From 32907611fb7efb188bbe47f159dd86a2114239ae Mon Sep 17 00:00:00 2001 From: Cornelius Roemer Date: Wed, 10 Jul 2024 22:30:23 +0200 Subject: [PATCH 1/8] Build raxml for osx-arm64 --- recipes/raxml/meta.yaml | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/recipes/raxml/meta.yaml b/recipes/raxml/meta.yaml index b98b2551cc414..7f23f373d4038 100644 --- a/recipes/raxml/meta.yaml +++ b/recipes/raxml/meta.yaml @@ -3,7 +3,7 @@ package: version: "8.2.13" build: - number: 1 + number: 2 run_exports: - {{ pin_subpackage('raxml', max_pin="x") }} @@ -33,6 +33,7 @@ about: extra: additional-platforms: - linux-aarch64 + - osx-arm64 identifiers: - biotools:raxml - doi:10.1093/bioinformatics/btu033 From 48ba84736939744d834a7ac921e3c2b28b5b7531 Mon Sep 17 00:00:00 2001 From: Cornelius Roemer Date: Thu, 11 Jul 2024 00:30:36 +0200 Subject: [PATCH 2/8] Disable failing arm64 builds --- recipes/raxml/build.sh | 27 +++++++++++++++++++-------- recipes/raxml/meta.yaml | 10 +++++----- 2 files changed, 24 insertions(+), 13 deletions(-) diff --git a/recipes/raxml/build.sh b/recipes/raxml/build.sh index 6dd8706245751..a6ea978219f76 100644 --- a/recipes/raxml/build.sh +++ b/recipes/raxml/build.sh @@ -1,19 +1,30 @@ #!/bin/bash -case `uname` in -Darwin) SUF=.mac;; -Linux) SUF=.gcc;; -*) echo "Unknown architecture"; exit 1;; +set -euxo pipefail + +PREFIX=prefix + +case $(uname) in +Darwin) SUF=.mac ;; +Linux) SUF=.gcc ;; +*) + echo "Unknown architecture" + exit 1 + ;; esac ARCH=$(uname -m) -mkdir -p $PREFIX/bin +mkdir -p "$PREFIX"/bin for PTHREADS in "" .PTHREADS; do for OPT in "" .SSE3 .AVX2; do - if [ "${ARCH}" == "aarch64" -a "${OPT}" == ".AVX2" ]; then + if [[ "${ARCH}" == "aarch64" && "${OPT}" == ".AVX2" ]]; then + continue + fi + + if [[ ${ARCH} == "arm64" && ("${OPT}" == ".AVX2" || "${OPT}" == ".SSE3" || "${PTHREADS}" == ".PTHREADS") ]]; then continue fi @@ -24,8 +35,8 @@ for PTHREADS in "" .PTHREADS; do else MAKEFILE=${MAKEFILE}.gcc fi - make -f ${MAKEFILE} CC=$CC - mv raxmlHPC* $PREFIX/bin + make -f ${MAKEFILE} + mv raxmlHPC* "$PREFIX"/bin make -f ${MAKEFILE} clean done done diff --git a/recipes/raxml/meta.yaml b/recipes/raxml/meta.yaml index 7f23f373d4038..b7e8de64fbd89 100644 --- a/recipes/raxml/meta.yaml +++ b/recipes/raxml/meta.yaml @@ -19,11 +19,11 @@ requirements: test: commands: - raxmlHPC -h > /dev/null - - raxmlHPC-PTHREADS -h > /dev/null - - raxmlHPC-SSE3 -h > /dev/null - - raxmlHPC-PTHREADS-SSE3 -h > /dev/null - - 'raxmlHPC-AVX2 -h > /dev/null' # [not aarch64] - - 'raxmlHPC-PTHREADS-AVX2 -h > /dev/null' # [not aarch64] + - raxmlHPC-PTHREADS -h > /dev/null # [not arm64] + - raxmlHPC-SSE3 -h > /dev/null # [not arm64] + - raxmlHPC-PTHREADS-SSE3 -h > /dev/null # [not arm64] + - 'raxmlHPC-AVX2 -h > /dev/null' # [not (aarch64 or arm64)] + - 'raxmlHPC-PTHREADS-AVX2 -h > /dev/null' # [not (aarch64 or arm64)] about: home: http://sco.h-its.org/exelixis/web/software/raxml/index.html From 62891a72e8ab520496a1baa8b50d1860cebb4d77 Mon Sep 17 00:00:00 2001 From: Cornelius Roemer Date: Thu, 11 Jul 2024 00:45:50 +0200 Subject: [PATCH 3/8] f --- recipes/raxml/build.sh | 4 +--- 1 file changed, 1 insertion(+), 3 deletions(-) diff --git a/recipes/raxml/build.sh b/recipes/raxml/build.sh index a6ea978219f76..ca76f01c78408 100644 --- a/recipes/raxml/build.sh +++ b/recipes/raxml/build.sh @@ -1,8 +1,6 @@ #!