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] 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] 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

2021-05-14 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] 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] 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] 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] 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] (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] 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] 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] 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] 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

2021-11-28 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

2021-12-08 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

[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] 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

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] 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] 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

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] 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] 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] 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] 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] 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] 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] 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] 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] 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] 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] 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] 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] 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] 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] 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] 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] 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] 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] 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 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] 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] 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 21:55, 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 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

2023-11-29 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] 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] 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] 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?

2023-12-14 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] 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] 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] 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] 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] 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] 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] 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] 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] 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] 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] 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] "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] "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] 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] [External] Re: try() in R CMD check --as-cran

2019-06-14 Thread Tomas Kalibera
The advantage of "abort" (R_Suicide) over the default (R error) is that it cannot be caught accidentally, so that one can detect more errors, and it may be easier to find where the error happened. To make the default behavior less surprising/more user friendly, and to allow intentional catching

Re: [R-pkg-devel] access is denied

2019-06-20 Thread Tomas Kalibera
If you have not already done so, I'd check the package directory (and its parent) is not opened in any application, including Windows Explorer, including current working directory in any command prompt. I'd also make sure the package is not loaded in any R session. The error message may be caus

Re: [R-pkg-devel] implications of staged install for data processing packages

2019-06-28 Thread Tomas Kalibera
On 6/28/19 5:16 PM, Florian Oswald wrote: oh ok i see: so i will always be able to do clean(path = "~/data.csv") for example? in that case I completely misunderstood this and there must indeed be some system.file call buried somewhere. will check. thanks! In case it is hard to find manually,

Re: [R-pkg-devel] Warning about "serialize/load".

2019-07-15 Thread Tomas Kalibera
On 7/15/19 2:06 AM, Travers Ching wrote: I think the major change was saving of alt-rep objects efficiently. Example save(1:1e8, file=...) is very efficient. I'm not sure if that is all that changed it, but I couldn't find documentation on the differences. Yes, format version 3 provides custom

Re: [R-pkg-devel] Single character in Fortran function and FCONE and FCLEN macros

2019-09-03 Thread Tomas Kalibera
On 9/3/19 3:07 PM, Benjamin Christoffersen wrote: > Dear Sirs, > > I have tried to update my 'dynamichazard' package on CRAN but I have > had some issues with the '-Wlto-type-mismatch' checks. In particular, > I have tried to follow "Writing R Extensions" section "Fortran > character strings" and d

Re: [R-pkg-devel] Linking with OpenBLAS complains lapacke not found

2019-09-09 Thread Tomas Kalibera
Please refer to BLAS_LIBS, LAPACK_LIBS in Writing R Extensions. For an example package that uses BLAS/LAPACK, see e.g. "stats" or "Matrix". The package will then use the BLAS/LAPACK implementation as chosen by the user/system administrator at dynamic linking time (see R Installation and Adminis

Re: [R-pkg-devel] R, BLAS, and FCLEN (solved)

2019-09-13 Thread Tomas Kalibera
Dear Göran, I can reproduce the problem with eha version 2.6.0. The reason for the type mismatch, and hence the LTO warning, is _not_ the calls to dgemv from Fortran code, but the calls to dgemv from the C code from the other source files in your package. There is no need to go through wrapper

Re: [R-pkg-devel] My test passes in OSx on Travis, but not in OSx on CRAN

2019-09-13 Thread Tomas Kalibera
The error seems to be because you are trying to write to the user's home directory. This is not allowed. Probably by accident your test creates "~/testcsv4.csv" (the same problem is present for other test files). Best Tomas On 9/13/19 1:21 PM, Vincent van Hees wrote: Dear all, I have a test

Re: [R-pkg-devel] Warning in system2(..., stdout = FALSE, stderr = FALSE) :, '"pdflatex"' not found

2019-09-19 Thread Tomas Kalibera
On 9/19/19 6:29 AM, Spencer Graves wrote: Update: A web search for 'installing pdflatex for "R CMD" on Windows 10?' suggested I install MiKTeX.  I did that from miktex.org, and it got me past that error.  Spencer Please note these things are documented in R Installation and Administration Man

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

2019-09-21 Thread Tomas Kalibera
On 9/20/19 2:43 AM, Aravind J. wrote: Hi, I was able to fix the issue and submit my package successfully to CRAN. However, the question remains, is there any way to replicate the CRAN pre-tests locally for future debugging, particularly in a windows environment? I had tried rhub platforms with

Re: [R-pkg-devel] unicode WARNING on solaris?

