Re: [R-pkg-devel] Replacement for SETLENGTH

2025-01-15 Thread Tomas Kalibera
On 1/15/25 05:26, Merlise Clyde, Ph.D. wrote: I am trying to determine the best way to eliminate the use of SETLENGTH to truncate over allocated vectors in my package BAS to eliminate the NOTES about non-API calls in anticipation of R 4.5.0. From WRE: "At times it can be useful to allocate

Re: [R-pkg-devel] long user + system time with CRAN special checks clang 19

2024-12-20 Thread Tomas Kalibera
On 12/20/24 10:04, Ivan Krylov via R-package-devel wrote: В Fri, 20 Dec 2024 11:30:04 +0300 Ivan Krylov via R-package-devel пишет: Unfortunately, it's still a puzzle why the function tesseract::TessBaseAPI::GetVariableAsString(char const*, std::string*) const fails to load from libtesseract.

Re: [R-pkg-devel] Non-reproducible ASAN flagged issue

2024-12-18 Thread Tomas Kalibera
On 12/17/24 20:26, David Cortes wrote: I am seeing a curious error in an ASAN package check which is not reproducible in the r-debug containers (https://github.com/wch/r-debug), and which I'm suspecting might be a compiler bug. Wanted to ask for a second opinion on whether this could actually be

Re: [R-pkg-devel] Creating and hosting static libraries for package installation on Windows

2024-12-12 Thread Tomas Kalibera
On 12/11/24 05:23, Satyaprakash Nayak wrote: Hi r-package-devel I am working on updating my package `sundialr` ( https://cran.r-project.org/web/packages/sundialr/index.html), wherein I was earlier bundling the C source files with the package, but now I am using `cmake` to create static libraries

Re: [R-pkg-devel] Cannot create C code with acceptable performance with respect to internal R command.

2024-12-06 Thread Tomas Kalibera
On 12/6/24 08:58, Avraham Adler wrote: Sent from my iPhone On Dec 5, 2024, at 4:11 PM, Sokol Serguei wrote: Luc, There can be many reasons explaining the difference in compiled code performances. Tuning such code to achieve a pick performance is generally a fine art. Optimizations techn

Re: [R-pkg-devel] Cannot create C code with acceptable performance with respect to internal R command.

2024-12-05 Thread Tomas Kalibera
On 12/5/24 14:21, Luc De Wilde wrote: Dear package developers, in creating a package lavaanC for use in lavaan, I need to perform some matrix computations involving matrix products and crossproducts. As far as I see I cannot directly call the C code in the R core. So I copied the code in the

Re: [R-pkg-devel] libarrow

2024-11-26 Thread Tomas Kalibera
On 11/26/24 11:18, Pham, T.V. via R-package-devel wrote: Dear all, I am planning to use libarrow for reading parquet files, chunk by chunk. It seems that by installing "arrow", one gets the libarrow library too (at least on Windows). On Windows, to properly use Apache Arrow with R, it would h

Re: [R-pkg-devel] Warnings related to functions from the survival package

2024-11-04 Thread Tomas Kalibera
On 11/1/24 17:40, Ivan Krylov wrote: On Fri, 1 Nov 2024 09:56:01 +0100 Tomas Kalibera wrote: isn't there a finer-grained way to suppress reports just of this particular issue, ideally at finer granularity than a function? The line saying "function:do_dotCode" in the suppre

Re: [R-pkg-devel] Warnings related to functions from the survival package

2024-11-01 Thread Tomas Kalibera
On 10/31/24 21:06, Ivan Krylov wrote: On Thu, 31 Oct 2024 17:59:01 +0100 Tomas Kalibera wrote: for now, if you know an elegant, minimal way how to suppress this, and have the time and energy, a patch would be welcome A fresh R-4.4.2 build compiled with clang-19 -fsanitize=function gives

Re: [R-pkg-devel] Warnings related to functions from the survival package

2024-10-31 Thread Tomas Kalibera
On 10/31/24 17:39, Ivan Krylov via R-package-devel wrote: В Thu, 31 Oct 2024 12:06:25 -0400 Kaifeng Lu пишет: /home/hornik/src/R/src/main/dotcode.c:1978:2: runtime error: call to function coxph_wtest through pointer to incorrect function type 'void (*)(void *, void *, void *, void *, void

Re: [R-pkg-devel] Properly referencing copied code

2024-07-13 Thread Tomas Kalibera
On 7/13/24 12:24, Simon Urbanek wrote: On 12 Jul 2024, at 10:07, Ivan Krylov via R-package-devel wrote: В Thu, 11 Jul 2024 20:58:53 + DRC via R-package-devel пишет: 1. How does linking to external libs differ from providing the source of a library and linking against that? I think

Re: [R-pkg-devel] "Writing R Extensions" manual needs update [was: Error handling in C code]

2024-06-25 Thread Tomas Kalibera
On 6/24/24 09:45, Agner Fog wrote: On 24/06/2024 08.56, Tomas Kalibera wrote: In principle it is the NEWS file that gives hints about important changes and then one can find the details in Writing R Extensions.  The NEWS file as of mid-April says that "R CMD check --as-cran" wil

Re: [R-pkg-devel] "Writing R Extensions" manual needs update [was: Error handling in C code]

2024-06-23 Thread Tomas Kalibera
On 6/24/24 08:25, Agner Fog wrote: Jarrod Hadfield wrote: Using Rf_error() rather than error() fixed the problem. Not sure why the problem was only flagged on Debian, but it seems to have been triggered by R_NO_REMAP being defined (which will be default in R 4.5.0). I had the same problem.

