Re: [R-pkg-devel] flang doesn't support derived types

2024-06-03 Thread Simon Urbanek
Othman, I'm not sure why you would expect a response from CRAN. The ball is in your court - you have to either fix your code (ideally) or provide a justification why you think it is safe. I have not seen any email from you to c...@r-project.org and you have not mentioned the name of the

Re: [R-pkg-devel] different build tools

2024-05-28 Thread Simon Urbanek
> On 29/05/2024, at 11:21 AM, Boylan, Ross wrote: > > Is it required that the package submitted to CRAN have been built with R CMD > build rather than some other tool? When you say "CRAN has nothing to do with > any of the above [different tools]" it sounds as if one can use anything; but

Re: [R-pkg-devel] different build tools

2024-05-28 Thread Simon Urbanek
Ross, R CMD build is the only offical way to build a (source) package in R. All other "tools" are just convenience wrappers by 3rd parties that call R CMD build eventually. There is no reason to assume that those tools should behave in a certain way - nor are you required to use them. They

Re: [R-pkg-devel] handling documentation build tools

2024-05-21 Thread Simon Urbanek
Ross, It's entirely up to you how you do this -- what you describe is something that has to happen before your run R CMD build, so it's not reflected in your package that you submit (and this has nothing to do with CRAN or R). There is nothing automatic as it requires you to do something in

Re: [R-pkg-devel] Trouble with dependencies on phyloseq and microViz

2024-05-12 Thread Simon Urbanek
the name of the package, otherwise the thread can quickly degrade to wild guesswork and misleading or incorrect answers from unrelated parties. Cheers, Simon > On 7/05/2024, at 6:56 PM, Simon Urbanek wrote: > > Ivan, > > sorry if it wasn't clear, but this thread was about stro

Re: [R-pkg-devel] Fast Matrix Serialization in R?

2024-05-09 Thread Simon Urbanek
> On 10/05/2024, at 12:31 PM, Henrik Bengtsson > wrote: > > On Thu, May 9, 2024 at 3:46 PM Simon Urbanek > wrote: >> >> FWIW serialize() is binary so there is no conversion to text: >> >>> serialize(1:10+0L, NULL) >> [1] 58 0a 00 00 00 03 00

Re: [R-pkg-devel] Fast Matrix Serialization in R?

2024-05-09 Thread Simon Urbanek
> On 9/05/2024, at 11:58 PM, Vladimir Dergachev wrote: > > > > On Thu, 9 May 2024, Sameh Abdulah wrote: > >> Hi, >> >> I need to serialize and save a 20K x 20K matrix as a binary file. This >> process is significantly slower in R compared to Python (4X slower). >> >> I'm not sure about

Re: [R-pkg-devel] Fast Matrix Serialization in R?

2024-05-08 Thread Simon Urbanek
Sameh, if it's a matrix, that's easy as you can write it directly which is the fastest possible way without compression - e.g. quick proof of concept: n <- 2^2 A <- matrix(runif(n), ncol = sqrt(n)) ## write (dim + payload) con <- file(description = "matrix_file", open = "wb") system.time({

Re: [R-pkg-devel] Trouble with dependencies on phyloseq and microViz

2024-05-07 Thread Simon Urbanek
this only affects R-oldrel so presumable Bioc upgrade may fix this so I'll have a look tomorrow. Cheers, Simon > On May 7, 2024, at 6:15 PM, Ivan Krylov wrote: > > On Tue, 7 May 2024 10:07:59 +1200 > Simon Urbanek wrote: > >> That doesn't work - additional reposit

Re: [R-pkg-devel] Trouble with dependencies on phyloseq and microViz

2024-05-06 Thread Simon Urbanek
> On 5/05/2024, at 4:32 AM, Ivan Krylov via R-package-devel > wrote: > > В Sat, 4 May 2024 15:53:25 + > Sharon Bewick пишет: > >> I have a dependency on phyloseq, which is available through GitHub >> but not on the CRAN site. I have a similar problem with microViz, >> however I’ve

Re: [R-pkg-devel] Error handling in C code

2024-05-05 Thread Simon Urbanek
Jarrod, could you point us to the code? There is not much to go by based on your email. One thing just in general: it's always safer to not re-map function names, especially since "error" can be defined in many random other headers, so it's better to use Rf_error() instead to avoid confusions

Re: [R-pkg-devel] re-exporting plot method?

2024-04-30 Thread Simon Urbanek
Kevin, welcome to the S4 world! ;) There is really no good solution since S4 only works at all if you attach the package since it relies on replacing the base S3 generic with its own - so the question remains what are your options to do it. The most obvious is to simply add Depends: Rgraphviz

Re: [R-pkg-devel] Problem with loading package "devtools" from CRAN.

