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-rw-r--r--gnu/packages/maths.scm102
1 files changed, 92 insertions, 10 deletions
diff --git a/gnu/packages/maths.scm b/gnu/packages/maths.scm
index d59028599f..f88f48b82b 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)))