From a4384dc970df534a2d1e96570e1e98abd8c85cd7 Mon Sep 17 00:00:00 2001 From: Marius Bakke Date: Tue, 8 Oct 2019 21:01:43 +0200 Subject: gnu: OpenBLAS: Incorporate grafted changes. * gnu/packages/maths.scm (openblas)[replacement]: Remove. [arguments]: Add NUM_THREADS in #:make-flags. (openblas/fixed-num-threads): Remove variable. --- gnu/packages/maths.scm | 29 +++++++---------------------- 1 file changed, 7 insertions(+), 22 deletions(-) (limited to 'gnu/packages/maths.scm') diff --git a/gnu/packages/maths.scm b/gnu/packages/maths.scm index fe9d59b69a..2664315674 100644 --- a/gnu/packages/maths.scm +++ b/gnu/packages/maths.scm @@ -3106,10 +3106,6 @@ parts of it.") (define-public openblas (package - ;; TODO: Incorporate 'openblas/fixed-num-threads' changes on the next - ;; rebuild cycle. - (replacement openblas/fixed-num-threads) - (name "openblas") (version "0.3.6") (source @@ -3137,6 +3133,13 @@ parts of it.") (list (string-append "PREFIX=" (assoc-ref %outputs "out")) "SHELL=bash" "MAKE_NB_JOBS=0" ;use jobserver for submakes + + ;; This is the maximum number of threads OpenBLAS will ever use (that + ;; is, if $OPENBLAS_NUM_THREADS is greater than that, then NUM_THREADS + ;; is used.) If we don't set it, the makefile sets it to the number + ;; of cores of the build machine, which is obviously wrong. + "NUM_THREADS=128" + ;; Build the library for all supported CPUs. This allows ;; switching CPU targets at runtime with the environment variable ;; OPENBLAS_CORETYPE=, where "type" is a supported CPU type. @@ -3191,24 +3194,6 @@ parts of it.") (synopsis "Optimized BLAS library based on GotoBLAS (ILP64 version)") (license license:bsd-3))) -(define openblas/fixed-num-threads - ;; TODO: Move that to 'openblas' proper on the next rebuild cycle. - (package - (inherit openblas) - (version (match (string-split (package-version openblas) #\.) - ((numbers ... (= string-length len)) - (string-join (append numbers - (list (make-string len #\a))) - ".")))) - (arguments - (substitute-keyword-arguments (package-arguments openblas) - ((#:make-flags flags ''()) - ;; This is the maximum number of threads OpenBLAS will ever use (that - ;; is, if $OPENBLAS_NUM_THREADS is greater than that, then NUM_THREADS - ;; is used.) If we don't set it, the makefile sets it to the number - ;; of cores of the build machine, which is obviously wrong. - `(cons "NUM_THREADS=128" ,flags)))))) - (define* (make-blis implementation #:optional substitutable?) "Return a BLIS package with the given IMPLEMENTATION (see config/ in the source tree for a list of implementations.) -- cgit v1.2.3 From 2ea095300a2e25a02b964711fa8a4b3a07f09843 Mon Sep 17 00:00:00 2001 From: Marius Bakke Date: Tue, 8 Oct 2019 21:03:16 +0200 Subject: gnu: OpenBLAS: Update to 0.3.7. * gnu/packages/maths.scm (openblas): Update to 0.3.7. --- 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 2664315674..c8df21fcde 100644 --- a/gnu/packages/maths.scm +++ b/gnu/packages/maths.scm @@ -3107,7 +3107,7 @@ parts of it.") (define-public openblas (package (name "openblas") - (version "0.3.6") + (version "0.3.7") (source (origin (method url-fetch) @@ -3116,7 +3116,7 @@ parts of it.") (file-name (string-append name "-" version ".tar.gz")) (sha256 (base32 - "1r2g9zzwq5dm8vjd19pxwggfvfzy56cvkmpmp5d014qr3svgmsap")))) + "0jbdjsi0qsxahdcm42agnn1y7xpmg0hrhwjsxg0zbhs9wwy3p568")))) (build-system