Re: [R-pkg-devel] [R] a question of etiquette

2020-06-02 Thread Avraham Adler
: > The obvious answer is simply to refer to GPL. It isn't necessary to > propagate a derogatory point of view by finding another word for an > incorrect idea. Try re-reading my previous words without trying to hold on > to a flawed interpretation. > > On June 2, 2020 5:33:56 PM

Re: [R-pkg-devel] [R] a question of etiquette

2020-06-02 Thread Avraham Adler
were trying to steal > something you did instead of protecting their code from being stolen. > Please refrain from being inflammatory. > > On June 2, 2020 4:49:25 PM PDT, Avraham Adler > wrote: > >IANAL, but the GPL family of licenses is VIRAL copy left so it infects > >

Re: [R-pkg-devel] [R] a question of etiquette

2020-06-02 Thread Avraham Adler
IANAL, but the GPL family of licenses is VIRAL copy left so it infects anything it touched, which is why many shy away and prefer something like the Mozilla Public License 2 (MPL) as a compromise between viral copyleft and the permissive MIT/ISC/BSD2. Avi On Tue, Jun 2, 2020 at 7:32 PM R. Mark

Re: [R-pkg-devel] [R] a question of etiquette

2020-06-02 Thread Avraham Adler
On Tue, Jun 2, 2020 at 5:04 PM Spencer Graves < spencer.gra...@effectivedefense.org> wrote: > QUESTION: How much money have people on this list received for what > they've written? I've received not one penny for any technical article > I've written or for software contributed to CRAN. > >

Re: [R-pkg-devel] For reproducibility issue

2020-01-17 Thread Avraham Adler
or. The output at the end of > running the functions kept having very similar results, but still have the > issue of reproducing exact results which I need it for relating work that is > based on the package. > > > > Many thanks, > > > > Waleed > > >

Re: [R-pkg-devel] For reproducibility issue

2020-01-17 Thread Avraham Adler
Hi. If it helps, I call the R RNG from Fortran in my Delaporte package [1], also using iso_c_bindings. Specifically, I have the following C code [2]: void F77_SUB(unifrnd) (int *n, double *x){ GetRNGstate(); for (int i = 0; i < *n; ++i){ *(x + i) = unif_rand(); } PutRNGstate(); } and call it in

Re: [R-pkg-devel] Using FORTRAN libraries and compiler options

2019-11-11 Thread Avraham Adler
If I’m not mistaken, dgemm is a BLAS call. That should be accessible from Fortran via an external call. I think the mvtnorm package calls BLAS/LAPACK from Fortran if that helps. Avi On Mon, Nov 11, 2019 at 6:40 AM Rampal S. Etienne wrote: > Hello, > > I am using FORTRAN code with the deSolve

Re: [R-pkg-devel] .Fortran opinion

2019-05-26 Thread Avraham Adler
If you read further in Drew's posts (which I highly recommend) he says that C++/Rcpp isn't the best for wrapping Fortran calls, and that it is faster and cleaner to use C. I have a relatively detailed blog post on building packages with Fortran (or raw C) code; I hope you may find it useful in

Re: [R-pkg-devel] registering native routines

2019-02-16 Thread Avraham Adler
https://stat.ethz.ch/pipermail/r-devel/2017-February/073755.html On Sat, Feb 16, 2019 at 3:22 PM Charles Geyer wrote: > > I just noticed that R package foo in the github repo > https://github.com/cjgeyer/foo no longer passes R CMD check --as-cran. The > problem seems to be that it does not

[R-pkg-devel] OpenMP & Fortran: Seemingly contradictory responses from CRAN

2019-01-27 Thread Avraham Adler
Hello. I am at my wits end as to how to comply with CRAN regarding my Delaporte package which uses Fortran and OpenMP [1]. Recently, it was announced [2] that going forward, OpenMP should be linked with SHLIB_OPENMP_CFLAGS. Moreover, I received an email from Professor Ripley, stating:

Re: [R-pkg-devel] package fails with parallel make - would forcing a serial version work?

2019-01-14 Thread Avraham Adler
If you want to use .NOTPARRALLEL, that’s considered non-portable as it’s GNU-make specific, (I got an email from Dr. Ripley this week) so you have to add Gnu Make to the system requirements in the DESCRIPTION or find the right sequence of targets to ensure order is maintained even in parallel

[R-pkg-devel] Best practices for R package requiring Fortran 2003

2018-12-03 Thread Avraham Adler
Following the news, I've been trying to clean up my package which uses Fortran in preparation for the changes that appear to be coming in R-devel. The package has implicitly been relying on Fortran 2003, since it uses iso_c_binding. In practice, is it proper that "-std=f2003" be explicitly added

Re: [R-pkg-devel] avoiding .mod files

2018-11-20 Thread Avraham Adler
On Tue, Nov 20, 2018 at 4:45 AM Rampal Etienne wrote: > > Dear Thomas, > > My FORTRAN code to be used with deSolve contains a module dimmod. During > build a file called dimmod.mod is created in the src directory. I can > avoid this by including it in the .RBuildignore file, but when I submit >

Re: [R-pkg-devel] Trying to compile R-3.5.1 with openblas for windows

2018-09-15 Thread Avraham Adler
Fantastic! Avi On Sat, Sep 15, 2018 at 7:26 PM Erin Hodgess wrote: > Finally got Openblas installed! The speed up is amazing! Thanks for your > help and patience. > > Sincerely, > Erin > > Erin Hodgess, PhD > mailto: erinm.hodg...@gmail.com > > > On Fri, Sep

