Re: [R-pkg-devel] RCMD check --as-cran on Windows

If it helps, in my experience, r-devel has those notes as well, so if you send your package to the r-devel option on winbuilder, and it comes back clean, you should be OK on all OSs, at least as respects the global function issues. Avi On Thu, Jul 2, 2015 at 10:51 AM, Fay, Michael (NIH/NIAID) [E]

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

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 wrote: >

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

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 know

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

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] Solaris SPARC, Fortran, and logical errors?

Hello. The Delaporte package works properly on all R-core platforms except Solaris SPARC, where it compiles properly but fails a number of its tests [1]. Not having access to a SPARC testbed, I'm limited in what kind of diagnostics I can do. One thing I have noticed is that a lot of the failures

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

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 -1 (all bits 1) as .t

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

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, there's a sunset date. > Is

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

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 -1 (all bits 1) as .t

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

On Sat, Apr 22, 2017 at 6:13 PM, Rolf Turner wrote: > > The foregoing "official" way would seem to apply to functions called by > ".Call" (which I never use; it is way over my head). What about functions > called by ".Fortran()" or ".C()"? > >> | (b) For the sake of completeness, how *does* o

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

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 > ways. Some are equivale

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

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 function. To hide i

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

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 (R CMD > build) and (R

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

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 package using (R CMD > b

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

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), and discussions between Gáb

Re: [R-pkg-devel] Question about preventing CRAN package archival

Exactly. Is square is just brow=ncol, is positive definite can be implemented as a check that all eigenvalues > 0, which can be done with base, and is.symmetric can be simply brute forced in a loop comparing i,j with j,i. The fewer dependencies a package has, the more robust it is. It’s a fine bal

Re: [R-pkg-devel] Question about preventing CRAN package archival

On the other hand, MIT does not restrict what you do with your own contributions, just the included code. GPL restricts rights on redistributing your own work if a component is GPL as well. Avi On Thu, Jun 3, 2021 at 6:51 AM Berwin A Turlach wrote: > > G'day Jeff, > > On Wed, 02 Jun 2021 11:34:2

Re: [R-pkg-devel] Tools beyond roxygen2 to write Rd documentation

I always write mine by hand. Used to do it in notepad++. Now I just do it as a text file in the Rstudio IDE. Avi On Thu, Aug 5, 2021 at 11:52 AM Martin Maechler wrote: > > Iago Giné-Vázquez > > on Thu, 05 Aug 2021 08:09:48 + writes: > > > Dear all, Are there any tools to edi

Re: [R-pkg-devel] "Connections left open" Error

On Fri, Aug 27, 2021 at 10:25 AM Uwe Ligges wrote: > > > On 23.08.2021 18:07, Alan Aw wrote: > > Hi, > > > > I submitted a package to CRAN, but it keeps failing a particular check > for > > Windows. This error shows up when I check my code examples. > > > > Error: connections left open: > >>

Re: [R-pkg-devel] CRAN no longer checking for solaris?

Would this mean we could start using little endian bit strings, as I think only the Solaris platform was big endian (or was it the other way around)? Avi On Sun, Dec 5, 2021 at 8:56 PM Dirk Eddelbuettel wrote: > > On 5 December 2021 at 17:23, Travers Ching wrote: > | I see that there doesn't ex

Re: [R-pkg-devel] Two problems with fda

mendations on how to ask for help. > > I remember he suggested submitting a question first to Stack Exchange or > > Stack Overflow or ..., but I can't find those recommendations, so I > > thought I'd here thank Avraham Adler and > > everyone else who has considered replying

Re: [R-pkg-devel] No package called 'scales' (r-oldrel-windows)

Scales is the package which is called when you use something like "dollar" or "comma" in scale_x_whatever(); perhaps you have a similar invocation without realizing it? Thanks, Avi On Tue, Aug 23, 2022 at 5:40 PM Paul Hibbing wrote: > > Hi all, > > I recently submitted an update to `PAutilities

[R-pkg-devel] Proper way to express Fortran 2008 dependence for R package

I would like to convert some of my hand-rolled Fortran code to Fortran intrinsics which entered the language in Fortran 2008, which should be extremely widely supported at this time. Specifically, I would like to use the log_gamma function and ieee_arithmetic functions and values. If it helps, the

Re: [R-pkg-devel] Proper way to express Fortran 2008 dependence for R package

t they are 5 or 15 years old by now :). Thank you, Avi [1]: https://developer.r-project.org/blosxom.cgi/R-devel/NEWS/2023/02/02#n2023-02-02 On Mon, Jan 30, 2023 at 12:12 AM Avraham Adler wrote: > > I would like to convert some of my hand-rolled Fortran code to Fortran > intrinsics which

Re: [R-pkg-devel] How to update "SystemRequirements: C++11"?

On Mon, Feb 6, 2023 at 9:46 PM Duncan Murdoch wrote: > > On 06/02/2023 4:01 p.m., Duncan Murdoch wrote: > > On 06/02/2023 3:46 p.m., Winston Chang wrote: > >> I recently submitted a package to CRAN with "SystemRequirements: C++11". > >> This raises the following NOTE on R-devel, and I was asked to

Re: [R-pkg-devel] How to update "SystemRequirements: C++11"?