Re: [R-pkg-devel] Flex missing in win-builder

2024-05-28 Thread Tomas Kalibera
On 5/28/24 06:18, drc via R-package-devel wrote: Is it possible to get flex in the win-builder windows environment? It's present in the debian environment. My package depends on cmake, bison, and flex. Each of these are listed in the `SystemRequirments` field of my DESCRIPTION file but flex is

Re: [R-pkg-devel] Fwd: using portable simd instructions

2024-03-27 Thread Tomas Kalibera
t require aligned operands (on the stack), aligned at 32-byte boundary. Tomas Op di 26 mrt 2024 om 15:51 schreef Tomas Kalibera : On 3/26/24 10:53, jesse koops wrote: Hello R-package-devel, I recently got inspired by the rcppsimdjson package to try out simd registers. It works fantastic on

Re: [R-pkg-devel] using portable simd instructions

2024-03-26 Thread Tomas Kalibera
On 3/26/24 10:53, jesse koops wrote: Hello R-package-devel, I recently got inspired by the rcppsimdjson package to try out simd registers. It works fantastic on my computer but I struggle to find information on how to make it portable. It doesn't help in this case that R and Rcpp make includin

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

2024-02-12 Thread Tomas Kalibera
On 2/12/24 01:35, Simon Urbanek wrote: 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 Ma

Re: [R-pkg-devel] New Package Removal because Shared Library Too Large from Debugging Symbols

2024-01-22 Thread Tomas Kalibera
On 1/22/24 15:42, Ivan Krylov via R-package-devel wrote: On Mon, 22 Jan 2024 12:30:46 +0100 Tomas Kalibera wrote: Thanks, ported now to R-patched. Thank you! Is it fine to mention problems like this one in the middle of an e-mail, or should I have left a note in the Bugzilla instead? In

Re: [R-pkg-devel] New Package Removal because Shared Library Too Large from Debugging Symbols

2024-01-22 Thread Tomas Kalibera
On 1/21/24 09:44, Ivan Krylov via R-package-devel wrote: В Sat, 20 Jan 2024 20:28:00 -0500 Johann Gaebler пишет: most likely there’s some error on my part in how I’ve set up cpp11, but it also seems possible that cpp11 should have detected that that header needs to be included and added it a

Re: [R-pkg-devel] ERROR building MixAll on Windows platform

2024-01-19 Thread Tomas Kalibera
On 1/19/24 15:18, Serge wrote: This post is a continuation of the post *[R-pkg-devel] Does dependencies up to date on the pretest CRAN infrastructure* I made more (unsuccessful) tries: - I installed a Windows 11 version in a VM on my compuiter and try to buid the MixAll package using Rtools42

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

2024-01-17 Thread Tomas Kalibera
On 1/17/24 08:37, Sameh Abdulah wrote: Hi All, We recently encountered an installation issue with our package on CRAN. We've been depending on CMake, assuming it is readily available by default, but it appears to be only available on the M1mac system but not on the others. Should we include

Re: [R-pkg-devel] Additional Issues: Intel

2024-01-17 Thread Tomas Kalibera
On 1/17/24 09:41, Ivan Krylov via R-package-devel wrote: В Wed, 17 Jan 2024 10:30:36 +1100 Hugh Parsonage пишет: I am unable to immediately see where in the test suite this error has occurred. Without testthat, you would have gotten a line by line printout of the code, letting you pinpoint

Re: [R-pkg-devel] Issue with flang-new (segfault from C stack overflow)

2023-12-18 Thread Tomas Kalibera
anks, Jisca On 18-12-2023 16:06, Tomas Kalibera wrote: On 12/18/23 15:09, Ivan Krylov wrote: В Mon, 18 Dec 2023 11:06:16 +0100 Jisca Huisman пишет: I isolated the problem in a minimal working example available here: https://github.com/JiscaH/flang_segfault_min_example . All that does i

Re: [R-pkg-devel] Issue with flang-new (segfault from C stack overflow)

2023-12-18 Thread Tomas Kalibera
On 12/18/23 15:09, Ivan Krylov wrote: В Mon, 18 Dec 2023 11:06:16 +0100 Jisca Huisman пишет: I isolated the problem in a minimal working example available here: https://github.com/JiscaH/flang_segfault_min_example . All that does is pass a vector of length N*N back and forth between R and Fo

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

2023-12-14 Thread Tomas Kalibera
On 12/14/23 19:39, McGrath, Justin M wrote: At this point, the policy appears to have nothing to do with tar, contrary to the error message. Thus, replacing tar with zip wouldn't address CRAN's concern. The policy given in this thread (and seemingly unstated anywhere public) is that CRAN wants

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

2023-12-13 Thread Tomas Kalibera
On 12/13/23 15:59, Dirk Eddelbuettel wrote: On 13 December 2023 at 15:32, Tomas Kalibera wrote: | Please don't forget about what has been correctly mentioned on this | thread already: there is essentially a 260 character limit on Windows | (see | https://blog.r-project.org/2023/03/07

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

2023-12-13 Thread Tomas Kalibera
On 12/13/23 14:56, McGrath, Justin M wrote: Thanks. Pursuing this a bit further, from ?tar "Known problems": > The handling of file paths of more than 100 bytes. These > were unsupported in early versions of ‘tar’, and supported in > one way by POSIX ‘tar’ and in another by GNU ‘

Re: [R-pkg-devel] Update timing of machines on CRAN?