gnu-build-system) (arguments `(#:test-target "test" -- cgit v1.2.3 From 3b7828cc7f938fcb369976cbe75d9c85f22583a1 Mon Sep 17 00:00:00 2001 From: Robert Smith Date: Sat, 16 Nov 2019 16:18:43 +0100 Subject: gnu: Add minisat. * gnu/packages/patches/minisat-friend-declaration.patch: New file. * gnu/packages/patches/minisat-install.patch: New file. * gnu/local.mk (dist_patch_DATA): Add both files above. * gnu/packages/maths.scm (minisat): New exported variable. Signed-off-by: Mathieu Othacehe --- gnu/local.mk | 2 ++ gnu/packages/maths.scm | 40 ++++++++++++++++++++++ .../patches/minisat-friend-declaration.patch | 25 ++++++++++++++ gnu/packages/patches/minisat-install.patch | 19 ++++++++++ 4 files changed, 86 insertions(+) create mode 100644 gnu/packages/patches/minisat-friend-declaration.patch create mode 100644 gnu/packages/patches/minisat-install.patch (limited to 'gnu/packages/maths.scm') diff --git a/gnu/local.mk b/gnu/local.mk index 8a52e98d3e..bb4dcbb17d 100644 --- a/gnu/local.mk +++ b/gnu/local.mk @@ -1131,6 +1131,8 @@ dist_patch_DATA = \ %D%/packages/patches/metabat-fix-compilation.patch \ %D%/packages/patches/mhash-keygen-test-segfault.patch \ %D%/packages/patches/mingw-w64-6.0.0-gcc.patch \ + %D%/packages/patches/minisat-friend-declaration.patch \ + %D%/packages/patches/minisat-install.patch \ %D%/packages/patches/mpc123-initialize-ao.patch \ %D%/packages/patches/module-init-tools-moduledir.patch \ %D%/packages/patches/monero-use-system-miniupnpc.patch \ diff --git a/gnu/packages/maths.scm b/gnu/packages/maths.scm index 16a9d97a47..32608ea2ff 100644 --- a/gnu/packages/maths.scm +++ b/gnu/packages/maths.scm @@ -32,6 +32,7 @@ ;;; Copyright © 2018 Amin Bandali ;;; Copyright © 2019 Nicolas Goaziou ;;; Copyright © 2019 Steve Sprang +;;; Copyright © 2019 Robert Smith ;;; ;;; This file is part of GNU Guix. ;;; @@ -5242,3 +5243,42 @@ fields of knowledge.") (home-page "http://speedcrunch.org/") (license license:gpl2+))) +(define-public minisat + ;; This is the last commit which is available upstream, no + ;; release happened since 2010. + (let ((commit "37dc6c67e2af26379d88ce349eb9c4c6160e8543") + (revision "1")) + (package + (name "minisat") + (version (string-append "2.2.0-" revision "." (string-take commit 7))) + (source + (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/niklasso/minisat.git") + (commit commit))) + (file-name (string-append name "-" version "-checkout")) + (sha256 + (base32 + "091hf3qkm197s5r7xcr3m07xsdwyz2rqk1hc9kj0hn13imz09irq")) + (patches + (search-patches "minisat-friend-declaration.patch" + "minisat-install.patch")))) + (build-system gnu-build-system) + (arguments + '(#:make-flags (list (string-append "prefix=" %output)) + #:tests? #f ;no check target + #:phases + (modify-phases %standard-phases + (delete 'configure)))) + (inputs + `(("zlib:static" ,zlib "static") + ("zlib" ,zlib))) + (synopsis + "Small, yet efficient, SAT solver") + (description + "MiniSat is a minimalistic, open-source SAT solver, developed to help +researchers and developers alike to get started on SAT.") + (home-page + "http://minisat.se/MiniSat.html") + (license license:expat)))) diff --git a/gnu/packages/patches/minisat-friend-declaration.patch b/gnu/packages/patches/minisat-friend-declaration.patch