From c5372cd48897c29ee5555708f8a52b16ecae0612 Mon Sep 17 00:00:00 2001 From: Ludovic Courtès Date: Fri, 23 Oct 2020 12:12:34 +0200 Subject: gnu: hdf5: Default to 1.10. This is a followup to 593096355501dfd76c2e92b1fbd87f940ab1d1f2. * gnu/packages/maths.scm (hdf5): Change to HDF5-1.10. (hdf-java, hdf-eos5, h5check, netcdf, matio)[inputs]: Use HDF5-1.8. * gnu/packages/java.scm (java-cisd-jhdf5)[inputs]: Likewise. --- gnu/packages/maths.scm | 15 +++++++++------ 1 file changed, 9 insertions(+), 6 deletions(-) (limited to 'gnu/packages/maths.scm') diff --git a/gnu/packages/maths.scm b/gnu/packages/maths.scm index 2a909ec1d4..f7565dd885 100644 --- a/gnu/packages/maths.scm +++ b/gnu/packages/maths.scm @@ -1203,7 +1203,7 @@ (define-public hdf5-1.10 (define-public hdf5 ;; Default version of HDF5. - hdf5-1.8) + hdf5-1.10) (define-public hdf-java (package @@ -1235,7 +1235,7 @@ (define-public hdf-java ("slf4j-simple" ,java-slf4j-simple))) (inputs `(("hdf4" ,hdf4) - ("hdf5" ,hdf5) + ("hdf5" ,hdf5-1.8) ("zlib" ,zlib) ("libjpeg" ,libjpeg-turbo) ("slf4j-api" ,java-slf4j-api))) @@ -1395,7 +1395,7 @@ (define-public hdf-eos5 `(("gfortran" ,gfortran))) (build-system gnu-build-system) (inputs - `(("hdf5" ,hdf5) + `(("hdf5" ,hdf5-1.8) ("zlib" ,zlib) ("gctp" ,gctp))) (arguments @@ -1496,7 +1496,7 @@ (define-public h5check (base32 "1gm76jbwhz9adbxgn14zx8cj33dmjdr2g5xcy0m9c2gakp8w59kj")))) (build-system gnu-build-system) - (inputs `(("hdf5" ,hdf5))) ;h5cc for tests + (inputs `(("hdf5" ,hdf5-1.8))) ;h5cc for tests (home-page "https://www.hdfgroup.org/products/hdf5_tools/h5check.html") (synopsis "HDF5 format checker") (description "@code{h5check} is a validation tool for verifying that an @@ -1556,7 +1556,10 @@ (define-public netcdf ("graphviz" ,graphviz))) (inputs `(("hdf4" ,hdf4-alt) - ("hdf5" ,hdf5) + + ;; XXX: The 'tst_nccopy4.sh' test fails when using hdf5-1.10. + ("hdf5" ,hdf5-1.8) + ("zlib" ,zlib) ("libjpeg" ,libjpeg-turbo))) (arguments @@ -4537,7 +4540,7 @@ (define-public matio (build-system gnu-build-system) (inputs `(("zlib" ,zlib) - ("hdf5" ,hdf5))) + ("hdf5" ,hdf5-1.8))) (home-page "http://matio.sourceforge.net/") (synopsis "Library for reading and writing MAT files") (description "Matio is a library for reading and writing MAT files. It -- cgit v1.2.3 From a9291a28b233dba20a523da679bb446643abf977 Mon Sep 17 00:00:00 2001 From: Christopher Baines Date: Sun, 25 Oct 2020 10:20:55 +0000 Subject: gnu: netcdf: Update to 4.7.4. This will fix an issue building qgis. * gnu/packages/maths.scm (netcdf): Update to 4.7.4. [source]: Remove the netcdf-tst_h_par.patch, also change the naming of the source tarball, as the name seems to have changed for recent releases. [inputs]: Update hdf5 and add curl. * gnu/packages/patches/netcdf-tst_h_par.patch: Delete. * gnu/local.mk (dist_patch_DATA): Remove deleted patch. --- gnu/local.mk | 1 - gnu/packages/maths.scm | 18 ++++++++---------- gnu/packages/patches/netcdf-date-time.patch | 6 +++--- gnu/packages/patches/netcdf-tst_h_par.patch | 21 --------------------- 4 files changed, 11 insertions(+), 35 deletions(-) delete mode 100644 gnu/packages/patches/netcdf-tst_h_par.patch (limited to 'gnu/packages/maths.scm') diff --git a/gnu/local.mk b/gnu/local.mk index 1a01360d72..0ada3b727b 100644 --- a/gnu/local.mk +++ b/gnu/local.mk @@ -1355,7 +1355,6 @@ dist_patch_DATA = \ %D%/packages/patches/m4-gnulib-libio.patch \ %D%/packages/patches/ncompress-fix-softlinks.patch \ %D%/packages/patches/netcdf-date-time.patch \ - %D%/packages/patches/netcdf-tst_h_par.patch \ %D%/packages/patches/netpbm-CVE-2017-2586.patch \ %D%/packages/patches/netpbm-CVE-2017-2587.patch \ %D%/packages/patches/netsurf-message-timestamp.patch \ diff --git a/gnu/packages/maths.scm b/gnu/packages/maths.scm index f7565dd885..d2631501aa 100644 --- a/gnu/packages/maths.scm +++ b/gnu/packages/maths.scm @@ -1538,17 +1538,17 @@ (define-public itpp (define-public netcdf (package (name "netcdf") - (version "4.4.1.1") + (version "4.7.4") (source (origin (method url-fetch) - (uri (string-append "ftp://ftp.unidata.ucar.edu/pub/netcdf/" - "netcdf-" version ".tar.gz")) + (uri (string-append + "https://www.unidata.ucar.edu/downloads/netcdf/ftp/" + "netcdf-c-" version ".tar.gz")) (sha256 (base32 - "1blc7ik5yin7i0ls2kag0a9xjk12m0dzx6v1x88az3ras3scci2d")) - (patches (search-patches "netcdf-date-time.patch" - "netcdf-tst_h_par.patch")))) + "1a2fpp15a2rl1m50gcvvzd9y6bavl6vjf9zzf63sz5gdmq06yiqf")) + (patches (search-patches "netcdf-date-time.patch")))) (build-system gnu-build-system) (native-inputs `(("m4" ,m4) @@ -1556,10 +1556,8 @@ (define-public netcdf ("graphviz" ,graphviz))) (inputs `(("hdf4" ,hdf4-alt) - - ;; XXX: The 'tst_nccopy4.sh' test fails when using hdf5-1.10. - ("hdf5" ,hdf5-1.8) - + ("hdf5" ,hdf5) + ("curl" ,curl) ("zlib" ,zlib) ("libjpeg" ,libjpeg-turbo))) (arguments diff --git a/gnu/packages/patches/netcdf-date-time.patch b/gnu/packages/patches/netcdf-date-time.patch index a4e7925aa1..0bdfc55299 100644 --- a/gnu/packages/patches/netcdf-date-time.patch +++ b/gnu/packages/patches/netcdf-date-time.patch @@ -3,9 +3,9 @@ @@ -13,7 +13,7 @@ #endif - /* Tell the user the version of netCDF. */ + /** @internal The version string for the library, used by + * nc_inq_libvers(). */ -static const char nc_libvers[] = PACKAGE_VERSION " of "__DATE__" "__TIME__" $"; -+static const char nc_libvers[] = PACKAGE_VERSION" $"; ++static const char nc_libvers[] = PACKAGE_VERSION " $"; /** - \defgroup lib_version Library Version diff --git a/gnu/packages/patches/netcdf-tst_h_par.patch b/gnu/packages/patches/netcdf-tst_h_par.patch deleted file mode 100644 index ac14a4c0a2..0000000000 --- a/gnu/packages/patches/netcdf-tst_h_par.patch +++ /dev/null @@ -1,21 +0,0 @@ -From a83702834938b23cc2e843589aa223e2024a7e6f Mon Sep 17 00:00:00 2001 -From: Orion Poplawski -Date: Tue, 29 Nov 2016 11:48:01 -0700 -Subject: [PATCH] Add