2024-04-29 Thread Simon Urbanek
Rolf, what do you mean by "broken"? Since you failed to include any proof nor details it's unlikely that anyone can help you, but chances are pretty high that it was a problem on your end. I just checked with R 4.4.0 on Ubuntu 22.04 and devtools install and load just fine, so it is certainly

Re: [R-pkg-devel] Package required but not available: ‘arrow’

2024-02-25 Thread Simon Urbanek
To quote Rob: "Version numbers are cheap" The way the policy is worded it is clear that you cannot complain if you didn't increase it as you are taking a risk. Also the the incoming FTP won't let you upload same version twice so it wasn't really a problem until more recently when there are

Re: [R-pkg-devel] CRAN uses an old version of clang

2024-02-11 Thread Simon Urbanek
Just to include the necessary details: macOS CRAN build uses Apple clang-14, so you cannot assume anything higher. Also the target is macOS 11 SDK. That said, LLVM does not support the special math functions at all according to the status report (see Mathematical Special Functions for C++17 at

Re: [R-pkg-devel] Warnings from upstream C library in CRAN submission

2024-02-03 Thread Simon Urbanek
Satyaprakash, those are clear bugs in the SUNDIALS library - they assume that "unsigned long" type is 64-bit wide (that assumption is also mentioned in the comments), but there is no such guarantee and on Windows it is only 32-bit wide, so the code has to be changed to replace "unsigned long"

Re: [R-pkg-devel] Clarifying CRAN's external libraries policy

2024-01-29 Thread Simon Urbanek
email > address) to c...@r-project.org on Mon, 23 Oct 2023. > > Thanks, > > Nic > > > On Mon, 29 Jan 2024 at 18:51, Simon Urbanek > wrote: >> >> Neal, >> >> generally, binaries are not allowed since CRAN cannot check the provenance >> s

Re: [R-pkg-devel] Clarifying CRAN's external libraries policy

2024-01-29 Thread Simon Urbanek
Neal, generally, binaries are not allowed since CRAN cannot check the provenance so it's not worth the risk, and it's close to impossible to maintain them over time across different systems, toolchains and architectures as they evolve. Historically, some packages allowed to provide binaries

Re: [R-pkg-devel] Possible malware(?) in a vignette

2024-01-27 Thread Simon Urbanek
First, let's take a step back, because I think there is way too much confusion here. The original report was about the vignette from the poweRlaw package version 0.70.6. That package contains a vignette file d_jss_paper.pdf with the SHA256 hash

Re: [R-pkg-devel] Possible malware(?) in a vignette

2024-01-27 Thread Simon Urbanek
mon > I don't think these are "false claims". > > Iñaki > > El sáb., 27 ene. 2024 11:19, Simon Urbanek <mailto:simon.urba...@r-project.org>> escribió: > Bob, > > I was not making assertions, I was only dismissing clearly false claims: CRAN > did NO

Re: [R-pkg-devel] Possible malware(?) in a vignette

2024-01-27 Thread Simon Urbanek
t least poke at more 2020 PDFs from CRAN vignette > builds (perhaps just the ones built that were JSS articles…it's possible the > header image sourced at that time was tampered with during some time window, > since image decoding issues have plagued Adobe Reader in buffer overflow land >

Re: [R-pkg-devel] Possible malware(?) in a vignette

2024-01-25 Thread Simon Urbanek
Iñaki, I think you got it backwards in your conclusions: CRAN has not generated that PDF file (and Windows machines are not even involved here), it is the contents of a contributed package, so CRAN itself is not compromised. Also it is far from clear that it is really a malware - in fact it's

Re: [R-pkg-devel] R-package-devel Digest, Vol 105, Issue 19

2024-01-24 Thread Simon Urbanek
This is a reminder why one should never build packages directly in their source directory since it can only be done once (for packages with native source code) - always use R CMD build --no-build-vignettes foo && R CMD INSTALL foo_*.tar.gz if you plan to edit files in the source directory and

Re: [R-pkg-devel] CMake on CRAN Systems

2024-01-17 Thread Simon Urbanek
I had a quick look and that package (assuming it's https://github.com/stsds/MPCR) does not adhere to any rules from R-exts (hence the removal from CRAN I presume) so the failure to detect cmake is the least problem. I would strongly recommend reading the R documentation as cmake is just the

Re: [R-pkg-devel] test failure: oldrel

2024-01-16 Thread Simon Urbanek
> On Jan 17, 2024, at 3:46 AM, Josiah Parry wrote: > > Hey folks! I've received note that a package of mine is failing tests on > oldrel. > > Check results: > https://www.r-project.org/nosvn/R.check/r-oldrel-windows-x86_64/arcgisutils-00check.html > > I think I've narrowed it down to the

