Re: [R-pkg-devel] is Fortran write still strictly forbidden?

Dear Berwin & Erin, Thanks for your replies. I should perhaps have clarified - this is for a package on CRAN. In my experience anything with Fortran write will get a NOTE from CRAN's auto-check: Check: compiled code, Result: NOTE File 'sequoia/libs/sequoia.so': Found '_gfortran_st_wri

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

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] is Fortran write still strictly forbidden?

Hi Jisca, On Wed, 8 May 2024 10:37:28 +0200 Jisca Huisman wrote: > I like to use write() in Fortran code [...] But from 'writing R > extensions' it seems that there have been quite a few changes with > respect to support for Fortran code, and it currently reads: > > 6.5.1 Printing from Fortran

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

Thanks! I want to save data from a matrix to a file and then retrieve it later while running R code, all within R. As long as the compression doesn't result in data loss, it should be suitable for my needs. Best, --Sameh From: Dirk Eddelbuettel Date: Thursday, May 9, 2024 at 6:35 AM To:

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

On 9 May 2024 at 03:20, Sameh Abdulah wrote: | I need to serialize and save a 20K x 20K matrix as a binary file. Hm that is an incomplete specification: _what_ do you want to do with it? Read it back in R? Share it with other languages (like Python) ? I.e. what really is your use case? Also, y

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

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 the best approach to optimize the below code. Is it possible to parallelize the serialization function to enhance performance? n

Re: [R-pkg-devel] is Fortran write still strictly forbidden?

Hi Jisca: I have used the write successfully. I’m not sure if this matters or not, but I am using WSL 2 with Ubuntu 22.04 installed. It works fine with R => 4.0. Hope this helps. Sincerely, Erin Erin Hodgess, PhD mailto: erinm.hodg...@gmail.com On Wed, May 8, 2024 at 6:49 PM Jisca Huisman

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

Hello everyone, this is my first post on the mailing list (as well as the first package I'm attempting to publish), so please forgive any obvious errors. I'm using a lot of Fortran code which relies on derived types to manage data structures. The package compiles fine on Windows, Linux and Mac a

[R-pkg-devel] is Fortran write still strictly forbidden?

Hello, I like to use write() in Fortran code to combine text with some integers & doubles, to pass runtime information to R in a way that is prettier and more legible than with intpr() & dblepr(). In the past any calls to write() were strictly forbidden in Fortran code, as apparently it messed

Re: [R-pkg-devel] Overcoming CRAN's 5mb vendoring requirement

On Wed, 8 May 2024, Josiah Parry wrote: Yes, prqlr is a great Rust-based package! My other Rust based packages that are on CRAN are based, in part on prqlr. If there are many packages based on Rust that require common code, would it make sense to make a single "rust" compatibility pack

Re: [R-pkg-devel] Overcoming CRAN's 5mb vendoring requirement

Zenodo and OSF (see e.g. ) are both non-profit organizations that support archiving -- that is, they both make stronger guarantees of permanent availability than GitHub does. Possibly Software Heritage https://www.softwareheritage.org/features/ ?

Re: [R-pkg-devel] Overcoming CRAN's 5mb vendoring requirement

That's a good point! My apologies for not making that abundantly clear. Regardless, I think it is a fair ask to not submit massive tarballs of dependencies. Clarifying how we might be able to store the dependencies *outside *of CRAN would be good to figure out. This would help packages like polars

Re: [R-pkg-devel] Overcoming CRAN's 5mb vendoring requirement

On 08.05.2024 17:56, Josiah Parry wrote: Thank you, Dirk. This was a direct email from a CRAN member and not part of the automatic checks. The whole email is below. I think the intent of the message is "please resubmit." Well, the CRAN maintainer has not spotted this is abour rust code. This

Re: [R-pkg-devel] Overcoming CRAN's 5mb vendoring requirement

Thank you, Ivan, for your really thoughtful feedback! I really appreciate it! - I'll see if there are any base R packages that support SHA-2 or SHA-3. - I'll see if I can get the configure.ac to make the appropriate Rscript call for configure.win. - I think the idea of having a sing

Re: [R-pkg-devel] Overcoming CRAN's 5mb vendoring requirement

В Wed, 8 May 2024 14:08:36 -0400 Josiah Parry пишет: > With ChatGPT's ability to write autoconf, I *think *I have something > that can work. You don't have to write autoconf if your configure.ac is mostly a plain shell script. You can write the configure script itself. Set the PATH and then exec

Re: [R-pkg-devel] Overcoming CRAN's 5mb vendoring requirement

Thank you, Neal! I took some inspiration from the arrow-r github repo and ch 1.2 of the manual *If your configure script needs auxiliary files, it is recommended that you > ship them in a tools directory (as R itself does).* With ChatGPT's ability to write autoconf, I *think *I have something t

Re: [R-pkg-devel] Overcoming CRAN's 5mb vendoring requirement

Thank you, Dirk. This was a direct email from a CRAN member and not part of the automatic checks. The whole email is below. I think the intent of the message is "please resubmit." Thanks, we see: >Size of tarball: 18099770 bytes Please reudce to less than 5 MB for a CRAN package. Best,

Re: [R-pkg-devel] Overcoming CRAN's 5mb vendoring requirement

On 8 May 2024 at 11:02, Josiah Parry wrote: | CRAN has rejected this package with: | | * Size of tarball: 18099770 bytes* | | *Please reudce to less than 5 MB for a CRAN package.* Are you by chance confusing a NOTE (issued, but can be overruled) with a WARNING (more severe, likely a must-be-

Re: [R-pkg-devel] package removed from CRAN

В Wed, 8 May 2024 17:30:46 +0200 "Jose V. Die Ramon" пишет: > Could anyone please help me understand the reasons behind this, or > suggest any steps I should take to resolve it? Here's what I could find in https://cran.r-project.org/src/contrib/PACKAGES.in: >> X-CRAN-Comment: Archived on 2024-0

Re: [R-pkg-devel] package removed from CRAN

According to the CRAN links , your package had an error on r-devel-windows-x86_64 and r-patched-linux-x86_64 which was not addressed. Specifically, some examples failed. See

[R-pkg-devel] package removed from CRAN

Hello, I just discovered that my package 'refseqR' was removed from the CRAN repository on April 30th. https://cran.r-project.org/web/packages/refseqR/index.html This news is extremely upsetting, especially because I did not receive any communication or warning regarding the issue. Could any

Re: [R-pkg-devel] Overcoming CRAN's 5mb vendoring requirement

CRAN policy [1] says: "If the sources are too large, it is acceptable to download them as part of installation, but do ensure that the download is of a fixed version rather than the latest." So you could try downloading the source in your configure script. Though be careful not to be bitten by this

[R-pkg-devel] Overcoming CRAN's 5mb vendoring requirement

I am sorry for blowing up this thread lately. I've submitted a package to CRAN that uses Rust which thus requires dependencies to be vendored. https://github.com/R-ArcGIS/arcgisutils/ The vendored dependencies are 18mb when zipped and 16.4mb when zipped with XZ -9e. The *installed package size is

Re: [R-pkg-devel] Cannot repro failing CRAN autochecks

Thanks to @yutannihilation for pointing out that the issue repros on r-universe https://github.com/r-universe/r-arcgis/actions/runs/8990426306/job/24695887245 . Do folks know if there are any templates for the linux CRAN check? It appears that the r-lib/actions linux checks don't cover all of the