Hi Ivan,
On 27 March 2021 at 19:11, Ivan Krylov wrote:
| Dirk, thank you a prompt reply!
|
| I see the issue you took part in solving:
| https://github.com/x13org/x13binary/issues/49
Yes. Temporary files are now written to a temporary directory which I make
sure to remove at end of examples (a
On 29 March 2021 at 23:29, Rasmus Liland wrote:
| can someone please guide me a little in
| installing RODBC[1] on FreeBSD 13?
|
| I believe it depends on unixodbc[2], but
| the compilation stops with at not
| finding unixodbc (I think):
|
| rasmus@iselin ~ % mkdir ~/src/RODBC
| ras
On 30 March 2021 at 15:19, Florian Rupprecht wrote:
| I am trying to add an optional system/C++ library to my package and was
| wondering if anyone could point me in the right direction on how to do this
| in the R package ecosystem.
|
| To be concrete, I want my graphics device package httpgd t
On 30 March 2021 at 01:10, Rasmus Liland wrote:
| Dirk, I did not realize libiodbc[1] is an
| alternative to unixODBC, how are you
| able to see this?
By studing the sources and README of the package you are trying to build.
| I also did not realize I had both of
| them installed ...
|
On 1 April 2021 at 18:39, Zhang, Wan wrote:
| Hello,
|
| In our package �BET� version 0.3.4 published on 2021-03-21, there is a
�memory not mapped� error on Solaris 10.
|
| https://www.r-project.org/nosvn/R.check/r-patched-solaris-x86/BET-00check.html
|
| I tried to replicate this error with R
On 2 April 2021 at 09:45, Duncan Murdoch wrote:
| On 01/04/2021 9:06 p.m., David Cortes wrote:
| > Is it allowed to use such functions in packages? I see a few packages
| > currently in CRAN have the same note in the checks, such as "iotools",
| > and am wondering if I should just email the CRAN
Tiago,
Looking at https://www.stats.ox.ac.uk/pub/bdr/noSuggests/pliman.out
we see it errors after trying '* checking examples ...':
* checking examples ... ERROR
Running examples in ‘pliman-Ex.R’ failed
The error most likely occurred in:
> ### Name: as_image
> ### Title: Crea
On 3 November 2024 at 11:02, Tiago Olivoto wrote:
| Today, I noticed that several stable packages, such as Rcpp and sf, were
| unavailable during the check process for this submission. This wasn’t an
| issue in the previously published version of pliman. Could this be a
| temporary problem with t
On 12 November 2024 at 12:40, Pepijn de Vries wrote:
| "Cannot create temporary file in D:\temp\2024_11_12_ 1_50_00_12637\: No such
file or directory"
Based on your quote and the log [1] it looks like you have a space in the
directory name. Windows can accommodate these but you must then quote
On 12 November 2024 at 12:40, Pepijn de Vries wrote:
| "Cannot create temporary file in D:\temp\2024_11_12_ 1_50_00_12637\: No such
file or directory"
Based on your quote and the log [1] it looks like you have a space in the
directory name. Windows can accommodate these but you must then quote
On 12 November 2024 at 10:47, Dirk Eddelbuettel wrote:
|
| On 12 November 2024 at 12:40, Pepijn de Vries wrote:
| | "Cannot create temporary file in D:\temp\2024_11_12_ 1_50_00_12637\: No
such file or directory"
|
| Based on your quote and the log [1] it looks like you have a sp
Hi John,
I think you are reading the text too literally. The intent of WRE is to
ensure that standard use of a RNG in an extension package uses the RNGs that
come with R (which includes an updated mersenne twister algorithm) so that
users are not "surprised". It explicitly mentions the problem
On 27 September 2024 at 16:58, John Clarke wrote:
| [...] -- the RNG state management strategy appears almost 'magical' to me
| especially inside RCPP. It is possible, I just don't understand how to use it.
See Section 6.3 of WRE: The pair of GetRNGstate() and PutRNGstate() is all
there is in te
On 17 November 2024 at 14:23, Patrick Giraudoux wrote:
| Le 17/11/2024 à 14:17, Ivan Krylov a écrit :
| > В Sun, 17 Nov 2024 14:04:56 +0100
| > Patrick Giraudoux пишет:
| >
| >> trying URL
| >> 'https://pbil.univ-lyon1.fr/CRAN/bin/windows/contrib/4.4/xfun_0.49.zip'
| >> Content type 'application/
On 15 November 2024 at 12:16, Mauricio Vargas Sepulveda wrote:
| [...] and I now asked Dr. Ligges for the possibility to know more about the
CRAN specific configuration to add it to R-Hub.