new file mode 100644 index 0000000000..14a886ae2f --- /dev/null +++ b/gnu/packages/patches/minisat-friend-declaration.patch @@ -0,0 +1,25 @@ +See https://groups.google.com/forum/#!topic/minisat/FCocZsC8oMQ +This seems to only be a problem with newer versions of g++, and +upstream development seems to have stopped in 2013. + +diff -rupN minisat-2.2.0/core/SolverTypes.h minisat-2.2.0.patched/core/SolverTypes.h +--- a/minisat/core/SolverTypes.h 2010-07-10 17:07:36.000000000 +0100 ++++ b/minisat/core/SolverTypes.h 2014-03-29 11:57:49.000000000 +0000 +@@ -47,7 +47,7 @@ struct Lit { + int x; + + // Use this as a constructor: +- friend Lit mkLit(Var var, bool sign = false); ++ //friend Lit mkLit(Var var, bool sign = false); + + bool operator == (Lit p) const { return x == p.x; } + bool operator != (Lit p) const { return x != p.x; } +@@ -55,7 +55,7 @@ struct Lit { + }; + + +-inline Lit mkLit (Var var, bool sign) { Lit p; p.x = var + var + (int)sign; return p; } ++inline Lit mkLit (Var var, bool sign = false) { Lit p; p.x = var + var + (int)sign; return p; } + inline Lit operator ~(Lit p) { Lit q; q.x = p.x ^ 1; return q; } + inline Lit operator ^(Lit p, bool b) { Lit q; q.x = p.x ^ (unsigned int)b; return q; } + inline bool sign (Lit p) { return p.x & 1; } diff --git a/gnu/packages/patches/minisat-install.patch b/gnu/packages/patches/minisat-install.patch new file mode 100644 index 0000000000..23cde89bec --- /dev/null +++ b/gnu/packages/patches/minisat-install.patch @@ -0,0 +1,19 @@ +Avoid the default dynamic executable, which depends on minisat.so +Instead install the release version, which is statically linked. + +diff --git a/Makefile b/Makefile +index ceb9d77..7b91906 100644 +--- a/Makefile ++++ b/Makefile +@@ -191,9 +191,9 @@ install-lib: $(BUILD_DIR)/release/lib/$(MINISAT_SLIB) $(BUILD_DIR)/dynamic/lib/$ + ln -sf $(MINISAT_DLIB).$(SOMAJOR) $(DESTDIR)$(libdir)/$(MINISAT_DLIB) + $(INSTALL) -m 644 $(BUILD_DIR)/release/lib/$(MINISAT_SLIB) $(DESTDIR)$(libdir) + +-install-bin: $(BUILD_DIR)/dynamic/bin/$(MINISAT) ++install-bin: $(BUILD_DIR)/release/bin/$(MINISAT) + $(INSTALL) -d $(DESTDIR)$(bindir) +- $(INSTALL) -m 755 $(BUILD_DIR)/dynamic/bin/$(MINISAT) $(DESTDIR)$(bindir) ++ $(INSTALL) -m 755 $(BUILD_DIR)/release/bin/$(MINISAT) $(DESTDIR)$(bindir) + + clean: + rm -f $(foreach t, release debug profile dynamic, $(foreach o, $(SRCS:.cc=.o), $(BUILD_DIR)/$t/$o)) \ -- cgit v1.2.3 From 3db9cbf67645caca8cd9ef4a921603751084c483 Mon Sep 17 00:00:00 2001 From: Tobias Geerinckx-Rice Date: Sat, 23 Nov 2019 01:50:24 +0100 Subject: gnu: r-desolve: Update to 1.25. * gnu/packages/maths.scm (r-desolve): Update to 1.25. --- gnu/packages/maths.scm | 5 ++--- 1 file changed, 2 insertions(+), 3 deletions(-) (limited to 'gnu/packages/maths.scm') diff --git a/gnu/packages/maths.scm b/gnu/packages/maths.scm index 32608ea2ff..29a1bfd768 100644 --- a/gnu/packages/maths.scm +++ b/gnu/packages/maths.scm @@ -4408,14 +4408,13 @@ are noisy or are discontinuous at the solution.") (define-public r-desolve (package (name "r-desolve") - (version "1.24") + (version "1.25") (source (origin (method url-fetch) (uri (cran-uri "deSolve" version)) (sha256 - (base32 - "0hkvspq0fp8j64l9zayab2l2nazazhwfgfym0jllh0xv5a12r99s")))) + (base32 "0735y3p5glhqx69rzrc8qgmvs7p7w0p98qxmvylb6bgqp6kp0cbp")))) (properties `((upstream-name . "deSolve"))) (build-system r-build-system) (native-inputs -- cgit v1.2.3 From ec9a15c2eb7aa6cf0ba9784d666dfa9419328e7f Mon Sep 17 00:00:00 2001 From: Tobias Geerinckx-Rice Date: Sat, 23 Nov 2019 01:51:35 +0100 Subject: gnu: r-quadprog: Update to 1.5-8. * gnu/packages/maths.scm (r-quadprog): Update to 1.5-8. --- gnu/packages/maths.scm | 5 ++--- 1 file changed, 2 insertions(+), 3 deletions(-) (limited to 'gnu/packages/maths.scm') diff --git a/gnu/packages/maths.scm b/gnu/packages/maths.scm index 29a1bfd768..e96a3199ff 100644 --- a/gnu/packages/maths.scm +++ b/gnu/packages/maths.scm @@ -2345,14 +2345,13 @@ sparse system of linear equations A x = b using Gaussian elimination.") (define-public r-quadprog (package (name "r-quadprog") - (version "1.5-7") + (version "1.5-8") (source (origin (method url-fetch) (uri (cran-uri "quadprog" version)) (sha256 - (base32 - "0vg7i9p241bwvfdspjbydjrsvgipl6nsb8bjigp0hbbgvxbixx0s")))) + (base32 "1ka9g8zak8sg4y2xbz93dfrldznlk9qpd4pq9z21cdcdn3b8s4i2")))) (build-system r-build-system) (native-inputs `(("gfortran" ,gfortran))) -- cgit v1.2.3 From 1e8609f2387905c06c42d0efe9d08391ca9354ea Mon Sep 17 00:00:00 2001 From: Kei Kebreau Date: Sat, 23 Nov 2019 15:33:14 -0500 Subject: gnu: wxmaxima: Update to 19.11.1. * gnu/packages/maths.scm (wxmaxima): Update to 19.11.1. --- 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 e96a3199ff..83ff9919ad 100644 --- a/gnu/packages/maths.scm +++ b/gnu/packages/maths.scm @@ -2991,7 +2991,7 @@ point numbers.") (define-public wxmaxima (package (name "wxmaxima") - (version "19.09.0") + (version "19.11.1") (source (origin (method git-fetch) @@ -3000,7 +3000,7 @@ point numbers.") (commit (string-append "Version-" version)))) (file-name (git-file-name name version)) (sha256 - (base32 "195j6j8z0jd6xg3a63ywbrbsc6dany795m3fb95nbx1vq0bqqvvn")))) + (base32 "16xizaddb27432n1083y89ir5zdqvllsgbwrzzk4jc2rw1ldxfsv")))) (build-system cmake-build-system) (native-inputs `(("gettext" ,gettext-minimal))) -- cgit v1.2.3 From 0eb59d9eac63068f382cf3fe6c0d4dd867c6256c Mon Sep 17 00:00:00 2001 From: zimoun Date: Wed, 27 Nov 2019 17:59:25 +0100 Subject: gnu: r-quadprog: Move to (gnu packages cran). * gnu/packages/maths.scm (r-quadprog): Move from here... * gnu/packages/cran.scm (r-quadprog): ...to here. Signed-off-by: Ricardo Wurmus --- gnu/packages/cran.scm | 20 ++++++++++++++++++++ gnu/packages/maths.scm | 20 -------------------- 2 files changed, 20 insertions(+), 20 deletions(-) (limited to 'gnu/packages/maths.scm') diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index 29aef19659..62113ab7e0 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -15741,3 +15741,23 @@ unique identifiers, and whether it is a certain length. In addition, files and to efficiently import multiple tabular data files into one data.table.") (license license:gpl3))) + +(define-public r-quadprog + (package + (name "r-quadprog") + (version "1.5-8") + (source + (origin + (method url-fetch) + (uri (cran-uri "quadprog" version)) + (sha256 + (base32 "1ka9g8zak8sg4y2xbz93dfrldznlk9qpd4pq9z21cdcdn3b8s4i2")))) + (build-system r-build-system) + (native-inputs + `(("gfortran" ,gfortran))) + (home-page "https://cran.r-project.org/web/packages/quadprog") + (synopsis "Functions to solve quadratic programming