From ae3a1e70ec69f64cfe1700c6784b4bd645b6be43 Mon Sep 17 00:00:00 2001 From: Aron Ahmadia Date: Tue, 24 Mar 2015 17:24:50 -0400 Subject: [PATCH 01/85] Add Shapely (Development branch) We can't use a release since we need https://github.com/Toblerity/Shapely/pull/241 This also requires: https://github.com/hashdist/hashdist/commit/d3a39c57 --- pkgs/geos.yaml | 4 ++++ pkgs/shapely.yaml | 16 ++++++++++++++++ 2 files changed, 20 insertions(+) create mode 100644 pkgs/shapely.yaml diff --git a/pkgs/geos.yaml b/pkgs/geos.yaml index ecbdd977c..e41b26ef6 100644 --- a/pkgs/geos.yaml +++ b/pkgs/geos.yaml @@ -3,3 +3,7 @@ extends: [autotools_package] sources: - url: http://download.osgeo.org/geos/geos-3.4.2.tar.bz2 key: tar.bz2:cxul7x36feehvfl3k2wfipvjvabscsa4 + +when_build_dependency: + - prepend_path: PATH + value: '${ARTIFACT}/bin' diff --git a/pkgs/shapely.yaml b/pkgs/shapely.yaml new file mode 100644 index 000000000..a28479bc3 --- /dev/null +++ b/pkgs/shapely.yaml @@ -0,0 +1,16 @@ +extends: [distutils_package] +dependencies: + build: [geos] + run: [geos] + +sources: +- key: git:76f5832e8df80ed86493fb4eb7a0cd7a17976822 + url: git@github.com:Toblerity/Shapely.git + +build_stages: +- name: check + after: install + handler: bash + bash: | + ${PYTHON} -c "from shapely import geos" + From 5be8186f0c2a7f2c6093a2184428900565115c04 Mon Sep 17 00:00:00 2001 From: Johannes Ring Date: Wed, 25 Mar 2015 14:31:00 +0100 Subject: [PATCH 02/85] Add libxml2 and pkg-config to build dependencies for mpich and set PKG_CONFIG_PATH (fixes issue #701). --- pkgs/mpich.yaml | 4 ++++ 1 file changed, 4 insertions(+) diff --git a/pkgs/mpich.yaml b/pkgs/mpich.yaml index 06ac8b90b..43a40295f 100644 --- a/pkgs/mpich.yaml +++ b/pkgs/mpich.yaml @@ -1,4 +1,6 @@ extends: [autotools_package] +dependencies: + build: [libxml2, pkg-config] build_stages: - name: configure @@ -27,3 +29,5 @@ when_build_dependency: - prepend_path: PATH value: ${ARTIFACT}/bin + - prepend_path: PKG_CONFIG_PATH + value: ${ARTIFACT}/lib/pkgconfig From ee4303d247e54a525da0ba8d39b16ef9ff1ed217 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Ond=C5=99ej=20=C4=8Cert=C3=ADk?= Date: Wed, 25 Mar 2015 16:20:06 -0600 Subject: [PATCH 03/85] Add the Libint package --- pkgs/libint.yaml | 5 +++++ 1 file changed, 5 insertions(+) create mode 100644 pkgs/libint.yaml diff --git a/pkgs/libint.yaml b/pkgs/libint.yaml new file mode 100644 index 000000000..815c56415 --- /dev/null +++ b/pkgs/libint.yaml @@ -0,0 +1,5 @@ +extends: [autotools_package] + +sources: +- key: git:5d9c42dccebed2e9207616794a933764ec4151ae + url: https://github.com/qsnake/libint.git From b9ab0242a09f1e15871d2a80fff808b032586d59 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Ond=C5=99ej=20=C4=8Cert=C3=ADk?= Date: Wed, 25 Mar 2015 17:03:53 -0600 Subject: [PATCH 04/85] Update Libint to the latest version --- pkgs/libint.yaml | 24 ++++++++++++++++++++++-- 1 file changed, 22 insertions(+), 2 deletions(-) diff --git a/pkgs/libint.yaml b/pkgs/libint.yaml index 815c56415..d4a9e1811 100644 --- a/pkgs/libint.yaml +++ b/pkgs/libint.yaml @@ -1,5 +1,25 @@ extends: [autotools_package] +dependencies: + build: [autoconf, automake, gmp, boost] + sources: -- key: git:5d9c42dccebed2e9207616794a933764ec4151ae - url: https://github.com/qsnake/libint.git +# When https://github.com/evaleev/libint/pull/30 is merged, we can switch to +# use the original repository, until then we use a clone with the necessary +# patches: +#- key: git:c1be4f680ada1797e71741fa882b68e926fc05a9 +# url: https://github.com/evaleev/libint +- key: git:c0a83fa7e2554ea71a14dbae47bce0a3559e1a54 + url: https://github.com/certik/libint-1 + +defaults: + # include/libint2/basis.h contains hard-coded path + relocatable: false + +build_stages: +- name: create_configure + after: prologue + before: configure + handler: bash + bash: | + ./autogen.sh From 1ccac063d4ed6e33de1e36ab60c88d626ed452f1 Mon Sep 17 00:00:00 2001 From: Jimmy Tang Date: Sun, 29 Mar 2015 09:52:56 +0100 Subject: [PATCH 05/85] ansible: Update to latest stable Signed-off-by: Jimmy Tang --- pkgs/ansible.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/pkgs/ansible.yaml b/pkgs/ansible.yaml index 283de6c12..78e7065b3 100644 --- a/pkgs/ansible.yaml +++ b/pkgs/ansible.yaml @@ -5,5 +5,5 @@ dependencies: run: [paramiko, jinja2, yaml] sources: -- key: tar.gz:2n6ajm5lz2nqg2tmqmi7zszwbrolypwi - url: https://pypi.python.org/packages/source/a/ansible/ansible-1.8.4.tar.gz +- key: tar.gz:wimt7wneaynlmjh2m4yrpfsbtj2z3ydl + url: https://pypi.python.org/packages/source/a/ansible/ansible-1.9.0.1.tar.gz From c15cc0dd4f8c3428b2a3ce1a0f42fab97c8a13bb Mon Sep 17 00:00:00 2001 From: Jimmy Tang Date: Sun, 29 Mar 2015 10:18:26 +0100 Subject: [PATCH 06/85] genshi: Initial add of genshi templating library Signed-off-by: Jimmy Tang --- pkgs/genshi.yaml | 9 +++++++++ 1 file changed, 9 insertions(+) create mode 100644 pkgs/genshi.yaml diff --git a/pkgs/genshi.yaml b/pkgs/genshi.yaml new file mode 100644 index 000000000..ed1c87048 --- /dev/null +++ b/pkgs/genshi.yaml @@ -0,0 +1,9 @@ +extends: [setuptools_package] + +dependencies: + build: [] + run: [] + +sources: +- key: zip:ptgbosdhel3aawcwn3pqmd6iy2xqvqkv + url: https://pypi.python.org/packages/source/G/Genshi/Genshi-0.7.zip From 29856aa40232c01a87584fba316882a7e77ed17c Mon Sep 17 00:00:00 2001 From: Aron Ahmadia Date: Mon, 30 Mar 2015 16:21:58 -0400 Subject: [PATCH 07/85] jinja needs markupsafe now --- pkgs/jinja2.yaml | 3 +++ 1 file changed, 3 insertions(+) diff --git a/pkgs/jinja2.yaml b/pkgs/jinja2.yaml index 2ede0bfa0..33850f06f 100644 --- a/pkgs/jinja2.yaml +++ b/pkgs/jinja2.yaml @@ -1,5 +1,8 @@ extends: [setuptools_package] +dependencies: + run: [MarkupSafe] + sources: - key: tar.gz:fyskyxiajw2xcslwubfmb2amnx3oi7uy url: https://pypi.python.org/packages/source/J/Jinja2/Jinja2-2.7.3.tar.gz From 2dde06abe28ff2d3948bf15948edc55a9c51b4d0 Mon Sep 17 00:00:00 2001 From: cekees Date: Tue, 31 Mar 2015 14:28:16 -0500 Subject: [PATCH 08/85] made relocatable cause it breaks on linux --- pkgs/pelican-bootstrap3.yaml | 3 +++ pkgs/pelican-plugins.yaml | 3 +++ 2 files changed, 6 insertions(+) diff --git a/pkgs/pelican-bootstrap3.yaml b/pkgs/pelican-bootstrap3.yaml index 014f20145..9b92e7b10 100644 --- a/pkgs/pelican-bootstrap3.yaml +++ b/pkgs/pelican-bootstrap3.yaml @@ -1,5 +1,8 @@ extends: [base_package] +defaults: + relocatable: false + sources: - key: git:0d473861e930e91a4a85a1770d926a62c05b8268 url: https://github.com/DandyDev/pelican-bootstrap3 diff --git a/pkgs/pelican-plugins.yaml b/pkgs/pelican-plugins.yaml index 30efa79a0..afd1319ad 100644 --- a/pkgs/pelican-plugins.yaml +++ b/pkgs/pelican-plugins.yaml @@ -1,5 +1,8 @@ extends: [base_package] +defaults: + relocatable: false + sources: - key: git:f7174a25b47675ed8429f432ef3a682c55c2fcf1 url: https://github.com/getpelican/pelican-plugins From d01464de08357a894c3a5fe227b15ec828bb2def Mon Sep 17 00:00:00 2001 From: Aron Ahmadia Date: Tue, 31 Mar 2015 16:33:00 -0400 Subject: [PATCH 09/85] Update proteus --- pkgs/proteus.yaml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/pkgs/proteus.yaml b/pkgs/proteus.yaml index 23a04434f..e852c8d09 100644 --- a/pkgs/proteus.yaml +++ b/pkgs/proteus.yaml @@ -4,7 +4,7 @@ dependencies: run: [daetk, ipython, matplotlib, nose, mpi4py, petsc4py, pytables, sphinx, superlu, sympy, tetgen, triangle] sources: - - key: git:1ee40338ff4a3ac6772c5837228752d6fb62b549 + - key: git:3d2bebca095ae8ac8baffde4c066c03590565510 url: https://github.com/erdc-cm/proteus # Proteus is a namespace package, do *not* link the Proteus directory itself in. From be3623ef706c7690642d5a770ead9203f5506b0c Mon Sep 17 00:00:00 2001 From: cmaurini Date: Wed, 1 Apr 2015 10:08:36 +0200 Subject: [PATCH 10/85] set OPENBLAS_DIR in openblas.yaml when build dependencies I found that the numpy package is not able to find openblas at compile time, because it is looking in `$OPENBLAS_DIR/lib` and `OPENBLAS_DIR` is not set in `openblas.yaml `. I think that this setting should be unable. At least with this change numpy finds openblas for me. --- pkgs/openblas.yaml | 1 + 1 file changed, 1 insertion(+) diff --git a/pkgs/openblas.yaml b/pkgs/openblas.yaml index 03942c318..1c6948aab 100644 --- a/pkgs/openblas.yaml +++ b/pkgs/openblas.yaml @@ -19,3 +19,4 @@ build_stages: when_build_dependency: - {set: 'BLAS_LDFLAGS', value: '-Wl,-rpath,${ARTIFACT}/lib -L${ARTIFACT}/lib -lopenblas'} - {set: 'LAPACK_LDFLAGS', value: '-Wl,-rpath,${ARTIFACT}/lib -L${ARTIFACT}/lib -lopenblas'} +- {set: 'OPENBLAS_DIR', value: '${ARTIFACT}'} From c6e646d9634c3f44ff845407113834d41e935bd7 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Ond=C5=99ej=20=C4=8Cert=C3=ADk?= Date: Wed, 1 Apr 2015 16:55:25 -0600 Subject: [PATCH 11/85] Keep the CPPFLAGS and LDFLAGS exported for make Otherwise the "make" command doesn't have the CPPFLAGS and LDFLAGS variables set, and then the build fails. Fixes #710. --- pkgs/gdb.yaml | 3 +++ 1 file changed, 3 insertions(+) diff --git a/pkgs/gdb.yaml b/pkgs/gdb.yaml index 4516b2d43..5483a394f 100644 --- a/pkgs/gdb.yaml +++ b/pkgs/gdb.yaml @@ -8,6 +8,9 @@ sources: url: http://ftp.gnu.org/gnu/gdb/gdb-7.7.1.tar.bz2 build_stages: + - name: configure + global_flags: true + - name: fail_on_osx before: prologue mode: replace From ef2671c1d90a384bab38469fcc9732c90cb3b687 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Ond=C5=99ej=20=C4=8Cert=C3=ADk?= Date: Wed, 1 Apr 2015 16:59:53 -0600 Subject: [PATCH 12/85] Make gdb not relocatable --- pkgs/gdb.yaml | 4 ++++ 1 file changed, 4 insertions(+) diff --git a/pkgs/gdb.yaml b/pkgs/gdb.yaml index 5483a394f..c19295f3e 100644 --- a/pkgs/gdb.yaml +++ b/pkgs/gdb.yaml @@ -7,6 +7,10 @@ sources: - key: tar.bz2:bw6veycan4nqy4h46at4msefe75n3ygn url: http://ftp.gnu.org/gnu/gdb/gdb-7.7.1.tar.bz2 +defaults: + # lib/libbfd.a contains hard-coded path + relocatable: false + build_stages: - name: configure global_flags: true From 0135f97121a54543b01a63dd4d34afa5811bb03d Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Ond=C5=99ej=20=C4=8Cert=C3=ADk?= Date: Wed, 1 Apr 2015 17:00:15 -0600 Subject: [PATCH 13/85] gdb: use readline from Hashstack --- pkgs/gdb.yaml | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/pkgs/gdb.yaml b/pkgs/gdb.yaml index c19295f3e..c659c2445 100644 --- a/pkgs/gdb.yaml +++ b/pkgs/gdb.yaml @@ -1,7 +1,7 @@ extends: [autotools_package] dependencies: - build: [python, expat, xz, ncurses, libiconv, zlib, {{build_with}}] + build: [python, expat, xz, ncurses, libiconv, zlib, readline, {{build_with}}] sources: - key: tar.bz2:bw6veycan4nqy4h46at4msefe75n3ygn @@ -14,6 +14,7 @@ defaults: build_stages: - name: configure global_flags: true + extra: ['--with-system-readline'] - name: fail_on_osx before: prologue From d5559b04f175de078e5df562f2baed4955bef9d7 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Ond=C5=99ej=20=C4=8Cert=C3=ADk?= Date: Wed, 1 Apr 2015 17:00:40 -0600 Subject: [PATCH 14/85] Update to gdb 7.9 --- pkgs/gdb.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/pkgs/gdb.yaml b/pkgs/gdb.yaml index c659c2445..ec6624d76 100644 --- a/pkgs/gdb.yaml +++ b/pkgs/gdb.yaml @@ -4,8 +4,8 @@ dependencies: build: [python, expat, xz, ncurses, libiconv, zlib, readline, {{build_with}}] sources: -- key: tar.bz2:bw6veycan4nqy4h46at4msefe75n3ygn - url: http://ftp.gnu.org/gnu/gdb/gdb-7.7.1.tar.bz2 +- key: tar.xz:tmyvmunbmuuppl4mpwbii2m7wdewlxzr + url: https://ftp.gnu.org/gnu/gdb/gdb-7.9.tar.xz defaults: # lib/libbfd.a contains hard-coded path From b12913630a9729fed0d5776f0fc4c437f13ee9fa Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Ond=C5=99ej=20=C4=8Cert=C3=ADk?