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 <e...@debian.org> 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 <karim.ra...@gmail.com> | 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 <e...@debian.org> | 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 <r-package-devel-boun...@r-project.org> on | > | >> behalf of Marta Karaś <marta.kar...@gmail.com> | > | >> | > Sent: Wednesday, September 9, 2020 9:09 PM | > | >> | > To: package-develop <r-package-devel@r-project.org> | > | >> | > Cc: karim.ra...@queensu.ca <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; | > | >> | > I am hoping maybe some Community members saw a similar error with | > | >> their dev | > | >> | > work and can suggest a hint/solution? | > | >> | > | > | >> | > Package GitHub: https://github.com/martakarass/runstats | > | >> | > Failed Travis job log: | > | >> | > https://travis-ci.com/github/martakarass/runstats/jobs/383037333 | > | >> | > | > | >> | > Error excerpt: | > | >> | > | > | >> | > * installing *source* package ‘fftwtools’ ... | > | >> | > ** package ‘fftwtools’ successfully unpacked and MD5 sums checked | > | >> | > ** using staged installation | > | >> | > ** libs | > | >> | > gcc -I"/opt/R/4.0.2/lib/R/include" -DNDEBUG | -I/usr/local/include | > | >> -fpic | > | >> | > -g -O2 -c fftwtools.c -o fftwtools.o | > | >> | > fftwtools.c:28:18: fatal error: fftw3.h: No such file or | directory | > | >> | > compilation terminated. | > | >> | > /opt/R/4.0.2/lib/R/etc/Makeconf:167: recipe for target | 'fftwtools.o' | > | >> failed | > | >> | > make: *** [fftwtools.o] Error 1 | > | >> | > ERROR: compilation failed for package ‘fftwtools’ | > | >> | > * removing ‘/home/travis/R/Library/fftwtools’ | > | >> | > Error in i.p(...) : | > | >> | > (converted from warning) installation of package ‘fftwtools’ | had | > | >> non-zero | > | >> | > exit status | > | >> | > Calls: <Anonymous> ... with_rprofile_user -> with_envvar -> | force -> | > | >> force | > | >> | > -> i.p | > | >> | > Execution halted | > | >> | > The command "Rscript -e 'deps <- | > | >> remotes::dev_package_deps(dependencies = | > | >> | > NA);remotes::install_deps(dependencies = TRUE);if | (!all(deps$package | > | >> %in% | > | >> | > installed.packages())) { message("missing: ", | > | >> paste(setdiff(deps$package, | > | >> | > installed.packages()), collapse=", ")); q(status = 1, save = | "no")}'" | > | >> | > failed and exited with 1 during . | > | >> | > Your build has been stopped. | > | >> | > | > | >> | > | > | >> | > Thank you, | > | >> | > | > | >> | > Marta | > | >> | > | > | >> | > [[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 | > | >> | > | >> -- | > | >> https://dirk.eddelbuettel.com | @eddelbuettel | e...@debian.org | > | >> | > | > | > | > -- | > https://dirk.eddelbuettel.com | @eddelbuettel | e...@debian.org -- https://dirk.eddelbuettel.com | @eddelbuettel | e...@debian.org ______________________________________________ R-package-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-package-devel
