Re: [R-pkg-devel] Fixing travis build fail due to fftwtools fatal error (fftw3.h: No such file or directory)
On 10 September 2020 at 14:14, Marta Karaś wrote: | Adding the following to .travis.yml: | | before_install: | - if [ "$TRAVIS_OS_NAME" = "linux" ]; then sudo apt-get -y install | libfftw3-dev ; fi | | did the trick! I think that is an example of the issue discussed in this blog post: http://dirk.eddelbuettel.com/blog/2020/08/26#029_introducing_bspm The RSPM system gets you the package, but it is by its (on purpose simple) design disconnected and unaware of the dependency required which sent you down a rabbit hole. (One could also suggest that maybe Karim should expand SystemRequirements: fftw3 (>= 3.1.2) to maybe list the packages offering fftw3 _headers_. Jeroen uses a pattern for this, eg curl has SystemRequirements: libcurl: libcurl-devel (rpm) or libcurl4-openssl-dev (deb). which is already one step better.) Only systems with actual dependency resolution can go further, but it is hard to do that cross-platform / cross-OS. On Linux we have both BSPM utilising the existing rpm and deb binaries, respectively, maintained by tireless volunteers, as well as the older use of directly using the binaries. Eg looking at the Ubuntu binary from the Rutter PPA shows that r-cran-fftwtools will bring the fftw3 runtime in: docker@08d894be427a:/work$ apt-cache show r-cran-fftwtools | grep ^Depends Depends: r-base-core, libfftw3-double3 (>= 3.3.5) docker@08d894be427a:/work$ That would be an easier binary install as it skips the 'from source' build step that sent Marta hunting for the required header. If I find some time I will try to set up some Travis CI examples utilizing BSPM. Until then, one can do as I have done for over half a decade and point Travis CI to these binaries via the (still maintained and simple) r-travis setup. Works for me. See http://eddelbuettel.github.io/r-travis/ and numerous .travis.yml in packages of mine and a few other users. Dirk | Thank you both for your attention to this issue! | | Bests, | Marta Karas | | | | | | On Thu, Sep 10, 2020 at 8:35 AM Karim Rahim wrote: | | > Thanks, | > | > That may be it. It is a missing dependency. | > | > It's been a while and I'm not sure which package exposes fftw3.h ... | > | > Karim | > | > On Thu, Sep 10, 2020 at 8:16 AM Dirk Eddelbuettel wrote: | > | >> | >> On 9 September 2020 at 23:45, Karim Rahim wrote: | >> | sudo apt-get install -y fftw3 | >> | >> Or maybe rather | >> | >>sudo apt-get install libfftw3-dev | >> | >> to get the development headers? | >> | >> Dirk | >> | >> | Then try again. | >> | | >> | Let me know if it doesn't work. | >> | | >> | Cheers! | >> | Karim | >> | | >> | On Wed, Sep 9, 2020 at 10:27 PM Max Turgeon | >> wrote: | >> | > | >> | > Hi Marta, | >> | > | >> | > One change I can see from your Git history that seems to match the | >> first failed build on Travis is when you added "Imports: fftwtools" to your | >> DESCRIPTION file. And it makes sense, because if we look at its DESCRIPTION | >> file, we can see that it has fftw3 as a SystemRequirements. In other words, | >> it needs to be installed on Travis before you can run the checks on your | >> package. | >> | > | >> | > As for solutions, I can see that Karim wrote a short description of | >> how to install the library on Linux, and there's a link for Mac; all this | >> is on the Github repo: https://github.com/krahim/fftwtools | >> | > | >> | > I also noticed that there is an R package wrapping fftw on CRAN ( | >> https://cran.r-project.org/package=fftw) and I can see that it's a | >> Suggested package for fftwtools. I haven't tried it, but presumably you | >> could install the fftw R package, instead of the fftw3 library. | >> | > | >> | > HTH, | >> | > | >> | > Max Turgeon | >> | > Assistant Professor | >> | > Department of Statistics | >> | > Department of Computer Science| >> | > University of Manitoba | >> | > maxturgeon.ca | >> | > | >> | > | >> | > | >> | > | >> | > From: R-package-devel on | >> behalf of Marta Karaś | >> | > Sent: Wednesday, September 9, 2020 9:09 PM | >> | > To: package-develop | >> | > Cc: karim.ra...