[R-pkg-devel] Fixing travis build fail due to fftwtools fatal error (fftw3.h: No such file or directory)

[Karim Rahim]

Hello,

There is only one fftw3 tar.gz  file that I see.

http://www.fftw.org/download.html

Once built it provides headers and static libraries to use fftw3 in cpp.

For an example of how it's used in cpp see:
http://www.fftw.org/fftw3_doc/Complex-One_002dDimensional-DFTs.html#Complex-One_002dDimensional-DFTs

As a general rule, you will need header files and to compile cpp code
using libraries.

This package basically provides a wrapper for fftw3 cpp routines. I
wrote it so I could easily swap fftw for fft in my multitaper package.

Ok I looked at the curl dependencies on the cran page.

If I do something similar, I would have:
libfftw3-dev (deb)
fftw-devel (rpm)

The documentation for these two packages state these contain the
header files and static libraries.

https://packages.debian.org/stretch/libfftw3-dev
http://rpmfind.net/linux/rpm2html/search.php?query=fftw-devel

I don't expect to rush this update, and I would appreciate
confirmation before doing this from a redhat user.

I appreciate that this is of use. I get less comments about this than
multitaper.

Kind regards,
Karim




On Fri., Sep. 11, 2020, 19:54 Dirk Eddelbuettel, <edd using debian.org> wrote:
>
>
> 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 <edd using debian.org> wrote:
> | >
> | >
> | > On 10 September 2020 at 14:14, Marta Karaś wrote:
> | > | Adding the following to .travis.yml:
> | > |
> | > | before_install:
> | > |   - if [ "$TRAVIS_OS_NAME" = "linux" ]; then sudo apt-get -y install
> | > | libfftw3-dev ; fi
> | > |
> | > | did the trick!
> | >
> | > I think that is an example of the issue discussed in this blog post:
> | >   http://dirk.eddelbuettel.com/blog/2020/08/26#029_introducing_bspm
> | >
> | > The RSPM system gets you the package, but it is by its (on purpose simple)
> | > design disconnected and unaware of the dependency required which sent you
> | > down a rabbit hole. (One could also suggest that maybe Karim should expand
> | >    SystemRequirements:  fftw3 (>= 3.1.2)
> | > to maybe list the packages offering fftw3 _headers_. Jeroen uses a pattern
> | > for this, eg curl has
> | >    SystemRequirements:  libcurl: libcurl-devel (rpm) or
> | libcurl4-openssl-dev (deb).
> | > which is already one step better.)
> | >
> | > Only systems with actual dependency resolution can go further, but it is
> | hard
> | > to do that cross-platform / cross-OS.  On Linux we have both BSPM
> | utilising
> | > the existing rpm and deb binaries, respectively, maintained by tireless
> | > volunteers, as well as the older use of directly using the binaries.
> | >
> | > Eg looking at the Ubuntu binary from the Rutter PPA shows that
> | > r-cran-fftwtools will bring the fftw3 runtime in:
> | >
> | >    docker using 08d894be427a:/work$ apt-cache show r-cran-fftwtools | grep
> | ^Depends
> | >    Depends: r-base-core, libfftw3-double3 (>= 3.3.5)
> | >    docker using 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.rahim using 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 <edd using 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.Turgeon using 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-bounces using r-project.org> on
> | > | >> behalf of Marta Karaś <marta.karass using gmail.com>
> | > | >> | > Sent: Wednesday, September 9, 2020 9:09 PM
> | > | >> | > To: package-develop <r-package-devel using r-project.org>
> | > | >> | > Cc: karim.rahim using queensu.ca <karim.rahim using 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 using r-project.org mailing list
> | > | >> | > https://stat.ethz.ch/mailman/listinfo/r-package-devel
> | > | >> |
> | > | >> | ______________________________________________
> | > | >> | R-package-devel using r-project.org mailing list
> | > | >> | https://stat.ethz.ch/mailman/listinfo/r-package-devel
> | > | >>
> | > | >> --
> | > | >> https://dirk.eddelbuettel.com | @eddelbuettel | edd using debian.org
> | > | >>
> | > | >
> | >
> | > --
> | > https://dirk.eddelbuettel.com | @eddelbuettel | edd using debian.org
>
> --
> https://dirk.eddelbuettel.com | @eddelbuettel | edd using debian.org