because of a bug [2],
> so you'll need to look at the results even if the build has passed.
>
> Gabor
>
> [1] https://r-hub.github.io/containers/
> [2] https://github.com/r-hub/actions/issues/16
>
> On Thu, May 16, 2024 at 10:27 PM Ralf Stubner wrote:
> >
> &g
Dear all,
I have been asked to fix a UBSAN error in my dqrng package. The error
itself and the necessary fix are quite straight forward. However, I
want to make 100% sure that I am really fixing the error. In the past
I had used rhub for tasks like that. But it seems like the new rhub v2
offers on
On Sat, Sep 23, 2023 at 7:30 PM Ivan Krylov wrote:
> You're right! Looking at the code, if R_useDynamicSymbols(dll, FALSE)
> has been called for a DLL, the branch that calls dlsym() or
> GetProcAddress() to find symbols from that library by their shared
> object symbol names gets completely disabl
On Sat, Sep 23, 2023 at 10:00 AM Duncan Murdoch
wrote:
> I don't know the answer here, but section 6.16 of WRE suggests that you
> could explicitly make your functions visible even if they default to
> invisible.
Thanks Duncan. Unfortunately at least in my tests the visibility
settings did not a
Hi everybody,
Section 5.4 of WRE suggests to use `R_useDynamicSymbols(dll, FALSE);`
when registering C/C++ routines in R packages, and Rcpp does so
automatically. ?Random.user describes a way to hook a user- defined
RNG into R. However, it looks like these two things are not
compatible, i.e. `user
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 of
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 simpl
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
xosh
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 p
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]’ [-Warray
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 src/Make
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 depen
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?
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 my
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
> insta
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 wch1/r-de
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
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 be
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
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 situati
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
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 w
Hi Christian,
in your NAMESPACE you import both mvtnorm and mclust completely. The
warning should go away if you change this to importFrom(...) with only
the methods you actually need, in particular dmvnorm either from
mvtnorm or from mclust. Alternatively, you could leave out the imports
and alwa
ner to add 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
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Ust.-IdN
deration 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
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
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Geschäftsfüh
will be 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
ponding vignette
https://cran.r-project.org/web/packages/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:
my drat repository.
In your case, you 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 1
; 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
it's worth, 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.
Greeti
; 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
daq
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
Senio
.Rout
--
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
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Geschäftsführer: Dr.-Ing. S
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
rsion deleted]]
>>
>> __
>> R-package-devel@r-project.org mailing list
>> https://stat.ethz.ch/mailman/listinfo/r-package-devel
>>
>
> __
> R-package-devel@r-project.org
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
evel/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
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
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
ems to 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
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
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
n:
https://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
olve/pull/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
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 2
more difficult than I thought since
it is #undefed 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
Core/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:
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