Re: [R-pkg-devel] checking CRAN incoming feasibility

2024-01-16 Thread Simon Urbanek
Ralf, that check always hangs for me (I don't think it likes NZ ;)), so I just use _R_CHECK_CRAN_INCOMING_REMOTE_=0 R CMD check --as-cran ... Cheers, Simon > On Jan 16, 2024, at 6:49 PM, Rolf Turner wrote: > > > On Tue, 16 Jan 2024 16:24:59 +1100 > Hugh Parsonage wrote: > >>> Surely the

Re: [R-pkg-devel] portability question

2023-12-20 Thread Simon Urbanek
This has nothing to do with Steven's question since he is creating a *static* library whereas install_name_tool changes install name ID entry of a *dynamic* library. Also the data.table example is effectively a no-op, because changing the ID makes no difference as it can't be linked against

Re: [R-pkg-devel] portability question

2023-12-20 Thread Simon Urbanek
Steven, no, I'm not aware of any negative effect, in fact having an index in the archive is always a good idea - some linkers require it, some work faster with it and at the worst the linker ignores it. And as far as I can tell all current system "ar" implementations support the -s flag (even

Re: [R-pkg-devel] Wrong mailing list: Could the 100 byte path length limit be lifted?

2023-12-12 Thread Simon Urbanek
Justin, now that you clarified what you are actually talking about, this is a question about the CRAN policies, so you should really direct it to the CRAN team as it is their decision (R-devel would be appropriate if this was a limitation in R itself, and R-package-devel would be appropriate

Re: [R-pkg-devel] Status of -mmacosx-version-min

2023-12-09 Thread Simon Urbanek
As discussed here before packages should *never* set -mmacosx-version-min or similar flags by hand. As documented in R-exts 1.2 packages should retrieve compiler flags from R (this includes compiling 3rd party dependencies). Incidentally, older versions of R have included -mmacosx-version-min

Re: [R-pkg-devel] macos x86 oldrel backups?

2023-12-05 Thread Simon Urbanek
Jon, The high-sierra build packages are currently not built due to hardware issues. The macOS version is so long out of support by Apple (over 6 years) that it is hard to maintain it. Only big-sur builds are supported at this point. Although it is possible that we may be able to restore the

Re: [R-pkg-devel] Cryptic error on Windows but not Debian

2023-11-18 Thread Simon Urbanek
the policy. (At > least, the CRAN volunteers seem to accept packages which use this approach.) > > Best, > Chris > > > From: R-package-devel on behalf of > Simon Urbanek > Sent: Saturday, November 18, 2023 6:14 PM > To: Adam > Cc: r-package-devel@r-project.

Re: [R-pkg-devel] Cryptic error on Windows but not Debian

2023-11-18 Thread Simon Urbanek
expect_false( > endsWith(Sys.getenv("MEGAMATION_URL"), "/") > ) > }) > > Best, > Adam > > > On Sat, Nov 18, 2023 at 4:52 PM Simon Urbanek <mailto:simon.urba...@r-project.org>> wrote: > Adam, > > > > On Nov 1

Re: [R-pkg-devel] Cryptic error on Windows but not Debian

2023-11-18 Thread Simon Urbanek
Adam, > On Nov 19, 2023, at 9:39 AM, Adam wrote: > > Dear Ivan, > > Thank you for explaining in such depth. I had not submitted to CRAN before. > I will look into tools::R_user_dir(). > > - May you point me toward the policy that the package should not edit > .Renviron? It is the policy

Re: [R-pkg-devel] Can -mmacosx-version-min be raised to 10.15 ?

2023-11-16 Thread Simon Urbanek
Dirk, > On 17/11/2023, at 10:28 AM, Dirk Eddelbuettel wrote: > > > Simon, > > On 17 November 2023 at 09:35, Simon Urbanek wrote: > | can you clarify where the flags come from? The current CRAN builds > (big-sur-x86_64 and big-sur-arm64) use > | > | exp

Re: [R-pkg-devel] Can -mmacosx-version-min be raised to 10.15 ?

2023-11-16 Thread Simon Urbanek
Dirk, can you clarify where the flags come from? The current CRAN builds (big-sur-x86_64 and big-sur-arm64) use export SDKROOT=/Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk export MACOSX_DEPLOYMENT_TARGET=11.0 so the lowest target is 11.0 and it is no longer forced it in the flags (so

Re: [R-pkg-devel] Matrix and Mac OS

2023-10-31 Thread Simon Urbanek
... > > Mikael > > On 2023-10-31 3:33 pm, Simon Urbanek wrote: >> Mikael, >> current Matrix fails checks on R-oldrel so that's why only the last working >> version is installed: >> https://cran.r-project.org/web/checks/check_results_Matrix.html >> Cheers

Re: [R-pkg-devel] Matrix and Mac OS

2023-10-31 Thread Simon Urbanek
Mikael, current Matrix fails checks on R-oldrel so that's why only the last working version is installed: https://cran.r-project.org/web/checks/check_results_Matrix.html Cheers, Simon > On 1/11/2023, at 4:05 AM, Mikael Jagan wrote: > > I am guessing that they mean EdSurvey: > >