2023-12-04 Thread Tomas Kalibera
On 12/4/23 15:44, SHIMA Tatsuya wrote: Thanks for your answer. Unlike Windows Server, which has a long support period, Fedora's support period is usually about one year, so it is surprising that the old Fedora continues to be used. And, unlike Windows, Linux uses the distribution standard pa

Re: [R-pkg-devel] Canonical way to Rprintf R_xlen_t

2023-11-29 Thread Tomas Kalibera
On 11/29/23 19:30, Henrik Bengtsson wrote: On Tue, Nov 28, 2023 at 1:21 PM Tomas Kalibera wrote: On 11/28/23 21:50, Henrik Bengtsson wrote: Daniel, I get those compiler warnings for '%td" MS Windows. It works fine on Linux. Please let me clarify. %td works in R on Windows in R

Re: [R-pkg-devel] Canonical way to Rprintf R_xlen_t

2023-11-28 Thread Tomas Kalibera
On 11/28/23 22:21, Tomas Kalibera wrote: On 11/28/23 21:50, Henrik Bengtsson wrote: Daniel, I get those compiler warnings for '%td" MS Windows. It works fine on Linux. Please let me clarify. %td works in R on Windows in R 4.3 and R-devel, when using the recommended toolchain

Re: [R-pkg-devel] Canonical way to Rprintf R_xlen_t

2023-11-28 Thread Tomas Kalibera
On 11/28/23 21:55, Daniel Kelley wrote: I hope it's okay to ask this on the present thread, rather than starting a new one... On this issue of the C format for various integer-type items, I am finding that checks made with devtools::check_win_devel() give different results than those made w

Re: [R-pkg-devel] Canonical way to Rprintf R_xlen_t

2023-11-28 Thread Tomas Kalibera
On 11/28/23 20:51, Ivan Krylov wrote: On Wed, 29 Nov 2023 06:11:23 +1100 Hugh Parsonage wrote: Rprintf("%lld", (long long) xlength(x)); This is fine. long longs are guaranteed to be at least 64 bits in size and are signed, just like lengths in R. Right, this has been my choice for R-devel,

Re: [R-pkg-devel] Canonical way to Rprintf R_xlen_t

2023-11-28 Thread Tomas Kalibera
On 11/28/23 21:50, Henrik Bengtsson wrote: Daniel, I get those compiler warnings for '%td" MS Windows. It works fine on Linux. Please let me clarify. %td works in R on Windows in R 4.3 and R-devel, when using the recommended toolchain, which is Rtools43. It also worked with R 4.2 and Rtools

Re: [R-pkg-devel] Package submission issue - OMP reduction (flang-new)

2023-11-14 Thread Tomas Kalibera
On 11/13/23 19:18, Ivan Krylov wrote: On Mon, 13 Nov 2023 16:39:45 +0100 (CET) Romain Pierlot wrote: Here is the error message, and the adequate code part is joint in the mail : error: loc("/data/gannet/ripley/R/packages/incoming/frailtypack.Rcheck/00_pkg_src/frailtypack/src/Integrale_mult_

Re: [R-pkg-devel] Package submission issue - OMP reduction (flang-new)

2023-11-13 Thread Tomas Kalibera
On 11/13/23 16:39, Romain Pierlot wrote: Hi everyone, I sent a first message a few weeks ago. I'm still in trouble for sending a package (Frailtypack) on the CRAN. It was removed because of reinforcement in CRAN requirements. We corrected the few issues, but more appeared, and one that I'm s

Re: [R-pkg-devel] Package bioOED has been removed from CRAN just for personal reasons

2023-11-01 Thread Tomas Kalibera
On 11/1/23 12:15, Alberto Garre wrote: Dear community, I feel dismay for having to write this email, but the issue must be brought up. On the 20th of October, I received an email from CRAN warning me of an issue with one of the packages I maintain (bioOED). The package depended on MEIGOR, a pa

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

2023-07-13 Thread Tomas Kalibera
On 7/13/23 05:08, Hiroaki Yutani wrote: I actually use cargo vendor. https://github.com/yutannihilation/string2path/blob/main/src/rust/vendor.sh One thing to note is that, prior to R 4.3.0, the vendored directories hit the Windows' path limit so I had to put them into a TAR file. I haven't te

Re: [R-pkg-devel] How to identify what flags "Additional Issues" for UBSAN

2023-03-23 Thread Tomas Kalibera
On 3/22/23 16:51, Kenny, Christopher wrote: Hi folks, I'm the maintainer of the redist package (https://cran.r-project.org/web/checks/check_results_redist.html) which was flagged for additional issues with clang-UBSAN and gcc-UBSAN. Both of the 00check.log files say that the status is "OK"

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

2023-03-01 Thread Tomas Kalibera
On 3/1/23 07:35, Matthias Gondan wrote: For the record, here's the documentation of the Prolog sandbox, https://www.swi-prolog.org/pldoc/doc/_SWI_/library/sandbox.pl You get an idea of the implementation by clicking at the ":-" icons. It does not seem too complicated, but I might be too opti

