Re: [R-pkg-devel] CXX14 not defined on Windows

2020-02-05 Thread Ralf Stubner
On Tue, Feb 4, 2020 at 5:51 PM Guido Kraemer wrote: > I have also set `~/.R/Makevars.win` as suggested in the manual "Writing > R extensions", Section 1.2.5 "Using C++14 code". What exactly do you have in src/Makevars.win? Just the simple CXX_STD = CXX14 or the more complex set-up from the end

Re: [R-pkg-devel] How to provide a finalized PDF file in a package?

2020-01-21 Thread Ralf Stubner
On Tue, Jan 21, 2020 at 5:50 PM Gábor Csárdi wrote: > > While R.rsp is a great workaround, I wish we had a better solution for > including a static PDF file in a package, one that does not require 6 > additional packages to leave a file exactly as it is One can use a Sweave vignette and

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

2020-01-17 Thread Ralf Stubner
On Fri, Jan 17, 2020 at 2:56 PM ‫وليد خلف معوض المطيرى‬‎ wrote:‬ > This might be because the RNG method used in random_number function is > different between the used version GCC 6 or less and the new ones GCC 8 or > greater. This is quite likely correct. The current gfortran docs [1] list

Re: [R-pkg-devel] Large Data Package CRAN Preferences

2019-12-15 Thread Ralf Stubner
On Sun, Dec 15, 2019 at 6:27 PM wrote: > Thanks for this information, and it makes sense to me. Is there a preferred > way to cache the data locally? Personally I like making an R package out of the data and hosting it in an "AdditionalRepository". This is quite easy with the help of the drat

Re: [R-pkg-devel] Compiler warning using C versions of base R integrate function

2019-11-22 Thread Ralf Stubner
On Thu, Nov 21, 2019 at 7:25 PM Devin Incerti wrote: > I'm attempting to submit a very minor update to my package where I replaced > a deprecated C++ function with an alternative. However, I'm receiving an > unrelated warning "*array subscript -1 is outside array bounds of ‘double > [52]’

Re: [R-pkg-devel] Use LAPACK, BLAS and CBLAS paths in configure file

2019-11-05 Thread Ralf Stubner
On Tue, Nov 5, 2019 at 10:12 AM Sameh M. Abdulah wrote: > 1- Use LAPACK, BLAS, and CBLAS paths in my configure file. What is the > command to use or what are the environment variables to read? According to WRE [1] you should include "$(LAPACK_LIBS) $(BLAS_LIBS) $(FLIBS)" in PKG_LIBS via

Re: [R-pkg-devel] Package or namespace load failed: undefined symbol

2019-09-27 Thread Ralf Stubner
On Thu, Sep 26, 2019 at 3:41 PM Sameh M. Abdulah wrote: > > I am installing my dependencies including OpenBLAS during the package > installation via the configure file. > What is surprising me that even all dependencies are installed successfully. > R cannot load one of the library > that

Re: [R-pkg-devel] Package or namespace load failed: undefined symbol

2019-09-26 Thread Ralf Stubner
On Wed, Sep 25, 2019 at 3:34 PM Sameh M. Abdulah wrote: > My package depends on another C-based software that needs LAPACKE to compile. > I do not know a lot about it. I think adding LAPACKE to my package will be a > good solution. > Could you please give me more information of how to do this?

Re: [R-pkg-devel] Package or namespace load failed: undefined symbol

2019-09-25 Thread Ralf Stubner
On Wed, Sep 25, 2019 at 10:29 AM Sameh M. Abdulah wrote: > I am installing OpenBLAS because I need LAPACKE libraries which I cannot find > on the current version of OpenBLAS on CRAN. > > I add the libraries directory in my package to the PKG_CONFIG_PATH. Is this > enough for the system to use

Re: [R-pkg-devel] Package or namespace load failed: undefined symbol

2019-09-25 Thread Ralf Stubner
On Tue, Sep 24, 2019 at 12:10 PM Sameh M. Abdulah wrote: > I am uploading my R package to CRAN. One of the dynamic libraries the package > requires depends on LAPACKE library which usually integrated with BLAS and > CBLAS in the same .so file (as I understand). CRAN has OpenBLAS already >

Re: [R-pkg-devel] Fwd: Reproducing CRAN pre-tests

2019-09-20 Thread Ralf Stubner
On Fri, Sep 20, 2019 at 11:44 AM Aravind J. wrote: > However, the question remains, is there any way to replicate the CRAN > pre-tests locally for future debugging, particularly in a windows > environment? > > I had tried rhub platforms without any success. I have found the docker image