= Date: Wed, 1 Apr 2015 17:09:17 -0600 Subject: [PATCH 15/85] Update Libint, remove local patches Now when https://github.com/evaleev/libint/pull/30 is merged, we can remove our local patches and just use the upstream repository. --- pkgs/libint.yaml | 9 ++------- 1 file changed, 2 insertions(+), 7 deletions(-) diff --git a/pkgs/libint.yaml b/pkgs/libint.yaml index d4a9e1811..e0158e7b0 100644 --- a/pkgs/libint.yaml +++ b/pkgs/libint.yaml @@ -4,13 +4,8 @@ dependencies: build: [autoconf, automake, gmp, boost] sources: -# When https://github.com/evaleev/libint/pull/30 is merged, we can switch to -# use the original repository, until then we use a clone with the necessary -# patches: -#- key: git:c1be4f680ada1797e71741fa882b68e926fc05a9 -# url: https://github.com/evaleev/libint -- key: git:c0a83fa7e2554ea71a14dbae47bce0a3559e1a54 - url: https://github.com/certik/libint-1 +- key: git:807677f7b7f0de46d9cc515ca0c75b0c4db3d2be + url: https://github.com/evaleev/libint defaults: # include/libint2/basis.h contains hard-coded path From 26ec0f509f3b60e82840a8b619d3082548ffe983 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Ond=C5=99ej=20=C4=8Cert=C3=ADk?= Date: Sat, 4 Apr 2015 12:33:47 -0600 Subject: [PATCH 16/85] Update the BDDC package --- pkgs/bddc.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/pkgs/bddc.yaml b/pkgs/bddc.yaml index 5999128a8..6232b750d 100644 --- a/pkgs/bddc.yaml +++ b/pkgs/bddc.yaml @@ -3,8 +3,8 @@ dependencies: build: [mpi, lapack, mumps, blopex, parmetis, scalapack] sources: -- url: https://github.com/certik/bddc.git - key: git:3d6cfa120682be5925861c022bd3a3f2c5d77940 +- key: git:e2b1c6e14fa96c2c53b5d8ec21e81cdea86001a0 + url: https://github.com/certik/bddc.git build_stages: From 6d4554788acdbad9a57ad74b67cbb0e5121ba94c Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Ond=C5=99ej=20=C4=8Cert=C3=ADk?= Date: Sat, 4 Apr 2015 14:42:49 -0600 Subject: [PATCH 17/85] BDDC: Explicitly use make -j1 --- pkgs/bddc.yaml | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/pkgs/bddc.yaml b/pkgs/bddc.yaml index 6232b750d..52a83c4f3 100644 --- a/pkgs/bddc.yaml +++ b/pkgs/bddc.yaml @@ -27,7 +27,8 @@ build_stages: BDDCML_LIBSCALAPACK="-L$SCALAPACK_DIR/lib -Wl,-rpath=${SCALAPACK_DIR}/lib -lscalapack" \ BDDCML_LIBLAPACK="-L$LAPACK_DIR/lib -Wl,-rpath=${LAPACK_DIR}/lib -llapack" \ BDDCML_LIBBLAS="-lblas" \ - BDDCML_LIBBLACS= + BDDCML_LIBBLACS= \ + -j 1 # The BDDC's makefile system doesn't work in parallel mkdir -p $ARTIFACT/bin cd examples cp bddcml_global bddcml_local poisson_on_cube $ARTIFACT/bin/ From f866843c0b88950a8c5813c7d3bc930466d8c917 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Ond=C5=99ej=20=C4=8Cert=C3=ADk?= Date: Sat, 4 Apr 2015 16:33:04 -0600 Subject: [PATCH 18/85] Install the interface module --- pkgs/bddc.yaml | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/pkgs/bddc.yaml b/pkgs/bddc.yaml index 52a83c4f3..7a0fb41ef 100644 --- a/pkgs/bddc.yaml +++ b/pkgs/bddc.yaml @@ -29,6 +29,7 @@ build_stages: BDDCML_LIBBLAS="-lblas" \ BDDCML_LIBBLACS= \ -j 1 # The BDDC's makefile system doesn't work in parallel - mkdir -p $ARTIFACT/bin + mkdir -p $ARTIFACT/bin $ARTIFACT/include + cp src/bddcml_interface_fortran.mod $ARTIFACT/include/ cd examples cp bddcml_global bddcml_local poisson_on_cube $ARTIFACT/bin/ From 160b27ca571d4b49d5587ea893b42dabbe7d6566 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Ond=C5=99ej=20=C4=8Cert=C3=ADk?= Date: Sat, 4 Apr 2015 17:09:32 -0600 Subject: [PATCH 19/85] Implement Debug and Release modes --- pkgs/bddc.yaml | 24 ++++++++++++++++++++++++ 1 file changed, 24 insertions(+) diff --git a/pkgs/bddc.yaml b/pkgs/bddc.yaml index 7a0fb41ef..72c8c8dec 100644 --- a/pkgs/bddc.yaml +++ b/pkgs/bddc.yaml @@ -6,8 +6,30 @@ sources: - key: git:e2b1c6e14fa96c2c53b5d8ec21e81cdea86001a0 url: https://github.com/certik/bddc.git +defaults: + # Build in Debug mode (debug symbols, bounds checks, ...) + debug: false + build_stages: +- when: debug + name: debug-flags + after: prologue + before: make-configure + handler: bash + bash: | + FFLAGS="-g -C -Wall -fbounds-check" + CFLAGS="-g -Wall" + +- when: not debug + name: debug-flags + after: prologue + before: make-configure + handler: bash + bash: | + FFLAGS="-C -Wall -O3 -march=native -ffast-math -funroll-loops" + CFLAGS="-Wall -O3 -march=native -ffast-math -funroll-loops" + - name: make-configure after: prologue handler: bash @@ -15,6 +37,8 @@ build_stages: cp make.inc.example make.inc make \ BDDCML_ROOT=$ARTIFACT \ + BDDCML_MPFFLAGS="$FFLAGS" \ + BDDCML_MPCFLAGS="$CFLAGS" \ BDDCML_INCPARMETIS=-I$PARMETIS_DIR/include \ BDDCML_LIBPARMETIS="-L$PARMETIS_DIR/lib -Wl,-rpath=${PARMETIS_DIR}/lib -lparmetis" \ BDDCML_INCMETIS= \ From 8cf9d91d5c6745a7ace69fdcf1cb090361384181 Mon Sep 17 00:00:00 2001 From: Hernan Villanueva Date: Sun, 5 Apr 2015 19:05:27 -0600 Subject: [PATCH 20/85] Valgrind profile --- pkgs/valgrind.yaml | 12 ++++++++++++ 1 file changed, 12 insertions(+) create mode 100644 pkgs/valgrind.yaml diff --git a/pkgs/valgrind.yaml b/pkgs/valgrind.yaml new file mode 100644 index 000000000..006617db4 --- /dev/null +++ b/pkgs/valgrind.yaml @@ -0,0 +1,12 @@ +extends: [autotools_package] + +defaults: + relocatable: false + +sources: +- key: tar.bz2:7ist3qtn3ntbwytj35mbitx7mb7kh53k + url: http://valgrind.org/downloads/valgrind-3.10.1.tar.bz2 + +when_build_dependency: +- prepend_path: PATH + value: '${ARTIFACT}/bin' From b70493e445314ee51e8ad6ecbab929120e6032cb Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Ond=C5=99ej=20=C4=8Cert=C3=ADk?= Date: Mon, 6 Apr 2015 12:23:40 -0600 Subject: [PATCH 21/85] Update to the newest version --- pkgs/bddc.yaml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/pkgs/bddc.yaml b/pkgs/bddc.yaml index 72c8c8dec..56e1812cb 100644 --- a/pkgs/bddc.yaml +++ b/pkgs/bddc.yaml @@ -3,7 +3,7 @@ dependencies: build: [mpi, lapack, mumps, blopex, parmetis, scalapack] sources: -- key: git:e2b1c6e14fa96c2c53b5d8ec21e81cdea86001a0 +- key: git:acd093697417f49ec856b69e2d8b442e5adbbe85 url: https://github.com/certik/bddc.git defaults: From c8d5d15470ec90e810502e2fcd3c7c3eb82a8018 Mon Sep 17 00:00:00 2001 From: Johannes Ring Date: Wed, 8 Apr 2015 14:37:16 +0200 Subject: [PATCH 22/85] superlu_dist: Remove -j option when building tests. --- pkgs/superlu_dist/superlu_dist.yaml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/pkgs/superlu_dist/superlu_dist.yaml b/pkgs/superlu_dist/superlu_dist.yaml index dd457e0db..ebb273788 100644 --- a/pkgs/superlu_dist/superlu_dist.yaml +++ b/pkgs/superlu_dist/superlu_dist.yaml @@ -54,7 +54,7 @@ build_stages: handler: bash bash: | cd EXAMPLE - make -j ${HASHDIST_CPU_COUNT} + make ${MPIEXEC} -np 4 ./pddrive -r 2 -c 2 g20.rua ${MPIEXEC} -np 10 ./pddrive4 g20.rua ${MPIEXEC} -np 4 ./pzdrive -r 2 -c 2 cg20.cua From fe6f5df0eadb947ff219d1aba14b3d65a7cac957 Mon Sep 17 00:00:00 2001 From: Johannes Ring Date: Thu, 9 Apr 2015 09:32:15 +0200 Subject: [PATCH 23/85] superlu_dist: remove -j option for make also when building the library. --- pkgs/superlu_dist/superlu_dist.yaml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/pkgs/superlu_dist/superlu_dist.yaml b/pkgs/superlu_dist/superlu_dist.yaml index ebb273788..ca09d32ad 100644 --- a/pkgs/superlu_dist/superlu_dist.yaml +++ b/pkgs/superlu_dist/superlu_dist.yaml @@ -34,7 +34,7 @@ build_stages: after: configure bash: | mkdir -p lib - make -j ${HASHDIST_CPU_COUNT} lib LAAUX="" + make lib LAAUX="" - name: install mode: replace From c8cce366a6f6b1592d17a0a2559d6d21aaf70c2c Mon Sep 17 00:00:00 2001 From: Johannes Ring Date: Thu, 9 Apr 2015 11:35:06 +0200 Subject: [PATCH 24/85] openblas: turn off threading by default. --- pkgs/openblas.yaml | 20 +++++++++++++++++++- 1 file changed, 19 insertions(+), 1 deletion(-) diff --git a/pkgs/openblas.yaml b/pkgs/openblas.yaml index 1c6948aab..1ddb992d2 100644 --- a/pkgs/openblas.yaml +++ b/pkgs/openblas.yaml @@ -7,13 +7,31 @@ sources: defaults: # cmake/OpenBLASConfig.cmake contains hard-coded path relocatable: false + # build single threaded version as default + use_thread: false build_stages: +- when: use_thread + name: use_thread + after: prologue + before: make_and_install + handler: bash + bash: | + export USE_THREAD=1 + +- when: not use_thread + name: use_thread + after: prologue + before: make_and_install + handler: bash + bash: | + export USE_THREAD=0 + - name: make_and_install after: prologue handler: bash bash: | - make {{extra_flags}} -j${HASDIST_CPU_COUNT} + make USE_THREAD=${USE_THREAD} {{extra_flags}} -j${HASDIST_CPU_COUNT} make {{extra_flags}} PREFIX=${ARTIFACT} install when_build_dependency: From 634f09d1ee048da05a7c14abf2d4bd971d6946f5 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Ond=C5=99ej=20=C4=8Cert=C3=ADk?= Date: Thu, 9 Apr 2015 10:36:23 -0600 Subject: [PATCH 25/85] Add the GLM package --- pkgs/glm.yaml | 7 +++++++ 1 file changed, 7 insertions(+) create mode 100644 pkgs/glm.yaml diff --git a/pkgs/glm.yaml b/pkgs/glm.yaml new file mode 100644 index 000000000..437bdb5a9 --- /dev/null +++ b/pkgs/glm.yaml @@ -0,0 +1,7 @@ +extends: [cmake_package] +dependencies: + build: [] + +sources: +- key: zip:crsrwvvrb6tibasenlfpniirnvllov6i + url: http://downloads.sourceforge.net/project/ogl-math/glm-0.9.6.3/glm-0.9.6.3.zip From 86319e761bd647098f61486499a6cc83a2b205fb Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Ond=C5=99ej=20=C4=8Cert=C3=ADk?= Date: Thu, 9 Apr 2015 09:16:24 -0600 Subject: [PATCH 26/85] Update Trilinos * Use the latest release * Add missing dependencies * Add Trilinos_ENABLE_DEVELOPMENT_MODE:BOOL=OFF CMake option. This option is OFF in the release tarballs, but ON in git. By always setting it, one can then just switch the sources to git and it will build. * Add teuchos_debug for optionally enabling Debug support in Teuchos --- pkgs/trilinos.yaml | 16 +++++++++++++--- 1 file changed, 13 insertions(+), 3 deletions(-) diff --git a/pkgs/trilinos.yaml b/pkgs/trilinos.yaml index db07d7656..1cbf3c106 100644 --- a/pkgs/trilinos.yaml +++ b/pkgs/trilinos.yaml @@ -1,14 +1,18 @@ extends: [cmake_package] dependencies: - build: [python, swig, mpi, numpy, openblas, suitesparse] + build: [python, swig, mpi, numpy, openblas, suitesparse, boost, netcdf4, + hdf5, glm] sources: -- key: tar.bz2:uqktsqkffhdfsbjgbm567y5o4ty52eav - url: http://trilinos.org/oldsite/download/files/trilinos-11.12.1-Source.tar.bz2 +- key: tar.bz2:wdbi4nvxaxpwimfb6p5cvszc4v52xnc5 + url: http://trilinos.org/oldsite/download/files/trilinos-11.14.2-Source.tar.bz2 defaults: # include/trilinos/Makefile.export.Trilinos contains hard-coded path relocatable: false + # Build Teuchos in Debug mode (RCP/Ptr dangling pointer checks, bounds + # checks, ...) + teuchos_debug: false build_stages: - name: configure @@ -33,8 +37,14 @@ build_stages: '-D UMFPACK_LIBRARY_DIRS:PATH=${SUITESPARSE_DIR}/lib', '-D UMFPACK_LIBRARY_NAMES:STRING="umfpack;cholmod;camd;ccolamd;colamd;amd;suitesparseconfig"', '-D SWIG_EXECUTABLE:FILEPATH=${SWIG_EXECUTABLE}', + '-D Trilinos_ENABLE_DEVELOPMENT_MODE:BOOL=OFF', '-D PYTHON_EXECUTABLE:FILEPATH=${PYTHON}'] +- when: teuchos_debug + name: configure + mode: update + extra: ['-D Teuchos_ENABLE_DEBUG:BOOL=ON'] + when_build_dependency: - prepend_path: PYTHONPATH value: '${ARTIFACT}/lib/python{{pyver}}/site-packages' From 714fe2dd7b25b6630cd30b70d8e6ee317c577b16 Mon Sep 17 00:00:00 2001 From: Johannes Ring Date: Fri, 10 Apr 2015 08:59:44 +0200 Subject: [PATCH 27/85] Bump netcdf4 to version 4.3.3.1, since 4.3.2 tarball has been removed (fixes issue #719). --- pkgs/netcdf4/netcdf4.