Re: [R-pkg-devel] Unable to load Windows NETIO.SYS and WINSPOOL.DRV DLLs

2023-02-14 Thread Tomas Kalibera
On 2/14/23 13:26, David Sterratt wrote: On Mon, 2023-02-13 at 19:08 +0100, Tomas Kalibera wrote: For reference, there is an old patch for RGtk2 package that I had created when working on Rtools42, though I am not very optimistic it will help in this case: https://svn.r-project.org/R-dev-web

Re: [R-pkg-devel] Unable to load Windows NETIO.SYS and WINSPOOL.DRV DLLs

2023-02-13 Thread Tomas Kalibera
On 2/12/23 17:37, David Sterratt wrote: On Sat, 2023-02-11 at 18:11 +0300, Ivan Krylov wrote: On Sat, 11 Feb 2023 11:19:42 + David Sterratt wrote: WinDbg output reveals errors loading "NETIO.SYS" and "WINSPOOL.DRV" when running "library(RGtk2)": 0c64:0640 @ 44312812 - LdrpProcessWo

Re: [R-pkg-devel] Inconsistent R CMD Check results

2023-01-24 Thread Tomas Kalibera
On 1/23/23 17:51, Ying Li via R-package-devel wrote: Dear all, Hope you are well! Recently, in the check before a re-submission, I got an unexpected note when doing R CMD Check using rhub::check_for_cran(), saying that "Examples with CPU (user + system) or elapsed time > 5s". I didn't expect

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

2023-01-24 Thread Tomas Kalibera
On 1/22/23 22:36, Uri Simonsohn wrote: This is not a perfect list for this question, but possibly a good list. I think this is a good match. I maintain 'groundhog', a package that seeks to simplify reproducibility of R code based on R packages. It has so far relied on MRAN for binaries of olde

Re: [R-pkg-devel] strange errors (non-ascii symbols) on win-builder R-devel

2023-01-23 Thread Tomas Kalibera
On 1/23/23 17:30, Maxim Nazarov wrote: Hello all, I am submitting a minor update to one of my CRAN package (BIGL), and get strange errors on R-devel on win-builder - https://win-builder.r-project.org/incoming_pretest/BIGL_1.6.7_20230119_225109/Windows/00check.log and https://win-builder.r-p

Re: [R-pkg-devel] Rcmd check skip example

2023-01-19 Thread Tomas Kalibera
On 1/19/23 05:00, mai zhou wrote: Hi, In the process of adding examples to the .RD file, I noticed Rcmd check seems to skip certain example code. I put my example code x%*%y%*%z (matrix multiplication) in the RD file. After running Rcmd check (on windows) and look into the xxx.Rcheck direct

Re: [R-pkg-devel] R-devel cannot install my package

2022-09-27 Thread Tomas Kalibera
On 9/28/22 00:50, Bailey, Paul wrote: Hi, I'm trying to update WeMix on CRAN and when I use R-devel (2022-09-26 r82921 ucrt) to R CMD check --as-cran R-devel will not install the package. This is the log file [snip] ** testing if installed package can be loaded from temporary location *** arc

Re: [R-pkg-devel] Unable to create manual

2022-09-17 Thread Tomas Kalibera
On 9/16/22 20:17, Edward Wei wrote: That is an interesting thought. I don't think I have downloaded LaTex explicitly, however, I do have MikTex and I added that file to PATH manually. This is what my current PATH calls: "c:/rtools42/x86_64-w64-mingw32.static.posix/bin;c:/rtools42/usr/bin;C:\\P

Re: [R-pkg-devel] About the CRAN policy on downloading pre-compiled binary

2022-07-27 Thread Tomas Kalibera
On 7/27/22 08:08, Tomas Kalibera wrote: On 7/27/22 00:30, Hiroaki Yutani wrote: Hi, Recently I got the following email from the CRAN maintainer about my package, string2path[1]. However, I do ensure the binary is the pinned version and verify if the hash matches with the embedded one in

Re: [R-pkg-devel] About the CRAN policy on downloading pre-compiled binary

2022-07-27 Thread Tomas Kalibera
his mailing list. > Thanks for your help! No problem, just please only regard it as my advice. Best Tomas > > Best, > Yutani > > 2022年7月27日(水) 15:08 Tomas Kalibera : > > > On 7/27/22 00:30, Hiroaki Yutani wrote: > > Hi, > > > > Recently I

Re: [R-pkg-devel] package stuck in CRAN 'pretest' for a day

2022-07-15 Thread Tomas Kalibera
On 7/15/22 14:50, Georgi Boshnakov wrote: Submitted package 'fGarch' has been stuck in CRAN 'pretest' for about 24 hours now. The same seems to hold for several other packages. Is this something that can be expected normally? The pretest service seems to work normally in that other packages co

Re: [R-pkg-devel] Changing optimization level when building package?

