From d8f46d52343972af6734c28cce94559e1c78481f Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Fri, 9 Mar 2018 11:20:22 +0100 Subject: gnu: hdf5: Do not record the build-time kernel version. * gnu/packages/maths.scm (hdf5)[arguments]: Patch libhdf5.settings to prevent the kernel version on the build node from affecting the output. --- gnu/packages/maths.scm | 6 +++++- 1 file changed, 5 insertions(+), 1 deletion(-) (limited to 'gnu/packages/maths.scm') diff --git a/gnu/packages/maths.scm b/gnu/packages/maths.scm index 8d0c10697f..cf3d8ae836 100644 --- a/gnu/packages/maths.scm +++ b/gnu/packages/maths.scm @@ -724,7 +724,11 @@ (define-public hdf5 ;; unnecessary store references to those compilers: (substitute* "src/libhdf5.settings" (("(/gnu/store/)([a-Z0-9]*)" all prefix hash) - (string-append prefix (string-take hash 10) "..."))) + (string-append prefix (string-take hash 10) "...")) + ;; Don't record the build-time kernel version to make the + ;; settings file reproducible. + (("Uname information:.*") + "Uname information: Linux\n")) #t)) (add-after 'install 'patch-references (lambda* (#:key inputs outputs #:allow-other-keys) -- cgit v1.2.3 From c0edb5b5430a5278a3ebc9aeea9d3c8ae9a2e1f1 Mon Sep 17 00:00:00 2001 From: Ludovic Courtès Date: Mon, 12 Mar 2018 16:06:17 +0100 Subject: gnu: arpack-ng: Update to 3.5.0; use 3.3.0 for julia. Partly fixes . * gnu/packages/maths.scm (arpack-ng): Update to 3.5.0. [native-inputs]: New field. (arpack-ng-3.3.0): New variable. * gnu/packages/julia.scm (julia)[inputs]: Use ARPACK-NG-3.3.0. --- gnu/packages/julia.scm | 7 ++++++- gnu/packages/maths.scm | 35 +++++++++++++++++++++++++++++------ 2 files changed, 35 insertions(+), 7 deletions(-) (limited to 'gnu/packages/maths.scm') diff --git a/gnu/packages/julia.scm b/gnu/packages/julia.scm index 41bbc66dd2..7a44abdec2 100644 --- a/gnu/packages/julia.scm +++ b/gnu/packages/julia.scm @@ -315,7 +315,12 @@ (define-public julia "USE_SYSTEM_OPENSPECFUN=1"))) (inputs `(("llvm" ,llvm) - ("arpack-ng" ,arpack-ng) + + ;; The bundled version is 3.3.0 so stick to that version. With other + ;; versions, we get test failures in 'linalg/arnoldi' as described in + ;; . + ("arpack-ng" ,arpack-ng-3.3.0) + ("coreutils" ,coreutils) ;for bindings to "mkdir" and the like ("lapack" ,lapack) ("openblas" ,openblas) ;Julia does not build with Atlas diff --git a/gnu/packages/maths.scm b/gnu/packages/maths.scm index cf3d8ae836..f9e5d2c3a2 100644 --- a/gnu/packages/maths.scm +++ b/gnu/packages/maths.scm @@ -12,7 +12,7 @@ ;;; Copyright © 2015 Fabian Harfert ;;; Copyright © 2016 Roel Janssen ;;; Copyright © 2016 Kei Kebreau -;;; Copyright © 2016, 2017 Ludovic Courtès +;;; Copyright © 2016, 2017, 2018 Ludovic Courtès ;;; Copyright © 2016 Leo Famulari ;;; Copyright © 2016, 2017 Thomas Danckaert ;;; Copyright © 2017 Paul Garlick @@ -418,18 +418,26 @@ (define-public cddlib (define-public arpack-ng (package (name "arpack-ng") - (version "3.2.0") + (version "3.5.0") + (home-page "https://github.com/opencollab/arpack-ng") (source (origin (method url-fetch) - (uri (string-append "https://github.com/opencollab/arpack-ng/archive/" - version ".tar.gz")) + (uri (string-append home-page "/archive/" version ".tar.gz")) (file-name (string-append name "-" version ".tar.gz")) (sha256 (base32 - "1fwch6vipms1ispzg2djvbzv5wag36f1dmmr3xs3mbp6imfyhvff")))) + "0f8jx3fifmj9qdp289zr7r651y1q48k1jya859rqxq62mvis7xsh")))) (build-system gnu-build-system) - (home-page "https://github.com/opencollab/arpack-ng") + (arguments + '(#:phases (modify-phases %standard-phases + (add-after 'unpack 'autoreconf + (lambda _ + (invoke "autoreconf" "-vfi")))))) + (native-inputs + `(("autoconf" ,autoconf) + ("automake" ,automake) + ("libtool" ,libtool))) (inputs `(("lapack" ,lapack) ("fortran" ,gfortran))) @@ -440,6 +448,21 @@ (define-public arpack-ng (license (license:non-copyleft "file://COPYING" "See COPYING in the distribution.")))) +(define-public arpack-ng-3.3.0 + (package + (inherit arpack-ng) + (version "3.3.0") + (name (package-name arpack-ng)) + (home-page (package-home-page arpack-ng)) + (source + (origin + (method url-fetch) + (uri (string-append home-page "/archive/" version ".tar.gz")) + (file-name (string-append name "-" version ".tar.gz")) + (sha256 + (base32 + "1cz53wqzcf6czmcpfb3vb61xi0rn5bwhinczl65hpmbrglg82ndd")))))) + (define-public arpack-ng-openmpi (package (inherit arpack-ng) (name "arpack-ng-openmpi") -- cgit v1.2.3 From 