missing #include "err_macros.h" to tst_h_par.c - ---- - h5_test/tst_h_par.c | 1 + - 1 file changed, 1 insertion(+) - -diff --git a/h5_test/tst_h_par.c b/h5_test/tst_h_par.c -index c3da7f4..a419d55 100644 ---- a/h5_test/tst_h_par.c -+++ b/h5_test/tst_h_par.c -@@ -11,6 +11,7 @@ - $Id: tst_h_par.c,v 1.15 2010/05/25 13:53:04 ed Exp $ - */ - #include -+#include "err_macros.h" - #include - - /* Defining USE_MPE causes the MPE trace library to be used (and you -- cgit v1.2.3 From d50ad6a7c66e26993a2e7467b8fa5c1ecbedd188 Mon Sep 17 00:00:00 2001 From: Christopher Baines Date: Sun, 25 Oct 2020 10:23:17 +0000 Subject: gnu: netcdf-fortran: Update to 4.5.3. This allows the package to build with netcdf 4.7.4. * gnu/packages/maths.scm (netcdf-fortran): Update to 4.5.3. --- 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 d2631501aa..ba46937f9a 100644 --- a/gnu/packages/maths.scm +++ b/gnu/packages/maths.scm @@ -1619,7 +1619,7 @@ (define-public netcdf-parallel-openmpi (define-public netcdf-fortran (package (name "netcdf-fortran") - (version "4.4.4") + (version "4.5.3") (source (origin (method url-fetch) (uri (string-append @@ -1627,7 +1627,7 @@ (define-public netcdf-fortran version ".tar.gz")) (sha256 (base32 - "0xaxdcg1p83zmypwml3swsnr3ccn38inwldyr1l3wa4dbwbrblxj")))) + "0x4acvfhbsx1q79dkkwrwbgfhm0w5ngnp4zj5kk92s1khihmqfhj")))) (build-system gnu-build-system) (arguments `(#:parallel-tests? #f)) -- cgit v1.2.3 From c6843f17517afe44a51593bcad1a9d12b296131a Mon Sep 17 00:00:00 2001 From: Paul Garlick Date: Wed, 11 Nov 2020 09:02:26 +0000 Subject: gnu: python-petsc4py: Fix build with python 3.8. * gnu/packages/maths.scm (python-petsc4py)[source]: Add snippet. [native-inputs]: New field. --- gnu/packages/maths.scm | 15 ++++++++++++++- 1 file changed, 14 insertions(+), 1 deletion(-) (limited to 'gnu/packages/maths.scm') diff --git a/gnu/packages/maths.scm b/gnu/packages/maths.scm index ba46937f9a..295e2dd35e 100644 --- a/gnu/packages/maths.scm +++ b/gnu/packages/maths.scm @@ -2470,7 +2470,18 @@ (define-public python-petsc4py (uri (pypi-uri "petsc4py" version)) (sha256 (base32 - "1rm1qj5wlkhxl39by9n78lh3gbmii31wsnb8j1rr5hvfr5xgbx2q")))) + "1rm1qj5wlkhxl39by9n78lh3gbmii31wsnb8j1rr5hvfr5xgbx2q")) + (modules '((guix build utils))) + (snippet + '(begin + ;; Ensure source file is regenerated in the build phase. + (delete-file "src/petsc4py.PETSc.c") + ;; Remove legacy GC code. See + ;; https://bitbucket.org/petsc/petsc4py/issues/125. + (substitute* "src/PETSc/cyclicgc.pxi" + ((".*gc_refs.*") "" ) + ((".*PyGC_Head.