2022-07-07 Thread Tomas Kalibera
On 7/5/22 16:11, Ivan Krylov wrote: On Tue, 5 Jul 2022 09:35:05 -0400 Duncan Murdoch wrote: I see the -O0 option that I added, but afterwards -O2 coming from somewhere in R. It seems to come from the CXXFLAGS macro defined in /etc/R/Makeconf. It's the last to be added to ALL_CXXFLAGS, so yo

Re: [R-pkg-devel] handling of byte-order-mark on r-devel-linux-x86_64-debian-clang machine

2022-04-06 Thread Tomas Kalibera
R handles BOMs in the "connections" code, ?connections, and it uses iconv for input conversion. Thanks Tomas On April 5, 2022 11:20:37 AM PDT, Tomas Kalibera wrote: On 3/28/22 13:16, Ivan Krylov wrote: On Mon, 28 Mar 2022 09:54:57 +0200 Tomas Kalibera wrote: Could you please cl

Re: [R-pkg-devel] cmake, Windows

2022-03-15 Thread Tomas Kalibera
R packages can be provided). If this is not possible and you need a new version of SWI Prolog on all systems, newer than normally available, perhaps best to write to CRAN and ask there about this specific case. Best Tomas > Best wishes, > > Matthias > > *Von: *Tomas Kalibera <

Re: [R-pkg-devel] Error in inDL(x, as.logical(local), as.logical(now), ...) unable to load shared object

2022-01-03 Thread Tomas Kalibera
Thanks again! -Ezra On 12/23/21 17:20, Tomas Kalibera wrote: On 12/23/21 4:52 PM, Ezra Tucker wrote: Hi Tomas and Dirk, Thanks for your suggestions! Between the two, got it working. I didn't know Windows didn't do rpath, I think that you're right that setting the PATH would have

Re: [R-pkg-devel] Error in inDL(x, as.logical(local), as.logical(now), ...) unable to load shared object

2021-12-23 Thread Tomas Kalibera
/23/21 09:34, Dirk Eddelbuettel wrote: On 23 December 2021 at 11:07, Tomas Kalibera wrote: | You can have a look at CRAN package Rblpapi which is using an external DLL. Yes with one big caveat: You have to make sure the library follows what is the "hour-glass pattern": it needs to have

Re: [R-pkg-devel] Error in inDL(x, as.logical(local), as.logical(now), ...) unable to load shared object

2021-12-23 Thread Tomas Kalibera
On 12/21/21 5:40 PM, Ezra Tucker wrote: Hi R package developers, I'm developing an R package that wraps NREL's SSC library (https://sam.nrel.gov/), which involves including one header file and linking to one dll. Thus far it is only tested in linux (works just fine there) but I am having trou

Re: [R-pkg-devel] New CRAN checks on r-devel-windows-x86_64-new-UL and the installed fonts

2021-12-16 Thread Tomas Kalibera
see. Maybe best then making the example more robust when no fonts are found, on different platforms. Best Tomas Best, Hiroaki Yutani 2021年12月17日(金) 0:52 Tomas Kalibera : On 12/16/21 4:17 PM, Hiroaki Yutani wrote: This would be an empty character vector on my Alpine Linux server as well. I s

Re: [R-pkg-devel] New CRAN checks on r-devel-windows-x86_64-new-UL and the installed fonts

2021-12-16 Thread Tomas Kalibera
On 12/16/21 4:17 PM, Hiroaki Yutani wrote: This would be an empty character vector on my Alpine Linux server as well. I see, thanks for the information. Sorry for my lack of consideration on this. So there are 127 *.ttf files installed, but systemfonts::system_fonts() does not find any of th

[R-pkg-devel] R/CRAN switch to UCRT on Windows

2021-12-08 Thread Tomas Kalibera
(My apologies for cross-posting to those reading also the R-devel mailing list) Please note an update concerning the support of UTF-8 as native encoding on Windows, which may at this point be of interest particularly to developers of packages with native code and to R users using R-devel (the

Re: [R-pkg-devel] socketConnection, delay when reading from

2021-12-08 Thread Tomas Kalibera
On 12/8/21 12:20 PM, Ben Engbers wrote: Op 07-12-2021 om 23:49 schreef Ben Engbers: After a long nightly session, I ended up with inserting a wait between sending the authentication nonce and reading the status byte. writeBin(auth, private$conn) Sys.sleep(.1) Accepted <- readBin(conn, what

Re: [R-pkg-devel] socketConnection, delay when reading from

2021-11-28 Thread Tomas Kalibera
On 11/28/21 5:10 PM, Ben Engbers wrote: Searching Google seems easy. But finding reaully usefull information is often very difficult. I alreay found hint #1. Thankfs for #2 and #3 Perhaps people who teach these things could give best recommendations (and those may not be reading this list).

Re: [R-pkg-devel] socketConnection, delay when reading from

2021-11-27 Thread Tomas Kalibera
On 11/27/21 8:05 PM, Tomas Kalibera wrote: On 11/27/21 5:24 PM, Ben Engbers wrote: Op 27-11-2021 om 17:03 schreef Jeff Newmiller: This is a null-terminated message protocol [1]. It has to be processed one byte at a time. [1] https://docs.basex.org/wiki/Server_Protocol The message may

Re: [R-pkg-devel] socketConnection, delay when reading from

2021-11-27 Thread Tomas Kalibera
On 11/27/21 5:24 PM, Ben Engbers wrote: Op 27-11-2021 om 17:03 schreef Jeff Newmiller: This is a null-terminated message protocol [1]. It has to be processed one byte at a time. [1] https://docs.basex.org/wiki/Server_Protocol The message may contain embedded 0x00's. To distinguish these emb

Re: [R-pkg-devel] LaTeX issues on r-devel-windows-x86_64-gcc10-UCRT?