problems") + (description + "This package contains routines and documentation for solving quadratic +programming problems.") + (license license:gpl3+))) diff --git a/gnu/packages/maths.scm b/gnu/packages/maths.scm index 83ff9919ad..cf78d0b7a4 100644 --- a/gnu/packages/maths.scm +++ b/gnu/packages/maths.scm @@ -2342,26 +2342,6 @@ sparse system of linear equations A x = b using Gaussian elimination.") (inputs (alist-delete "pt-scotch" (package-inputs mumps-openmpi))))) -(define-public r-quadprog - (package - (name "r-quadprog") - (version "1.5-8") - (source - (origin - (method url-fetch) - (uri (cran-uri "quadprog" version)) - (sha256 - (base32 "1ka9g8zak8sg4y2xbz93dfrldznlk9qpd4pq9z21cdcdn3b8s4i2")))) - (build-system r-build-system) - (native-inputs - `(("gfortran" ,gfortran))) - (home-page "https://cran.r-project.org/web/packages/quadprog") - (synopsis "Functions to solve quadratic programming problems") - (description - "This package contains routines and documentation for solving quadratic -programming problems.") - (license license:gpl3+))) - (define-public r-pracma (package (name "r-pracma") -- cgit v1.2.3 From 9bd56b1a77e7011a044e9da6d4f7a00226eb01e0 Mon Sep 17 00:00:00 2001 From: zimoun Date: Wed, 27 Nov 2019 18:04:18 +0100 Subject: gnu: r-desolve: Move to (gnu packages cran). * gnu/packages/maths.scm (r-desolve): Move from here... * gnu/packages/cran.scm (r-desolve): ...to here. Signed-off-by: Ricardo Wurmus --- gnu/packages/cran.scm | 28 ++++++++++++++++++++++++++++ gnu/packages/maths.scm | 28 ---------------------------- 2 files changed, 28 insertions(+), 28 deletions(-) (limited to 'gnu/packages/maths.scm') diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index 62113ab7e0..943cd0deec 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -15761,3 +15761,31 @@ data.table.") "This package contains routines and documentation for solving quadratic programming problems.") (license license:gpl3+))) + +(define-public r-desolve + (package + (name "r-desolve") + (version "1.25") + (source + (origin + (method url-fetch) + (uri (cran-uri "deSolve" version)) + (sha256 + (base32 "0735y3p5glhqx69rzrc8qgmvs7p7w0p98qxmvylb6bgqp6kp0cbp")))) + (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+))) diff --git a/gnu/packages/maths.scm b/gnu/packages/maths.scm index cf78d0b7a4..9108150de9 100644 --- a/gnu/packages/maths.scm +++ b/gnu/packages/maths.scm @@ -4384,34 +4384,6 @@ 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 "1.25") - (source - (origin - (method url-fetch) - (uri (cran-uri "deSolve" version)) - (sha256 - (base32 "0735y3p5glhqx69rzrc8qgmvs7p7w0p98qxmvylb6bgqp6kp0cbp")))) - (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+))) - (define-public tcalc (package (name "tcalc") -- cgit v1.2.3 From 682768deb036b730c25694adbd81cd1574b37dfd Mon Sep 17 00:00:00 2001 From: zimoun Date: Wed, 27 Nov 2019 18:07:02 +0100 Subject: gnu: r-pracma: Move to (gnu packages cran). * gnu/packages/maths.scm (r-pracma): Move from here... * gnu/packages/cran.scm (r-pracma): ...to here. Signed-off-by: Ricardo Wurmus --- gnu/packages/cran.scm | 20 +++++++++++++++++++- gnu/packages/maths.scm | 18 ------------------ 2 files changed, 19 insertions(+), 19 deletions(-) (limited to 'gnu/packages/maths.scm') diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index 