2019-09-24 Thread Tomas Kalibera
On 9/24/19 1:57 AM, Toby Hocking wrote: Hi all, is there a known fix for this WARNING which I am getting on solaris for my newly submitted nc package? https://www.r-project.org/nosvn/R.check/r-patched-solaris-x86/nc-00check.html It seems that deparse() came across some non-printable characters

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

2019-09-25 Thread Tomas Kalibera
On 9/25/19 1:00 PM, Ralf Stubner wrote: On Wed, Sep 25, 2019 at 10:29 AM Sameh M. Abdulah wrote: I am installing OpenBLAS because I need LAPACKE libraries which I cannot find on the current version of OpenBLAS on CRAN. I add the libraries directory in my package to the PKG_CONFIG_PATH. Is thi

Re: [R-pkg-devel] unicode WARNING on solaris?

2019-09-25 Thread Tomas Kalibera
es. I see \u4e8c \u4e09 \U0001F60E. Tomas > > On Tue, Sep 24, 2019 at 1:38 AM Tomas Kalibera > mailto:tomas.kalib...@gmail.com>> wrote: > > On 9/24/19 1:57 AM, Toby Hocking wrote: > > Hi all, > > > > is there a known fix for this WARNING which I

Re: [R-pkg-devel] How reproduce CRAN check

2019-09-25 Thread Tomas Kalibera
On 9/17/19 6:17 PM, Cristiane Hayumi Taniguti wrote: Hello, thanks for all the answers. I did the new tests with all suggestions. I included the Rprintf in my script, however it did not show any NaN when running with my examples (the same that CRAN check pointed the error) The approach of add

Re: [R-pkg-devel] invalid multibyte string on solaris?

2019-11-01 Thread Tomas Kalibera
On 10/31/19 12:58 AM, Toby Hocking wrote: Hi all, I am getting an "invalid multibyte string" error from one of my examples when it is run on solaris, which results in check FAILURE: https://www.r-project.org/nosvn/R.check/r-patched-solaris-x86/nc-00check.html To fix this I guess I could just del

Re: [R-pkg-devel] install.R running out of memory

2019-11-04 Thread Tomas Kalibera
On 11/3/19 1:05 PM, Viktor Gal wrote: ah yeah i forgot to mention. it’s the same, i.e. it’s not the byte code compilation that causes this behaviour but the preparation for lazy loading. R is not optimized for these cases (generated code, source file with >100,000 lines of code), but R has bi

Re: [R-pkg-devel] netcdf question

2019-11-04 Thread Tomas Kalibera
On 11/4/19 8:40 PM, Roy Mendelssohn - NOAA Federal via R-package-devel wrote: Hi All: I am wondering if it is possible to find out when packages that use the netcdf libraries are built on the CRAN machines (such as ncdf4) what versions of the netcdf library are being used on at least Mac and W

Re: [R-pkg-devel] Updating package with a dependency (rJava) that doesn't build on all flavours

2019-11-13 Thread Tomas Kalibera
On 11/13/19 10:19 AM, Tomáš Kliegr wrote: Hello, This question has not stirred much discussion ... If this is the wrong place to ask, I was wondering if some one point me to where I should ask, or who to approach? If I understand this issue correctly, it does not affect only my package, but

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

2019-11-28 Thread Tomas Kalibera
On 11/21/19 7:25 PM, Devin Incerti wrote: Hi, I'm attempting to submit a very minor update to my package where I replaced a deprecated C++ function with an alternative. However, I'm receiving an unrelated warning "*array subscript -1 is outside array bounds of ‘double [52]’ [-Warray-bounds] *" o

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

2020-03-05 Thread Tomas Kalibera
On 3/5/20 4:26 AM, John Lawson wrote: > I see this error on the CRAN Check report > >> ### ** Examples >> >> #Definitive Screening Design >> library(daewr) >> set.seed(1234) >> x <- DefScreen(m=5,c=0) >> colnames(x) <- paste("x",1:5,sep="") >> x$y <- 3*x$x1 + 2*x$x2 + 2*x$x4*x$x5 + x$x3^2 + 2*x$x1^

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 == "("

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] 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

2020-03-20 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] 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

2020-03-21 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] 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] 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] 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] 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] 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] 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] 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?

2020-09-21 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] 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] 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-

  1   2   >