From n@@@j@v@nderve|den @end|ng |rom gm@||@com Mon Jan 13 17:05:46 2025 From: n@@@j@v@nderve|den @end|ng |rom gm@||@com (Niels van der Velden) Date: Mon, 13 Jan 2025 12:05:46 -0400 Subject: [R-pkgs] Announcing geneviewer v0.1.10 Now Available on CRAN Message-ID: Dear all, I am happy to announce that {geneviewer*}* v0.1.10 is now on CRAN. *{geneviewer}* is an R package for plotting gene clusters and transcripts. It imports data from GenBank, FASTA, and GFF files, performs BlastP and MUMmer alignments, and displays results on gene arrow maps. The package offers extensive customization options, including legends, labels, annotations, scales, colors, tooltips, and more. - *CRAN:* https://cran.r-project.org/web/packages/geneviewer/index.html - *GitHub Repository:* https://github.com/nvelden/geneviewer - *Package website: *https://nvelden.github.io/geneviewer/ - *Bug Reports:* https://github.com/nvelden/geneviewer/issues I hope you find {*geneviewer}* helpful. Please feel free to reach out with feedback or questions. Thanks, Niels van der Velden [[alternative HTML version deleted]] From j@g@nmn2 @end|ng |rom gm@||@com Mon Feb 24 01:34:48 2025 From: j@g@nmn2 @end|ng |rom gm@||@com (Mikael Jagan) Date: Sun, 23 Feb 2025 19:34:48 -0500 Subject: [R-pkgs] R package 'flint', an interface to the FLINT C library, now available on CRAN Message-ID: <554f296f-3f0f-41a4-ae35-852a4ed12ee9@gmail.com> Dear R-packages/R-help subscribers, Just writing to advertise that R package 'flint', interfacing the FLINT C library for number theory, is now available on CRAN. https://cran.r-project.org/package=flint https://github.com/jaganmn/flint https://flintlib.org/ Thanks very much to the CRAN Team for its early guidance and clear documentation on the correct approach to adding external libraries to the CRAN check servers: https://cran.r-project.org/web/packages/external_libs.html I copy the R package description here and add some comments below for early users. Description: An R interface to 'FLINT' , a C library for number theory. 'FLINT' extends GNU 'MPFR' and GNU 'MP' with support for arithmetic in standard rings (the integers, the integers modulo n, the rational, p-adic, real, and complex numbers) as well as vectors, matrices, polynomials, and power series over rings. 'FLINT' implements midpoint-radius interval arithmetic, also known as ball arithmetic, in the real and complex numbers, enabling computation in arbitrary precision with rigorous propagation of errors; see Johansson (2017) . Finally, 'FLINT' provides ball arithmetic implementations of many special mathematical functions, with high coverage of reference works such as the NIST Digital Library of Mathematical Functions . The R interface defines S4 classes, generic functions, and methods for representation and basic operations as well as plain R functions mirroring and vectorizing entry points in the C library. Comments: * The C library is expansive: https://flintlib.org/doc/ The R package makes no attempt to interface every C entry point. Rather, users wanting an R interface to a C entry point are encouraged to file an issue requesting an implementation. In this way, the interface will grow organically and "as needed" by the community of R users. * Of particular interest to applied mathematicians and statisticians will be special mathematical functions of real and complex arguments not previously supported by R or any R package available on CRAN (or, where supported, not defined over the complex numbers, to arbitrary precision, or beyond the radius of convergence of a power series representation). Use help.search(package = "flint", keyword = "math") to get an index of special mathematical functions currently interfaced. At the moment, this list excludes the (inverse) trigonometric, (inverse) hyperbolic, logarithmic, exponential, and other functions for which R provides S4 group generic functions 'Math', 'Math2', and 'Complex', for which the R package provides *methods* rather than plain R functions. * The interface to traditional number theoretic functionality (concerning integers, the integers modulo n, polynomials over the integers, ...) is small right now. I don't personally have use for it. But it can be expanded, again by request of users. * Installation from sources depends on FLINT, GNU MPFR, and GNU MP headers and libraries. Use your operating system's package manager to install these ... $ pacman -S flint $ apt install libflint-dev $ dnf install flint-devel $ pkg install flint $ port install flint $ brew install flint ... unless ... (1) The repositories provide a too old (< 3.0.0) version of FLINT, in which case consider building FLINT from a recent (>= 3.0.0) source tarball obtained here: https://github.com/flintlib/flint/releases (2) You use Windows and obtained R from CRAN, in which case use the headers and libraries from a recent enough Rtools (>= Rtools44 r6414) https://cran.r-project.org/bin/windows/Rtools/ https://cran.r-project.org/bin/windows/Rtools/rtools44/news.html choosing the Rtools installer built for your architecture (x86_64 or aarch64). (3) You use macOS and obtained R from CRAN, in which case install the macOS binaries (for flint, mpfr, and gmp) maintained by Simon Urbanek https://mac.r-project.org/bin/ https://mac.r-project.org/bin/darwin20/x86_64/ https://mac.r-project.org/bin/darwin20/arm64/ choosing the binaries built for your architecture (x86_64 or arm64). Comments from early users are very much welcome and appreciated. Mikael