@queensu.ca | >> | > Subject: [R-pkg-devel] Fixing travis build fail due to fftwtools | >> fatal error (fftw3.h: No such file or directory) | >> | > | >> | > | >> | > Caution: This message was sent from outside the University of | >> Manitoba. | >> | > | >> | > | >> | > Dear all, | >> | > | >> | > I have been facing travis build fail on linux xenial due to *fftwtools | >> | > fatal error* (fftw3.h: No such file or directory) with my R package. | >> The | >> | > error appeared at a random time a few months ago (at a random time := | >> I do | >> | > not link it with any fftwtools-function related change commit I did) | >> and | >> | > persists. | >> | > | >> | > There is not much I achieved in googling and trying to decipher it, | >> sadly; | >> |
Re: [R-pkg-devel] Fixing travis build fail due to fftwtools fatal error (fftw3.h: No such file or directory)
Hi Dirk, Thanks for resolving this! It's been awhile since I've worked on this... So for dependencies, I'd like to keep it as simple as possible. I agree fftw3 may need to be updated. It's my understanding that if one were to install the latest fftw (3.3.8) from source then it would expose the header file. Is this incorrect? If this is the case, then it becomes about the various distribution specific packages. So then I want to aim people in the right direction. How about? fftw3 (>= 3.1.2; ensure fftw3.h is exposed - libfftw3-dev in Ubuntu) Kind Regards, Karim On Fri, Sep 11, 2020 at 11:20 AM Dirk Eddelbuettel wrote: > > > On 10 September 2020 at 14:14, Marta Karaś wrote: > | Adding the following to .travis.yml: > | > | before_install: > | - if [ "$TRAVIS_OS_NAME" = "linux" ]; then sudo apt-get -y install > | libfftw3-dev ; fi > | > | did the trick! > > I think that is an example of the issue discussed in this blog post: > http://dirk.eddelbuettel.com/blog/2020/08/26#029_introducing_bspm > > The RSPM system gets you the package, but it is by its (on purpose simple) > design disconnected and unaware of the dependency required which sent you > down a rabbit hole. (One could also suggest that maybe Karim should expand >SystemRequirements: fftw3 (>= 3.1.2) > to maybe list the packages offering fftw3 _headers_. Jeroen uses a pattern > for this, eg curl has >SystemRequirements: libcurl: libcurl-devel (rpm) or libcurl4-openssl-dev (deb). > which is already one step better.) > > Only systems with actual dependency resolution can go further, but it is hard > to do that cross-platform / cross-OS. On Linux we have both BSPM utilising > the existing rpm and deb binaries, respectively, maintained by tireless > volunteers, as well as the older use of directly using the binaries. > > Eg looking at the Ubuntu binary from the Rutter PPA shows that > r-cran-fftwtools will bring the fftw3 runtime in: > >docker@08d894be427a:/work$ apt-cache show r-cran-fftwtools | grep ^Depends >Depends: r-base-core, libfftw3-double3 (>= 3.3.5) >docker@08d894be427a:/work$ > > That would be an easier binary install as it skips the 'from source' build > step that sent Marta hunting for the required header. > > If I find some time I will try to set up some Travis CI examples utilizing > BSPM. Until then, one can do as I have done for over half a decade and point > Travis CI to these binaries via the (still maintained and simple) r-travis > setup. Works for me. See http://eddelbuettel.github.io/r-travis/ and > numerous .travis.yml in packages of mine and a few other users. > > Dirk > > | Thank you both for your attention to this issue! > | > | Bests, > | Marta Karas > | > | > | > | > | > | On Thu, Sep 10, 2020 at 8:35 AM Karim Rahim wrote: > | > | > Thanks, > | > > | > That may be it. It is a missing dependency. > | > > | > It's been a while and I'm not sure which package exposes fftw3.h ... > | > > | > Karim > | > > | > On Thu, Sep 10, 2020 at 8:16 AM Dirk Eddelbuettel wrote: > | > > | >> > | >> On 9 September 2020 at 23:45, Karim Rahim wrote: > | >> | sudo apt-get install -y fftw3 > | >> > | >> Or maybe rather > | >> > | >>sudo apt-get install libfftw3-dev > | >> > | >> to get the development headers? > | >> > | >> Dirk > | >> > | >> | Then try again. > | >> | > | >> | Let me know if it doesn't work. > | >> | > | >> | Cheers! > | >> | Karim > | >> | > | >> | On Wed, Sep 9, 2020 at 10:27 PM Max Turgeon < max.turg...