Re: [R-pkg-devel] Matrix and Mac OS

2023-10-30 Thread Simon Urbanek
Paul, can you give us a bit more detail? Which package, which build and where you got the errors? Older builds may not have the latest Matrix. Cheers, Simon > On 31/10/2023, at 11:26 AM, Bailey, Paul via R-package-devel > wrote: > > Hi, > > I'm the maintainer for a few packages, one of

Re: [R-pkg-devel] Failing to write config file in linux

2023-10-23 Thread Simon Urbanek
>From CRAN policy (which you agreed to when you submitted your package) - note >in particular the "nor anywhere else on the file system" part and also note >that it tells you what to do in your case: Packages should not write in the user’s home filespace (including clipboards), nor anywhere

Re: [R-pkg-devel] Suppressing long-running vignette code in CRAN submission

2023-10-17 Thread Simon Urbanek
discussed to death so I didn't comment on those. Cheers, Simon > On 18/10/2023, at 11:03 AM, Dirk Eddelbuettel wrote: > > > On 18 October 2023 at 08:51, Simon Urbanek wrote: > | John, > | > | the short answer is it won't work (it defeats the purpose of vignettes). > &

Re: [R-pkg-devel] Suppressing long-running vignette code in CRAN submission

2023-10-17 Thread Simon Urbanek
John, the short answer is it won't work (it defeats the purpose of vignettes). However, this sounds like a purely hypothetical question - CRAN policies allow long-running vignettes if they declared. Cheers, Simon > On 18/10/2023, at 3:02 AM, John Fox wrote: > > Hello Dirk, > > Thank you

Re: [R-pkg-devel] Question about Clang 17 Error

2023-10-11 Thread Simon Urbanek
packages directly to the CRAN's clang17 setup? I > can enable verbose output for CMake and compare the output, but I'd rather > not clog up the CRAN incoming queue just to debug a linker error? > > On Wed, Sep 27, 2023 at 2:43 PM Simon Urbanek <mailto:simon.urba...@r-project.org&g

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

2023-10-08 Thread Simon Urbanek
Franz, it means that the author(s) have abandoned the package: as the note says it was failing checks and the authors have not fixed the problems so it has been removed from CRAN (more than a year ago). Cheers, Simon > On 9/10/2023, at 10:28 AM, Dr. Franz Király wrote: > > Dear all, > >

Re: [R-pkg-devel] CXX_VISIBILITY on macOS

2023-10-08 Thread Simon Urbanek
Matthias, this has nothing to do with R, but rather your code. You have the wrong order of headers: the SWI headers mess up visibility macros, so you have to include them *after* Rcpp.h. Cheers, Simon > On 9/10/2023, at 8:41 AM, Matthias Gondan wrote: > > Dear developers and CRAN people, >

Re: [R-pkg-devel] Question about Clang 17 Error

2023-09-27 Thread Simon Urbanek
It looks like a C++ run-time mismatch between what cmake is using to build the static library and what is used by R. Unfortunately, cmake hides the actual compiler calls so it's hard to tell the difference, but that setup relies on the correct sequence of library paths. The rhub manually

Re: [R-pkg-devel] R_orderVector1 - algo: radix, shell, or another?

2023-09-24 Thread Simon Urbanek
I think the logic Jeff had in mind is that R order() uses C do_order() for method="shell" and since do_order() uses orderVector1() by induction it is the shell-sort implementation. order() itself uses whatever you specify in method=. Cheers, Simon > On Sep 25, 2023, at 7:10 AM, Jan Gorecki

Re: [R-pkg-devel] published packages not showing updated macOS results

2023-09-14 Thread Simon Urbanek
Aron, one package managed to spawn a separate process that was blocking the build process (long story) and I was on the other side of the world. It should be fixed now, but it may take up to a day before the backlog is processed. In the future for faster response, please contact me directly -

Re: [R-pkg-devel] What to do when a package is archived from CRAN

2023-08-26 Thread Simon Urbanek
n't check - thus just trying reverse-engineer what happens by looking at the dependencies which leads to GitHub). > Sorry for nitpicking. > Sure, good to get the fact straight. Cheers, Simon > Best, > Yutani > > 2023年8月27日(日) 6:57 Simon Urbanek <mailto:simon.urba...@r-project.or

Re: [R-pkg-devel] What to do when a package is archived from CRAN

2023-08-26 Thread Simon Urbanek
Tatsuya, What you do is contact CRAN. I don't think anyone here can answer your question, only CRAN can, so ask there. Generally, packages with sufficiently many Rust dependencies have to be handled manually as they break the size limit, so auto-rejections are normal. Archival is unusual, but

