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

[Marta Karaś]

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!

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
>>
>

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