Re: [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,  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  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 
> | 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 ...
> | > | >
> | > | > 

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

[Dirk Eddelbuettel]

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  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 
| 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 
| 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
| > | >> | >
| > | >> 

Re: [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  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 
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 
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  on
> | >> behalf of Marta Karaś 
> | >> | > Sent: Wednesday, September 9, 2020 9:09 PM
> | >> | > To: package-develop 
> | 

Re: [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@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  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  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 
| >> 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  on
| >> behalf of Marta Karaś 
| >> | > Sent: Wednesday, September 9, 2020 9:09 PM
| >> | > To: package-develop 
| >> | > Cc: 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;
| >> 

Re: [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  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  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 
>> 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  on
>> behalf of Marta Karaś 
>> | > Sent: Wednesday, September 9, 2020 9:09 PM
>> | > To: package-develop 
>> | > Cc: 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:  ... 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
>> |
>> | 

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

[Karim Rahim]

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  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 
> 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  on
> behalf of Marta Karaś 
> | > Sent: Wednesday, September 9, 2020 9:09 PM
> | > To: package-develop 
> | > Cc: 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:  ... 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
>

[[alternative HTML version deleted]]

__
R-package-devel@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-package-devel

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

[Dirk Eddelbuettel]

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  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  on behalf of 
Marta Karaś 
| > Sent: Wednesday, September 9, 2020 9:09 PM
| > To: package-develop 
| > Cc: 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:  ... 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

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

[Karim Rahim]

 sudo apt-get install -y fftw3

Then try again.

Let me know if it doesn't work.

Cheers!
Karim

On Wed, Sep 9, 2020 at 10:27 PM Max Turgeon  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  on behalf of 
> Marta Karaś 
> Sent: Wednesday, September 9, 2020 9:09 PM
> To: package-develop 
> Cc: 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:  ... 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

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

[Max Turgeon]

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  on behalf of 
Marta Kara� 
Sent: Wednesday, September 9, 2020 9:09 PM
To: package-develop 
Cc: 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:  ... 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]]

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