diff options
Diffstat (limited to 'gnu/packages/maths.scm')
| -rw-r--r-- | gnu/packages/maths.scm | 102 |
1 files changed, 92 insertions, 10 deletions
diff --git a/gnu/packages/maths.scm b/gnu/packages/maths.scm index 49c8de8979..5e0df6e409 100644 --- a/gnu/packages/maths.scm +++ b/gnu/packages/maths.scm @@ -30,6 +30,7 @@ ;;; Copyright © 2018 Eric Brown <brown@fastmail.com> ;;; Copyright © 2018 Julien Lepiller <julien@lepiller.eu> ;;; Copyright © 2018 Amin Bandali <bandali@gnu.org> +;;; Copyright © 2019 Nicolas Goaziou <mail@nicolasgoaziou.fr> ;;; ;;; This file is part of GNU Guix. ;;; @@ -774,14 +775,25 @@ incompatible with HDF5.") (inputs `(("zlib" ,zlib))) (native-inputs - `(("gfortran" ,gfortran))) + `(("gfortran" ,gfortran) + ("perl" ,perl))) ;part of the test machinery needs Perl (outputs '("out" ; core library "fortran")) ; fortran interface (arguments `(;; Some of the users, notably Flann, need the C++ interface. #:configure-flags '("--enable-cxx" "--enable-fortran" - "--enable-fortran2003") + "--enable-fortran2003" + + ;; Build a thread-safe library. Unfortunately, + ;; 'configure' invites you to either turn off C++, + ;; Fortran, and the high-level interface (HL), or + ;; to pass '--enable-unsupported'. Debian + ;; packagers chose to pass '--enable-unsupported' + ;; and we follow their lead here. + "--enable-threadsafe" + "--with-pthread" + "--enable-unsupported") ;; Use -fPIC to allow the R bindings to link with the static libraries #:make-flags (list "CFLAGS=-fPIC" "CXXFLAGS=-fPIC") @@ -1093,7 +1105,9 @@ Swath).") (arguments (substitute-keyword-arguments (package-arguments hdf5) ((#:configure-flags flags) - ``("--enable-parallel" ,@(delete "--enable-cxx" ,flags))) + ``("--enable-parallel" + ,@(delete "--enable-cxx" + (delete "--enable-threadsafe" ,flags)))) ((#:phases phases) `(modify-phases ,phases (add-after 'build 'mpi-setup @@ -1102,7 +1116,7 @@ Swath).") (lambda _ ;; OpenMPI's mpirun will exit with non-zero status if it ;; detects an "abnormal termination", i.e. any process not - ;; calling MPI_Finalize(). Since the test is explicitely + ;; calling MPI_Finalize(). Since the test is explicitly ;; avoiding MPI_Finalize so as not to have at_exit and thus ;; H5C_flush_cache from being called, mpirun will always ;; complain, so turn this test off. @@ -2168,7 +2182,7 @@ IORDERINGSC = $(IPORD) $(IMETIS) $(ISCOTCH)" (synopsis "Multifrontal sparse direct solver") (description "MUMPS (MUltifrontal Massively Parallel sparse direct Solver) solves a -sparse system of linear equations A x = b using Guassian elimination.") +sparse system of linear equations A x = b using Gaussian elimination.") (license license:cecill-c))) (define-public mumps-metis @@ -2206,14 +2220,14 @@ sparse system of linear equations A x = b using Guassian elimination.") (define-public r-quadprog (package (name "r-quadprog") - (version "1.5-6") + (version "1.5-7") (source (origin (method url-fetch) (uri (cran-uri "quadprog" version)) (sha256 (base32 - "1fnwaz70dhiq4av8apc4wr3yrrpwc2i6lksf8pfi6jw8vzzyahql")))) + "0vg7i9p241bwvfdspjbydjrsvgipl6nsb8bjigp0hbbgvxbixx0s")))) (build-system r-build-system) (native-inputs `(("gfortran" ,gfortran))) @@ -4868,13 +4882,12 @@ built on top of DUNE, the Distributed and Unified Numerics Environment.") (uri (string-append "https://mersenneforum.org/mayer/src/C/mlucas_v" version ".txz")) (sha256 - (base32 - "1ax12qj9lyvnx4vs3gx7l8r3wx5gjbsdswp5f00ik9z0wz7xf297")))) + (base32 "0h4xj6pyyac79ka5ibqjilfa3s9j3yxnzgpwc57b54kfh2bj3447")))) (build-system gnu-build-system) (inputs `(("python2" ,python-2))) (arguments - `(#:tests? #f ; no tests + `(#:tests? #f ; no tests #:phases (modify-phases %standard-phases (replace 'configure @@ -4908,3 +4921,72 @@ coordinated fashion, as part of the Great Internet Mersenne Prime Search (GIMPS). Mlucas also includes a simple Python script for assignment management via the GIMPS project's Primenet server.") (license license:gpl2+))) + +(define-public nauty + (package + (name "nauty") + (version "2.6r11") + (source (origin + (method url-fetch) + (uri (string-append + "https://pallini.di.uniroma1.it/" + "nauty" (string-join (string-split version #\.) "") + ".tar.gz")) + (sha256 + (base32 + "05z6mk7c31j70md83396cdjmvzzip1hqb88pfszzc6k4gy8h3m2y")))) + (build-system gnu-build-system) + (outputs '("out" "lib")) + (arguments + `(#:test-target "checks" + #:phases + (modify-phases %standard-phases + ;; Default make target does not build all available + ;; executables. Create them now. + (add-after 'build 'build-extra-programs + (lambda _ + (for-each (lambda (target) (invoke "make" target)) + '("blisstog" "bliss2dre" "checks6" "sumlines")) + #t)) + ;; Upstream does not provide any install target. + (replace 'install + (lambda* (#:key outputs #:allow-other-keys) + (let* ((out (assoc-ref outputs "out")) + (lib-output (assoc-ref outputs "lib")) + (bin (string-append out "/bin")) + (doc (string-append out "/share/doc/nauty/")) + (include (string-append lib-output "/include/nauty")) + (lib (string-append lib-output "/lib/nauty"))) + (for-each (lambda (f) (install-file f bin)) + '("dreadnaut" "NRswitchg" "addedgeg" "amtog" "biplabg" + "blisstog" "bliss2dre" "catg" "checks6" "complg" + "converseg" "copyg" "countg" "cubhamg" "deledgeg" + "delptg" "directg" "dretodot" "dretog" "genbg" + "genbgL" "geng" "genquarticg" "genrang" "genspecialg" + "gentourng" "gentreeg" "hamheuristic" "labelg" + "linegraphg" "listg" "multig" "newedgeg" "pickg" + "planarg" "ranlabg" "shortg" "showg" "subdivideg" + "sumlines" "twohamg" "vcolg" "watercluster2")) + (for-each (lambda (f) (install-file f include)) + (find-files "." "\\.h$")) + (for-each (lambda (f) (install-file f lib)) + (find-files "." "\\.a$")) + (for-each (lambda (f) (install-file f doc)) + (append '("formats.txt" "README" "schreier.txt") + (find-files "." "\\.pdf$"))))))))) + (inputs + `(("gmp" ,gmp))) ;for sumlines + (home-page "https://pallini.di.uniroma1.it/") + (synopsis "Library for graph automorphisms") + (description "@code{nauty} (No AUTomorphisms, Yes?) is a set of +procedures for computing automorphism groups of graphs and digraphs. + +@code{nauty} computes graph information in the form of a set of +generators, the size of the group, and the orbits of the group; it can +also produce a canonical label. The @code{nauty} suite is written in +C and comes with a command-line interface, a collection of +command-line tools, and an Application Programming Interface (API). + +This package provides the static libraries required to run programs +compiled against the nauty library.") + (license license:asl2.0))) |