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/pkgs/netcdf4/netcdf4.yaml b/pkgs/netcdf4/netcdf4.yaml index 65a6f6ad3..c816129e2 100644 --- a/pkgs/netcdf4/netcdf4.yaml +++ b/pkgs/netcdf4/netcdf4.yaml @@ -3,8 +3,8 @@ dependencies: build: [mpi, hdf5, curl] sources: -- key: tar.gz:k4egwq4dz2jdf4c2vvyhmhbkma2ldiga - url: ftp://ftp.unidata.ucar.edu/pub/netcdf/netcdf-4.3.2.tar.gz +- key: tar.gz:xxpd3cyojdxnffeovvs7qlc47n2zamj3 + url: ftp://ftp.unidata.ucar.edu/pub/netcdf/netcdf-4.3.3.1.tar.gz defaults: increase_max_dims: false From 1dab3f2f670ff32fa654906a38a374e16356fb6f Mon Sep 17 00:00:00 2001 From: Johannes Ring Date: Fri, 10 Apr 2015 14:44:57 +0200 Subject: [PATCH 28/85] netcdf4: remove patches that has been applied upstream. --- pkgs/netcdf4/fix_genlib.patch | 11 --- pkgs/netcdf4/hdf5-1.8.13_fix.patch | 129 ----------------------------- pkgs/netcdf4/netcdf4.yaml | 22 ----- 3 files changed, 162 deletions(-) delete mode 100644 pkgs/netcdf4/fix_genlib.patch delete mode 100644 pkgs/netcdf4/hdf5-1.8.13_fix.patch diff --git a/pkgs/netcdf4/fix_genlib.patch b/pkgs/netcdf4/fix_genlib.patch deleted file mode 100644 index 9191fa843..000000000 --- a/pkgs/netcdf4/fix_genlib.patch +++ /dev/null @@ -1,11 +0,0 @@ -diff --unified -r netcdf4/ncgen3/genlib.h netcdf4-fix-genlib/ncgen3/genlib.h ---- netcdf4/ncgen3/genlib.h 2013-11-21 15:57:21.000000000 -0500 -+++ netcdf4-fix-genlib/ncgen3/genlib.h 2014-03-14 22:12:06.000000000 -0400 -@@ -5,6 +5,7 @@ - * See netcdf/COPYRIGHT file for copying and redistribution conditions. - * $Header: /upc/share/CVS/netcdf-3/ncgen3/genlib.h,v 1.15 2009/12/29 18:42:35 dmh Exp $ - *********************************************************************/ -+#include - #include - #include - diff --git a/pkgs/netcdf4/hdf5-1.8.13_fix.patch b/pkgs/netcdf4/hdf5-1.8.13_fix.patch deleted file mode 100644 index bd7555710..000000000 --- a/pkgs/netcdf4/hdf5-1.8.13_fix.patch +++ /dev/null @@ -1,129 +0,0 @@ -diff --git a/RELEASE_NOTES.md b/RELEASE_NOTES.md -index 27f228c..1a69d17 100644 ---- a/RELEASE_NOTES.md -+++ b/RELEASE_NOTES.md -@@ -9,6 +9,8 @@ This file contains a high-level description of this package's evolution. Release - - ### 4.3.3-rc1 Released TBD - -+* When the NC_MPIPOSIX flag is given for parallel I/O access and the HDF5 library does not have the MPI-POSIX VFD configured in, the NC_MPIPOSIX flag is transparently aliased to the NC_MPIIO flag within the netCDF-4 library. -+ - ## 4.3.2 Released 2014-04-23 - - * As part of an ongoing project, the Doxygen-generated netcdf documentation has been reorganized. The goal is to make the documentation easier to parse, and to eliminate redundant material. This project is ongoing. -diff --git a/libsrc4/nc4file.c b/libsrc4/nc4file.c -index ec3bb0c..5c957be 100644 ---- a/libsrc4/nc4file.c -+++ b/libsrc4/nc4file.c -@@ -308,12 +308,21 @@ nc4_create_file(const char *path, int cmode, MPI_Comm comm, MPI_Info info, - if (H5Pset_fapl_mpio(fapl_id, comm, info) < 0) - BAIL(NC_EPARINIT); - } -+#ifdef USE_PARALLEL_POSIX - else /* MPI/POSIX */ - { - LOG((4, "creating parallel file with MPI/posix")); - if (H5Pset_fapl_mpiposix(fapl_id, comm, 0) < 0) - BAIL(NC_EPARINIT); - } -+#else /* USE_PARALLEL_POSIX */ -+ /* Should not happen! Code in NC4_create/NC4_open should alias the -+ * NC_MPIPOSIX flag to NC_MPIIO, if the MPI-POSIX VFD is not -+ * available in HDF5. -QAK -+ */ -+ else /* MPI/POSIX */ -+ BAIL(NC_EPARINIT); -+#endif /* USE_PARALLEL_POSIX */ - - /* Keep copies of the MPI Comm & Info objects */ - if (MPI_SUCCESS != MPI_Comm_dup(comm, &nc4_info->comm)) -@@ -465,6 +474,17 @@ NC4_create(const char* path, int cmode, size_t initialsz, int basepe, - ) - return NC_EINVAL; - -+#ifndef USE_PARALLEL_POSIX -+/* If the HDF5 library has been compiled without the MPI-POSIX VFD, alias -+ * the NC_MPIPOSIX flag to NC_MPIIO. -QAK -+ */ -+ if(cmode & NC_MPIPOSIX) -+ { -+ cmode &= ~NC_MPIPOSIX; -+ cmode |= NC_MPIIO; -+ } -+#endif /* USE_PARALLEL_POSIX */ -+ - cmode |= NC_NETCDF4; - - /* Apply default create format. */ -@@ -2168,12 +2188,21 @@ nc4_open_file(const char *path, int mode, MPI_Comm comm, - if (H5Pset_fapl_mpio(fapl_id, comm, info) < 0) - BAIL(NC_EPARINIT); - } -+#ifdef USE_PARALLEL_POSIX - else /* MPI/POSIX */ - { - LOG((4, "opening parallel file with MPI/posix")); - if (H5Pset_fapl_mpiposix(fapl_id, comm, 0) < 0) - BAIL(NC_EPARINIT); - } -+#else /* USE_PARALLEL_POSIX */ -+ /* Should not happen! Code in NC4_create/NC4_open should alias the -+ * NC_MPIPOSIX flag to NC_MPIIO, if the MPI-POSIX VFD is not -+ * available in HDF5. -QAK -+ */ -+ else /* MPI/POSIX */ -+ BAIL(NC_EPARINIT); -+#endif /* USE_PARALLEL_POSIX */ - - /* Keep copies of the MPI Comm & Info objects */ - if (MPI_SUCCESS != MPI_Comm_dup(comm, &nc4_info->comm)) -@@ -2640,6 +2669,17 @@ NC4_open(const char *path, int mode, int basepe, size_t *chunksizehintp, - (mode & NC_MPIIO && mode & NC_MPIPOSIX)) - return NC_EINVAL; - -+#ifndef USE_PARALLEL_POSIX -+/* If the HDF5 library has been compiled without the MPI-POSIX VFD, alias -+ * the NC_MPIPOSIX flag to NC_MPIIO. -QAK -+ */ -+ if(mode & NC_MPIPOSIX) -+ { -+ mode &= ~NC_MPIPOSIX; -+ mode |= NC_MPIIO; -+ } -+#endif /* USE_PARALLEL_POSIX */ -+ - - /* Depending on the type of file, open it. */ - -diff --git a/nc_test4/tst_nc4perf.c b/nc_test4/tst_nc4perf.c -index 47af70e..3528b82 100644 ---- a/nc_test4/tst_nc4perf.c -+++ b/nc_test4/tst_nc4perf.c -@@ -244,6 +244,11 @@ int test_pio_4d(size_t cache_size, int facc_type, int access_flag, MPI_Comm comm - return 0; - } - -+/* Note: When the MPI-POSIX VFD is not compiled in to HDF5, the NC_MPIPOSIX -+ * flag will be aliased to the NC_MPIIO flag within the library, and -+ * therefore this test will exercise the aliasing, with the MPI-IO VFD, -+ * under that configuration. -QAK -+ */ - #define NUM_MODES 2 - #define NUM_FACC 2 - #define NUM_CHUNK_COMBOS_2D 3 -diff --git a/nc_test4/tst_parallel3.c b/nc_test4/tst_parallel3.c -index 27f9c98..9fa534f 100644 ---- a/nc_test4/tst_parallel3.c -+++ b/nc_test4/tst_parallel3.c -@@ -129,6 +129,11 @@ int main(int argc, char **argv) - if (mpi_rank == 0) - SUMMARIZE_ERR; - -+/* Note: When the MPI-POSIX VFD is not compiled in to HDF5, the NC_MPIPOSIX -+ * flag will be aliased to the NC_MPIIO flag within the library, and -+ * therefore this test will exercise the aliasing, with the MPI-IO VFD, -+ * under that configuration. -QAK -+ */ - if (mpi_rank == 0) - printf("*** Testing parallel IO for raw-data with MPIPOSIX-IO (driver)..."); - facc_type = NC_NETCDF4|NC_MPIPOSIX; diff --git a/pkgs/netcdf4/netcdf4.yaml b/pkgs/netcdf4/netcdf4.yaml index c816129e2..0509bf09c 100644 --- a/pkgs/netcdf4/netcdf4.yaml +++ b/pkgs/netcdf4/netcdf4.yaml @@ -23,28 +23,6 @@ build_stages: append: {LDFLAGS: {{DYNAMIC_EXE_LINKER_FLAGS}}} extra: ['--host=cray','--with-pic'] -# http://www.unidata.ucar.edu/software/netcdf/docs/known_problems.html#clang-ncgen3 -- when: platform == 'Darwin' - files: [fix_genlib.patch] - name: fix_genlib - handler: bash - before: make - bash: | - patch -p1 < _hashdist/fix_genlib.patch - -# HDF5 1.8.13 removes symbols related to MPI POSIX VFD, leading to -# errors when linking hdf5 and netcdf4 such as "undefined reference to -# `_H5Pset_fapl_mpiposix`". This patch fixes those errors, and has been -# added upstream. It should be unnecessary once NetCDF releases a new -# stable version. -# https://github.com/Unidata/netcdf-c/commit/435d8a03ed28bb5ad63aff12cbc6ab91531b6bc8.diff -- files: [hdf5-1.8.13_fix.patch] - name: hdf5-1.8.13_fix - handler: bash - before: make - bash: | - patch -p1 < _hashdist/hdf5-1.8.13_fix.patch - - when: increase_max_dims files: [max_dims.patch] name: max_dims From 5b4985ff3761955c378c8a7b349688ffd557fe92 Mon Sep 17 00:00:00 2001 From: Johannes Ring Date: Fri, 10 Apr 2015 15:01:02 +0200 Subject: [PATCH 29/85] netcdf4: mark as not relocatable. --- pkgs/netcdf4/netcdf4.yaml | 2 ++ 1 file changed, 2 insertions(+) diff --git a/pkgs/netcdf4/netcdf4.yaml b/pkgs/netcdf4/netcdf4.yaml index 0509bf09c..64d48c814 100644 --- a/pkgs/netcdf4/netcdf4.yaml +++ b/pkgs/netcdf4/netcdf4.yaml @@ -8,6 +8,8 @@ sources: defaults: increase_max_dims: false + # lib/libnetcdf.settings contains hard-coded path + relocatable: false build_stages: From 7941f25891f0967be948da3a7ee0eb04ae9580e4 Mon Sep 17 00:00:00 2001 From: Volker Braun Date: Sat, 11 Apr 2015 10:21:17 +0200 Subject: [PATCH 30/85] Update Python --- pkgs/python/python.yaml | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/pkgs/python/python.yaml b/pkgs/python/python.yaml index 008ab1127..da943479e 100644 --- a/pkgs/python/python.yaml +++ b/pkgs/python/python.yaml @@ -2,8 +2,8 @@ extends: [autotools_package] when pyver == '2.7': sources: - - key: tar.gz:otlqxeknurehviozoirlfhuvktief6bf - url: http://python.org/ftp/python/2.7.8/Python-2.7.8.tgz + - key: tar.gz:zc52gptgvqzadwv5yvlpb2t47zvmcgkg + url: http://python.org/ftp/python/2.7.9/Python-2.7.9.tgz when pyver == '3.2': sources: - key: tar.gz:7qpecklofhkhn5uwga5mvyutvz5cgehq @@ -14,8 +14,8 @@ when pyver == '3.3': url: https://www.python.org/ftp/python/3.3.6/Python-3.3.6.tgz when pyver == '3.4': sources: - - key: tar.gz:isr4d3y4psr6j7jfeqvpqdwxfwuucib4 - url: https://www.python.org/ftp/python/3.4.2/Python-3.4.2.tgz + - key: tar.gz:rn2d6vxj4uf7ber3t2oelxmspqdr26vf + url: https://www.python.org/ftp/python/3.4.3/Python-3.4.3.tgz From 24e562f3664787c4e40674fb2fec8f56968f701d Mon Sep 17 00:00:00 2001 From: Volker Braun Date: Sat, 11 Apr 2015 11:11:54 +0200 Subject: [PATCH 31/85] Update to nodejs 0.12.2 --- pkgs/node.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/pkgs/node.yaml b/pkgs/node.yaml index 2fa4fae32..4476789c4 100644 --- a/pkgs/node.yaml +++ b/pkgs/node.yaml @@ -6,5 +6,5 @@ defaults: relocatable: false sources: -- key: tar.gz:xhl5dubjjphem2dlcoqf3jx4lmphoq5v - url: http://nodejs.org/dist/v0.10.36/node-v0.10.36.tar.gz +- key: tar.gz:vr7hrlpjhzrt47wwfbjsxohgkdflude4 + url: http://nodejs.org/dist/v0.12.2/node-v0.12.2.tar.gz From 315d410e2685da6e383119521a800dabf2baa12c Mon Sep 17 00:00:00 2001 From: Volker Braun Date: Sat, 11 Apr 2015 11:20:38 +0200 Subject: [PATCH 32/85] Update pip 6.1.1 --- pkgs/pip.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/pkgs/pip.yaml b/pkgs/pip.yaml index a5945e990..a791605a3 100644 --- a/pkgs/pip.yaml +++ b/pkgs/pip.yaml @@ -5,5 +5,5 @@ dependencies: run: [] sources: - - url: https://pypi.python.org/packages/source/p/pip/pip-1.5.6.tar.gz - key: tar.gz:wgsk4zv26inx5mc2lzhtprime4dpukhk + - url: https://pypi.python.org/packages/source/p/pip/pip-6.1.1.tar.gz + key: tar.gz:rhz3mjwsexqi47za3biejl5eb5qs5mzi From 63be7dc03acd1af49a28eeb8dac0848f9874675b Mon Sep 17 00:00:00 2001 From: Volker Braun Date: Sun, 12 Apr 2015 13:43:59 +0200 Subject: [PATCH 33/85] Add coffeescript --- pkgs/coffeescript.yaml | 20 ++++++++++++++++++++ 1 file changed, 20 insertions(+) create mode 100644 pkgs/coffeescript.yaml diff --git a/pkgs/coffeescript.yaml b/pkgs/coffeescript.yaml new file mode 100644 index 000000000..fa79d493c --- /dev/null +++ b/pkgs/coffeescript.yaml @@ -0,0 +1,20 @@ +extends: [base_package] +dependencies: + build: [node] + +defaults: + relocatable: false + +sources: +- key: tar.gz:uwx36n3nhdu7dwxtwp46sffv3t3orhtw + url: https://github.com/jashkenas/coffeescript/archive/1.9.1.tar.gz + +build_stages: +- name: install + mode: replace + handler: bash + after: prologue + bash: | + "$NODE_DIR"/bin/npm --proxy 127.0.0.1:2 --production --global \ + --prefix="$ARTIFACT" install . + From 2467a55f5d2718404b86c31c6a36835853f45cb0 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Ond=C5=99ej=20=C4=8Cert=C3=ADk?= Date: Wed, 15 Apr 2015 12:43:08 -0600 Subject: [PATCH 34/85] netcdf: apply the patch before configure To fail early if it fails to apply. --- pkgs/netcdf4/netcdf4.yaml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/pkgs/netcdf4/netcdf4.yaml b/pkgs/netcdf4/netcdf4.yaml index 64d48c814..a95555835 100644 --- a/pkgs/netcdf4/netcdf4.yaml +++ b/pkgs/netcdf4/netcdf4.yaml @@ -29,6 +29,6 @@ build_stages: files: [max_dims.patch] name: max_dims handler: bash - before: make + before: configure bash: | patch -p1 < _hashdist/max_dims.patch From e1c260593d0c6a061d8bce4c356b8498d7dc771a Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Ond=C5=99ej=20=C4=8Cert=C3=ADk?