41835f947e84b99d2b8aa5e32c68db2016c7437a Mon Sep 17 00:00:00 2001 From: Leo Famulari Date: Sat, 17 Feb 2018 16:47:57 -0500 Subject: gnu: Add r-subplex. gnu/packages/maths.scm (r-subplex): New variable. --- gnu/packages/maths.scm | 23 +++++++++++++++++++++++ 1 file changed, 23 insertions(+) (limited to 'gnu/packages/maths.scm') diff --git a/gnu/packages/maths.scm b/gnu/packages/maths.scm index f9e5d2c3a2..5382260f3c 100644 --- a/gnu/packages/maths.scm +++ b/gnu/packages/maths.scm @@ -23,6 +23,7 @@ ;;; Copyright © 2017, 2018 Tobias Geerinckx-Rice ;;; Copyright © 2017 Dave Love ;;; Copyright © 2018 Jan Nieuwenhuizen +;;; Copyright © 2018 Joshua Sierles, Nextjournal ;;; ;;; This file is part of GNU Guix. ;;; @@ -3754,3 +3755,25 @@ (define-public mcrl2 analysed.") (home-page "http://mcrl2.org") (license license:boost1.0))) + +(define-public r-subplex + (package + (name "r-subplex") + (version "1.5-2") + (source + (origin + (method url-fetch) + (uri (cran-uri "subplex" version)) + (sha256 + (base32 + "1v9xrnkapnq7v1jbhlg32ignklzf2vn8rqpayc8pzk8wvz53r33g")))) + (build-system r-build-system) + (native-inputs + `(("gfortran" ,gfortran))) + (home-page "https://cran.r-project.org/web/packages/subplex") + (synopsis "Unconstrained optimization using the subplex algorithm") + (description "This package implements the Subplex optimization algorithm. +It solves unconstrained optimization problems using a simplex method on +subspaces. The method is well suited for optimizing objective functions that +are noisy or are discontinuous at the solution.") + (license license:gpl3+))) -- cgit v1.2.3 From 799ad71bfc05f084d595ee11b608745a9c56eb10 Mon Sep 17 00:00:00 2001 From: Leo Famulari Date: Sat, 17 Feb 2018 16:55:07 -0500 Subject: gnu: Add r-desolve. * gnu/packages/maths.scm (r-desolve): New variable. --- gnu/packages/maths.scm | 29 +++++++++++++++++++++++++++++ 1 file changed, 29 insertions(+) (limited to 'gnu/packages/maths.scm') diff --git a/gnu/packages/maths.scm b/gnu/packages/maths.scm index 5382260f3c..b372ad9874 100644 --- a/gnu/packages/maths.scm +++ b/gnu/packages/maths.scm @@ -3777,3 +3777,32 @@ (define-public r-subplex subspaces. The method is well suited for optimizing objective functions that are noisy or are discontinuous at the solution.") (license license:gpl3+))) + +(define-public r-desolve + (package + (name "r-desolve") + (version "1.20") + (source + (origin + (method url-fetch) + (uri (cran-uri "deSolve" version)) + (sha256 + (base32 + "18nx3maww979a8p8ly4hv63y65mnjx8vbj2fpipd6rhcbf1lbsan")))) + (properties `((upstream-name . "deSolve"))) + (build-system r-build-system) + (native-inputs + `(("gfortran" ,gfortran))) + (home-page "https://desolve.r-forge.r-project.org/") + (synopsis "Solvers for initial value problems of differential equations") + (description "This package provides functions that solve initial +value problems of a system of first-order ordinary differential equations (ODE), +of partial differential equations (PDE), of differential algebraic equations +(DAE), and of delay differential equations. The functions provide an interface +to the FORTRAN functions lsoda, lsodar, lsode, lsodes of the ODEPACK collection, +to the FORTRAN functions dvode and daspk and a C-implementation of solvers of +the Runge-Kutta family with fixed or variable time steps. The package contains +routines designed for solving ODEs resulting from 1-D, 2-D and 3-D partial +differential equations (PDE) that have been converted to ODEs by numerical +differencing.") + (license license:gpl2+))) -- cgit v1.2.3 From 47653b39332977e899e756305d6378c322c0c52c Mon Sep 17 00:00:00 2001 From: Tobias Geerinckx-Rice Date: Thu, 15 Mar 2018 00:17:26 +0100 Subject: gnu: octave: Update to 4.2.2. * gnu/packages/maths.scm (octave): Update to 4.2.2. --- gnu/packages/maths.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages/maths.scm') diff --git a/gnu/packages/maths.scm b/gnu/packages/maths.scm index b372ad9874..64fe13b9bc 100644 --- a/gnu/packages/maths.scm +++ b/gnu/packages/maths.scm @@ -1308,7 +1308,7 @@ (define-public ceres (define-public octave (package (name "octave") - (version "4.2.1") + (version "4.2.2") (source (origin (method url-fetch) @@ -1316,7 +1316,7 @@ (define-public octave version ".tar.lz")) (sha256 (base32 - "09zhhch79jw3ynw39vizx0i2cbd2bjz3sp38pjdzraqrbivpwp92")))) + "0pkkz1vazsh7ipffb09q0nc2jgx6q27pkkngygjij6jrpcly5zsp")))) (build-system gnu-build-system) (inputs `(("lapack" ,lapack) -- cgit v1.2.3