It is (and has always been) documented in a text file on the server
https://www.stats.ox.ac.uk/pub/bd
On 14 November 2024 at 16:24, Mauricio Vargas Sepulveda wrote:
| After enabling the SAN flags, I cannot reproduce the gcc-san error [2].
|
| Should I report this as a false positive?
No.
Replicating ASAN/UBSAN issues is known to be potentially tricky.
It drove me so batty a decade ago that I
Luc,
As Tomas mentioned, matrix-multiplication can take advantage of multiple
threads, and the 'text book' nexted loops do not do that. Now, one
alternative that appeals a lot to me is to farm out to Armadillo which also
calls LAPACK for you (as R does). And via RcppArmadillo, the setup becomes
On 2 January 2025 at 13:41, Henrik Bengtsson wrote:
| Agree, it would be neat if a package could clean up after itself when
| uninstalled.
Indeed many things could be nicer if we had more package manager integrations
and hooks besides `cleanup` and `configure`. Someone would have to start
with
On 30 December 2024 at 11:24, Kevin Coombes wrote:
| Thanks; I suspected as much. I will try changing the name of the algorithm
| (in the manuscript) to uppercase, and leave the package name alone.
Some (software-centric) journals (JSS, R Journal, ...) use a distinct font
for software components
On 4 February 2025 at 16:16, Graeme Hickey wrote:
| Having spent the best part of a month troubleshooting an almost
| identical issue, I came across Dirk's blog post here: https://
| dirk.eddelbuettel.com/blog/2023/10/31/. He discusses how to throttle the
number
| of threads, and exports 2 handy
On 7 February 2025 at 05:05, Richard M. Heiberger wrote:
| Michael and Brian.
|
| thank you
| exactly correct.
For completeness: this check is a fairly recent addition to r-devel and hence
a 'policy change'.
Dirk
--
dirk.eddelbuettel.com | @eddelbuettel | e...@debian.org
___
On 7 February 2025 at 11:15, Duncan Murdoch wrote:
| On 2025-02-07 10:09 a.m., Dirk Eddelbuettel wrote:
| >
| > On 7 February 2025 at 05:05, Richard M. Heiberger wrote:
| > | Michael and Brian.
| > |
| > | thank you
| > | exactly correct.
| >
| > For completeness: this
Hi Wolfgang,
On 31 January 2025 at 15:02, Wolfgang Rolke via R-package-devel wrote:
| In the vignette of my package Rgof I create a function written in Rcpp, which
is then passed and executed in some of the routines included in Rgof. The
package passes all the checks on the various platform wit
On 18 December 2024 at 19:46, Bielow, Chris wrote:
| hoping this is the right place for this:
| I stumbled upon documentation regarding the use of `assert` in C++ code, in
| particular, https://cran.r-project.org/web/packages/policies.html states
| that
|
| ```
| Thus C/C++ calls to assert/abort
On 19 December 2024 at 06:06, Duncan Murdoch wrote:
| I think it would be really misleading to have code that routinely
| ignored the assert() calls. In a year would you remember that those
| asserts were effectively just comments, not being acted on without some
| trickery to enable them?
Or
On 17 November 2024 at 15:16, Patrick Giraudoux wrote:
| Thus, this latter works fine. Does this help to identify the trouble ?
I think this resonates with the fine work Ivan had already done. I suspect
you have a bad local with the repo information (possible PACKAGE.rds) and it
does not get ove
Lukas,
It is, as you noticed, complicated.