@umanitoba.ca> > | >> wrote: > | >> | > > | >> | > Hi Marta, > | >> | > > | >> | > One change I can see from your Git history that seems to match the > | >> first failed build on Travis is when you added "Imports: fftwtools" to your > | >> DESCRIPTION file. And it makes sense, because if we look at its DESCRIPTION > | >> file, we can see that it has fftw3 as a SystemRequirements. In other words, > | >> it needs to be installed on Travis before you can run the checks on your > | >> package. > | >> | > > | >> | > As for solutions, I can see that Karim wrote a short description of > | >> how to install the library on Linux, and there's a link for Mac; all this > | >> is on the Github repo: https://github.com/krahim/fftwtools > | >> | > > | >> | > I also noticed that there is an R package wrapping fftw on CRAN ( > | >> https://cran.r-project.org/package=fftw) and I can see that it's a > | >> Suggested package for fftwtools. I haven't tried it, but presumably you > | >> could install the fftw R package, instead of the fftw3 library. > | >> | > > | >> | > HTH, > | >> | > > | >> | > Max Turgeon > | >> | > Assistant Professor > | >> | > Department of Statistics > | >> | > Department of Computer Science| > >> | > University of Manitoba > | >> | > maxturgeon.ca > | >> | > > | >> | > > | >> | > > | >> | > > | >> | > From: R-package-devel on > | >> behalf of Marta Karaś > | >> | > Sent: Wednesday, September 9, 2020 9:09 PM > | >> | > To: package-develop > | >
Re: [R-pkg-devel] Fixing travis build fail due to fftwtools fatal error (fftw3.h: No such file or directory)
Hi Karim, On 11 September 2020 at 13:09, Karim Rahim wrote: | Thanks for resolving this! It's been awhile since I've worked on this... | | So for dependencies, I'd like to keep it as simple as possible. I agree | fftw3 may need to be updated. | | It's my understanding that if one were to install the latest fftw (3.3.8) | from source then it would expose the header file. Not necessarily and it depends on how the package is setup. In general you want a '-dev' or '-devel' package but I do not know what this one is called in the Fedora/RH/CentOS world. | Is this incorrect? | | If this is the case, then it becomes about the various distribution | specific packages. | So then I want to aim people in the right direction. | | How about? | | fftw3 (>= 3.1.2; ensure fftw3.h is exposed - libfftw3-dev in Ubuntu) So per the above I would suggest you reconsider the curl example I emailed earlier and do something like fftw3 development package: libfftw3-dev (deb), . (rpm) Maybe someone can help with the rpm package name. Cheers, Dirk | | Kind Regards, | Karim | | | | | | On Fri, Sep 11, 2020 at 11:20 AM Dirk Eddelbuettel wrote: | > | > | > On 10 September 2020 at 14:14, Marta Karaś wrote: | > | Adding the following to .travis.yml: | > | | > | before_install: | > | - if [ "$TRAVIS_OS_NAME" = "linux" ]; then sudo apt-get -y install | > | libfftw3-dev ; fi | > | | > | did the trick! | > | > I think that is an example of the issue discussed in this blog post: | > http://dirk.eddelbuettel.com/blog/2020/08/26#029_introducing_bspm | > | > The RSPM system gets you the package, but it is by its (on purpose simple) | > design disconnected and unaware of the dependency required which sent you | > down a rabbit hole. (One could also suggest that maybe Karim should expand | >SystemRequirements: fftw3 (>= 3.1.2) | > to maybe list the packages offering fftw3 _headers_. Jeroen uses a pattern | > for this, eg curl has | >SystemRequirements: libcurl: libcurl-devel (rpm) or | libcurl4-openssl-dev (deb). | > which is already one step better.) | > | > Only systems with actual dependency resolution can go further, but it is | hard | > to do that cross-platform / cross-OS. On Linux we have both BSPM | utilising | > the existing rpm and deb binaries, respectively, maintained by tireless | > volunteers, as well as the older use of directly using the binaries. | > | > Eg looking at the Ubuntu binary from the Rutter PPA shows that | > r-cran-fftwtools will bring the fftw3 runtime in: | > | >docker@08d894be427a:/work$ apt-cache show r-cran-fftwtools | grep | ^Depends | >Depends: r-base-core, libfftw3-double3 (>= 3.3.5) | >docker@08d894be427a:/work$ | > | > That would be an easier binary install as it skips the 'from source' build | > step that sent Marta hunting for the required header. | > | > If I find some time I will try to set up some Travis CI examples utilizing | > BSPM. Until then, one can do as I have done for over half a decade and | point | > Travis CI to these binaries via the (still maintained and simple) r-travis | > setup. Works for me. See http://eddelbuettel.github.io/r-travis/ and | > numerous .travis.yml in packages of mine and a few other users. | > | > Dirk | > | > | Thank you both for your attention to this issue! | > | | > | Bests, | > | Marta Karas | > | | > | | > | | > | | > | | > | On Thu, Sep 10, 2020 at 8:35 AM Karim Rahim | wrote: | > | | > | > Thanks, | > | > | > | > That may be it. It is a missing dependency. | > | > | > | > It's been a while and I'm not sure which package exposes fftw3.h ... | > | > | > | > Karim | > | > | > | > On Thu, Sep 10, 2020 at 8:16 AM Dirk Eddelbuettel | wrote: | > | > | > | >> | > | >> On 9 September 2020 at 23:45, Karim Rahim wrote: | > | >> | sudo apt-get install -y fftw3 | > | >> | > | >> Or maybe rather | > | >> | > | >>sudo apt-get install libfftw3-dev | > | >> | > | >> to get the development headers? | > | >> | > | >> Dirk | > | >> | > | >> | Then try again. | > | >> | | > | >> | Let me know if it doesn't work. | > | >> | | > | >> | Cheers! | > | >> | Karim | > | >> | | > | >> | On Wed, Sep 9, 2020 at 10:27 PM Max Turgeon < | max.turg...@umanitoba.ca> | > | >> wrote: | > | >> | > | > | >> | > Hi Marta, | > | >> | > | > | >> | > One change I can see from your Git history that seems to match | the | > | >> first failed build on Travis is when you added "Imports: fftwtools" | to your | > | >> DESCRIPTION file. And it makes sense, because if we look at its | DESCRIPTION | > | >> file, we can see that it has fftw3 as a SystemRequirements. In other | words, | > | >> it needs to be installed on Travis before you can run the checks on | your | > | >> package. | > | >> | > | > | >> | > As for solutions, I can see that Karim wrote a short description | of | > | >> how to install the library on Linux, and there's a link for Mac; all | this | > | >> is on the Github repo: https://github.com/krahim/fftwtools | > | >> | > | > | >>
[R-pkg-devel] Rcpp with clang++ -stdlib=libc++ ?
I can compile a package under clang++ with -stdlib=libstdc++, but with
-stdlib=libc++ I get
"
In file included from
/home/jo/R/x86_64-pc-linux-gnu-library/4.0/Rcpp/include/Rcpp/r/headers.h:67:
/home/jo/R/x86_64-pc-linux-gnu-library/4.0/Rcpp/include/Rcpp/platform/compiler.h:100:10:
fatal error: 'cmath' file not found
#include
^~~
1 error generated.
"
Is there any howto for using Rcpp with -stdlib=libc++ ?
Greetings from Munich
Jens Oehlschlägel
P.S.
Package Makevars
CXX_STD = CXX17
PKG_CXXFLAGS=-O3 -march=native -pthread
PKG_LIBS=-latomic -pthread
~.R/Makevars
CXX17 = clang++ -stdlib=libc++
CXX17FLAGS = -fstack-protector-strong -D_FORTIFY_SOURCE=2 -g $(LTO)
CXX17STD = -std=c++17
> packageVersion("Rcpp")
[1] ‘1.0.5’
> version
_
platform x86_64-pc-linux-gnu
arch x86_64
os linux-gnu
system x86_64, linux-gnu
status
major 4
minor 0.2
year 2020
month 06
day 22
svn rev 78730
language R
version.string R version 4.0.2 (2020-06-22)
nickname Taking Off Again
__
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