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

2023-08-25 Thread Simon Urbanek
> On Aug 26, 2023, at 11:01 AM, Dirk Eddelbuettel wrote: > > > On 25 August 2023 at 18:45, Duncan Murdoch wrote: > | The real problem is that there are two stubborn groups opposing each > | other: the data.table developers and the CRAN maintainers. The former > | think users should by

Re: [R-pkg-devel] gdb availability on r-devel-linux-x86_64-fedora-gcc

2023-08-13 Thread Simon Urbanek
> On 14/08/2023, at 5:25 AM, Jamie Lentin wrote: > > Thanks both! > > On 2023-08-12 23:52, Uwe Ligges wrote: >> On 12.08.2023 23:19, Dirk Eddelbuettel wrote: >>> On 12 August 2023 at 18:12, Uwe Ligges wrote: >>> | On 12.08.2023 15:10, Jamie Lentin wrote: >>> | > The system call in question

Re: [R-pkg-devel] macOS results not mirrored/updated at CRAN

2023-08-10 Thread Simon Urbanek
Dirk, thanks - one of those annoying cases where a script works in the login shell, but not in the cron job -- hopefully fixed. Cheers, Simon > On 9/08/2023, at 12:45 AM, Dirk Eddelbuettel wrote: > > > Simon, > > This is still an issue for arm64. Uploaded tiledb and RQuantLib yesterday,

Re: [R-pkg-devel] macOS results not mirrored/updated at CRAN

2023-07-22 Thread Simon Urbanek
Drik, thanks. I have tried to address the problem and the actual sync problem for big-sur-x86_64 was fixed (as you can the see the results have been updated after you reported it), but apparently there was another, independent, problem with the cron jobs on that machine. I have changed the way

Re: [R-pkg-devel] macOS results not mirrored/updated at CRAN

2023-07-15 Thread Simon Urbanek
I looked into it and there was no issue on the build machine or staging server, so it will require some more digging in the international waters .. hopefully sometime next week… Cheers, Simon > On 16/07/2023, at 11:25, Dirk Eddelbuettel wrote: > >  > Simon, > > On 12 July 2023 at 19:02,

Re: [R-pkg-devel] Feedback on "Using Rust in CRAN packages"

2023-07-13 Thread Simon Urbanek
> On Jul 14, 2023, at 11:19 AM, Hadley Wickham wrote: > >>> If CRAN cannot trust even the official one of Rust, why does CRAN have Rust >>> at all? >>> >> >> I don't see the connection - if you downloaded something in the past it >> doesn't mean you will be able to do so in the future.

Re: [R-pkg-devel] Feedback on "Using Rust in CRAN packages"

2023-07-13 Thread Simon Urbanek
Yutani, [moving back to the original thread, please don't cross-post] > On Jul 13, 2023, at 3:34 PM, Hiroaki Yutani wrote: > > Hi Simon, > > Thanks for the response. I thought > >> download a specific version from a secure site and check that the > download is the expected code by some sort

Re: [R-pkg-devel] Feedback on "Using Rust in CRAN packages"

2023-07-12 Thread Simon Urbanek
> Presumedly, the vendored sources would be built using the versions specified > in an accompanying Cargo.lock as well. > > https://doc.rust-lang.org/cargo/commands/cargo-vendor.html > > > On Wed, Jul 12, 2023, 7:35 PM Simon Urbanek > wrote: > Yutani, > &g

Re: [R-pkg-devel] Feedback on "Using Rust in CRAN packages"

2023-07-12 Thread Simon Urbanek
Yutani, I'm not quite sure your reading fully matches the intent of the policy. Cargo.lock is not sufficient, it is expected that the package will provide *all* the sources, it is not expected to use cargo to resolve them from random (possibly inaccessible) places. So the package author is

Re: [R-pkg-devel] Best practices for CRAN package using Go

2023-07-12 Thread Simon Urbanek
Dewey, you will definitely need to include all the necessary sources for your package. You may want to have a look at the "Using Rust"[1] document linked from the CRAN policy. I think Go is quite similar to Rust in that sense so you should use the same approach, i.e. checking for system and

Re: [R-pkg-devel] gfortran: command not found

2023-07-05 Thread Simon Urbanek
To quote from the page you downloaded R from: This release uses Xcode 14.2/14.3 and GNU Fortran 12.2. If you wish to compile R packages which contain Fortran code, you may need to download the corresponding GNU Fortran compiler from https://mac.R-project.org/tools. > On Jul 6, 2023, at

Re: [R-pkg-devel] Convention or standards for using header library (e.g. Eigen)

2023-06-23 Thread Simon Urbanek
Stephen, If you want to give the system version a shot, I would simply look for pkg-config, add the supplied CPPFLAGS to the package R flags if present and then test (regardless of pkg-config) with AC_CHECK_HEADER (see standard R-exts autoconf rules for packages). If that fails then use your