2021-09-23 Thread Tomas Kalibera
Dear Stephan, On 9/21/21 8:10 PM, Struckmann, Stephan wrote: Dear Thomas, thank you for your quick reply. I'll consider then writing to the CRAN address earler, if I have strong hints that the build/check system may cause a warning/error. So, I'll wait for the next check-run then. If I can he

Re: [R-pkg-devel] LaTeX issues on r-devel-windows-x86_64-gcc10-UCRT?

2021-09-21 Thread Tomas Kalibera
Dear Stephan, On 9/21/21 3:31 PM, Stephan Struckmann wrote: > Dear all, > > lately, an error and two warnings occurred for our package dataquieR on the > platform r-devel-windows-x86_64-gcc10-UCRT > (https://cran.r-project.org/web/checks/check_results_dataquieR.html). > > Unfortunately, error me

Re: [R-pkg-devel] (R-devel unknown warning: 'memory.limit()' is no longer supported)

2021-09-03 Thread Tomas Kalibera
Dear Cristhian, memory.limit() is called by package "ff" when it is loaded. Your new package uses "ff" via "propagate". Perhaps the easiest option for you is to re-try the submission once "ff" is adapted to this change in R-devel. Best Tomas On 9/3/21 7:10 PM, Cristhian Paredes Cardona wrote

Re: [R-pkg-devel] Unicode Name Warnings for Package Constant

2021-09-02 Thread Tomas Kalibera
In the current R releases, R symbol names are in the native encoding, which on Windows in R (the normal MSVCRT builds up to R 4.1) cannot be UTF-8 nor any other Unicode encoding. So you can't portably use such characters e.g. in names of vector elements or of bindings in an environment, so not

Re: [R-pkg-devel] UX for "WARNING unable to translate to native encoding"?

2021-08-16 Thread Tomas Kalibera
On 8/16/21 12:42 PM, Ivan Krylov wrote: On Mon, 16 Aug 2021 09:05:54 + David Norris wrote: Unicode U+00d7 (times), U+00b1 (plus-minus) and U+03bc (mu) have equivalents in Latin-1 encoding, and I have used these without difficulty in strings, neither U+2206 (INCREMENT) nor U+0394 (Greek D

Re: [R-pkg-devel] speeding up package code/build/test cycle

2021-06-24 Thread Tomas Kalibera
On 6/24/21 11:31 PM, Duncan Murdoch wrote: On 24/06/2021 4:52 p.m., Dirk Eddelbuettel wrote: On 24 June 2021 at 16:31, Duncan Murdoch wrote: | This does the full compile again, so it's slow. ccache fixes that (as it has its own cache). It also works on macOS. I haven't tried ccache:  shoul

Re: [R-pkg-devel] Valgrind warning: invalid size of 4, is it due to a simple overrun?

2021-06-10 Thread Tomas Kalibera
On 6/2/21 3:01 AM, Hugh Parsonage wrote: Hello, I received a valgrind warning about my package, hutilscpp, from CRAN (thank you). I believe I've tracked down and fixed the problem, but I wasn't able to reproduce the error on rhub (including with --leak-check=full etc) so I'd like to know if I

Re: [R-pkg-devel] Passing CRAN checks for a package linking to a system library on CRAN machines

2021-05-14 Thread Tomas Kalibera
encies on native libraries, and someone has to do this work. Installing libraries manually on the check machines is not going to scale and may be too much burden for many end users, apart from difficulties with repeatability, maintenance, etc. Best Tomas > > Thanks again for your help

Re: [R-pkg-devel] Fwd: Passing CRAN checks for a package linking to a system library on CRAN machines

2021-05-13 Thread Tomas Kalibera
On 5/13/21 7:29 AM, Sokol Serguei wrote: Le 13/05/2021 à 07:06, SN248 a écrit : I am working on a package which provides an interface to the libsbml C++ library (http://sbml.org/Software/libSBML) in R. The source code of this package (r2sbml) can be found at the following link https://github.

Re: [R-pkg-devel] Passing CRAN checks for a package linking to a system library on CRAN machines

2021-05-12 Thread Tomas Kalibera
On 5/13/21 7:06 AM, SN248 wrote: I am working on a package which provides an interface to the libsbml C++ library (http://sbml.org/Software/libSBML) in R. The source code of this package (r2sbml) can be found at the following link https://github.com/sn248/r2sbml The package passes CRAN checks

Re: [R-pkg-devel] winUCRT failures

2021-04-26 Thread Tomas Kalibera
On 4/25/21 2:49 PM, Duncan Murdoch wrote: The current CRAN release of rgl fails on winUCRT because of missing dependencies: 'htmlwidgets', 'htmltools', 'knitr', 'jsonlite', 'shiny', 'magrittr', 'crosstalk', 'manipulateWidget'. Tracing `htmlwidgets` shows it also fails because of missing d

Re: [R-pkg-devel] how to address CRAN FAIL on r-devel-windows-x86_64-gcc10-UCRT?