= Date: Wed, 15 Apr 2015 12:46:27 -0600 Subject: [PATCH 35/85] netcdf: Rebase the patch on top of the latest code Previously it failed to apply (due to white space), now it works again. --- pkgs/netcdf4/max_dims.patch | 18 +++++++++--------- 1 file changed, 9 insertions(+), 9 deletions(-) diff --git a/pkgs/netcdf4/max_dims.patch b/pkgs/netcdf4/max_dims.patch index 1fa28fb3c..b6527f2a8 100644 --- a/pkgs/netcdf4/max_dims.patch +++ b/pkgs/netcdf4/max_dims.patch @@ -1,24 +1,24 @@ -commit c3e8003955febdb8e46c760d21fe891f958dd245 +commit 9e8b68aae32f9fda89625a7a9c9cc391feb455e3 Author: Ondřej Čertík -Date: Sun Dec 7 23:11:01 2014 -0700 +Date: Wed Apr 15 12:44:47 2015 -0600 Increase max dimensions - + In order to handle larger meshes in libraries like ExodusII and Moab. diff --git a/include/netcdf.h b/include/netcdf.h -index 5d556bc..a642b71 100644 +index c9ca0af..ac27c2d 100644 --- a/include/netcdf.h +++ b/include/netcdf.h -@@ -225,9 +225,9 @@ created with the ::NC_CLASSIC_MODEL flag. +@@ -226,9 +226,9 @@ created with the ::NC_CLASSIC_MODEL flag. As a rule, NC_MAX_VAR_DIMS <= NC_MAX_DIMS. */ /**@{*/ --#define NC_MAX_DIMS 1024 +-#define NC_MAX_DIMS 1024 +#define NC_MAX_DIMS 65536 - #define NC_MAX_ATTRS 8192 --#define NC_MAX_VARS 8192 + #define NC_MAX_ATTRS 8192 +-#define NC_MAX_VARS 8192 +#define NC_MAX_VARS 524288 - #define NC_MAX_NAME 256 + #define NC_MAX_NAME 256 #define NC_MAX_VAR_DIMS 1024 /**< max per variable dimensions */ /**@}*/ From 3295b85cb8c18aa287e76be170bc1b0a597a8fdb Mon Sep 17 00:00:00 2001 From: Johannes Ring Date: Tue, 21 Apr 2015 09:12:41 +0200 Subject: [PATCH 36/85] Add more host packages. --- pkgs/host-ncurses.yaml | 1 + pkgs/host-png.yaml | 1 + pkgs/host-sed.yaml | 1 + pkgs/host-ssl.yaml | 1 + 4 files changed, 4 insertions(+) create mode 100644 pkgs/host-ncurses.yaml create mode 100644 pkgs/host-png.yaml create mode 100644 pkgs/host-sed.yaml create mode 100644 pkgs/host-ssl.yaml diff --git a/pkgs/host-ncurses.yaml b/pkgs/host-ncurses.yaml new file mode 100644 index 000000000..7393088d6 --- /dev/null +++ b/pkgs/host-ncurses.yaml @@ -0,0 +1 @@ +extends: [host_package] diff --git a/pkgs/host-png.yaml b/pkgs/host-png.yaml new file mode 100644 index 000000000..7393088d6 --- /dev/null +++ b/pkgs/host-png.yaml @@ -0,0 +1 @@ +extends: [host_package] diff --git a/pkgs/host-sed.yaml b/pkgs/host-sed.yaml new file mode 100644 index 000000000..7393088d6 --- /dev/null +++ b/pkgs/host-sed.yaml @@ -0,0 +1 @@ +extends: [host_package] diff --git a/pkgs/host-ssl.yaml b/pkgs/host-ssl.yaml new file mode 100644 index 000000000..7393088d6 --- /dev/null +++ b/pkgs/host-ssl.yaml @@ -0,0 +1 @@ +extends: [host_package] From 90b2f2067b6b53a2d4655e55aff39879fa0b4819 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Hern=C3=A1n=20Villanueva?= Date: Thu, 23 Apr 2015 22:03:09 -0600 Subject: [PATCH 37/85] Update doxygen.yaml to set dependency on Flex --- pkgs/doxygen.yaml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/pkgs/doxygen.yaml b/pkgs/doxygen.yaml index c02a94a0b..704bf68cd 100644 --- a/pkgs/doxygen.yaml +++ b/pkgs/doxygen.yaml @@ -1,7 +1,7 @@ extends: [autotools_package] dependencies: - build: [bison] + build: [bison,flex] sources: - url: https://github.com/doxygen/doxygen.git From 5815793cb2048ec6eb503d9f95ae2d0bc44513af Mon Sep 17 00:00:00 2001 From: Jaroslav Hron Date: Wed, 29 Apr 2015 22:46:22 +0200 Subject: [PATCH 38/85] The rpath-fix should be applied to the real library not to the symlink. If applied to the symlink, the symlink is changed to a copy of the file and the rpath of the original library file is not fixed. --- pkgs/hypre.yaml | 5 +++-- 1 file changed, 3 insertions(+), 2 deletions(-) diff --git a/pkgs/hypre.yaml b/pkgs/hypre.yaml index 6c79e6a1e..8c0a8011b 100644 --- a/pkgs/hypre.yaml +++ b/pkgs/hypre.yaml @@ -112,13 +112,14 @@ build_stages: mode: update extra: ["--enable-shared"] +### needs to fix rpath on the real library not the link - when: platform == 'linux' name: rpath-fix after: install handler: bash bash: | - oldRPath=$(${PATCHELF} --print-rpath ${ARTIFACT}/lib/libHYPRE.so) - ${PATCHELF} --set-rpath ${oldRPath}:${ARTIFACT}/lib:${BLAS_DIR}/lib:${LAPACK_DIR}/lib:${MPI_DIR}/lib ${ARTIFACT}/lib/libHYPRE.so + oldRPath=$(${PATCHELF} --print-rpath ${ARTIFACT}/lib/libHYPRE-*.so) + ${PATCHELF} --set-rpath ${oldRPath}:${ARTIFACT}/lib:${BLAS_DIR}/lib:${LAPACK_DIR}/lib:${MPI_DIR}/lib ${ARTIFACT}/lib/libHYPRE-*.so - when: platform != 'linux' name: rpath-fix From ed1e1e5e946d688bdc77514e2764cb4dba6a7542 Mon Sep 17 00:00:00 2001 From: Jimmy Tang Date: Thu, 30 Apr 2015 21:54:28 +0100 Subject: [PATCH 39/85] Fix up dependencies for buildbot and bcfg2 --- pkgs/buildbot.yaml | 4 ++-- pkgs/cryptography.yaml | 2 +- pkgs/lockfile.yaml | 3 +++ pkgs/pbr.yaml | 8 ++++++++ 4 files changed, 14 insertions(+), 3 deletions(-) create mode 100644 pkgs/pbr.yaml diff --git a/pkgs/buildbot.yaml b/pkgs/buildbot.yaml index 9152d93ab..9549187bc 100644 --- a/pkgs/buildbot.yaml +++ b/pkgs/buildbot.yaml @@ -1,8 +1,8 @@ extends: [distutils_package] dependencies: - build: [SQLAlchemy, SQLAlchemy-Migrate, jinja2, Twisted, sqlite, python-dateutil, setuptools] - run: [SQLAlchemy, SQLAlchemy-Migrate, jinja2, Twisted, sqlite, python-dateutil] + build: [SQLAlchemy, SQLAlchemy-Migrate, jinja2, Twisted, sqlite, python-dateutil, Tempita, decorator, MarkupSafe, zope-interface, setuptools] + run: [SQLAlchemy, SQLAlchemy-Migrate, jinja2, Twisted, sqlite, python-dateutil, Tempita, decorator, MarkupSafe, zope-interface] sources: - key: zip:tsyafdgdsontllm5ujazrcbcnysx3o2g diff --git a/pkgs/cryptography.yaml b/pkgs/cryptography.yaml index b3d32d3d1..aa505f015 100644 --- a/pkgs/cryptography.yaml +++ b/pkgs/cryptography.yaml @@ -1,7 +1,7 @@ extends: [setuptools_package] dependencies: - build: [six, cffi, cryptography-vectors, openssl, pytest] + build: [six, cffi, cryptography-vectors, openssl, pytest, pycparser] run: [] sources: diff --git a/pkgs/lockfile.yaml b/pkgs/lockfile.yaml index 2b12c63d8..51d486aaf 100644 --- a/pkgs/lockfile.yaml +++ b/pkgs/lockfile.yaml @@ -1,5 +1,8 @@ extends: [setuptools_package] +dependencies: + build: [pbr, pip] + sources: - url: https://pypi.python.org/packages/source/l/lockfile/lockfile-0.10.2.tar.gz key: tar.gz:tzbcklyx2hoyt3rrorpayt56lcdcyjiu diff --git a/pkgs/pbr.yaml b/pkgs/pbr.yaml new file mode 100644 index 000000000..6f060051f --- /dev/null +++ b/pkgs/pbr.yaml @@ -0,0 +1,8 @@ +extends: [setuptools_package] + +dependencies: + build: [pip] + +sources: + - key: tar.gz:u5awkddjpk7j3u62aabzuv5elik2n3wq + url: https://pypi.python.org/packages/source/p/pbr/pbr-0.10.8.tar.gz From 2fd676304bb88555ec92b9df599a49fc48bbcd0f Mon Sep 17 00:00:00 2001 From: Jimmy Tang Date: Thu, 30 Apr 2015 22:03:28 +0100 Subject: [PATCH 40/85] httpie: initial add of package, this is a curl alternative --- pkgs/httpie.yaml | 8 ++++++++ 1 file changed, 8 insertions(+) create mode 100644 pkgs/httpie.yaml diff --git a/pkgs/httpie.yaml b/pkgs/httpie.yaml new file mode 100644 index 000000000..c11a00a54 --- /dev/null +++ b/pkgs/httpie.yaml @@ -0,0 +1,8 @@ +extends: [setuptools_package] + +dependencies: + build: [pygments] + +sources: + - key: tar.gz:v44yfvaxipmymyepd7toin6qje67ej4z + url: https://pypi.python.org/packages/source/h/httpie/httpie-0.9.2.tar.gz From 0b30635024319dfca7187268da19245dd2c31256 Mon Sep 17 00:00:00 2001 From: Jimmy Tang Date: Thu, 30 Apr 2015 22:04:11 +0100 Subject: [PATCH 41/85] Add missing packages --- pkgs/Tempita.yaml | 9 +++++++++ pkgs/decorator.yaml | 9 +++++++++ 2 files changed, 18 insertions(+) create mode 100644 pkgs/Tempita.yaml create mode 100644 pkgs/decorator.yaml diff --git a/pkgs/Tempita.yaml b/pkgs/Tempita.yaml new file mode 100644 index 000000000..a57d07eb5 --- /dev/null +++ b/pkgs/Tempita.yaml @@ -0,0 +1,9 @@ +extends: [setuptools_package] + +dependencies: + build: [] + run: [] + +sources: + - key: tar.gz:ha4sxnyiueasqqm7ox5jcifg2lencnyb + url: https://pypi.python.org/packages/source/T/Tempita/Tempita-0.5.3dev.tar.gz diff --git a/pkgs/decorator.yaml b/pkgs/decorator.yaml new file mode 100644 index 000000000..cf6c180ec --- /dev/null +++ b/pkgs/decorator.yaml @@ -0,0 +1,9 @@ +extends: [setuptools_package] + +dependencies: + build: [] + run: [] + +sources: + - key: tar.gz:omqaalhgdxvgvisk3skf3hlyggzwnfkt + url: https://pypi.python.org/packages/source/d/decorator/decorator-3.4.2.tar.gz From 6c512eb6d3674ea97878e9f7f06c2dbb3db4da5f Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Hern=C3=A1n=20Villanueva?= Date: Thu, 30 Apr 2015 16:24:06 -0600 Subject: [PATCH 42/85] Update doxygen.yaml --- pkgs/doxygen.yaml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/pkgs/doxygen.yaml b/pkgs/doxygen.yaml index 704bf68cd..ba3bb3222 100644 --- a/pkgs/doxygen.yaml +++ b/pkgs/doxygen.yaml @@ -1,7 +1,7 @@ extends: [autotools_package] dependencies: - build: [bison,flex] + build: [bison, flex] sources: - url: https://github.com/doxygen/doxygen.git From 9492f747168786557f4330e82e05a8296d44bb51 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Ond=C5=99ej=20=C4=8Cert=C3=ADk?= Date: Mon, 13 Apr 2015 16:26:15 -0600 Subject: [PATCH 43/85] Update gmp --- pkgs/gmp.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/pkgs/gmp.yaml b/pkgs/gmp.yaml index c1d6895f6..e57e4dcaf 100644 --- a/pkgs/gmp.yaml +++ b/pkgs/gmp.yaml @@ -4,8 +4,8 @@ dependencies: build: [m4] sources: -- url: http://mirrors.kernel.org/gnu/gmp/gmp-5.1.3.tar.bz2 - key: tar.bz2:ouqhsuqli2ifgelr2d2fglsa6cdaaik7 +- key: tar.bz2:p6hjvacltrwqofsm65kca67ihdwocimu + url: http://mirrors.kernel.org/gnu/gmp/gmp-6.0.0a.tar.bz2 build_stages: - name: configure From 417f279f8252bacc4fd4bbdc774d65fbccc7a7c5 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Ond=C5=99ej=20=C4=8Cert=C3=ADk?= Date: Fri, 1 May 2015 00:18:20 -0600 Subject: [PATCH 44/85] GMP: add a patch for OS X 10.10 --- pkgs/{ => gmp}/gmp.yaml | 6 ++++++ pkgs/gmp/osx_10_10_fix.patch | 34 ++++++++++++++++++++++++++++++++++ 2 files changed, 40 insertions(+) rename pkgs/{ => gmp}/gmp.yaml (67%) create mode 100644 pkgs/gmp/osx_10_10_fix.patch diff --git a/pkgs/gmp.yaml b/pkgs/gmp/gmp.yaml similarity index 67% rename from pkgs/gmp.yaml rename to pkgs/gmp/gmp.yaml index e57e4dcaf..55a6cbb51 100644 --- a/pkgs/gmp.yaml +++ b/pkgs/gmp/gmp.yaml @@ -8,6 +8,12 @@ sources: url: http://mirrors.kernel.org/gnu/gmp/gmp-6.0.0a.tar.bz2 build_stages: +- name: rpath_patch + before: configure + files: [osx_10_10_fix.patch] + handler: bash + bash: | + patch -up1 < _hashdist/osx_10_10_fix.patch - name: configure extra: ['--enable-cxx'] diff --git a/pkgs/gmp/osx_10_10_fix.patch b/pkgs/gmp/osx_10_10_fix.patch new file mode 100644 index 000000000..fbd4ab765 --- /dev/null +++ b/pkgs/gmp/osx_10_10_fix.patch @@ -0,0 +1,34 @@ +commit 4519b66df0c8a175270c2caf4338c44159e594cb +Author: Ondřej Čertík +Date: Fri May 1 00:08:15 2015 -0600 + + Make configure scripts detect OS X 10.10 properly + + Previously it treated 10.10 as 10.1. + +diff --git a/aclocal.m4 b/aclocal.m4 +index 11222f5..37c1162 100644 +--- a/aclocal.m4 ++++ b/aclocal.m4 +@@ -1066,7 +1066,7 @@ _LT_EOF + case ${MACOSX_DEPLOYMENT_TARGET-10.0},$host in + 10.0,*86*-darwin8*|10.0,*-darwin[[91]]*) + _lt_dar_allow_undefined='${wl}-undefined ${wl}dynamic_lookup' ;; +- 10.[[012]]*) ++ 10.[[012]][[,.]]*) + _lt_dar_allow_undefined='${wl}-flat_namespace ${wl}-undefined ${wl}suppress' ;; + 10.*) + _lt_dar_allow_undefined='${wl}-undefined ${wl}dynamic_lookup' ;; +diff --git a/configure b/configure +index 60c6bd5..b223c18 100755 +--- a/configure ++++ b/configure +@@ -14809,7 +14809,7 @@ $as_echo "$lt_cv_ld_force_load" >&6; } + case ${MACOSX_DEPLOYMENT_TARGET-10.0},$host in + 10.0,*86*-darwin8*|10.0,*-darwin[91]*) + _lt_dar_allow_undefined='${wl}-undefined ${wl}dynamic_lookup' ;; +- 10.[012]*) ++ 10.[012][,.]*) + _lt_dar_allow_undefined='${wl}-flat_namespace ${wl}-undefined ${wl}suppress' ;; + 10.