Re: [R-pkg-devel] set pkg_config for 3rd party software

2019-09-06 Thread Ralf Stubner
On Thu, Sep 5, 2019 at 6:36 PM Martin Maechler wrote: > For me (on Fedora 30) > > $ R CMD config LDFLAGS > -L/usr/lib64 This looks wrong. I would expect that /usr/lib64 is one of the standard directories that are searched anyway. So why put it into the very beginning of the search? BTW, this

Re: [R-pkg-devel] set pkg_config for 3rd party software

2019-09-05 Thread Ralf Stubner
On Thu, Sep 5, 2019 at 12:27 PM Martin Maechler wrote: > Now what is the officially / best way to have either 'configure' > or Makevars.{in,win} use the 'pkg-config' information > *dynamically*, i.e., > if I update my MPFR from 4.0.1 to 4.0.2 the newer 4.0.2 is found ? I don't know what is

Re: [R-pkg-devel] third part software dependency

2019-08-30 Thread Ralf Stubner
On Fri, Aug 30, 2019 at 11:10 AM Serguei Sokol wrote: > I am preparing a new package r2sundials for submission to cran. It > depends on third part software > (https://computing.llnl.gov/projects/sundials). Are you aware of the sundialr package? https://cran.r-project.org/package=sundialr > This

Re: [R-pkg-devel] Difficulty installing my package from drat repository

2019-07-10 Thread Ralf Stubner
On Wed, Jul 10, 2019 at 11:54 AM Alex Hallam wrote: > My hunch is that this has to do with the tar ball being tracked with "git > large file storage". This is because the file size of my tar ball is 154.9 > MB which exceeds github's 100 MB file size limit. What options can I try in > this

Re: [R-pkg-devel] Reproducing address sanitizer errors

2019-07-08 Thread Ralf Stubner
On Sat, Jul 6, 2019 at 10:45 PM Ralf Stubner wrote: > I have been informed that the most recent upload of our swephR package > triggers stack-buffer-overflow. See for example > https://www.stats.ox.ac.uk/pub/bdr/memtests/clang-ASAN/swephR. The > reason seems to be quite obvious (an ar

[R-pkg-devel] Reproducing address sanitizer errors

2019-07-06 Thread Ralf Stubner
Dear List, I have been informed that the most recent upload of our swephR package triggers stack-buffer-overflow. See for example https://www.stats.ox.ac.uk/pub/bdr/memtests/clang-ASAN/swephR. The reason seems to be quite obvious (an array has been declared with 36 instead of 37 elements), but I

Re: [R-pkg-devel] Compilation used the "non-portable flag"

2019-05-10 Thread Ralf Stubner
a suitable ~/.R/Makevars file. Greetings Ralf -- Ralf Stubner Senior Software Engineer / Trainer daqana GmbH Dortustraße 48 14467 Potsdam T: +49 331 23 61 93 11 F: +49 331 23 61 93 90 M: +49 162 20 91 196 Mail: ralf.stub...@daqana.com Sitz: Potsdam Register: AG Potsdam HRB 27966 Ust.-IdNr.: DE3000

Re: [R-pkg-devel] data in R package

2019-04-29 Thread Ralf Stubner
nsideration should be given to a separate data-only package which can be updated only rarely (since older versions of packages are archived in perpetuity). Besides these technical questions, one also has to consider legal questions: Under which license may one distribute the data? Greetings Ralf

Re: [R-pkg-devel] dtrti2 error on CRAN checks

2019-04-18 Thread Ralf Stubner
BLAS/LAPACK. cheerio ralf -- Ralf Stubner Senior Software Engineer / Trainer daqana GmbH Dortustraße 48 14467 Potsdam T: +49 331 23 61 93 11 F: +49 331 23 61 93 90 M: +49 162 20 91 196 Mail: ralf.stub...@daqana.com Sitz: Potsdam Register: AG Potsdam HRB 27966 Ust.-IdNr.: DE300072622 Geschäftsfüh

Re: [R-pkg-devel] Package suggested but not available for checking: 'rPeaks'; Additional_repositories

2019-04-16 Thread Ralf Stubner
e there as long as rPeaks is not on CRAN, c.f. https://cran.r-project.org/web/checks/check_results_swephR.html One could argue that it's another reason to try to get rPeaks onto CRAN. cheerio ralf -- Ralf Stubner Senior Software Engineer / Trainer daqana GmbH Dortustraße 48 14467 Potsdam T: +49 331 23

Re: [R-pkg-devel] Package suggested but not available for checking: 'rPeaks'; Additional_repositories

2019-04-16 Thread Ralf Stubner
s/drat/vignettes/DratForPackageAuthors.html for the full details. cheerio ralf -- Ralf Stubner Senior Software Engineer / Trainer daqana GmbH Dortustraße 48 14467 Potsdam T: +49 331 23 61 93 11 F: +49 331 23 61 93 90 M: +49 162 20 91 196 Mail: ralf.stub...@daqana.com Sitz: Potsdam Register: AG Pot