2021-04-03 Thread Tomas Kalibera
On 4/2/21 1:05 PM, Daniel Kelley wrote: The "oce" package for oceanographic analysis is failing a check on the r-devel-windows-x86_64-gcc10-UCRT system (see https://www.r-project.org/nosvn/R.check/r-devel-windows-x86_64-gcc10-UCRT/oce-00check.html). The problem seems to relate to the checking v

Re: [R-pkg-devel] R package check stuck on “checking use of S3 registration …”

2021-02-12 Thread Tomas Kalibera
On 2/11/21 8:28 AM, Evan Biederstedt wrote: Hi there Creating an R package here which I plan to upload to CRAN. Upon checking the tarball created with `R CMD BUILD`, I try to use `R CMD CHECK` as follows: ``` R CMD CHECK my_package.tar.gz --as-cran ``` This normally works smoothly. However, in

Re: [R-pkg-devel] Package Encoding and Literal Strings

2020-12-21 Thread Tomas Kalibera
oblem... You can compile native code locally on Windows, the toolchain includes a native compiler and I build R packages natively as well. Cross-compilation is used to build the compiler toolchain and external libraries for packages. Cheers Tomas > > Cheers, > Joris > > >

Re: [R-pkg-devel] [Re] warning: type of ‘zhpevx_’ does not match original declaration [-Wlto-type-mismatch]

2020-12-21 Thread Tomas Kalibera
hat by redefining FC_LEN_T and Rcomplex, without any runtime overhead, but that would be hiding potential problems as well. Best Tomas > > Thank you again all for sharing your precious time. > > Kind regards, > Pierre L. > ---

Re: [R-pkg-devel] Package Encoding and Literal Strings

2020-12-18 Thread Tomas Kalibera
on in there I wrote that displays the bytes straight from R's > CHAR to be sure no conversion is happening. > I would expect that the mathotString had "C3 B4" for "ô" but instead > it gets "F4". As you can see when you run > `utf8StringsPkg::testutf

Re: [R-pkg-devel] Package Encoding and Literal Strings

2020-12-18 Thread Tomas Kalibera
On 12/17/20 6:43 PM, jo...@jorisgoosen.nl wrote: > > > On Thu, 17 Dec 2020 at 18:22, Tomas Kalibera <mailto:tomas.kalib...@gmail.com>> wrote: > > On 12/17/20 5:17 PM, jo...@jorisgoosen.nl > <mailto:jo...@jorisgoosen.nl> wrote: >> >> >&g

Re: [R-pkg-devel] [Re] warning: type of ‘zhpevx_’ does not match original declaration [-Wlto-type-mismatch]

2020-12-18 Thread Tomas Kalibera
ns (but does not include the complex type). Best, Tomas > > Have a nice day. > > Kind regards, > Pierre > -------- > *From:* Ivan Krylov > *Sent:* Friday, 18 December 2020 18:16 > *To:* Pierre Lafaye de Micheaux &g

Re: [R-pkg-devel] Package Encoding and Literal Strings

2020-12-17 Thread Tomas Kalibera
On 12/17/20 5:17 PM, jo...@jorisgoosen.nl wrote: > > > On Thu, 17 Dec 2020 at 10:46, Tomas Kalibera <mailto:tomas.kalib...@gmail.com>> wrote: > > On 12/16/20 11:07 PM, jo...@jorisgoosen.nl > <mailto:jo...@jorisgoosen.nl> wrote: > > David,

Re: [R-pkg-devel] Package Encoding and Literal Strings

2020-12-17 Thread Tomas Kalibera
On 12/16/20 11:07 PM, jo...@jorisgoosen.nl wrote: David, Thanks for the response! So the problem is a bit worse then just setting `encoding="UTF-8"` on functions like readLines. I'll describe our setup a bit: So we run R embedded in a separate executable and through a whole bunch of C(++) magic

Re: [R-pkg-devel] warning: type of ‘zhpevx_’ does not match original declaration [-Wlto-type-mismatch]

2020-12-15 Thread Tomas Kalibera
t match original declaration ). > > My version of fortran: GNU Fortran (Debian 8.3.0-6) 8.3.0 under Debian 10. > > Thank you very much for any further help you could provide so that I > could have my package back to the CRAN. > > Kind regards, > Pierre L. > > >

Re: [R-pkg-devel] detritus in temp

2020-10-20 Thread Tomas Kalibera
This was a bug in R-devel, already fixed. (specific to Unix, and only 3 R-devel revisions) Sorry for the inconvenience, Tomas On 10/20/20 4:48 PM, Cristoforo Simonetto wrote: Dear all, last week I tried to upload for the first time a package to CRAN but my submission was refused: Flavor: r-

Re: [R-pkg-devel] Check: for detritus in the temp directory, Result: NOTE

2020-10-16 Thread Tomas Kalibera
This is was a bug in R-devel, already fixed. Sorry for the inconvenience, Tomas On 10/17/20 12:06 AM, John Mount wrote: I am trying to move the wrapr package from RUnit to tinytest. All seemed well on my tests, but when I submitted to CRAN I got: Flavor: r-devel-linux-x86_64-debian-gcc Check:

Re: [R-pkg-devel] Anyone Know How To Setup Wine for Windows Testing?

2020-09-21 Thread Tomas Kalibera
On 9/18/20 11:56 PM, Steve Bronder wrote: > inline > > > On Wed, Sep 9, 2020 at 3:35 AM Tomas Kalibera > mailto:tomas.kalib...@gmail.com>> wrote: > > On 7/16/20 7:57 PM, Steve Bronder wrote: > > On Wed, Jul 15, 2020 at 2:22 PM Neal Fultz

Re: [R-pkg-devel] Compiling 32-bit on Windows using 64-bit gcc and -m32

2020-09-09 Thread Tomas Kalibera
On 9/7/20 7:07 PM, b...@denney.ws wrote: Hello, My question is: Can I use the 64-bit gcc to build a 32-bit package with the -m32 command line option with Rtools? And, can that work for CRAN? Or more generally, is there a work-around for needing lots of RAM during compilation with the 32-

Re: [R-pkg-devel] Anyone Know How To Setup Wine for Windows Testing?