Re: [R-pkg-devel] NOTE about missing package ‘emmeans’ on macos-x86_64

2023-06-23 Thread Simon Urbanek
> On Jun 24, 2023, at 12:19 AM, Uwe Ligges > wrote: > > > > On 23.06.2023 11:27, Helmut Schütz wrote: >> Dear all, >> since a while (January?) we face NOTEs in package checks >> (https://cran.r-project.org/web/checks/check_results_PowerTOST.html): >> Version: 1.5-4 >> Check: package

Re: [R-pkg-devel] Questions regarding a new (seperated package) and how to submit them to cran

2023-06-22 Thread Simon Urbanek
Bernd, the sequence in which you submit doesn't matter - the packages have to work regardless of the sequence. Suggests means that the dependency is optional, not that it can break tests. You have to skip the tests that cannot be run due to missing dependencies (see 1.1.3.1 in R-exts) Cheers,

Re: [R-pkg-devel] clang linker error: Symbol not found: _objc_msgSend$UTF8String

2023-06-18 Thread Simon Urbanek
Andreas, Xcode update fixed the issue as expected so in due time the ERRORs should disappear. Cheers, Simon > On 18/06/2023, at 10:29 AM, Simon Urbanek wrote: > > Andreas, > > that is actually not your problem - the stubs are generated in glib, so your > package ca

Re: [R-pkg-devel] clang linker error: Symbol not found: _objc_msgSend$UTF8String

2023-06-17 Thread Simon Urbanek
Andreas, that is actually not your problem - the stubs are generated in glib, so your package can do nothing about it, your compile flags won't change it. The only way to fix it is on my end, the proper way is to upgrade to Xcode 14 for the package builds, but that requires some changes to the

Re: [R-pkg-devel] [External] Test fails on M1 Mac on CRAN, but not on macOS builder

2023-05-22 Thread Simon Urbanek
Florian, ok, understood. It works for me on both M1 build machines, so can't really help. I'd simply submit the new version on CRAN. Of course it would help if the tests were more informative such as actually showing the values involved on failure so you could at least have an idea from the

Re: [R-pkg-devel] Test fails on M1 Mac on CRAN, but not on macOS builder

2023-05-21 Thread Simon Urbanek
Florian, looking at the notes for 2.1-4 it says the tolerance has the wrong sign, i.e. you're adding it to the value on both sides of the interval (instead of subtracting for the lower bound). In your latest version the tolerances get added everywhere so that makes even less sense to me, but

Re: [R-pkg-devel] Problems with devtools::build() in R

2023-05-17 Thread Simon Urbanek
This thread went way off the rails and was cross-posted so the solution is on R-SIG-Mac. It was simply wrong Fortran with wrong R - installing latest R and Fortran (from CRAN or https://mac.r-project.org/tools/) is the easiest way to solve the problem. Note that R binaries and tools go

Re: [R-pkg-devel] Are the CRAN macOS builders down?

2023-05-17 Thread Simon Urbanek
volve cron jobs which is why the total time from upload to published binary can take a bit of time. Cheers, Simon > On 17/05/2023, at 10:55 AM, Dirk Eddelbuettel wrote: > > > On 17 May 2023 at 10:39, Simon Urbanek wrote: > | Dirk, > | > | thanks, ok, now I get wh

Re: [R-pkg-devel] Are the CRAN macOS builders down?

2023-05-16 Thread Simon Urbanek
, Simon > On 17/05/2023, at 8:39 AM, Dirk Eddelbuettel wrote: > > > Simon: > > On 17 May 2023 at 07:57, Simon Urbanek wrote: > | builds are immediate, so it is a matter of seconds for most packages. I > don't see any issues on the Mac Builder server. > | If you hav

Re: [R-pkg-devel] Are the CRAN macOS builders down?

2023-05-16 Thread Simon Urbanek
Dirk, builds are immediate, so it is a matter of seconds for most packages. I don't see any issues on the Mac Builder server. If you have a problem, please be more specific and include the check link returned at submission. Cheers, Simon > On 17/05/2023, at 4:27 AM, Dirk Eddelbuettel

Re: [R-pkg-devel] Please install cmake on macOS builders

2023-05-11 Thread Simon Urbanek
I think it would be quite useful to have some community repository of code snippets dealing with such situations. R-exts gives advice and pieces of code which are useful, but they are not complete solutions and situations like Dirk's example are not that uncommon. (E.g., I recall some of the

Re: [R-pkg-devel] Please install cmake on macOS builders

2023-05-10 Thread Simon Urbanek
Dirk, can you be more specific, please? I suspect that it may be rather an issue in your package. All build machines have the official cmake releases installed and there are many packages that use it successfully. Here is the report on the currently installed versions. If you require more