"If a package does have a src/Makevars[.win] file then also setting the make variable ‘CXX_STD’ there is recommended," Avi On Mon, Feb 6, 2023 at 10:58 PM Iñaki Ucar wrote: > > On Mon, 6 Feb 2023 at 23:27, Avraham Adler wrote: > > > > On Mon, Feb 6, 2023 at 9:46 P

Re: [R-pkg-devel] How to update "SystemRequirements: C++11"?

On Tue, Feb 7, 2023 at 12:10 AM Iñaki Ucar wrote: > > On Tue, 7 Feb 2023 at 00:09, Avraham Adler wrote: > > > > "If a package does have a src/Makevars[.win] file then also setting > > the make variable ‘CXX_STD’ there is recommended," > > That doesn

Re: [R-pkg-devel] Package PowerSDI NOTES

Hello, Gabriel. CRAN policy is to rarely, if ever, allow long-running examples. It would be best if you could give an example of the function which requires as little run time as possible. Perhaps pre-compute some stages? Avi Sent from my iPhone > On Jul 18, 2023, at 9:07 PM, Gabriel Constan

Re: [R-pkg-devel] status of "possibly invalid URL/403 error" NOTEs?

I had a similar issue with a paper on JSTOR. Usually CRAN let it through. However, I eventually switched from URL to DOI and now the user needs to find the free source so to rid myself of the constant hassle. CRAN really doesn’t like redirects. I guess you could wrap it in \code{} so as not to h

Re: [R-pkg-devel] Re-building vignettes had CPU time 9.2 times elapsed time

To be fair, data.table defaults to using 1/2 the available cores; they do not take the entire machine by default. Avi Sent from my iPhone > On Aug 25, 2023, at 6:46 PM, Duncan Murdoch wrote: > > On 25/08/2023 6:13 p.m., Toby Hocking wrote: >> Thanks Dirk. I agree. >> data.table is not in a

Re: [R-pkg-devel] Modernizing legacy Fortran:, REAL(kind=8)

I’ve had no issues using the iso_c_binding schema. Avi Sent from my iPhone > On Aug 30, 2023, at 2:43 AM, Thomas Petzoldt > wrote: > > Hi, > > some package maintainers including me got a reminder from Prof. Brian Ripley > to modernize REAL and INTEGER declarations using the KIND option:

Re: [R-pkg-devel] Modernizing legacy Fortran:, REAL(kind=8)

Hi, Thomas. Since all the Fortran code must talk to R through SEXP's written in C, wouldn't it make sense to use " C_DOUBLE_COMPLEX" and " C_DOUBLE" to ensure maximum compatibility? Thanks, Avi On Thu, Aug 31, 2023 at 9:42 AM Thomas Petzoldt < thomas.petzo...@tu-dresden.de> wrote: > On 30.08.2

Re: [R-pkg-devel] Spelling of PDB in Package Description

Regarding PDB, in Rd format it’s best to wrap that in an \acronym{} tag. See section 2.3 of https://cran.r-project.org/doc/manuals/R-exts.html#Marking-text Avi Sent from my iPhone > On Sep 14, 2023, at 3:40 PM, Leonard Mada via R-package-devel > wrote: > > Dear List Members, > > After resu

Re: [R-pkg-devel] What happened to mlr3proba on CRAN?

https://cran-archive.r-project.org/web/checks/2022/2022-05-16_check_results_mlr3proba.html On Mon, Oct 9, 2023 at 12:37 AM Dr. Franz Király wrote: > Dear all, > > can someone explain to me what exactly happened to mlr3proba on CRAN? > https://cran.r-project.org/web/packages/mlr3proba/index.html

[R-pkg-devel] Unable to access log operator in C

I am hoping the solution to this question is simple, but I have not been able to find one. I am building a routine in C to be called from R. I am including Rmath.h. However, when I have a call to "log", I get the error "called object 'log' is not a function or a function pointer. When I "trick" it

Re: [R-pkg-devel] Unable to access log operator in C

28, 2024 at 7:14 PM Dirk Eddelbuettel wrote: > > > On 28 February 2024 at 19:05, Avraham Adler wrote: > | I am hoping the solution to this question is simple, but I have not > | been able to find one. I am building a routine in C to be called from > | R. I am including Rmath.h. H

[R-pkg-devel] Check results on r-devel-windows claiming error but tests seem to pass?

I noticed that a few of my packages appear to be failing on "r-devel-windows-x86_64". Specficially, Delaporte [1], lamW [2], and revss[3]. However, checking the output of the tests shows that all passed. Is this a hiccup or is there something that needs to be changed? And why would my other two pac

Re: [R-pkg-devel] package removed from CRAN

According to the CRAN links , your package had an error on r-devel-windows-x86_64 and r-patched-linux-x86_64 which was not addressed. Specifically, some examples failed. See

Re: [R-pkg-devel] SIAM Wilkinson prize

Seems as if it is restricted to people with PhDs. Avi On Fri, May 18, 2018 at 1:13 PM J C Nash wrote: > It occurs to me that there could be packages developed by early career R > developers that might fit > this prize which is considered quite prestigious (not to mention the cash) > in the nume

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

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 Openbl

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

.o:Csparse.c:(.text+0xd3d): undefined reference to > `cholmod_copy_sparse' > Csparse.o:Csparse.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?

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

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] avoiding .mod files

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 > th

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

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 to

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

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 make.

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

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: ---ST

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

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 regis

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

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 your

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

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 pa

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

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 F

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

re not major. 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] [R] a question of etiquette

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] [R] a question of etiquette

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 Sh

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

as if they 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

: > 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 5:33:5