*") "")) + #t)))) (build-system python-build-system) (arguments `(#:phases @@ -2482,6 +2493,8 @@ (define-public python-petsc4py #t)) (add-before 'check 'mpi-setup ,%openmpi-setup)))) + (native-inputs + `(("python-cython" ,python-cython))) (inputs `(("petsc" ,petsc-openmpi) ("python-numpy" ,python-numpy))) -- cgit v1.2.3 From 7ea957e2c5886c7b93c3ae31a1a5c41c2bf679dd Mon Sep 17 00:00:00 2001 From: Tobias Geerinckx-Rice Date: Sun, 15 Nov 2020 00:25:49 +0100 Subject: gnu: superlu: Update to 5.2.2. * gnu/packages/maths.scm (superlu): Update to 5.2.2. --- 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 295e2dd35e..b2f7f02f05 100644 --- a/gnu/packages/maths.scm +++ b/gnu/packages/maths.scm @@ -2908,14 +2908,14 @@ (define-public ruby-asciimath (define-public superlu (package (name "superlu") - (version "5.2.1") + (version "5.2.2") (source (origin (method url-fetch) (uri (string-append "https://portal.nersc.gov/project/sparse/superlu/" "superlu_" version ".tar.gz")) (sha256 - (base32 "0qzlb7cd608q62kyppd0a8c65l03vrwqql6gsm465rky23b6dyr8")) + (base32 "13520vk6fqspyl22cq4ak2jh3rlmhja4czq56j75fdx65fkk80s7")) (modules '((guix build utils))) (snippet ;; Replace the non-free implementation of MC64 with a stub adapted -- cgit v1.2.3 From dc2de508a38d8e0a3f93e8d6ded225d3a7e32548 Mon Sep 17 00:00:00 2001 From: Martin Becze Date: Thu, 5 Nov 2020 07:59:44 -0600 Subject: gnu: z3: Update to 4.8.9. * gnu/packages/maths.scm (z3): Update to 4.8.9. Signed-off-by: Christopher Baines --- gnu/packages/maths.scm | 5 +++-- 1 file changed, 3 insertions(+), 2 deletions(-) (limited to 'gnu/packages/maths.scm') diff --git a/gnu/packages/maths.scm b/gnu/packages/maths.scm index b2f7f02f05..c4c30483d5 100644 --- a/gnu/packages/maths.scm +++ b/gnu/packages/maths.scm @@ -41,6 +41,7 @@ ;;; Copyright © 2020 B. Wilson ;;; Copyright © 2020 Vinicius Monego ;;; Copyright © 2020 Simon Tournier +;;; Copyright © 2020 Martin Becze ;;; ;;; This file is part of GNU Guix. ;;; @@ -4716,7 +4717,7 @@ (define-public jacal (define-public z3 (package (name "z3") - (version "4.8.8") + (version "4.8.9") (home-page "https://github.com/Z3Prover/z3") (source (origin (method git-fetch) @@ -4725,7 +4726,7 @@ (define-public z3 (file-name (git-file-name name version)) (sha256 (base32 - "1rn538ghqwxq0v8i6578j8mflk6fyv0cp4hjfqynzvinjbps56da")))) + "1hnbzq10d23drd7ksm3c1n2611c3kd0q0yxgz8y78zaafwczvwxx")))) (build-system gnu-build-system) (arguments `(#:imported-modules ((guix build python-build-system) -- cgit v1.2.3 From 1b16727c18c926eb1bb69dffb55e5074f5c3a0a8 Mon Sep 17 00:00:00 2001 From: Tobias Geerinckx-Rice Date: Tue, 17 Nov 2020 22:20:50 +0100 Subject: gnu: units: Update to 2.21. * gnu/packages/maths.scm (units): Update to 2.21. --- 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 c4c30483d5..d3f3539e26 100644 --- a/gnu/packages/maths.scm +++ b/gnu/packages/maths.scm @@ -307,13 +307,13 @@ (define-public python2-cvxopt (define-public units (package (name "units") - (version "2.19") + (version "2.21") (source (origin (method url-fetch) (uri (string-append "mirror://gnu/units/units-" version ".tar.gz")) (sha256 (base32 - "0mk562g7dnidjgfgvkxxpvlba66fh1ykmfd9ylzvcln1vxmi6qj2")))) + "1bybhqs4yrly9myb5maz3kdmf8k4fhk2m1d5cbcryn40z6lq0gkc")))) (build-system gnu-build-system) (inputs `(("readline" ,readline) -- cgit v1.2.3