2020-09-09 Thread Tomas Kalibera
On 7/16/20 7:57 PM, Steve Bronder wrote: On Wed, Jul 15, 2020 at 2:22 PM Neal Fultz wrote: If you don't mind multi-gig docker containers, this can be helpful: https://github.com/scottyhardy/docker-wine It doesn't work with 64 bit versions of R as far as I could tell, but 32 bit did install a

Re: [R-pkg-devel] warning: type of ‘zhpevx_’ does not match original declaration [-Wlto-type-mismatch]

2020-07-06 Thread Tomas Kalibera
My recommendation would be to try to minimize the example (package) as much as possible so that it still has the problem, and then try to investigate why exactly/where is the type mismatch. This is what helped me debug similar issues - sometimes it was hard to tell from the Fortran warnings whe

Re: [R-pkg-devel] data and load version 3

2020-06-30 Thread Tomas Kalibera
On 6/30/20 11:48 AM, Göran Broström wrote: On 2020-06-30 01:07, Jeff Newmiller wrote: Your choice. Do you want to support people using older versions of R, or not? Is that all? No point at all with version 3 in packages? Why was it introduced? I have seen an argument for version 2: "... nee

Re: [R-pkg-devel] how to prevent a small package from yielding a large installed size?

2020-06-15 Thread Tomas Kalibera
On 6/15/20 6:52 PM, Duncan Murdoch wrote: On 15/06/2020 12:30 p.m., Daniel Kelley wrote: Duncan, thanks very much for that very helpful hint.  I got as follows.   My guess is that the first column in rdx$variables is an address offset, and so it seems that the lion's share of the storage is de

Re: [R-pkg-devel] use of getNativeSymbolInfo

2020-03-24 Thread Tomas Kalibera
On 2/9/20 5:14 PM, Benjamin Tyner wrote: Hello, Using package nlme as an example, where there is a registered routine fit_gnls: > library(nlme) > getDLLRegisteredRoutines("nlme")$.C$fit_gnls $name [1] "fit_gnls" $address attr(,"class") [1] "RegisteredNativeSymbol" $dll DLL name: nlme Filen

Re: [R-pkg-devel] Problem with Check --as-cran

2020-03-23 Thread Tomas Kalibera
The problem is with if (class(data) != "matrix") stop("The data field should be an array or a data frame") Please use inherits() instead of checking class(), see this for more details https://developer.r-project.org/Blog/public/2019/11/09/when-you-think-class.-think-again Best Tomas On 3/2

Re: [R-pkg-devel] Errors in make check in Windows 10 with OpenBLAS

2020-03-21 Thread Tomas Kalibera
> Riconv.def win_iconv.o > > Just the  -march=native -pipe > > Erin Hodgess, PhD > mailto: erinm.hodg...@gmail.com <mailto:erinm.hodg...@gmail.com> > > > On Fri, Mar 20, 2020 at 9:01 AM Tomas Kalibera > mailto:tomas.kalib...@gmail.com>> wrote: > >

Re: [R-pkg-devel] Errors in make check in Windows 10 with OpenBLAS

2020-03-20 Thread Tomas Kalibera
2;LC_MONETARY=English_United > States.1252;LC_NUMERIC=C;LC_TIME=English_United States.1252" > > enc2native("\uff21") > [1] "A" > > enc2native("\u4e2d") > [1] "" > > Sys.setlocale("LC_CTYPE", "English

Re: [R-pkg-devel] Errors in make check in Windows 10 with OpenBLAS

2020-03-20 Thread Tomas Kalibera
     > c.ch <http://c.ch> w.ch <http://w.ch> c.fw w.fw >      > 64   64   32   64 >     >> stopifnot(unname(ncc) == c(64,64, 32, 64)) >     >> ## nchar.max: 1st line needs an increase of  2 in order to > see  1  (in >      > UTF-$ >

Re: [R-pkg-devel] Strange leftovers after check by CRAN

2020-03-20 Thread Tomas Kalibera
On 3/19/20 6:03 PM, Max Turgeon wrote: > Is there perhaps a typo in the environment variable name? This line suggests > there should be an underscore at the beginning too: > > https://github.com/wch/r-source/blob/trunk/src/library/tools/R/check.R#L6028 Also the correct name is in R Internals, whe

Re: [R-pkg-devel] Errors in make check in Windows 10 with OpenBLAS

2020-03-19 Thread Tomas Kalibera
Hi Erin, this comes from examples in ?str. Could you please try to find a minimal example to reproduce on your system based on that? I would look for "line needs" in ?str and experiment with reducing the example there while still getting the error. Once it is minimal, could you please try als

Re: [R-pkg-devel] [FORGED] Re: Help on Windows CRAN Check

2020-03-05 Thread Tomas Kalibera
On 3/5/20 9:45 AM, Rolf Turner wrote: On 5/03/20 9:04 pm, Tomas Kalibera wrote: On 3/5/20 4:26 AM, John Lawson wrote: I see this error on the CRAN Check report Fatal error: the condition has length > 1 The problem is that the condition t1 == "I" & t2 == "("

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