Re: [R-pkg-devel] Unfortunate function name generic.something

2023-05-09 Thread Simon Urbanek
of "local" registration and then replacing the name-based search up the call chain with local registration search - but probably again at the cost of performance. Cheers, Simon > On May 9, 2023, at 11:23 AM, Duncan Murdoch wrote: > > On 08/05/2023 6:58 p.m., Simon Urbanek w

Re: [R-pkg-devel] Unfortunate function name generic.something

2023-05-08 Thread Simon Urbanek
> On 8/05/2023, at 11:58 PM, Duncan Murdoch wrote: > > There really isn't such a thing as "a function that looks like an S3 method, > but isn't". If it looks like an S3 method, then in the proper circumstances, > it will be called as one. > I disagree - that was the case in old

Re: [R-pkg-devel] How to declare Bioconductor Dependencies in the Description File of my R Package

2023-05-03 Thread Simon Urbanek
> On May 4, 2023, at 3:36 AM, Martin Morgan wrote: > > CRAN is fine with Bioconductor Depends: and Imports: dependencies, as > previously mentioned. This is because the CRAN maintainers explicitly > configure their system to know about Bioconductor package repositories. > That is not

Re: [R-pkg-devel] 'Default' macos (x86) download URL now gone?

2023-04-24 Thread Simon Urbanek
Dirk, thanks - the problem is that there is not a single installer package (for several years now), so that URL is ambiguous. Whether the missing link is a good or bad depends on how it is used. I would argue that any link to that URL is inherently bad, because there is no way of knowing that

Re: [R-pkg-devel] Discovering M1mac cowpads

2023-03-24 Thread Simon Urbanek
John, you provide no details to go on, but generally the main difference is that arm64 uses 64-bit precision for long double (which is permitted by the C standard), while Intel uses 80-bits of precision (on systems that enable it). That leads to differences in results, e.g. when computing long

Re: [R-pkg-devel] How to declare Bioconductor Dependencies in the Description File of my R Package

2023-03-17 Thread Simon Urbanek
Packages can only be installed from the repositories listed and only CRAN is the default so only CRAN package are guaranteed to work. I'd like to add that the issue below is exactly why, personally, I would not recommend using Bioconductor package as strong dependency (imports/depends), because

Re: [R-pkg-devel] Sanitize Input Code for a Shiny App

2023-02-26 Thread Simon Urbanek
Bill, the short answer is you can't limit anything at R level. Any attempts to create a list of "bad" commands are trivial to circumvent since you can compute on the language in R, so you can construct and call functions with trivial operations. Similarly, since R allows the loading of binary

Re: [R-pkg-devel] R OpenCL on an AMD GPU

2023-02-07 Thread Simon Urbanek
Quirin, this is a contributed package question, so you should either use the GitHub issues (https://github.com/s-u/OpenCL/issues) for the package or contact the maintainer (me). But before you do so, you have to provide a lot more details including exact code you used and the full output of

Re: [R-pkg-devel] Best current way to hook into the event loop?

2023-02-02 Thread Simon Urbanek
Duncan, I don't know if it is best, but you can have a look at "background"[1] which is I believe what "later" was inspired by. It is a very minimal example so should give you ideas on how to do that in your package - it runs the R code on the main thread so it should be as close to safe as

Re: [R-pkg-devel] If you had to choose one binary to preserve for a pkg, which would it be?

2023-01-24 Thread Simon Urbanek
Uri, I can speak only for macOS package binaries and they have been rarely re-built. The only time when a re-build is necessary is when a dependency is updated and breaks its backward-compatibility (sadly, yes, that happens). It is relatively rare, but recently Matrix was one example with

Re: [R-pkg-devel] NOTE about use of `:::`

2022-12-14 Thread Simon Urbanek
David, why not call[[1]] <- parse_args The assignment is evaluated in your namespace so that makes sure the call is that of your function. The only downside I see is that in a stack trace you'll see the definition instead of the name. Or possibly do.call(parse_args, as.list(call[-1]))

Re: [R-pkg-devel] Minimum macOS version ?

2022-12-08 Thread Simon Urbanek
el wrote: > > > Simon, > > On 9 December 2022 at 10:00, Simon Urbanek wrote: > | the minimum required version for the high-sierra build is 10.13 and for > big-sur build is 11.0 (as the names imply). Although it is not unrealistic to > move Intel to macOS 10.14, it wou

Re: [R-pkg-devel] Minimum macOS version ?

