date:20200912

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

2020-09-12 Thread 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 ...
> | > | >
> | > | > Kar

Re: [R-pkg-devel] Rcpp with clang++ -stdlib=libc++ ?

2020-09-12 Thread Dirk Eddelbuettel



Hi Jens,

On 11 September 2020 at 21:00, Dr. Jens Oehlschlägel wrote:
| I can compile a package under clang++ with -stdlib=libstdc++, but with 
-stdlib=libc++ I get
| 
| "
| In file included from 
/home/jo/R/x86_64-pc-linux-gnu-library/4.0/Rcpp/include/Rcpp/r/headers.h:67:
| 
/home/jo/R/x86_64-pc-linux-gnu-library/4.0/Rcpp/include/Rcpp/platform/compiler.h:100:10:
 fatal error: 'cmath' file not found
| #include 
|  ^~~
| 1 error generated.
| "
| 
| Is there any howto for using Rcpp with -stdlib=libc++ ?

That has zero to do with Rcpp.  You are lacking a C++ library header when
switching the C++ standard library along with clang. Nothing that Rcpp ships,
or governs, or selects.  

I am forgetting the fine details here (and someone may hopefully fill in
fuller details) but in short, "that is just the way it is".  I think we
simply pivot back to the g++ standard C++ library even when using clang++.

Cheers from Chicago,  Dirk

| Greetings from Munich
| 
| Jens Oehlschlägel
| 
|  
| P.S.
| 
| Package Makevars
| CXX_STD = CXX17
| PKG_CXXFLAGS=-O3 -march=native -pthread
| PKG_LIBS=-latomic -pthread
| 
| ~.R/Makevars
| CXX17 = clang++ -stdlib=libc++
| CXX17FLAGS = -fstack-protector-strong -D_FORTIFY_SOURCE=2 -g $(LTO)
| CXX17STD = -std=c++17
| 
| > packageVersion("Rcpp")
| [1] ‘1.0.5’
| 
| > version
|    _  
| platform   x86_64-pc-linux-gnu
| arch   x86_64 
| os linux-gnu  
| system x86_64, linux-gnu  
| status
| major  4  
| minor  0.2
| year   2020   
| month  06 
| day    22 
| svn rev    78730  
| language   R  
| version.string R version 4.0.2 (2020-06-22)
| nickname   Taking Off Again
| 
| __
| R-package-devel@r-project.org mailing list
| https://stat.ethz.ch/mailman/listinfo/r-package-devel

-- 
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[R-pkg-devel] failing on win and debian -- because of new submission?

2020-09-12 Thread Simit Patel

hello,

 
i am submitting my first package for CRAN, but am failing pre-check on windows 
and debian. below is an excerpt from the failure message:

 

package wordpressr_0.1.0.tar.gz does not pass the incoming checks 
automatically, please see the following pre-tests:
Windows: 

Status: 1 NOTE
Debian: 

Status: 1 NOTE

 
as the logs confirm, the only note is related to this being a new submission. 
should i email CRAN staff noting that this is a false-positive that should be 
reviewed? 

 
any and all help is most appreciated!

 
thanks

simit 

 
-- 

URL: https://sixjupiter.com

Email: si...@sixjupiter.com

Phone/SMS/whatsapp: +1 646 327 3895

Skype: simitp_1

Telegram: @SimitPatel

 

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Re: [R-pkg-devel] failing on win and debian -- because of new submission?

2020-09-12 Thread Jeff Newmiller

I would not read anything into this. Does [1] help?

[1] https://jef.works/blog/2018/06/18/get-your-package-on-cran-in-10-steps/

On September 12, 2020 1:58:15 PM PDT, Simit Patel  wrote:
>hello,
>
> 
>i am submitting my first package for CRAN, but am failing pre-check on
>windows and debian. below is an excerpt from the failure message:
>
> 
>
>package wordpressr_0.1.0.tar.gz does not pass the incoming checks
>automatically, please see the following pre-tests:
>Windows:
>
>Status: 1 NOTE
>Debian:
>
>Status: 1 NOTE
>
> 
>as the logs confirm, the only note is related to this being a new
>submission. should i email CRAN staff noting that this is a
>false-positive that should be reviewed? 
>
> 
>any and all help is most appreciated!
>
> 
>thanks
>
>simit 
>
> 
>-- 
>
>URL: https://sixjupiter.com
>
>Email: si...@sixjupiter.com
>
>Phone/SMS/whatsapp: +1 646 327 3895
>
>Skype: simitp_1
>
>Telegram: @SimitPatel
>
> 
>
>   [[alternative HTML version deleted]]
>
>__
>R-package-devel@r-project.org mailing list
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Re: [R-pkg-devel] failing on win and debian -- because of new submission?

2020-09-12 Thread Max Turgeon

Hi Simit,

There's actually more happening in the NOTE than simply a reminder that this is 
a new submission. You get a message about a possibly invalid URL because of a 
redirect, and you also get this:

Package has a VignetteBuilder field but no prebuilt vignette index.

