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

[Karim Rahim]

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 <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

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