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

[Dirk Eddelbuettel]

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