2022-12-08 Thread Simon Urbanek
Dirk, the minimum required version for the high-sierra build is 10.13 and for big-sur build is 11.0 (as the names imply). Although it is not unrealistic to move Intel to macOS 10.14, it would be more problematic to move to 10.15 since it is the version that killed 32-bit support so 10.14 is

Re: [R-pkg-devel] LAPACK errors in r-devel only

2022-11-28 Thread Simon Urbanek
Louis, you didn't provide any details (please always post a link to the sources you're talking about!), but I suspect you are missing character length arguments, Lapack.h has: F77_NAME(dgeevx)(const char* balanc, const char* jobvl, const char* jobvr, const char* sense, const

Re: [R-pkg-devel] Resubmission of archived package after email change

2022-11-24 Thread Simon Urbanek
Have you followed the instructions? > CRAN Repository Policy > > Submission > [...] > Explain any change in the maintainer’s email address and if possible send > confirmation from the previous address (by a separate email to > cran-submissi...@r-project.org) or explain why it is not possible.

Re: [R-pkg-devel] R, Rust and CRAN

2022-11-12 Thread Simon Urbanek
community to do. Cheers, Simon > On Nov 13, 2022, at 9:20 AM, Dirk Eddelbuettel wrote: > > > On 13 November 2022 at 08:15, Simon Urbanek wrote: > | sorry, I think you misunderstood: CRAN machines have the compilers, but the > packages were not detecting it properly and

Re: [R-pkg-devel] R, Rust and CRAN

2022-11-12 Thread Simon Urbanek
to make the same mistakes over again. Cheers, Simon > On Nov 13, 2022, at 7:27 AM, Jeroen Ooms wrote: > > On Sat, Nov 12, 2022 at 12:49 AM Simon Urbanek > wrote: >> >> this does not directly address your question, but I think it would make a >> lot of sense to

Re: [R-pkg-devel] R, Rust and CRAN

2022-11-11 Thread Simon Urbanek
Florian, this does not directly address your question, but I think it would make a lot of sense to standardize the process, given how many issues there were with packages using Rust (mainly not detecting compilers correctly, not supplying source code, unsolicited writing into user's

Re: [R-pkg-devel] Issue handling datetimes: possible differences between computers

2022-10-10 Thread Simon Urbanek
Liam, I think I have failed to convey my main point in the last e-mail - which was that you want to parse the date/time in the timezone that you care about so in your example that would be > foo <- as.Date(33874, origin = "1899-12-30") > foo [1] "1992-09-27" > as.POSIXlt(as.character(foo),

Re: [R-pkg-devel] Issue handling datetimes: possible differences between computers

2022-10-09 Thread Simon Urbanek
Alexandre, it's better to parse the timestamp in correct timezone: > foo = as.POSIXlt("2021-10-01", "UTC") > as.POSIXct(as.character(foo), "Europe/Berlin") [1] "2021-10-01 CEST" The issue stems from the fact that you are pretending like your timestamp is UTC (which it is not) while you want to

Re: [R-pkg-devel] R build fail without a message

2022-09-26 Thread Simon Urbanek
Paul, I wouldn't worry about oldrel - that's likely an incomplete run (I don't see that error anymore), but I would worry about the failure on R-release: https://www.r-project.org/nosvn/R.check/r-release-macos-arm64/EdSurvey-00check.html You can always check with the Mac Builder before you

Re: [R-pkg-devel] windows i386

2022-09-14 Thread Simon Urbanek
Florian, since there was no direct response and given the earlier discussion I figured I chime. The main problem seems to be your build system that doesn't work. Since you didn't post the actual version of the package, I can only see the CRAN version which still don't set any of the necessary

Re: [R-pkg-devel] How to fix Tcl/Tk Error on Mac OS build

2022-04-26 Thread Simon Urbanek
Thanks, indeed, as part of full re-install for R 4.2.0 package builds the Tcl/Tk libraries were missing. Now fixed and summarytools check with * checking data for non-ASCII characters ... NOTE Note: found 78 marked UTF-8 strings Status: 1 NOTE I'll just repeat the important link that Tomas

Re: [R-pkg-devel] Package accepted, then an error to fix by 3/22

2022-03-08 Thread Simon Urbanek
Michael, I can replicate the problem on macOS so this is not system-specific - did you actually try to re-build the vignette? As can be seen from the output the problem is is the following line: one_rec %>% pull(abstract_text) %>% print

Re: [R-pkg-devel] UTF-8 characters inside R functions for data transformation

2021-12-21 Thread Simon Urbanek
Xavier, short answer is no, because there is no guarantee that user's system supports any encoding other than ASCII, so that code wouldn't run. Hence you can't use non-ASCII characters in symbols. That said, you can use Unicode _strings_, so metadata[["\u00e1cc\u00e9nts"]] will work in

Re: [R-pkg-devel] pandoc missing on r-{release,oldrel}-macos-x86_64

2021-12-16 Thread Simon Urbanek
Sure, installed pandoc 2.16.2. Cheers, Simon > On Dec 17, 2021, at 9:21 AM, Dirk Eddelbuettel wrote: > > > CRAN results flag NOTEs on the two platforms > r-release-macos-x86_64 > r-oldrel-macos-x86_64 > because `pandoc` is apparently missing. These platforms being somewhat > common,

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