*) + _lt_dar_allow_undefined='${wl}-undefined ${wl}dynamic_lookup' ;; From f6e5331c7c2e9bf2e06c2b71544708e03c0e6000 Mon Sep 17 00:00:00 2001 From: Jimmy Tang Date: Sun, 3 May 2015 09:20:41 +0100 Subject: [PATCH 45/85] terraform: update package to recent stable version Signed-off-by: Jimmy Tang --- pkgs/terraform.yaml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/pkgs/terraform.yaml b/pkgs/terraform.yaml index bf1d5034b..159730fd5 100644 --- a/pkgs/terraform.yaml +++ b/pkgs/terraform.yaml @@ -7,7 +7,7 @@ defaults: relocatable: false sources: -- key: git:751822b53f9a3d08fed3983e7037008c5034f263 +- key: git:cc7f4edd27ae79f08c11aaafa0b9abb2838a0a1e url: https://github.com/hashicorp/terraform.git build_stages: From ef7fc3aaf60799e4e95dd6a7f2556bf5922f3240 Mon Sep 17 00:00:00 2001 From: Min RK Date: Sun, 3 May 2015 08:29:02 -0500 Subject: [PATCH 46/85] add pillow used for proteus parallel plotting --- examples/proteus.Darwin.yaml | 1 + examples/proteus.linux2.yaml | 1 + pkgs/pillow.yaml | 7 +++++++ 3 files changed, 9 insertions(+) create mode 100644 pkgs/pillow.yaml diff --git a/examples/proteus.Darwin.yaml b/examples/proteus.Darwin.yaml index e4e182b4f..1bdaea30e 100644 --- a/examples/proteus.Darwin.yaml +++ b/examples/proteus.Darwin.yaml @@ -44,6 +44,7 @@ packages: debug: false petsc4py: with_conf: true + pillow: pytables: sphinx: superlu: diff --git a/examples/proteus.linux2.yaml b/examples/proteus.linux2.yaml index b4834e6ec..4ae9108cf 100644 --- a/examples/proteus.linux2.yaml +++ b/examples/proteus.linux2.yaml @@ -43,6 +43,7 @@ packages: debug: false petsc4py: with_conf: true + pillow: pytables: sphinx: superlu: diff --git a/pkgs/pillow.yaml b/pkgs/pillow.yaml new file mode 100644 index 000000000..1cc90b543 --- /dev/null +++ b/pkgs/pillow.yaml @@ -0,0 +1,7 @@ +extends: [setuptools_package] +dependencies: + build: [png] + +sources: +- key: tar.gz:q5qmcgfaefplufr7o6bbcdt67tn3cx4k + url: https://pypi.python.org/packages/source/P/Pillow/Pillow-2.8.1.tar.gz From fa4deed873f7317a4526bc258c31e9171ea2bd76 Mon Sep 17 00:00:00 2001 From: Min RK Date: Sat, 2 May 2015 12:18:04 -0500 Subject: [PATCH 47/85] update IPython to 3.1 - add missing dependency on markupsafe to jinja2 - add missing dependency on jsonschema to ipython - update tornado to 4.1 (required for IPython 3) - add backports.ssl_match_hostname (required for tornado 4) --- pkgs/backports-ssl_match_hostname.yaml | 9 +++++++++ pkgs/ipython.yaml | 6 +++--- pkgs/jinja2.yaml | 3 +++ pkgs/tornado.yaml | 7 +++++-- 4 files changed, 20 insertions(+), 5 deletions(-) create mode 100644 pkgs/backports-ssl_match_hostname.yaml diff --git a/pkgs/backports-ssl_match_hostname.yaml b/pkgs/backports-ssl_match_hostname.yaml new file mode 100644 index 000000000..647407c77 --- /dev/null +++ b/pkgs/backports-ssl_match_hostname.yaml @@ -0,0 +1,9 @@ +extends: [setuptools_package] + +dependencies: + build: [] + run: [] + +sources: +- key: tar.gz:a5aq475qtkvxxwxv4ymn4zwd3lee4lr5 + url: https://pypi.python.org/packages/source/b/backports.ssl_match_hostname/backports.ssl_match_hostname-3.4.0.2.tar.gz diff --git a/pkgs/ipython.yaml b/pkgs/ipython.yaml index b4064e3ad..ac849e164 100644 --- a/pkgs/ipython.yaml +++ b/pkgs/ipython.yaml @@ -1,7 +1,7 @@ extends: [distutils_package] dependencies: - run: [pyzmq, tornado, jinja2, pygments, sphinx] + run: [pyzmq, tornado, jinja2, jsonschema, pygments, sphinx] sources: - - url: https://pypi.python.org/packages/source/i/ipython/ipython-2.3.0.tar.gz - key: tar.gz:ul4bv7r6zjoiwlum6twdkump2ad2herr + - url: https://pypi.python.org/packages/source/i/ipython/ipython-3.1.0.tar.gz + key: tar.gz:kmqjfu7qn6bldwgr4xbxbf7k4gp46as7 diff --git a/pkgs/jinja2.yaml b/pkgs/jinja2.yaml index 2ede0bfa0..33850f06f 100644 --- a/pkgs/jinja2.yaml +++ b/pkgs/jinja2.yaml @@ -1,5 +1,8 @@ extends: [setuptools_package] +dependencies: + run: [MarkupSafe] + sources: - key: tar.gz:fyskyxiajw2xcslwubfmb2amnx3oi7uy url: https://pypi.python.org/packages/source/J/Jinja2/Jinja2-2.7.3.tar.gz diff --git a/pkgs/tornado.yaml b/pkgs/tornado.yaml index 0b41a52d6..f15d4836d 100644 --- a/pkgs/tornado.yaml +++ b/pkgs/tornado.yaml @@ -1,5 +1,8 @@ extends: [distutils_package] +dependencies: + run: [backports-ssl_match_hostname] + sources: - - url: https://pypi.python.org/packages/source/t/tornado/tornado-3.1.1.tar.gz - key: tar.gz:grmqjp7eudhf22dsap3yhgdkoph5pxb2 + - url: https://pypi.python.org/packages/source/t/tornado/tornado-4.1.tar.gz + key: tar.gz:tgv5hlw6ixetoojun3ttqttraeqbehbx From 50e27ce93ea3452cdb929e7ffe471d9100144935 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Ond=C5=99ej=20=C4=8Cert=C3=ADk?= Date: Wed, 6 May 2015 11:36:53 -0600 Subject: [PATCH 48/85] Add Ninja --- pkgs/ninja.yaml | 17 +++++++++++++++++ 1 file changed, 17 insertions(+) create mode 100644 pkgs/ninja.yaml diff --git a/pkgs/ninja.yaml b/pkgs/ninja.yaml new file mode 100644 index 000000000..82a6f841e --- /dev/null +++ b/pkgs/ninja.yaml @@ -0,0 +1,17 @@ +extends: [base_package] + +dependencies: + build: [python] + +sources: +- key: git:3309498174411e02e7680ea8b470bb7d1d70bdb8 + url: https://github.com/martine/ninja + +build_stages: +- name: build + after: prologue + handler: bash + bash: | + ./configure.py --bootstrap + mkdir -p $ARTIFACT/bin + cp ninja $ARTIFACT/bin/ From 094956323b4e7e0d8e0461cbfcfb38d7ad1ba79a Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Ond=C5=99ej=20=C4=8Cert=C3=ADk?= Date: Wed, 6 May 2015 12:02:24 -0600 Subject: [PATCH 49/85] Use a release tarball instead of a git repository --- pkgs/ninja.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/pkgs/ninja.yaml b/pkgs/ninja.yaml index 82a6f841e..fe1301f79 100644 --- a/pkgs/ninja.yaml +++ b/pkgs/ninja.yaml @@ -4,8 +4,8 @@ dependencies: build: [python] sources: -- key: git:3309498174411e02e7680ea8b470bb7d1d70bdb8 - url: https://github.com/martine/ninja +- key: tar.gz:psktwwt4e3h42cbiqlr7hywnbd7orbek + url: https://github.com/martine/ninja/archive/v1.5.3.tar.gz build_stages: - name: build From e3b65154d15de65fb081f711b73f0b1d5e370ed6 Mon Sep 17 00:00:00 2001 From: cekees Date: Thu, 7 May 2015 23:18:00 -0500 Subject: [PATCH 50/85] pexpect 3.3 from github zip --- pkgs/pexpect.yaml | 9 +++++++++ 1 file changed, 9 insertions(+) create mode 100644 pkgs/pexpect.yaml diff --git a/pkgs/pexpect.yaml b/pkgs/pexpect.yaml new file mode 100644 index 000000000..45a749880 --- /dev/null +++ b/pkgs/pexpect.yaml @@ -0,0 +1,9 @@ +extends: [setuptools_package] + +dependencies: + build: [] + run: [] + +sources: +- key: zip:lrupabyl3nnmb7kdcric42o77blww42n + url: https://github.com/pexpect/pexpect/archive/3.3.zip From 1d9a7cc30b7fa81889f5705543ff25856bf524d0 Mon Sep 17 00:00:00 2001 From: cekees Date: Thu, 7 May 2015 23:19:25 -0500 Subject: [PATCH 51/85] openjpeg 1.5.1 from dev site, used by grib_api Note: I couldn't get pillow to use this as its jpeg2000 lib --- pkgs/openjpeg.yaml | 24 ++++++++++++++++++++++++ 1 file changed, 24 insertions(+) create mode 100644 pkgs/openjpeg.yaml diff --git a/pkgs/openjpeg.yaml b/pkgs/openjpeg.yaml new file mode 100644 index 000000000..016e77318 --- /dev/null +++ b/pkgs/openjpeg.yaml @@ -0,0 +1,24 @@ +extends: [cmake_package] + +# version 1.5 of openjpeg +# later versions should go in openjpeg2 + +dependencies: + build: [] + +defaults: + relocatable: false + +sources: +- key: tar.gz:nt5tbf5bzduvkajrwf3ghwxze72cob54 + url: https://openjpeg.googlecode.com/files/openjpeg-1.5.1.tar.gz + +build_stages: + +# grib_api, at least, expects not to find this namespaced +- name: fix_include + after: install + handler: bash + bash: | + ln -s ${ARTIFACT}/include/openjpeg-1.5/openjpeg.h ${ARTIFACT}/include/openjpeg.h + From 5aa0a7f25095667665a06c5d97e05cdc23ba5f5e Mon Sep 17 00:00:00 2001 From: cekees Date: Thu, 7 May 2015 23:28:34 -0500 Subject: [PATCH 52/85] gdal Python wrappers --- pkgs/GDAL.yaml | 8 ++++++++ 1 file changed, 8 insertions(+) create mode 100644 pkgs/GDAL.yaml diff --git a/pkgs/GDAL.yaml b/pkgs/GDAL.yaml new file mode 100644 index 000000000..3e6ff5df6 --- /dev/null +++ b/pkgs/GDAL.yaml @@ -0,0 +1,8 @@ +extends: [setuptools_package] + +dependencies: + build: [gdal] + +sources: +- key: tar.gz:zwdszwufyivezzpltv6j6t5vntntdbgb + url: https://pypi.python.org/packages/source/G/GDAL/GDAL-1.11.1.tar.gz From b40f53fd2a8ec30a1e51bd21d41b80a37462b345 Mon Sep 17 00:00:00 2001 From: cekees Date: Thu, 7 May 2015 23:34:22 -0500 Subject: [PATCH 53/85] added pygrib and dependencies --- pkgs/grib_api.yaml | 16 ++++++++++++++++ pkgs/jasper.yaml | 23 +++++++++++++++++++++++ pkgs/pygrib.yaml | 21 +++++++++++++++++++++ pkgs/pyproj.yaml | 8 ++++++++ 4 files changed, 68 insertions(+) create mode 100644 pkgs/grib_api.yaml create mode 100644 pkgs/jasper.yaml create mode 100644 pkgs/pygrib.yaml create mode 100644 pkgs/pyproj.yaml diff --git a/pkgs/grib_api.yaml b/pkgs/grib_api.yaml new file mode 100644 index 000000000..3b5ec924c --- /dev/null +++ b/pkgs/grib_api.yaml @@ -0,0 +1,16 @@ +extends: [autotools_package] + +dependencies: + build: [jasper, openjpeg] + +defaults: + relocatable: false + +sources: +- key: tar.gz:fvfqkqzmtao4yk2zmb6vb3vscsx63q4u + url: https://software.ecmwf.int/wiki/download/attachments/3473437/grib_api-1.12.3.tar.gz + +build_stages: + - name: configure + mode: override + extra: ['--with-jasper=${JASPER_DIR}'] diff --git a/pkgs/jasper.yaml b/pkgs/jasper.yaml new file mode 100644 index 000000000..b9da68a68 --- /dev/null +++ b/pkgs/jasper.yaml @@ -0,0 +1,23 @@ +extends: [autotools_package] + +sources: +- key: zip:noifvhbkzixcovkeeetgn3x4j22e3foq + url: http://www.ece.uvic.ca/~frodo/jasper/software/jasper-1.900.1.zip + +defaults: + relocatable: false + +build_stages: +- name: configure + handler: bash + mode: replace + bash: | + bash configure --prefix=${ARTIFACT} --enable-shared + +- when: platform == 'Cygwin' + name: configure + handler: bash + mode: replace + bash: | + cp /usr/share/automake-1.9/config.guess acaux + bash configure --prefix=${ARTIFACT} --enable-shared diff --git a/pkgs/pygrib.yaml b/pkgs/pygrib.yaml new file mode 100644 index 000000000..b51c460f0 --- /dev/null +++ b/pkgs/pygrib.yaml @@ -0,0 +1,21 @@ +extends: [distutils_package] + +dependencies: + build: [python,jasper,grib_api,pyproj,numpy] + run: [python,pyproj] + +sources: +- key: tar.gz:u4hhkrnmmbciyv2qjzajx4ne3em2l5mb + url: https://pygrib.googlecode.com/files/pygrib-1.9.8.tar.gz + +build_stages: +- name: create-setup.cfg + before: install + handler: bash + bash: | + cat > setup.cfg << EOF + [directories] + grib_api_dir=${GRIB_API_DIR} + jasper_dir=${JASPER_DIR} + EOF + diff --git a/pkgs/pyproj.yaml b/pkgs/pyproj.yaml new file mode 100644 index 000000000..06e095ce9 --- /dev/null +++ b/pkgs/pyproj.yaml @@ -0,0 +1,8 @@ +extends: [distutils_package] +dependencies: + build: [python] + run: [python] + +sources: +- key: tar.gz:sexnq3c6ib7qshiphudwlffpj62wtyt4 + url: https://pyproj.googlecode.com/files/pyproj-1.9.3.tar.gz From 7faf1a0231a94e6f9e2f68436c6409deb5314d0f Mon Sep 17 00:00:00 2001 From: cekees Date: Thu, 7 May 2015 23:43:15 -0500 Subject: [PATCH 54/85] add rdp 0.5 from pypi --- pkgs/rdp.yaml | 9 +++++++++ 1 file changed, 9 insertions(+) create mode 100644 pkgs/rdp.yaml diff --git a/pkgs/rdp.yaml b/pkgs/rdp.yaml new file mode 100644 index 000000000..2e3daabda --- /dev/null +++ b/pkgs/rdp.yaml @@ -0,0 +1,9 @@ +extends: [setuptools_package] +dependencies: + run: [numpy] + +sources: +- key: tar.gz:36tbip4bzxitlhsoaj5d2m4r4gb2lq5k + url: https://pypi.python.org/packages/source/r/rdp/rdp-0.5.tar.gz + + From c3421a1c76a6569013447a42f0ef5a5bcf387427 Mon Sep 17 00:00:00 2001 From: cekees Date: Thu, 7 May 2015 23:46:42 -0500 Subject: [PATCH 55/85] add pydap and dependencies --- pkgs/httplib2.yaml | 5 +++++ pkgs/paver.yaml | 5 +++++ pkgs/pydap.yaml | 9 +++++++++ 3 files changed, 19 insertions(+) create mode 100644 pkgs/httplib2.yaml create mode 100644 pkgs/paver.yaml create mode 100644 pkgs/pydap.yaml diff --git a/pkgs/httplib2.yaml b/pkgs/httplib2.yaml new file mode 100644 index 000000000..2eba81faf --- /dev/null +++ b/pkgs/httplib2.yaml @@ -0,0 +1,5 @@ +extends: [distutils_package] + +sources: +- key: git:0197ec868a4fc638c08358b94200ffd6ddb1bf50 + url: https://github.com/jcgregorio/httplib2 diff --git a/pkgs/paver.yaml b/pkgs/paver.yaml new file mode 100644 index 000000000..5d0685229 --- /dev/null +++ b/pkgs/paver.yaml @@ -0,0 +1,5 @@ +extends: [distutils_package] + +sources: +- key: tar.gz:dzvyiiupdv3zc33kmb5gaofyxuxapefe + url: https://pypi.python.org/packages/source/P/Paver/Paver-1.2.2.tar.gz diff --git a/pkgs/pydap.yaml b/pkgs/pydap.yaml new file mode 100644 index 000000000..703c530f4 --- /dev/null +++ b/pkgs/pydap.yaml @@ -0,0 +1,9 @@ +extends: [namespace_package] + +dependencies: + build: [paver] + run: [httplib2] + +sources: +- key: tar.gz:ggxvshjej45j2n42b4bbousdqlkhh7je + url: https://pypi.python.org/packages/source/P/Pydap/Pydap-3.1.1.tar.gz From 78f695fbca728b7e983f7db5b953144b692088b6 Mon Sep 17 00:00:00 2001 From: cekees Date: Thu, 7 May 2015 23:54:31 -0500 Subject: [PATCH 56/85] added snapshot of pymatbridge and host-matlab pkg --- pkgs/host-matlab.yaml | 2 ++ pkgs/pymatbridge.yaml | 37 +++++++++++++++++++++++++++++++++++++ 2 files changed, 39 insertions(+) create mode 100644 pkgs/host-matlab.yaml create mode 100644 pkgs/pymatbridge.yaml diff --git a/pkgs/host-matlab.yaml b/pkgs/host-matlab.yaml new file mode 100644 index 000000000..7ed5ecbed --- /dev/null +++ b/pkgs/host-matlab.yaml @@ -0,0 +1,2 @@ +when_build_dependency: + - {set: 'MATLAB', value: '{{HOST_MATLAB}}'} diff --git a/pkgs/pymatbridge.yaml b/pkgs/pymatbridge.yaml new file mode 100644 index 000000000..c3231551e --- /dev/null +++ b/pkgs/pymatbridge.yaml @@ -0,0 +1,37 @@ +extends: [distutils_package] +dependencies: + build: [python, ipython, zmq, pyzmq, matlab] + run: [python, ipython, zmq, pyzmq, matlab] + +sources: +- key: git:1c589c39713218f38b9e59e882330b7a1355d8a1 + url: https://github.com/arokem/python-matlab-bridge.git + +build_stages: +- when: platform == 'linux' + name: config + after: setup_dirs + before: install + handler: bash + bash: | + cd messenger/mexa64 + echo "MATLAB_BIN=$(dirname $MATLAB)" > local.cfg + echo "HEADER_PATH=$ZMQ_DIR/include" >> local.cfg + echo "LIB_PATH=$ZMQ_DIR/lib" >> local.cfg + MATLAB=$(dirname $(dirname $MATLAB)) $PYTHON make.py + cp messenger.mexa64 ../../pymatbridge/matlab + cd ../.. + +- when: platform == 'Darwin' + name: config + after: setup_dirs + before: install + handler: bash + bash: | + cd messenger/mexmaci64 + echo "MATLAB_BIN=$(dirname $MATLAB)" > local.cfg + echo "HEADER_PATH=$ZMQ_DIR/include" >> local.cfg + echo "LIB_PATH=$ZMQ_DIR/lib" >> local.cfg + MATLAB=$(dirname $(dirname $MATLAB)) $PYTHON make.py + cp messenger.mexmaci64 ../../pymatbridge/matlab + cd ../.. From 2fb63863d49c1267cce040ca16900eed11625498 Mon Sep 17 00:00:00 2001 From: cekees Date: Thu, 7 May 2015 23:58:50 -0500 Subject: [PATCH 57/85] adding rtree plus libspatialindex dependency --- pkgs/libspatialindex.yaml | 5 +++++ pkgs/rtree.yaml | 17 +++++++++++++++++ 2 files changed, 22 insertions(+) create mode 100644 pkgs/libspatialindex.yaml create mode 100644 pkgs/rtree.yaml diff --git a/pkgs/libspatialindex.yaml b/pkgs/libspatialindex.yaml new file mode 100644 index 000000000..b0dd7dc3a --- /dev/null +++ b/pkgs/libspatialindex.yaml @@ -0,0 +1,5 @@ +extends: [autotools_package] + +sources: +- key: tar.bz2:tzl3a7gnmszjicwee44tqluejetrn4mg + url: http://download.osgeo.org/libspatialindex/spatialindex-src-1.8.1.tar.bz2 diff --git a/pkgs/rtree.yaml b/pkgs/rtree.yaml new file mode 100644 index 000000000..38260b47f --- /dev/null +++ b/pkgs/rtree.yaml @@ -0,0 +1,17 @@ +extends: [setuptools_package] +dependencies: + build: [libspatialindex] + run: [libspatialindex] + +# rtree currently looks for libspatialindex using CDLL, which doesn't know how to do a local search... +# note, this is a decent build-time hack, but will require another hack to make this build relocatable. +build_stages: +- name: patch_library_path + before: install + handler: bash + bash: | + sed -i -e "s|CDLL(lib_name)|CDLL('${LIBSPATIALINDEX_DIR}/lib/'+lib_name)|g" rtree/core.py + +sources: +- key: tar.gz:z6kqsl4g4znjefsflhsu6cbegpon6g6t + url: https://pypi.python.org/packages/source/R/Rtree/Rtree-0.7.0.tar.gz From ad3a06902a8611f15b61ab26463c9e7dd23c35e3 Mon Sep 17 00:00:00 2001 From: cekees Date: Fri, 8 May 2015 00:20:26 -0500 Subject: [PATCH 58/85] added scored mesh tools and zoltan partitioner dep. --- pkgs/scorec.yaml | 36 ++++++++++++++++++++++++++++++++++++ pkgs/zoltan.yaml | 32 ++++++++++++++++++++++++++++++++ 2 files changed, 68 insertions(+) create mode 100644 pkgs/scorec.yaml create mode 100644 pkgs/zoltan.yaml diff --git a/pkgs/scorec.yaml b/pkgs/scorec.yaml new file mode 100644 index 000000000..7e7e8bdba --- /dev/null +++ b/pkgs/scorec.yaml @@ -0,0 +1,36 @@ +extends: [cmake_package] +dependencies: + build: [mpi, parmetis, zoltan, simmetrix] + +sources: +- key: git:ccd43aaab35fbc471f24f20860025985595a3b3a + url: git@bitbucket.org:ibaned/scorec.git + +defaults: + relocatable: false + +build_stages: + +- name: setup_builddir + after: prologue + handler: bash + bash: | + mkdir -p _build + cd _build + +- name: configure + extra: [ + '-DCMAKE_C_COMPILER=${MPICC}', + '-DCMAKE_CXX_COMPILER=${MPICXX}', + '-DENABLE_ZOLTAN=ON', + '-DMETIS_LIBRARY=${PARMETIS_DIR}/lib/libmetis.so', + '-DPARMETIS_LIBRARY=${PARMETIS_DIR}/lib/libparmetis.so', + '-DPARMETIS_INCLUDE_DIR=${PARMETIS_DIR}/include', + '-DZOLTAN_LIBRARY=${ZOLTAN_DIR}/lib/libzoltan.a', + '-DZOLTAN_INCLUDE_DIR=${ZOLTAN_DIR}/include', + '-DBUILD_SHARED_LIBS=True', + '-DSIM_MPI=mpich2', + '-DSIMMETRIX_LIB_DIR=${SIMMETRIX_LIB}', + '-DSIMMETRIX_INCLUDE_DIR=${SIMMETRIX_INCLUDE}' + ] + diff --git a/pkgs/zoltan.yaml b/pkgs/zoltan.yaml new file mode 100644 index 000000000..da583de12 --- /dev/null +++ b/pkgs/zoltan.yaml @@ -0,0 +1,32 @@ +extends: [autotools_package] +dependencies: + build: [mpi, {{build_with}}] + +sources: +- key: tar.gz:lpoumvepxhdtwis3xtz5ebwfldbrrszj + url: http://www.cs.sandia.gov/~kddevin/Zoltan_Distributions/zoltan_distrib_v3.8.tar.gz + +defaults: + #include/Makefile.export.zoltan.macros + relocatable: false + +build_stages: + + - name: setup_builddir + after: prologue + handler: bash + bash: | + mkdir -p _build + cd _build + + - name: setEnv + after: setup_builddir + handler: bash + bash: | + export MPI_DIR=$(dirname $(dirname $MPICC) ) + export LD_LIBRARY_PATH=${MPI_DIR}/lib + + - name: configure + after: setEnv + configure_path: ".." + extra: ['--with-cflags=-fPIC', '--with-cxxflags=-fPIC'] From 799d32cb1b7c0f2c831b67bdb9cc85af0b701207 Mon Sep 17 00:00:00 2001 From: cekees Date: Sat, 9 May 2015 20:21:43 -0500 Subject: [PATCH 59/85] removed empty dependency section --- pkgs/pexpect.yaml | 4 ---- 1 file changed, 4 deletions(-) diff --git a/pkgs/pexpect.yaml b/pkgs/pexpect.yaml index 45a749880..154d67e74 100644 --- a/pkgs/pexpect.yaml +++ b/pkgs/pexpect.yaml @@ -1,9 +1,5 @@ extends: [setuptools_package] -dependencies: - build: [] - run: [] - sources: - key: zip:lrupabyl3nnmb7kdcric42o77blww42n url: https://github.com/pexpect/pexpect/archive/3.3.zip From f17217de2fd2d0115036ab64e61266c7580ef1a7 Mon Sep 17 00:00:00 2001 From: cekees Date: Sat, 9 May 2015 20:25:20 -0500 Subject: [PATCH 60/85] updated source and version of openjpeg --- pkgs/openjpeg.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/pkgs/openjpeg.yaml b/pkgs/openjpeg.yaml index 016e77318..aa9e64596 100644 --- a/pkgs/openjpeg.yaml +++ b/pkgs/openjpeg.yaml @@ -10,8 +10,8 @@ defaults: relocatable: false sources: -- key: tar.gz:nt5tbf5bzduvkajrwf3ghwxze72cob54 - url: https://openjpeg.googlecode.com/files/openjpeg-1.5.1.tar.gz +- key: tar.gz:cizlxakp3cgy5uyuzfhqx7v3appikwky + url: http://sourceforge.net/projects/openjpeg.mirror/files/2.1.0/openjpeg-2.1.0.tar.gz build_stages: From 540201ebd91c14921fdda9a370d713924c9c7f5e Mon Sep 17 00:00:00 2001 From: cekees Date: Sat, 9 May 2015 21:45:40 -0500 Subject: [PATCH 61/85] added options for <#> versions of png(zlib), freetype, and jpeg2K --- pkgs/pillow.yaml | 16 +++++++++++++++- 1 file changed, 15 insertions(+), 1 deletion(-) diff --git a/pkgs/pillow.yaml b/pkgs/pillow.yaml index 1cc90b543..fff105c0a 100644 --- a/pkgs/pillow.yaml +++ b/pkgs/pillow.yaml @@ -1,7 +1,21 @@ extends: [setuptools_package] dependencies: - build: [png] + build: [zlib,png,freetype,openjpeg] sources: - key: tar.gz:q5qmcgfaefplufr7o6bbcdt67tn3cx4k url: https://pypi.python.org/packages/source/P/Pillow/Pillow-2.8.1.tar.gz + +build_stages: +- name: install + mode: replace + handler: bash + bash: | + ${PYTHON} -c 'import setuptools; __file__="setup.py"; exec(open(__file__).read())' \ + build_ext \ + --enable-zlib --enable-freetype --enable-jpeg2000 \ + --include-dirs="${ZLIB_DIR}/include:${PNG_DIR}/include:${FREETYPE_DIR}/include:${OPENJPEG_DIR}/include" \ + --library-dirs="${ZLIB_DIR}/lib:${PNG_DIR}/lib:${FREETYPE_DIR}/lib:${OPENJPEG_DIR}/lib" \ + install \ + --prefix=. --root=${ARTIFACT} \ + --single-version-externally-managed From 72448256d30faec2c6f3dd7dbc5bb1b7e82168f6 Mon Sep 17 00:00:00 2001 From: cekees Date: Sat, 9 May 2015 21:50:35 -0500 Subject: [PATCH 62/85] updated sources to commits on github --- pkgs/pygrib.yaml | 8 ++++---- pkgs/pyproj.yaml | 4 ++-- 2 files changed, 6 insertions(+), 6 deletions(-) diff --git a/pkgs/pygrib.yaml b/pkgs/pygrib.yaml index b51c460f0..bb8eb91f7 100644 --- a/pkgs/pygrib.yaml +++ b/pkgs/pygrib.yaml @@ -1,12 +1,12 @@ extends: [distutils_package] dependencies: - build: [python,jasper,grib_api,pyproj,numpy] - run: [python,pyproj] + build: [python, jasper, grib_api, pyproj, numpy] + run: [python, pyproj] sources: -- key: tar.gz:u4hhkrnmmbciyv2qjzajx4ne3em2l5mb - url: https://pygrib.googlecode.com/files/pygrib-1.9.8.tar.gz +- key: git:db179ce3dccee59bb41ca812c4b02750be74239f + url: https://github.com/jswhit/pygrib.git build_stages: - name: create-setup.cfg diff --git a/pkgs/pyproj.yaml b/pkgs/pyproj.yaml index 06e095ce9..cb49c3cbf 100644 --- a/pkgs/pyproj.yaml +++ b/pkgs/pyproj.yaml @@ -4,5 +4,5 @@ dependencies: run: [python] sources: -- key: tar.gz:sexnq3c6ib7qshiphudwlffpj62wtyt4 - url: https://pyproj.googlecode.com/files/pyproj-1.9.3.tar.gz +- key: git:bb005aca2d933d77b78c0018f8b5d04c471b4608 + url: https://github.com/jswhit/pyproj.git From ba409733d7bfa68935845aea7969812ddf9970f2 Mon Sep 17 00:00:00 2001 From: Min RK Date: Sat, 9 May 2015 21:37:20 -0700 Subject: [PATCH 63/85] remove unnecessary dependencies from backports-ssl_match_hostname --- pkgs/backports-ssl_match_hostname.yaml | 4 ---- 1 file changed, 4 deletions(-) diff --git a/pkgs/backports-ssl_match_hostname.yaml b/pkgs/backports-ssl_match_hostname.yaml index 647407c77..bfdb1b056 100644 --- a/pkgs/backports-ssl_match_hostname.yaml +++ b/pkgs/backports-ssl_match_hostname.yaml @@ -1,9 +1,5 @@ extends: [setuptools_package] -dependencies: - build: [] - run: [] - sources: - key: tar.gz:a5aq475qtkvxxwxv4ymn4zwd3lee4lr5 url: https://pypi.python.org/packages/source/b/backports.ssl_match_hostname/backports.ssl_match_hostname-3.4.0.2.tar.gz From 82c7f22e4cd993808882239c111155234ba88d6a Mon Sep 17 00:00:00 2001 From: cekees Date: Wed, 13 May 2015 13:25:55 -0500 Subject: [PATCH 64/85] updated approach to build_ext options --- base/setuptools_package.yaml | 1 + pkgs/pillow.yaml | 11 ++++------- 2 files changed, 5 insertions(+), 7 deletions(-) diff --git a/base/setuptools_package.yaml b/base/setuptools_package.yaml index 98185993c..5f875fd97 100644 --- a/base/setuptools_package.yaml +++ b/base/setuptools_package.yaml @@ -22,6 +22,7 @@ build_stages: handler: bash bash: | ${PYTHON} -c 'import setuptools; __file__="setup.py"; exec(open(__file__).read())' \ + ${SETUPTOOLS_PACKAGE_EXTRA_OPTIONS} \ install \ --prefix=. --root=${ARTIFACT} \ --single-version-externally-managed diff --git a/pkgs/pillow.yaml b/pkgs/pillow.yaml index fff105c0a..d3a61ea1d 100644 --- a/pkgs/pillow.yaml +++ b/pkgs/pillow.yaml @@ -7,15 +7,12 @@ sources: url: https://pypi.python.org/packages/source/P/Pillow/Pillow-2.8.1.tar.gz build_stages: -- name: install +- name: build_ext_options mode: replace + before: install handler: bash bash: | - ${PYTHON} -c 'import setuptools; __file__="setup.py"; exec(open(__file__).read())' \ - build_ext \ + SETUPTOOLS_PACKAGE_EXTRA_OPTIONS=build_ext \ --enable-zlib --enable-freetype --enable-jpeg2000 \ --include-dirs="${ZLIB_DIR}/include:${PNG_DIR}/include:${FREETYPE_DIR}/include:${OPENJPEG_DIR}/include" \ - --library-dirs="${ZLIB_DIR}/lib:${PNG_DIR}/lib:${FREETYPE_DIR}/lib:${OPENJPEG_DIR}/lib" \ - install \ - --prefix=. --root=${ARTIFACT} \ - --single-version-externally-managed + --library-dirs="${ZLIB_DIR}/lib:${PNG_DIR}/lib:${FREETYPE_DIR}/lib:${OPENJPEG_DIR}/lib" From