with CPU or elapsed time > 10s user system elapsed cfa 10.62 0.23 12 * checking for unstated dependencies in 'tests' ... OK * checking tests ... ** running tests for arch 'i386' ... [25s] OK Running 'testthat.R' [24s] ** running tests for arch 'x64' ... [32s] OK Running 'testthat.R' [31s] I'm not sure why you're saying it's taking too long to run your tests when the output is telling you that it's your examples that are taking too long to run. It's also not taking 24 and 28 seconds - I believe that is just a timestamp telling you that it's producing that note 24 and 28 seconds into the check but I could be wrong. Either way the relevant output for how long the examples take look like: user system elapsed cfa 8.05 0.36 10.08 That which tells you total it took 10.08 seconds to run the examples for arch 'i386'. -Dason Kurkiewicz On Mon, Jun 5, 2017 at 8:23 AM, Jonathon Love wrote: hi, i've uploaded a version of my package to the win-builder service, but it is reporting that one of my tests takes > 10 seconds to run. examining the log here: https://win-builder.r-project.org/BvR4nreDE9qP/00check.log the win-builder is taking 24 and 28 seconds to run this test. on my local machine, this same test runs in 600ms can anyone shed any light on this? why is the win-builder so slow? with thanks jonathon __ 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 __ R-package-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-package-devel