Re: [R-pkg-devel] Package suggested but not available for checking: 'rPeaks'; Additional_repositories

2019-04-15 Thread Ralf Stubner
u could either ask the rPeaks author to create a drat repo or do that yourself (possibly with the author's consent). Greetings Ralf -- Ralf Stubner Senior Software Engineer / Trainer daqana GmbH Dortustraße 48 14467 Potsdam T: +49 331 23 61 93 11 F: +49 331 23 61 93 90 M: +49 162 20 91 196

Re: [R-pkg-devel] CRAN review

2019-03-29 Thread Ralf Stubner
; y) > { > return x + (y-x) * Scalar(std::rand()) / Scalar(RAND_MAX); > } The link between the two seems to be rounding.h which contains: // pick a random rotation MT R = MT::Random(n,n); cheerio ralf -- Ralf Stubner Senior Software Engineer / Trainer daqana GmbH Dortustr

Re: [R-pkg-devel] CRAN review

2019-03-29 Thread Ralf Stubner
h, neither does BH: > https://cran.r-project.org/web/checks/check_results_BH.html Both RcppEigen and BH provide header only libraries which are only compiled by packages making use of it. And the rand symbol is only searched for in the resulting/compiled libraries. Greetings Ralf -- R

Re: [R-pkg-devel] What to do when a dependency falls off CRAN

2019-03-25 Thread Ralf Stubner
; on the two latest tarballs reveals only some NOTEs, though, the most serious one from my point of view is usage of 'rand()' via 'random_shuffle()' https://github.com/cran/maxent/blob/master/src/sgd.cpp#L77. Greetings Ralf -- Ralf Stubner Senior Software Engineer / Trainer daqana GmbH Dortustraße

Re: [R-pkg-devel] active bindings in package namespace

2019-03-25 Thread Ralf Stubner
via drat, c.f. https://journal.r-project.org/archive/2017/RJ-2017-026/RJ-2017-026.pdf. The original 'hurricaneexposure' package has meanwhile been archived. However, I have successfully used this method in https://cran.r-project.org/package=swephR. Greetings Ralf -- Ralf Stubner Senior Software

[R-pkg-devel] Handling ERROR on Solaris

2019-03-05 Thread Ralf Stubner
-- Ralf Stubner Senior Software Engineer / Trainer daqana GmbH Dortustraße 48 14467 Potsdam T: +49 331 23 61 93 11 F: +49 331 23 61 93 90 M: +49 162 20 91 196 Mail: ralf.stub...@daqana.com Sitz: Potsdam Register: AG Potsdam HRB 27966 Ust.-IdNr.: DE300072622 Geschäftsführer: Dr.-Ing. Stefan

[R-pkg-devel] How to handle UBSAN false positives

2019-03-01 Thread Ralf Stubner
832. What would be best practice for handling this in the next upload? 1. Mention it in the upload comments as a false positive? 2. Disable the tests on CRAN? 3. Something else? Thanks Ralf [1] https://cran.r-project.org/web/checks/check_results_dqrng.html -- Ralf Stubner Senior Software Engineer

Re: [R-pkg-devel] Problem on rand() in packaging

2019-02-21 Thread Ralf Stubner
ted]] >> >> __ >> R-package-devel@r-project.org mailing list >> https://stat.ethz.ch/mailman/listinfo/r-package-devel >> > > __ > R-package-devel@r-project.org mailing l

Re: [R-pkg-devel] use g++ instead of clang++ on Mac OS

2019-01-24 Thread Ralf Stubner
at fie is included after R_HOME/etc/Makeconf. But I have never tried that and it is strongly discouraged in WRE. I would expect that a package doing something like that will not pass the CRAN checks. Greetings Ralf -- Ralf Stubner Senior Software Engineer / Trainer daqana GmbH Dortustraße 48

Re: [R-pkg-devel] use g++ instead of clang++ on Mac OS

2019-01-24 Thread Ralf Stubner
e-devel/2017q4/002087.html. You have to use $HOME/.R/Makevars or $R_HOME/etc/Makeconf for that. Greetings Ralf -- Ralf Stubner Senior Software Engineer / Trainer daqana GmbH Dortustraße 48 14467 Potsdam T: +49 331 23 61 93 11 F: +49 331 23 61 93 90 M: +49 162 20 91 196 Mail: ralf.stub...@daqana.com

Re: [R-pkg-devel] Incorporating external library licensces (zstd license) within package

2019-01-10 Thread Ralf Stubner
qrng/blob/master/LICENSE) Greetings Ralf -- Ralf Stubner Senior Software Engineer / Trainer daqana GmbH Dortustraße 48 14467 Potsdam T: +49 331 23 61 93 11 F: +49 331 23 61 93 90 M: +49 162 20 91 196 Mail: ralf.stub...@daqana.com Sitz: Potsdam Register: AG Potsdam HRB 27966 Ust.-IdNr.: DE30007