Re: [R-pkg-devel] Trying to compile R-3.5.1 with openblas for windows

2018-09-14 Thread Avraham Adler
parse.c:(.text+0xd4c): undefined reference to > `cholmod_free_sparse' > Csparse.o:Csparse.c:(.text+0xdf9): undefined reference to `cholmod_copy' > > Does this look familiar, please? > > Thanks, > Erin > > Erin Hodgess, PhD > mailto: erinm.hodg...@gmail.com > > > On

Re: [R-pkg-devel] Trying to compile R-3.5.1 with openblas for windows

2018-09-14 Thread Avraham Adler
Try following the directions here. They have worked for me for years. Please see the comments too. https://www.avrahamadler.com/r-tips/build-openblas-for-windows-r64/ Hope that helps, Avi On Fri, Sep 14, 2018 at 2:34 PM Erin Hodgess wrote: > Hello! > > I'm building a package that needs

Re: [R-pkg-devel] Trouble installing XML on Windows 7 (64-bit)

2017-12-15 Thread Avraham Adler
On Fri, Dec 15, 2017 at 12:02 PM, Haigh, Rowan wrote: > Hi Duncan, > > Well I finally managed to install XML from source in Windows under R-devel. > Basically it was a clue provided by user wlandau-lilly (last message on > https://github.com/igraph/igraph/issues/915),

Re: [R-pkg-devel] New package submission error (ieee_arithmetic)

2017-11-30 Thread Avraham Adler
On Wed, Nov 29, 2017 at 4:37 PM, Waleed Almutiry wrote: > Hi all, > > I tried to upload my package to CRAN and did not pass the the incoming > checks. This was because the use of ieee_arithmetic module in a fortran > subroutine in the src folder. I built and checked the

Re: [R-pkg-devel] New package submission error (ieee_arithmetic)

2017-11-30 Thread Avraham Adler
On Wed, Nov 29, 2017 at 4:37 PM, Waleed Almutiry wrote: > I tried to upload my package to CRAN and did not pass the the incoming > checks. This was because the use of ieee_arithmetic module in a fortran > subroutine in the src folder. I built and checked the package using

Re: [R-pkg-devel] R_registerRoutines, etc.

2017-04-23 Thread Avraham Adler
On Sun, Apr 23, 2017 at 7:51 PM, Dirk Eddelbuettel wrote: > > On 24 April 2017 at 11:47, Rolf Turner wrote: > > And per Duncan's last (and his earlier emails) maybe you need to call from R > into C (for finer control over the interface) and only then call your Fortran > worker

Re: [R-pkg-devel] R_registerRoutines, etc.

2017-04-23 Thread Avraham Adler
On Sun, Apr 23, 2017 at 7:36 PM, Duncan Murdoch wrote: > On 23/04/2017 6:18 PM, Rolf Turner wrote: [SNIP] > This is important: *there is no way to pass a Fortran "LOGICAL" from R to > Fortran*. > > The issue is that different Fortran compilers store LOGICAL in different

Re: [R-pkg-devel] Solaris SPARC, Fortran, and logical errors?

2017-03-31 Thread Avraham Adler
On Wed, Mar 15, 2017 at 12:19 PM, William Dunlap wrote: > I don't know about the current Sparc Fortran compilers, but over the > years have learned not to try to pass logicals and character strings > between C and Fortran. I have seen Fortran compilers that treated > integer

Re: [R-pkg-devel] Solaris SPARC, Fortran, and logical errors?

2017-03-15 Thread Avraham Adler
On Wed, Mar 15, 2017 at 11:09 AM, J C Nash wrote: > Possibly tangential, but has there been any effort to set up a Sparc > testbed? It > seems we could use a network-available (virtual?) machine, since this > platform is > often the unfortunate one. Unless, of course,

Re: [R-pkg-devel] Solaris SPARC, Fortran, and logical errors?

2017-03-15 Thread Avraham Adler
On Wed, Mar 15, 2017 at 12:19 PM, William Dunlap wrote: > I don't know about the current Sparc Fortran compilers, but over the > years have learned not to try to pass logicals and character strings > between C and Fortran. I have seen Fortran compilers that treated > integer

[R-pkg-devel] Packages which use Fortran call "rwarn" for warnings?

2017-02-15 Thread Avraham Adler
Hello. Would anyone know of a package which uses the rwarn subroutine, as described in Writing R extensions 6.2.1, for error handling from Fortran? I'm experimenting with it and getting overwhelmed with stack errors and crashes, and could benefit from seeing it used properly. Thank you, Avi

[R-pkg-devel] Delaporte: Test Errors on Sun Sparc

2017-02-05 Thread Avraham Adler
I recently changed the back-end compiled code for the Delaporte package from C++ to Fortran/C, and after some birthing pains (and a lot of patience shown by CRAN), it's fully functional _except_ on sparc-sun-solaris2.10 [1]. There, 10 of the 44 tests return errors. I've done enough research to

Re: [R-pkg-devel] recreating CRAN Testing environment

2015-07-20 Thread Avraham Adler
Even if you don't use Windows, it pays to submit your package to the Winbuilder test of buth R-release and R-devel. The error reports, if any, are often not-OS dependant and will serve as a good gaage as to how the real CRAN will respond. Avi On Mon, Jul 20, 2015 at 1:59 PM, Ben Bolker