One way forward might be to rely on what you can rely on (i.e. a suitable
system fftw on two of the three platforms) and to embed and locally build
where not. Nowadays a number of packages embedding external libraries and
resorting to eg cmake to build
On 21 January 2025 at 12:04, Jonathan Berrisch wrote:
| first of all: I'm not an expert on this and don't really know if there
| is a recommended way.
|
| However, you may look at my 'rcpptimer' package and how it includes
| 'cpptimer' as a submodule.
|
| You can find the repository here: htt
On 19 January 2025 at 20:42, Pepijn de Vries wrote:
| I think I could write a similar test as used by `cpp11tesseract`:
|
|
https://github.com/pachadotdev/cpp11tesseract/blob/2ea8287ef2c27901446bafa402728014d99904d4/configure#L66-L85
Taking an example from a package not on CRAN 'for policy vio
On 28 January 2025 at 14:27, Iñaki Ucar wrote:
| El mar., 28 ene. 2025 14:25, John Clarke
| escribió:
|
| > Hi all,
| >
| > I'm wondering if there is a way to point an R package installer to a
| > pre-compiled release on Github rather than rely on CRAN.
|
|
| Yes, see https://r-universe.dev/
Excellent (as usual) sleuthing by Ivan -- colour me impressed (again).
As an aside, your package makes wide use of the excellent resources provided
by other CRAN packages. But with this comes added complexity. Depending on
over sixty (!!) other packages (when counting recursively, over seventy
Thank you for actually posting a reference to your package and its source
code. That allows us to take a closer look.
On 28 January 2025 at 16:07, Guillermo Vinue wrote:
| Thank you for your help, Ben and Ivan. Unfortunately, the note persists:
|
https://win-builder.r-project.org/incoming_prete
On 15 February 2025 at 19:50, Simon Urbanek wrote:
| Github is not reliable enough for reproducible research (your files can
| disappear at any point - or can change without notice),
I'm curious: Do you have a concrete example of a no-longer-reproducible study
whose data or other support files
On 24 March 2025 at 09:10, Josiah Parry wrote:
| In trying to address new WARNINGs on R-devel I'm trying to rebuild my
| package environment on R 4.6 (r88038) so I can try and remediate. However,
| I'm encountering a segfault when doing so which doesn't occur for R 4.5.0
| alpha (2025-03-18 r8799
On 19 March 2025 at 09:29, Michael Chirico wrote:
| data.table is doing the same in a number of places, Ivan even went so far
| as to pin down a specific SVN commit for those as well:
|
| #if R_VERSION < R_Version(4, 5, 0) || R_SVN_REVISION < 86702
| # define isDataFrame(x) isFrame(x) // #6180
On 19 March 2025 at 11:16, Ben Bolker wrote:
|FWIW Rcpp handles this (for CLOENV) with an ifdef:
|
| #if (defined(R_VERSION) && R_VERSION >= R_Version(4,5,0))
| return R_ClosureEnv(fun);
| #else
| return CLOENV(fun);
| #endif
On 6 April 2025 at 01:25, Lluís Revilla wrote:
| To solve it, it might be as simple as writing nimDim <- NULL inside your
| package or there might be a real issue there.
Or call utils::globalVariables(c("nimDim")) where, if needed, you could add
to that argument vector any other variables listed
Hi Thierry,
On 17 February 2025 at 09:16, Thierry Onkelinx wrote:
| Zenodo does offer storage. The default quota are 50GB and 100 files per record
| (version). See https://help.zenodo.org/docs/deposit/manage-files/#prepare
So TIL! Thanks for the heads-up and correction.
Dirk
--
dirk.eddelbue
Something that had happened to the Rcpp package in the past (but seemingly
went away on its own ?) is now apparently hitting package RcppArmadillo.
I received private email from the CRAN maintainers reporting, without
offering a fix as there seems to be none, that one of the two pdf vignettes
(w
This really is Dadaism (or maybe Absurdism? Where are our art historians?)