Re: [R-pkg-devel] Submitting CORELS (Certifiably Optimal Rule Lists) package with/without Windows support

2018-12-20 Thread Ralf Stubner
db/ for more info on gdb. Greetings Ralf -- Ralf Stubner Senior Software Engineer / Trainer daqana GmbH Dortustraße 48 14467 Potsdam T: +49 331 23 61 93 11 F: +49 331 23 61 93 90 M: +49 162 20 91 196 Mail: ralf.stub...@daqana.com Sitz: Potsdam Register: AG Potsdam HRB 27966 Ust.-IdNr.: DE30007

Re: [R-pkg-devel] Submitting CORELS (Certifiably Optimal Rule Lists) package with/without Windows support

2018-12-20 Thread Ralf Stubner
o require GMP and GSL libraries, which can impose problems on Windows if not handled correctly. Have a look at CRAN for how other packages using these libraries handle it. Greetinga Ralf -- Ralf Stubner Senior Software Engineer / Trainer daqana GmbH Dortustraße 48 14467 Potsdam T: +49 331 23 61 9

Re: [R-pkg-devel] FOSS license and restricted use by further dependence

2018-11-22 Thread Ralf Stubner
r details. cheerio Ralf -- Ralf Stubner Senior Software Engineer / Trainer daqana GmbH Dortustraße 48 14467 Potsdam T: +49 331 23 61 93 11 F: +49 331 23 61 93 90 M: +49 162 20 91 196 Mail: ralf.stub...@daqana.com Sitz: Potsdam Register: AG Potsdam HRB 27966 Ust.-IdNr.: DE300072622 Geschäftsf

Re: [R-pkg-devel] R package submission: does not pass the incoming checks automatically,

2018-10-01 Thread Ralf Stubner
Hi Bernd, On 10/1/18 2:39 PM, Müller, Bernd wrote: > * checking CRAN incoming feasibility ... NOTE > Maintainer: ‘Bernd Mueller ’ This NOTE is expected for a new package. It acts as a reminder to THE CRAN team to look at the package manually. Greetings Ralf -- Ralf Stubner Senior So

Re: [R-pkg-devel] Submission to CRAN when package needs personal data (API key)

2018-09-07 Thread Ralf Stubner
//github.com/r-lib/testthat/commit/0a7d27bb9ea545be7da1a10e511962928d888302 Greetings Ralf -- Ralf Stubner Senior Software Engineer / Trainer daqana GmbH Dortustraße 48 14467 Potsdam T: +49 331 23 61 93 11 F: +49 331 23 61 93 90 M: +49 162 20 91 196 Mail: ralf.stub...@daqana.com Sitz: Potsdam Register: AG Potsdam H

Re: [R-pkg-devel] Lapack: undefined symbol: zgbsv_

2018-02-14 Thread Ralf Stubner
ll/1 for one way to do this. With this change it works in my test Docker image together with the dev version(!) of RcppArmadillo. Greetings Ralf -- Ralf Stubner Senior Software Engineer / Trainer R Institute GmbH Dortustraße 48 14467 Potsdam T: +49 331 23 70 81 66 F: +49 331 23 70 81

Re: [R-pkg-devel] Lapack: undefined symbol: zgbsv_

2018-02-13 Thread Ralf Stubner
the way RcppArmadillo does it. If my understanding above is correct, the number of users with ARMA_CRIPPLED_LAPACK in your package but not in RcppArmadillo will be quite small. Greetings Ralf -- Ralf Stubner Senior Software Engineer / Trainer R Institute GmbH Dortustraße 48 14467 Potsdam T: +49 331 23 70 81

Re: [R-pkg-devel] Lapack: undefined symbol: zgbsv_

2017-12-19 Thread Ralf Stubner
in the RcppArmadillo-Config. Short of editing that file, you can add this to src/Makevars PKG_CXXFLAGS=-DARMA_CRIPPLED_LAPACK -DRcppArmadillo__RcppArmadilloConfigGenerated__h I hope there is a better way ... Greetings Ralf -- Ralf Stubner Senior Software Engineer / Trainer R Institute GmbH Dortustra

Re: [R-pkg-devel] Lapack: undefined symbol: zgbsv_

2017-12-18 Thread Ralf Stubner
RcppArmadillo/blob/f20cc71ad6b1c730a79f2e5609733f741172b399/inst/include/armadillo_bits/auxlib_meat.hpp#L4599), but I have not checked any side effects. Greetings Ralf -- Ralf Stubner Senior Software Engineer / Trainer R Institute GmbH Dortustraße 48 14467 Potsdam T: +49 331 23 70 81 66 F: +49 331 23 70 81 67 M: +49 1