d5cf3af73d54378c882eb5b3d0bf5ed98e2b8eb0 Mon Sep 17 00:00:00 2001 From: cekees Date: Wed, 13 May 2015 13:31:07 -0500 Subject: [PATCH 65/85] added export --- pkgs/pillow.yaml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/pkgs/pillow.yaml b/pkgs/pillow.yaml index d3a61ea1d..6bcab1eb8 100644 --- a/pkgs/pillow.yaml +++ b/pkgs/pillow.yaml @@ -12,7 +12,7 @@ build_stages: before: install handler: bash bash: | - SETUPTOOLS_PACKAGE_EXTRA_OPTIONS=build_ext \ + export SETUPTOOLS_PACKAGE_EXTRA_OPTIONS=build_ext \ --enable-zlib --enable-freetype --enable-jpeg2000 \ --include-dirs="${ZLIB_DIR}/include:${PNG_DIR}/include:${FREETYPE_DIR}/include:${OPENJPEG_DIR}/include" \ --library-dirs="${ZLIB_DIR}/lib:${PNG_DIR}/lib:${FREETYPE_DIR}/lib:${OPENJPEG_DIR}/lib" From 5377049a6b298d63103be00230c9cc69e9bc2a6d Mon Sep 17 00:00:00 2001 From: cekees Date: Wed, 13 May 2015 13:50:50 -0500 Subject: [PATCH 66/85] fixed options string --- pkgs/pillow.yaml | 5 +---- 1 file changed, 1 insertion(+), 4 deletions(-) diff --git a/pkgs/pillow.yaml b/pkgs/pillow.yaml index 6bcab1eb8..8e07d62b2 100644 --- a/pkgs/pillow.yaml +++ b/pkgs/pillow.yaml @@ -12,7 +12,4 @@ build_stages: before: install handler: bash bash: | - export SETUPTOOLS_PACKAGE_EXTRA_OPTIONS=build_ext \ - --enable-zlib --enable-freetype --enable-jpeg2000 \ - --include-dirs="${ZLIB_DIR}/include:${PNG_DIR}/include:${FREETYPE_DIR}/include:${OPENJPEG_DIR}/include" \ - --library-dirs="${ZLIB_DIR}/lib:${PNG_DIR}/lib:${FREETYPE_DIR}/lib:${OPENJPEG_DIR}/lib" + export SETUPTOOLS_PACKAGE_EXTRA_OPTIONS="build_ext --enable-zlib --enable-freetype --enable-jpeg2000 --include-dirs=${ZLIB_DIR}/include:${PNG_DIR}/include:${FREETYPE_DIR}/include:${OPENJPEG_DIR}/include --library-dirs=${ZLIB_DIR}/lib:${PNG_DIR}/lib:${FREETYPE_DIR}/lib:${OPENJPEG_DIR}/lib" From 3550e37117e914e458e8fafa610b27a74210bdba Mon Sep 17 00:00:00 2001 From: cekees Date: Wed, 13 May 2015 13:52:17 -0500 Subject: [PATCH 67/85] fixed comma spacing --- pkgs/pillow.yaml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/pkgs/pillow.yaml b/pkgs/pillow.yaml index 8e07d62b2..430151538 100644 --- a/pkgs/pillow.yaml +++ b/pkgs/pillow.yaml @@ -1,6 +1,6 @@ extends: [setuptools_package] dependencies: - build: [zlib,png,freetype,openjpeg] + build: [zlib, png, freetype, openjpeg] sources: - key: tar.gz:q5qmcgfaefplufr7o6bbcdt67tn3cx4k From 6e0b16a37c6e5c88902cb20337860beb8a74a3e8 Mon Sep 17 00:00:00 2001 From: cekees Date: Wed, 13 May 2015 18:13:33 -0500 Subject: [PATCH 68/85] applied rpath fixes for linux --- pkgs/openssl/openssl.yaml | 19 +++++++++++++++++-- 1 file changed, 17 insertions(+), 2 deletions(-) diff --git a/pkgs/openssl/openssl.yaml b/pkgs/openssl/openssl.yaml index 58f6d31e6..c2d29f18c 100644 --- a/pkgs/openssl/openssl.yaml +++ b/pkgs/openssl/openssl.yaml @@ -1,7 +1,7 @@ extends: [autotools_package] dependencies: - build: [pkg-config, zlib] + build: [pkg-config, zlib, patchelf] sources: - url: https://www.openssl.org/source/openssl-1.0.1g.tar.gz @@ -23,13 +23,20 @@ build_stages: bash: | patch -p1 < _hashdist/0001-POD-Fix-item-numbering.patch +- when: platform == 'linux' + name: set_flags + before: configure + handler: bash + bash: | + export OPENSSL_EXTRA_FLAGS="-Wl,-rpath=$ARTIFACT/lib -Wl,-rpath=$ZLIB_DIR/lib" + - name: configure after: fix_docs handler: bash mode: replace bash: | #./config --prefix=$ARTIFACT shared zlib-dynamic -I$ZLIB_DIR/include -Wl,-rpath=$ARTIFACT/lib -Wl,-rpath=$ZLIB_DIR/lib - ./config --prefix=$ARTIFACT shared zlib-dynamic -I$ZLIB_DIR/include + ./config --prefix=$ARTIFACT shared zlib-dynamic -I$ZLIB_DIR/include $OPENSSL_EXTRA_FLAGS # parallel build is racy, can fail with "libcrypto.a(cryptlib.o) in archive is not an object" - name: make @@ -47,6 +54,14 @@ build_stages: #./config --prefix=$ARTIFACT shared zlib-dynamic -I$ZLIB_DIR/include -Wl,-rpath=$ARTIFACT/lib -Wl,-rpath=$ZLIB_DIR/lib ./Configure --prefix=$ARTIFACT shared zlib-dynamic -I$ZLIB_DIR/include darwin64-x86_64-cc enable-ec_nistp-64_gcc_128 +- when: platform == 'linux' + name: fix_rpath + after: install + handler: bash + bash: | + $PATCHELF --set-rpath $ARTIFACT/lib:$ZLIB_DIR/lib $ARTIFACT/lib/engines/libgost.so + when_build_dependency: - prepend_path: PKG_CONFIG_PATH value: '${ARTIFACT}/lib/pkgconfig' + From f9a23b5af14ec10ac293bea1422122da1ffac8dc Mon Sep 17 00:00:00 2001 From: cekees Date: Wed, 13 May 2015 18:37:58 -0500 Subject: [PATCH 69/85] updated scorec url and removed simmetrix dep from public stack --- pkgs/scorec.yaml | 8 +++----- 1 file changed, 3 insertions(+), 5 deletions(-) diff --git a/pkgs/scorec.yaml b/pkgs/scorec.yaml index 7e7e8bdba..ab97db06c 100644 --- a/pkgs/scorec.yaml +++ b/pkgs/scorec.yaml @@ -1,10 +1,10 @@ extends: [cmake_package] dependencies: - build: [mpi, parmetis, zoltan, simmetrix] + build: [mpi, parmetis, zoltan] sources: -- key: git:ccd43aaab35fbc471f24f20860025985595a3b3a - url: git@bitbucket.org:ibaned/scorec.git +- key: git:1d2f5438d3dff3f1120649577bb2a05f9ac8c556 + url: https://github.com/SCOREC/core.git defaults: relocatable: false @@ -30,7 +30,5 @@ build_stages: '-DZOLTAN_INCLUDE_DIR=${ZOLTAN_DIR}/include', '-DBUILD_SHARED_LIBS=True', '-DSIM_MPI=mpich2', - '-DSIMMETRIX_LIB_DIR=${SIMMETRIX_LIB}', - '-DSIMMETRIX_INCLUDE_DIR=${SIMMETRIX_INCLUDE}' ] From fcc4165fe006dc60d64471eb849ac2a1fa6840ea Mon Sep 17 00:00:00 2001 From: cekees Date: Thu, 14 May 2015 12:12:41 -0500 Subject: [PATCH 70/85] add -R switch to ode python bindings --- pkgs/ode.yaml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/pkgs/ode.yaml b/pkgs/ode.yaml index bdecfef5d..d93366012 100644 --- a/pkgs/ode.yaml +++ b/pkgs/ode.yaml @@ -24,4 +24,4 @@ build_stages: handler: bash bash: | cd bindings/python - PKG_CONFIG_PATH=../.. ${PYTHON} setup.py install --prefix=${ARTIFACT} + PKG_CONFIG_PATH=../.. ${PYTHON} setup.py build_ext -R ${ARTIFACT}/lib install --prefix=${ARTIFACT} From 09ab7bc3b88fc52952bac71e35be6e6452eae648 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Ond=C5=99ej=20=C4=8Cert=C3=ADk?= Date: Thu, 14 May 2015 14:06:15 -0600 Subject: [PATCH 71/85] CMake: update to 3.2.2 --- pkgs/cmake.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/pkgs/cmake.yaml b/pkgs/cmake.yaml index 4da397372..c7cb7a72f 100644 --- a/pkgs/cmake.yaml +++ b/pkgs/cmake.yaml @@ -1,8 +1,8 @@ extends: [autotools_package] sources: -- key: tar.gz:kcrzjtzo7wnjfxkbctv6fgmurgmezzxg - url: http://www.cmake.org/files/v3.2/cmake-3.2.0-rc1.tar.gz +- key: tar.gz:vxuu43rwaodxivs7flwyqzsbkrbuit5x + url: http://www.cmake.org/files/v3.2/cmake-3.2.2.tar.gz build_stages: - name: configure From 835f05b0ac7c2717f007f0ffef1ecc2b96616888 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Ond=C5=99ej=20=C4=8Cert=C3=ADk?= Date: Thu, 14 May 2015 14:07:20 -0600 Subject: [PATCH 72/85] CMake: use our zlib, bzip2 and curl This way CMake does not build its own versions, but rather uses Hashstack versions. We also made sure the proper RPATH will be used in the `cmake` executable via the CMAKE_PREFIX_PATH option. Only three other libraries are still build as part of CMake: expat, jsoncpp, libarchive, so we commented out options that disable them for now. As a bonus, this patch also fixes a problem on OSX 10.10 where the curl component of CMake fails to build with gcc (we now use Hashstack's version that builds). --- pkgs/cmake.yaml | 14 +++++++++++++- 1 file changed, 13 insertions(+), 1 deletion(-) diff --git a/pkgs/cmake.yaml b/pkgs/cmake.yaml index c7cb7a72f..f948e7899 100644 --- a/pkgs/cmake.yaml +++ b/pkgs/cmake.yaml @@ -1,12 +1,24 @@ extends: [autotools_package] +dependencies: + build: [zlib, bzip2, curl] + sources: - key: tar.gz:vxuu43rwaodxivs7flwyqzsbkrbuit5x url: http://www.cmake.org/files/v3.2/cmake-3.2.2.tar.gz build_stages: - name: configure - extra: ['--parallel=${HASHDIST_CPU_COUNT}'] + extra: ['--parallel=${HASHDIST_CPU_COUNT}', + '--system-bzip2', + '--system-curl', + #'--system-expat', + #'--system-jsoncpp', + #'--system-libarchive', + '--system-zlib', + '--', + '-DCMAKE_PREFIX_PATH=${CURL_DIR}/lib;${ZLIB_DIR}/lib;${BZIP2_DIR}/lib', + ] when_build_dependency: - set: CMAKE From 34c798afd4388f7c0dd356b06971b36a43a26fc8 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Ond=C5=99ej=20=C4=8Cert=C3=ADk?= Date: Thu, 14 May 2015 14:12:22 -0600 Subject: [PATCH 73/85] CMake: set OSX specific variables properly On OSX 10.10, one gets errors of the type: [cmake] CMake Error at Modules/Platform/Darwin.cmake:76 (message): [cmake] CMAKE_OSX_DEPLOYMENT_TARGET is '10.10' but CMAKE_OSX_SYSROOT: [cmake] [cmake] "" [cmake] [cmake] is not set to a MacOSX SDK with a recognized version. Either set [cmake] CMAKE_OSX_SYSROOT to a valid SDK or set CMAKE_OSX_DEPLOYMENT_TARGET to [cmake] empty. [cmake] Call Stack (most recent call first): [cmake] Modules/CMakeSystemSpecificInformation.cmake:36 (include) [cmake] CMakeLists.txt:16 (project) Unless the CMAKE_OSX_DEPLOYMENT_TARGET is set to empty. We set it to empty by unsetting the MACOSX_DEPLOYMENT_TARGET environment variable. Similar problem happens when cmake is used to build other packages. There the fix is to unset the CMAKE_OSX_DEPLOYMENT_TARGET variable on the command line. --- base/cmake_package.py | 3 +++ pkgs/cmake.yaml | 8 ++++++++ 2 files changed, 11 insertions(+) diff --git a/base/cmake_package.py b/base/cmake_package.py index ad83dfbfe..853c85b95 100644 --- a/base/cmake_package.py +++ b/base/cmake_package.py @@ -34,6 +34,9 @@ def configure(ctx, stage_args): else: conf_lines.append('-DCMAKE_BUILD_TYPE:STRING=Release') + if ctx.parameters['platform'] == 'Darwin': + conf_lines.append('-DCMAKE_OSX_DEPLOYMENT_TARGET:STRING=""') + #cmake needs to be given all the dependency dirs as prefix paths #so that we search the hashdist directories before the system directories #CMake doesn't use the CPPFLAGS implicitly to find libraries diff --git a/pkgs/cmake.yaml b/pkgs/cmake.yaml index f948e7899..135252f12 100644 --- a/pkgs/cmake.yaml +++ b/pkgs/cmake.yaml @@ -8,6 +8,14 @@ sources: url: http://www.cmake.org/files/v3.2/cmake-3.2.2.tar.gz build_stages: +- when: platform == 'Darwin' + name: fix_deployment_target + after: prologue + before: configure + handler: bash + bash: | + unset MACOSX_DEPLOYMENT_TARGET + - name: configure extra: ['--parallel=${HASHDIST_CPU_COUNT}', '--system-bzip2', From aa3c2f706cb83bf5f41f5c28320559a08896d6fc Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Ond=C5=99ej=20=C4=8Cert=C3=ADk?= Date: Thu, 14 May 2015 17:03:29 -0600 Subject: [PATCH 74/85] CMake: fix the $ORIGIN problem ld does not seem to follow the $ORIGIN in recursive dependencies properly. The workaround is to specify the recursive dependencies (in this case openssl, libidn) explicitly, then the rpath is properly constructed and things work at link time. Also add full include paths to the dependencies. --- pkgs/cmake.yaml | 5 ++++- 1 file changed, 4 insertions(+), 1 deletion(-) diff --git a/pkgs/cmake.yaml b/pkgs/cmake.yaml index 135252f12..04052e0e2 100644 --- a/pkgs/cmake.yaml +++ b/pkgs/cmake.yaml @@ -1,7 +1,7 @@ extends: [autotools_package] dependencies: - build: [zlib, bzip2, curl] + build: [zlib, bzip2, curl, openssl, libidn] sources: - key: tar.gz:vxuu43rwaodxivs7flwyqzsbkrbuit5x @@ -26,6 +26,9 @@ build_stages: '--system-zlib', '--', '-DCMAKE_PREFIX_PATH=${CURL_DIR}/lib;${ZLIB_DIR}/lib;${BZIP2_DIR}/lib', + '-DCURL_INCLUDE_DIR=${CURL_DIR}/include', + '-DZLIB_INCLUDE_DIR=${ZLIB_DIR}/include', + '-DBZIP2_INCLUDE_DIR=${BZIP2_DIR}/include', ] when_build_dependency: From 9aed1265a8886a5e514ba78813953fd2c94e16d5 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Ond=C5=99ej=20=C4=8Cert=C3=ADk?