943cd0deec..9a49602fff 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -2,7 +2,7 @@ ;;; Copyright © 2015, 2016, 2017, 2018, 2019 Ricardo Wurmus ;;; Copyright © 2015 Andreas Enge ;;; Copyright © 2016, 2017 Ben Woodcroft -;;; Copyright © 2017, 2018 Roel Janssen +;;; Copyright © 2016, 2017, 2018 Roel Janssen ;;; Copyright © 2017, 2018, 2019 Tobias Geerinckx-Rice ;;; Copyright © 2017 Raoul Bonnal ;;; Copyright © 2018 Vijayalakshmi Vedantham @@ -15789,3 +15789,21 @@ 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+))) + +(define-public r-pracma + (package + (name "r-pracma") + (version "2.2.5") + (source (origin + (method url-fetch) + (uri (cran-uri "pracma" version)) + (sha256 + (base32 "0isd3s0i4mzmva8lkh0j76hwjy1w50q7d1n9lhxsnnkgalx3xs1g")))) + (build-system r-build-system) + (home-page "https://cran.r-project.org/web/packages/pracma/") + (synopsis "Practical numerical math functions") + (description "This package provides functions for numerical analysis and +linear algebra, numerical optimization, differential equations, plus some +special functions. It uses Matlab function names where appropriate to simplify +porting.") + (license license:gpl3+))) diff --git a/gnu/packages/maths.scm b/gnu/packages/maths.scm index 9108150de9..c8e0e39343 100644 --- a/gnu/packages/maths.scm +++ b/gnu/packages/maths.scm @@ -2342,24 +2342,6 @@ sparse system of linear equations A x = b using Gaussian elimination.") (inputs (alist-delete "pt-scotch" (package-inputs mumps-openmpi))))) -(define-public r-pracma - (package - (name "r-pracma") - (version "2.2.5") - (source (origin - (method url-fetch) - (uri (cran-uri "pracma" version)) - (sha256 - (base32 "0isd3s0i4mzmva8lkh0j76hwjy1w50q7d1n9lhxsnnkgalx3xs1g")))) - (build-system r-build-system) - (home-page "https://cran.r-project.org/web/packages/pracma/") - (synopsis "Practical numerical math functions") - (description "This package provides functions for numerical analysis and -linear algebra, numerical optimization, differential equations, plus some -special functions. It uses Matlab function names where appropriate to simplify -porting.") - (license license:gpl3+))) - (define-public ruby-asciimath (package (name "ruby-asciimath") -- cgit v1.2.3 From ef7944b94f38a1ed92f164ca6b37c8c9ad4bcbee Mon Sep 17 00:00:00 2001 From: zimoun Date: Wed, 27 Nov 2019 18:13:56 +0100 Subject: gnu: r-subplex: Move to (gnu packages cran). * gnu/packages/maths.scm (r-subplex): Move from here... * gnu/packages/cran.scm (r-subplex): ...to here. Signed-off-by: Ricardo Wurmus --- gnu/packages/cran.scm | 23 +++++++++++++++++++++++ gnu/packages/maths.scm | 22 ---------------------- 2 files changed, 23 insertions(+), 22 deletions(-) (limited to 'gnu/packages/maths.scm') diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index 9a49602fff..0797897acd 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -15807,3 +15807,26 @@ linear algebra, numerical optimization, differential equations, plus some special functions. It uses Matlab function names where appropriate to simplify porting.") (license license:gpl3+))) + +(define-public r-subplex + (package + (name "r-subplex") + (version "1.5-4") + (source + (origin + (method url-fetch) + (uri (cran-uri "subplex" version)) + (sha256 + (base32 + "10cbgbx1bgsax5z7gz6716g360xpq4mvq19cf4qqrxv02mmwz57z")))) + (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+))) diff --git a/gnu/packages/maths.scm b/gnu/packages/maths.scm index c8e0e39343..16bb85efbc 100644 --- a/gnu/packages/maths.scm +++ b/gnu/packages/maths.scm @@ -4344,28 +4344,6 @@ analysed.") (arguments '(#:configure-flags '("-DMCRL2_ENABLE_GUI_TOOLS=OFF"))))) -(define-public r-subplex - (package - (name "r-subplex") - (version "1.5-4") - (source - (origin - (method url-fetch) - (uri (cran-uri "subplex" version)) - (sha256 - (base32 - "10cbgbx1bgsax5z7gz6716g360xpq4mvq19cf4qqrxv02mmwz57z")))) - (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+))) - (define-public tcalc (package (name "tcalc") -- cgit v1.2.3 From f3640e7395b54c801bde8ba40ad08bdad488453d Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Wed, 27 Nov 2019 18:29:32 +0100 Subject: gnu: Remove obsolete import of R build system module. * gnu/packages/maths.scm: Remove import of (guix build-system r). --- gnu/packages/maths.scm | 1 - 1 file changed, 1 deletion(-) (limited to 'gnu/packages/maths.scm') diff --git a/gnu/packages/maths.scm b/gnu/packages/maths.scm index 16bb85efbc..16e070eeff 100644 --- a/gnu/packages/maths.scm +++ b/gnu/packages/maths.scm @@ -62,7 +62,6 @@ #:use-module (guix build-system cmake) #:use-module (guix build-system gnu) #:use-module (guix build-system python) - #:use-module (guix build-system r) #:use-module (guix build-system ruby) #:use-module (gnu packages algebra) #:use-module (gnu packages audio) -- cgit v1.2.3 From 1ff64c503ae5028077afd615d98260955c970307 Mon Sep 17 00:00:00 2001 From: Tobias Geerinckx-Rice Date: Sat, 30 Nov 2019 23:14:57 +0100 Subject: gnu: nauty: Update to 2.6r12. * gnu/packages/maths.scm (nauty): Update to 2.6r12. --- 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 16e070eeff..0d303dc53e 100644 --- a/gnu/packages/maths.scm +++ b/gnu/packages/maths.scm @@ -5015,7 +5015,7 @@ management via the GIMPS project's Primenet server.") (define-public nauty (package (name "nauty") - (version "2.6r11") + (version "2.6r12") (source (origin (method url-fetch) (uri (string-append @@ -5024,7 +5024,7 @@ management via the GIMPS project's Primenet server.") ".tar.gz")) (sha256 (base32 - "05z6mk7c31j70md83396cdjmvzzip1hqb88pfszzc6k4gy8h3m2y")))) + "1p4mxf8q5wm47nxyskxbqwa5p1vvkycv1zgswvnk9nsn6vff0al6")))) (build-system gnu-build-system) (outputs '("out" "lib")) (arguments -- cgit v1.2.3 From dbef037ff48460ec8f7bb4dbb3139c74403a9378 Mon Sep 17 00:00:00 2001 From: Tobias Geerinckx-Rice Date: Sun, 1 Dec 2019 00:48:07 +0100 Subject: gnu: z3: Update to 4.8.7. * gnu/packages/maths.scm (z3): Update to 4.8.7. --- 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 0d303dc53e..b9d1dce97a 100644 --- a/gnu/packages/maths.scm +++ b/gnu/packages/maths.scm @@ -4108,7 +4108,7 @@ as equations, scalars, vectors, and matrices.") (define-public z3 (package (name "z3") - (version "4.8.6") + (version "4.8.7") (home-page "https://github.com/Z3Prover/z3") (source (origin (method git-fetch) @@ -4117,7 +4117,7 @@ as equations, scalars, vectors, and matrices.") (file-name (git-file-name name version)) (sha256 (base32 - "1sywcqj5y8yp28m4cdvzsgw74kd6zr1s3y1x17ky8pr9prvpvl6x")))) + "0hprcdwhhyjigmhhk6514m71bnmvqci9r8gglrqilgx424r6ff7q")))) (build-system gnu-build-system) (arguments `(#:phases -- cgit v1.2.3