By now I heard from one of the affected scientists via a private slack
message. A choice quote:
basically the pdf is moved into quarantine, and our IT are now threatening
us to format all our laptops
This is beyon
On 18 February 2025 at 15:14, Iñaki Ucar wrote:
| What happened in Rcpp is that the antivirus were detecting an old
| version of ghostscript that could produce potentially vulnerable
| outputs. We solved it by rebuilding the vignettes with a newer version
| of ghostscript. This is most likely the
On 18 February 2025 at 16:26, Ivan Krylov wrote:
| On Tue, 18 Feb 2025 07:05:06 -0600
| Dirk Eddelbuettel wrote:
|
| > one of the two pdf vignettes (which I happen to create as a shallow
| > Rnw -> pdf wrapper around a pre-made pdf, here that inner pdf had not
| > changed in five
On 9 March 2025 at 15:03, Stephen Abrams wrote:
| Hi again - I'm working through the final details of a submission. My
| current problem is that I make use of a dependency of the caret package
| (kernlab) in one of my vignettes. If I don't include kernlab in my
| DESCRIPTION file, I get the follo
On 24 February 2025 at 22:08, Viechtbauer, Wolfgang (NP) wrote:
| Like Duncan's rgl package, the mathjaxr package
(https://cran.r-project.org/package=mathjaxr) also contains JS code (for
MathJax). And one of the requirements to get the package onto CRAN was that the
source package had to conta
On 12 May 2025 at 16:45, Adam Loy wrote:
| Hi all,
|
| I am having trouble getting past the pre-checks for CRAN, but things check
| out in my testing localling in the cloud. I get this message on Debian:
|
| Error: package or namespace load failed for ‘HLMdiag’ in
| dyn.load(file, DLLpath = DLL
On 10 May 2025 at 12:34, Tyler wrote:
| I recently submitted the package `libdeflate`, which successfully made
| its way to the CRAN
| (https://cran.r-project.org/web/packages/libdeflate/index.html) but
| has failed to install on macOS:
[...]
| I see that WRE also recommends checking
| "/Applicat
On 13 May 2025 at 21:07, Ben Bolker wrote:
| threaded computations. I don't think CRAN multithreads by default (and I
| don't know if they test on MKL at all ...?)
CRAN itself writes at https://cran.r-project.org/CRAN_team.htm :
CRAN QA
CRAN package checks on combinations of various plat
[ If you could, please set your email software up such that posts to a
mailing lists are not signed, it makes reading them more cumbersome. It
also means I can't reply (easily) inline now. ]
In most cases environment variables need to be set before the process
starts. Setting them inside the
On 14 May 2025 at 15:18, smallepsilon wrote:
| Ben,
|
| No need to apologize. I hope the following example helps clarify what I mean.
Suppose that modify_matrix(mat, other_args) is a function that, among other
things, applies eigen() to mat. For good reasons, other_args has no default
value.
On 21 May 2025 at 13:55, Peiyuan Zhu wrote:
| Thanks Kasper, but I don’t know how exactly to accomplish this. As Dirk says
| the system overwrites it every time.
That is *not* what Dirk said.
Dirk
--
dirk.eddelbuettel.com | @eddelbuettel | e...@debian.org
_
On 21 May 2025 at 09:34, Peiyuan Zhu wrote:
| I'm happy to just use O3 but it sounds like this isn't something doable in
C++.
It is called -O3, not 'O3'. (Also Rcpp, not RCpp.)
We do not know what you did because you never posted anything even remotely
close to reproducible.
| Maybe I should
Andrew,
On 21 May 2025 at 12:48, andrew--- via R-package-devel wrote:
| I'm currently having difficulty replicating an ODR violation that is being
raised by the gcc-asan check here:
https://www.stats.ox.ac.uk/pub/bdr/memtests/gcc-ASAN/RcppPlanc/00install.out.
Perhaps weirder, it seems to be t
On 20 May 2025 at 19:39, Peiyuan Zhu wrote:
| How to use the O4 flag in an RCpp project? Every time when I load_all it
| starts using the O2 flag or the debug flag. What should I put into Makevar?
| Can I still do remote::install.github(...)?
Given that this mailing list can need explicit approv
Also, and while it won't help for the non-standard field in question here,
the standard fields are all compiled into what tools::CRAN_package_db()
returns. Very handy for many use cases, and possibly not as well known as it
should be.
Dirk
--
dirk.eddelbuettel.com | @eddelbuettel | e...@debian
|
| On Sun, May 18, 2025, 7:59 AM Dirk Eddelbuettel wrote:
|
|
| Also, and while it won't help for the non-standard field in question here,
| the standard fields are all compiled into what tools::CRAN_package_db()
| returns. Very handy for many use cases, and possibly not
On 22 November 2022 at 14:15, Jaihee Choi wrote:
| I was trying to resubmit a package but was notified that it did not pass
| the initial checks due to the following error message regarding compiling
| my vignette:
|
| Error: .onLoad failed in loadNamespace() for 'rje', details:
| call: getEng
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