You may get this message when the "vignettes.rds" file is omitted because of a 
line in .Rbuildignore; see for example this: 
https://stackoverflow.com/questions/39649133/package-has-a-vignettebuilder-field-but-no-prebuilt-vignette-index
[https://cdn.sstatic.net/Sites/stackoverflow/Img/apple-touch-i...@2.png?v=73d79a89bded]
r - Package has a VignetteBuilder field but no prebuilt vignette index - Stack 
Overflow
I am submitting a package to CRAN and I have got the below warning from the 
reviewers team: Package has a VignetteBuilder field but no prebuilt vignette 
index. that I have in fact seen also when
stackoverflow.com

Max Turgeon
Assistant Professor
Department of Statistics
Department of Computer Science
University of Manitoba
maxturgeon.ca

From: R-package-devel  on behalf of Jeff 
Newmiller 
Sent: Saturday, September 12, 2020 6:47 PM
To: r-package-devel@r-project.org ; Simit Patel 
; r-package-devel@r-project.org 

Subject: Re: [R-pkg-devel] failing on win and debian -- because of new 
submission?

Caution: This message was sent from outside the University of Manitoba.

I would not read anything into this. Does [1] help?

[1] https://jef.works/blog/2018/06/18/get-your-package-on-cran-in-10-steps/

On September 12, 2020 1:58:15 PM PDT, Simit Patel  wrote:
>hello,
>
>
>i am submitting my first package for CRAN, but am failing pre-check on
>windows and debian. below is an excerpt from the failure message:
>
>
>
>package wordpressr_0.1.0.tar.gz does not pass the incoming checks
>automatically, please see the following pre-tests:
>Windows:
>
>Status: 1 NOTE
>Debian:
>
>Status: 1 NOTE
>
>
>as the logs confirm, the only note is related to this being a new
>submission. should i email CRAN staff noting that this is a
>false-positive that should be reviewed?
>
>
>any and all help is most appreciated!
>
>
>thanks
>
>simit
>
>
>--
>
>URL: https://sixjupiter.com
>
>Email: si...@sixjupiter.com
>
>Phone/SMS/whatsapp: +1 646 327 3895
>
>Skype: simitp_1
>
>Telegram: @SimitPatel
>
>
>
>   [[alternative HTML version deleted]]
>
>__
>R-package-devel@r-project.org mailing list
>https://stat.ethz.ch/mailman/listinfo/r-package-devel

--
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Re: [R-pkg-devel] Rcpp with clang++ -stdlib=libc++ ?

2020-09-12 Thread Kevin Ushey

My understanding is that many Linux OSes package the clang compiler, the
libc++ standard library, and the headers used by the libc++ standard
library separately. To install those headers, you likely need (e.g. on
Ubuntu):

sudo apt install libc++-dev libc++abi-dev

to be able to build and compile programs against libc++.

This also comes with the caveat that mixing programs built against
different standard library implementations is in general a bad idea, so you
may see issues if you mix libraries compiled with libstdc++ and libc++ in
the same R session. (This can come up with R packages that link to other
libraries installed on the system, which will typically be built with and
linked against the "default" system compiler + standard library
implementations.) I'm not sure if this will be an issue in practice with
what you're doing, but it's worth being aware of.

Best,
Kevin

On Sat, Sep 12, 2020 at 5:50 AM Dirk Eddelbuettel  wrote:

>
> Hi Jens,
>
> On 11 September 2020 at 21:00, Dr. Jens Oehlschlägel wrote:
> | I can compile a package under clang++ with -stdlib=libstdc++, but with
> -stdlib=libc++ I get
> |
> | "
> | In file included from
> /home/jo/R/x86_64-pc-linux-gnu-library/4.0/Rcpp/include/Rcpp/r/headers.h:67:
> |
> /home/jo/R/x86_64-pc-linux-gnu-library/4.0/Rcpp/include/Rcpp/platform/compiler.h:100:10:
> fatal error: 'cmath' file not found
> | #include 
> |  ^~~
> | 1 error generated.
> | "
> |
> | Is there any howto for using Rcpp with -stdlib=libc++ ?
>
> That has zero to do with Rcpp.  You are lacking a C++ library header when
> switching the C++ standard library along with clang. Nothing that Rcpp
> ships,
> or governs, or selects.
>
> I am forgetting the fine details here (and someone may hopefully fill in
> fuller details) but in short, "that is just the way it is".  I think we
> simply pivot back to the g++ standard C++ library even when using clang++.
>
> Cheers from Chicago,  Dirk
>
> | Greetings from Munich
> |
> | Jens Oehlschlägel
> |
> |
> | P.S.
> |
> | Package Makevars
> | CXX_STD = CXX17
> | PKG_CXXFLAGS=-O3 -march=native -pthread
> | PKG_LIBS=-latomic -pthread
> |
> | ~.R/Makevars
> | CXX17 = clang++ -stdlib=libc++
> | CXX17FLAGS = -fstack-protector-strong -D_FORTIFY_SOURCE=2 -g $(LTO)
> | CXX17STD = -std=c++17
> |
> | > packageVersion("Rcpp")
> | [1] ‘1.0.5’
> |
> | > version
> |_
> | platform   x86_64-pc-linux-gnu
> | arch   x86_64
> | os linux-gnu
> | system x86_64, linux-gnu
> | status
> | major  4
> | minor  0.2
> | year   2020
> | month  06
> | day22
> | svn rev78730
> | language   R
> | version.string R version 4.0.2 (2020-06-22)
> | nickname   Taking Off Again
> |
> | __
> | 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
>
> __
> R-package-devel@r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/r-package-devel
>

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

Re: [R-pkg-devel] Rcpp with clang++ -stdlib=libc++ ?

[R-pkg-devel] failing on win and debian -- because of new submission?

Re: [R-pkg-devel] failing on win and debian -- because of new submission?

Re: [R-pkg-devel] failing on win and debian -- because of new submission?

Re: [R-pkg-devel] Rcpp with clang++ -stdlib=libc++ ?

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