= Date: Thu, 14 May 2015 17:16:41 -0600 Subject: [PATCH 75/85] CMake: use our own expat library --- pkgs/cmake.yaml | 7 ++++--- 1 file changed, 4 insertions(+), 3 deletions(-) diff --git a/pkgs/cmake.yaml b/pkgs/cmake.yaml index 04052e0e2..01ae25dec 100644 --- a/pkgs/cmake.yaml +++ b/pkgs/cmake.yaml @@ -1,7 +1,7 @@ extends: [autotools_package] dependencies: - build: [zlib, bzip2, curl, openssl, libidn] + build: [zlib, bzip2, curl, openssl, libidn, expat] sources: - key: tar.gz:vxuu43rwaodxivs7flwyqzsbkrbuit5x @@ -20,15 +20,16 @@ build_stages: extra: ['--parallel=${HASHDIST_CPU_COUNT}', '--system-bzip2', '--system-curl', - #'--system-expat', + '--system-expat', #'--system-jsoncpp', #'--system-libarchive', '--system-zlib', '--', - '-DCMAKE_PREFIX_PATH=${CURL_DIR}/lib;${ZLIB_DIR}/lib;${BZIP2_DIR}/lib', + '-DCMAKE_PREFIX_PATH=${CURL_DIR}/lib;${ZLIB_DIR}/lib;${BZIP2_DIR}/lib;${EXPAT_DIR}/lib', '-DCURL_INCLUDE_DIR=${CURL_DIR}/include', '-DZLIB_INCLUDE_DIR=${ZLIB_DIR}/include', '-DBZIP2_INCLUDE_DIR=${BZIP2_DIR}/include', + '-DEXPAT_INCLUDE_DIR=${EXPAT_DIR}/include', ] when_build_dependency: From 6fff3ace320030c0fa8819cb81b537bb11e2df97 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Ond=C5=99ej=20=C4=8Cert=C3=ADk?= Date: Fri, 1 May 2015 11:30:45 -0600 Subject: [PATCH 76/85] gcc: install fixed dispatch/object.h header file Fixes #742. --- pkgs/gcc/gcc.yaml | 8 ++++++++ 1 file changed, 8 insertions(+) diff --git a/pkgs/gcc/gcc.yaml b/pkgs/gcc/gcc.yaml index 8710ab881..dd87891a9 100644 --- a/pkgs/gcc/gcc.yaml +++ b/pkgs/gcc/gcc.yaml @@ -22,6 +22,14 @@ build_stages: patch -up1 < _hashdist/rpath.patch sed -i "s|@@ARTIFACT@@|${ARTIFACT}|g" gcc/config/i386/gnu-user.h gcc/config/i386/gnu-user64.h + - when: platform == 'Darwin' + name: fix_object_h + before: configure + handler: bash + bash: | + mkdir -p "$ARTIFACT/include/dispatch" + sed 's+typedef void (\^dispatch_block_t)(void)+typedef void* dispatch_block_t+' /usr/include/dispatch/object.h > "$ARTIFACT/include/dispatch/object.h" + - name: link_lib64_to_lib after: install handler: bash From bf2217371d561578861b5b8218c9cba8dfc65dd4 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Ond=C5=99ej=20=C4=8Cert=C3=ADk?= Date: Fri, 15 May 2015 14:16:03 -0600 Subject: [PATCH 77/85] gcc: check that the file exists before patching it --- pkgs/gcc/gcc.yaml | 6 ++++-- 1 file changed, 4 insertions(+), 2 deletions(-) diff --git a/pkgs/gcc/gcc.yaml b/pkgs/gcc/gcc.yaml index dd87891a9..d6e103935 100644 --- a/pkgs/gcc/gcc.yaml +++ b/pkgs/gcc/gcc.yaml @@ -27,8 +27,10 @@ build_stages: before: configure handler: bash bash: | - mkdir -p "$ARTIFACT/include/dispatch" - sed 's+typedef void (\^dispatch_block_t)(void)+typedef void* dispatch_block_t+' /usr/include/dispatch/object.h > "$ARTIFACT/include/dispatch/object.h" + if [ -f /usr/include/dispatch/object.h ]; then + mkdir -p "$ARTIFACT/include/dispatch" + sed 's+typedef void (\^dispatch_block_t)(void)+typedef void* dispatch_block_t+' /usr/include/dispatch/object.h > "$ARTIFACT/include/dispatch/object.h" + fi - name: link_lib64_to_lib after: install From 29d8a92a98f0a9415b626fd82f274ca9e4f2005f Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Ond=C5=99ej=20=C4=8Cert=C3=ADk?= Date: Fri, 1 May 2015 12:04:32 -0600 Subject: [PATCH 78/85] Update git to 2.4.0 --- pkgs/git.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/pkgs/git.yaml b/pkgs/git.yaml index 4e7be7d35..6854f4f7e 100644 --- a/pkgs/git.yaml +++ b/pkgs/git.yaml @@ -4,8 +4,8 @@ dependencies: build: [curl, pcre, openssl, libiconv, gettext, expat, zlib, perl] sources: -- key: tar.gz:xix6qfhhbgs5b4bu5pucba74477o2cez - url: http://www.kernel.org/pub/software/scm/git/git-2.3.0.tar.gz +- key: tar.gz:2wghm2ua3bvf4gcgybghiymotc76yfmh + url: https://www.kernel.org/pub/software/scm/git/git-2.4.0.tar.gz defaults: # /bin/git contains hard-coded path From 293863d99c321a3e5164a0fd1ba14d19c1547279 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Ond=C5=99ej=20=C4=8Cert=C3=ADk?= Date: Fri, 1 May 2015 12:54:32 -0600 Subject: [PATCH 79/85] git: allow to set NO_APPLE_COMMON_CRYPTO=1 This fixes a build failure on OS X 10.10. Unfortunately, this disabled https access, so it is only enabled if 'disable_crypto' parameter is 'true'. --- pkgs/git.yaml | 8 ++++++++ 1 file changed, 8 insertions(+) diff --git a/pkgs/git.yaml b/pkgs/git.yaml index 4e7be7d35..c230a4fac 100644 --- a/pkgs/git.yaml +++ b/pkgs/git.yaml @@ -10,6 +10,7 @@ sources: defaults: # /bin/git contains hard-coded path relocatable: false + disable_crypto: false build_stages: @@ -19,6 +20,13 @@ build_stages: bash: | export PERL_PATH="/usr/bin/env perl" +- when: platform == 'Darwin' and disable_crypto + name: fix_crypto_compile_failure + before: configure + handler: bash + bash: | + export NO_APPLE_COMMON_CRYPTO=1 + - name: configure mode: override extra: ['--with-libpcre=${PCRE_DIR}', '--with-zlib=${ZLIB_DIR}', '--with-iconv=${LIBICONV_DIR}', '--with-expat=${EXPAT_DIR}', '--with-curl=${CURL_DIR}'] From ed3d5254544720cab7b371f4714d37596f329c34 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Ond=C5=99ej=20=C4=8Cert=C3=ADk?= Date: Fri, 15 May 2015 14:39:02 -0600 Subject: [PATCH 80/85] Rename GDAL Fixes #770. We should make sure that all files in our git repository are unique on case insensitive filesystems. --- pkgs/{GDAL.yaml => python-gdal.yaml} | 0 1 file changed, 0 insertions(+), 0 deletions(-) rename pkgs/{GDAL.yaml => python-gdal.yaml} (100%) diff --git a/pkgs/GDAL.yaml b/pkgs/python-gdal.yaml similarity index 100% rename from pkgs/GDAL.yaml rename to pkgs/python-gdal.yaml From 9c993f59034f0663d590c9e8391a9f41abe3b613 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Ond=C5=99ej=20=C4=8Cert=C3=ADk?= Date: Fri, 15 May 2015 15:11:47 -0600 Subject: [PATCH 81/85] Add hd_base example profile for OS X --- examples/hd_base.Darwin.yaml | 41 ++++++++++++++++++++++++++++++++++++ 1 file changed, 41 insertions(+) create mode 100644 examples/hd_base.Darwin.yaml diff --git a/examples/hd_base.Darwin.yaml b/examples/hd_base.Darwin.yaml new file mode 100644 index 000000000..a72dc3ab4 --- /dev/null +++ b/examples/hd_base.Darwin.yaml @@ -0,0 +1,41 @@ +# This profile builds with the default clang compiler on Mac OS X 10.10 +# Yosemite. In particular it builds gcc (g++, gcc, gfortran). This profile can +# then be used as a base for building the rest of Hashstack. + +extends: + - file: config.yaml + +parameters: + platform: Darwin + fortran: false + PATH: /usr/bin:/bin:/usr/sbin:/sbin + PROLOGUE: | + export MACOSX_DEPLOYMENT_TARGET=$(sw_vers -productVersion | sed -E "s/([0-9]+\.[0-9]+).*/\1/") + +packages: + + launcher: + blas: + use: host-osx-framework-accelerate + lapack: + use: host-osx-framework-accelerate + mpi: + use: mpich + python: + link: shared + swig: + build_with: | + perl + ipython: + nose: + numpy: + sphinx: + sympy: + gmp: + matplotlib: + doxygen: + breathe: + gcc: + git: + perl: + pyliblzma: From 337d25c774fd992a0be3aaa17eefc25d683688cd Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Ond=C5=99ej=20=C4=8Cert=C3=ADk?= Date: Fri, 15 May 2015 16:16:35 -0600 Subject: [PATCH 82/85] Update ncurses to 5.9-20141206 Upstream only distributes the 5.9 version plus the 20141206 patch in a form that is not easy to apply, so I pushed it into a git repository. The clang-fix.patch, even though it applies, actually makes clang fail to build it and removing the patch fixes it. The package now builds on OS X 10.10 both with the native clang as well as with Hashstack's gcc. --- pkgs/ncurses/clang-fix.patch | 42 ------------------------------------ pkgs/ncurses/ncurses.yaml | 11 ++-------- 2 files changed, 2 insertions(+), 51 deletions(-) delete mode 100644 pkgs/ncurses/clang-fix.patch diff --git a/pkgs/ncurses/clang-fix.patch b/pkgs/ncurses/clang-fix.patch deleted file mode 100644 index ce33049bf..000000000 --- a/pkgs/ncurses/clang-fix.patch +++ /dev/null @@ -1,42 +0,0 @@ -diff -ruNp ncurses-5.8.orig/c++/cursesf.h ncurses-5.8/c++/cursesf.h ---- ncurses-5.8.orig/c++/cursesf.h 2005-08-13 21:08:24.000000000 +0300 -+++ ncurses-5.8/c++/cursesf.h 2011-04-03 18:29:29.000000000 +0300 -@@ -681,7 +681,7 @@ public: - const T* p_UserData = STATIC_CAST(T*)(0), - bool with_frame=FALSE, - bool autoDelete_Fields=FALSE) -- : NCursesForm (Fields, with_frame, autoDelete_Fields) { -+ : NCursesForm (&Fields, with_frame, autoDelete_Fields) { - if (form) - set_user (const_cast(p_UserData)); - }; -@@ -694,7 +694,7 @@ public: - const T* p_UserData = STATIC_CAST(T*)(0), - bool with_frame=FALSE, - bool autoDelete_Fields=FALSE) -- : NCursesForm (Fields, nlines, ncols, begin_y, begin_x, -+ : NCursesForm (&Fields, nlines, ncols, begin_y, begin_x, - with_frame, autoDelete_Fields) { - if (form) - set_user (const_cast(p_UserData)); -diff -ruNp ncurses-5.8.orig/c++/cursesm.h ncurses-5.8/c++/cursesm.h ---- ncurses-5.8.orig/c++/cursesm.h 2005-08-13 21:10:36.000000000 +0300 -+++ ncurses-5.8/c++/cursesm.h 2011-04-03 18:31:42.000000000 +0300 -@@ -639,7 +639,7 @@ public: - const T* p_UserData = STATIC_CAST(T*)(0), - bool with_frame=FALSE, - bool autoDelete_Items=FALSE) -- : NCursesMenu (Items, with_frame, autoDelete_Items) { -+ : NCursesMenu (&Items, with_frame, autoDelete_Items) { - if (menu) - set_user (const_cast(p_UserData)); - }; -@@ -651,7 +651,7 @@ public: - int begin_x = 0, - const T* p_UserData = STATIC_CAST(T*)(0), - bool with_frame=FALSE) -- : NCursesMenu (Items, nlines, ncols, begin_y, begin_x, with_frame) { -+ : NCursesMenu (&Items, nlines, ncols, begin_y, begin_x, with_frame) { - if (menu) - set_user (const_cast(p_UserData)); - }; diff --git a/pkgs/ncurses/ncurses.yaml b/pkgs/ncurses/ncurses.yaml index f1ad68afd..55419d3f0 100644 --- a/pkgs/ncurses/ncurses.yaml +++ b/pkgs/ncurses/ncurses.yaml @@ -1,20 +1,13 @@ extends: [autotools_package] sources: - - url: http://ftp.gnu.org/pub/gnu/ncurses/ncurses-5.9.tar.gz - key: tar.gz:sbdctd5uiazezhkbgxwou6dz77wykrw5 + - key: git:2031c7bde2dfb2189b9c724946f19c089596eac4 + url: https://github.com/certik/ncurses defaults: relocatable: false build_stages: - - name: patch - before: configure - files: [clang-fix.patch] - handler: bash - bash: | - patch -up1 < _hashdist/clang-fix.patch - - name: configure mode: override extra: ['--with-shared', '--without-profile', '--without-debug', From f8b50d103b598b17eb2df5aad360337dfc8244fc Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Ond=C5=99ej=20=C4=8Cert=C3=ADk?= Date: Sat, 16 May 2015 09:17:53 -0600 Subject: [PATCH 83/85] Move the repository to hashdist/pkg-ncurses --- pkgs/ncurses/ncurses.yaml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/pkgs/ncurses/ncurses.yaml b/pkgs/ncurses/ncurses.yaml index 55419d3f0..8ab8292a1 100644 --- a/pkgs/ncurses/ncurses.yaml +++ b/pkgs/ncurses/ncurses.yaml @@ -2,7 +2,7 @@ extends: [autotools_package] sources: - key: git:2031c7bde2dfb2189b9c724946f19c089596eac4 - url: https://github.com/certik/ncurses + url: https://github.com/hashdist/pkg-ncurses defaults: relocatable: false From 13268bb7eb2b7aa4d273d654c4f71f8ea56689c3 Mon Sep 17 00:00:00 2001 From: Johannes Ring Date: Tue, 19 May 2015 14:58:55 +0200 Subject: [PATCH 84/85] boost: run patchelf on the libraries, not on the symlinks (fixes issue #781) --- pkgs/boost/boost.yaml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/pkgs/boost/boost.yaml b/pkgs/boost/boost.yaml index 64f50e8dd..ae613b6f9 100644 --- a/pkgs/boost/boost.yaml +++ b/pkgs/boost/boost.yaml @@ -91,7 +91,7 @@ build_stages: after: bjam handler: bash bash: | - for lib in ${ARTIFACT}/lib/*.so; do + for lib in ${ARTIFACT}/lib/*.so.*; do ${PATCHELF} --set-rpath ${ARTIFACT}/lib:${BZIP2_DIR}/lib:${ZLIB_DIR}/lib ${lib} done From 90bcb1c5882349a5fdb4d478fe510d6a575e327d Mon Sep 17 00:00:00 2001 From: Jaroslav Hron Date: Wed, 20 May 2015 22:07:01 +0200 Subject: [PATCH 85/85] update source URL for mesa 10.2.4 --- pkgs/mesa.yaml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/pkgs/mesa.yaml b/pkgs/mesa.yaml index 22ec5a051..fc14140be 100644 --- a/pkgs/mesa.yaml +++ b/pkgs/mesa.yaml @@ -6,7 +6,7 @@ dependencies: sources: - key: tar.bz2:a2rdiese5oc4fa7vt5ybmhqg33iqn6bv - url: ftp://ftp.freedesktop.org/pub/mesa/10.2.4/MesaLib-10.2.4.tar.bz2 + url: ftp://ftp.freedesktop.org/pub/mesa/older-versions/10.x/10.2.4/MesaLib-10.2.4.tar.bz2 build_stages: # Needed because of https://bugs.freedesktop.org/show_bug.cgi?id=63615