/bin/bash -set -euxo pipefail - -PREFIX=prefix +set -exo pipefail case $(uname) in Darwin) SUF=.mac ;; From afafb7ca5ed9bf66de7743282dfeef547b9b202c Mon Sep 17 00:00:00 2001 From: Cornelius Roemer Date: Thu, 11 Jul 2024 01:02:07 +0200 Subject: [PATCH 4/8] Apply patch to not overwrite CC env variable --- recipes/raxml/meta.yaml | 2 + recipes/raxml/patch | 179 ++++++++++++++++++++++++++++++++++++++++ 2 files changed, 181 insertions(+) create mode 100644 recipes/raxml/patch diff --git a/recipes/raxml/meta.yaml b/recipes/raxml/meta.yaml index b7e8de64fbd89..72587490ca912 100644 --- a/recipes/raxml/meta.yaml +++ b/recipes/raxml/meta.yaml @@ -10,6 +10,8 @@ build: source: url: https://github.com/stamatak/standard-RAxML/archive/refs/tags/v8.2.13.tar.gz sha256: 28e500793324bd7d330b396ef27ea49c9186fa5e1edb3d5439036dc6c33e6067 + patches: + - patch requirements: build: diff --git a/recipes/raxml/patch b/recipes/raxml/patch new file mode 100644 index 0000000000000..4b62d04b52139 --- /dev/null +++ b/recipes/raxml/patch @@ -0,0 +1,179 @@ +diff --git a/Makefile.SSE3.PTHREADS.mac b/Makefile.SSE3.PTHREADS.mac +--- a/Makefile.SSE3.PTHREADS.mac ++++ b/Makefile.SSE3.PTHREADS.mac +@@ -1,7 +1,6 @@ + # Makefile for SSE3 with Pthreads on Mac + # + +-CC = clang + CFLAGS = -O3 -msse3 -pthread + LDFLAGS = -pthread + TARGET = my_program + +diff --git a/Makefile.AVX2.mac b/Makefile.AVX2.mac +--- a/Makefile.AVX2.mac ++++ b/Makefile.AVX2.mac +@@ -1,7 +1,6 @@ + # Makefile for AVX2 on Mac + # + +-CC = clang + CFLAGS = -O3 -mavx2 + LDFLAGS = + TARGET = my_program + +diff --git a/Makefile.AVX.mac b/Makefile.AVX.mac +--- a/Makefile.AVX.mac ++++ b/Makefile.AVX.mac +@@ -1,7 +1,6 @@ + # Makefile for AVX on Mac + # + +-CC = clang + CFLAGS = -O3 -mavx + LDFLAGS = + TARGET = my_program + +diff --git a/Makefile.PTHREADS.mac b/Makefile.PTHREADS.mac +--- a/Makefile.PTHREADS.mac ++++ b/Makefile.PTHREADS.mac +@@ -1,7 +1,6 @@ + # Makefile for Pthreads on Mac + # + +-CC = clang + CFLAGS = -O3 -pthread + LDFLAGS = -pthread + TARGET = my_program + +diff --git a/Makefile.SSE3.mac b/Makefile.SSE3.mac +--- a/Makefile.SSE3.mac ++++ b/Makefile.SSE3.mac +@@ -1,7 +1,6 @@ + # Makefile for SSE3 on Mac + # + +-CC = clang + CFLAGS = -O3 -msse3 + LDFLAGS = + TARGET = my_program + +diff --git a/Makefile.AVX2.PTHREADS.mac b/Makefile.AVX2.PTHREADS.mac +--- a/Makefile.AVX2.PTHREADS.mac ++++ b/Makefile.AVX2.PTHREADS.mac +@@ -1,7 +1,6 @@ + # Makefile for AVX2 with Pthreads on Mac + # + +-CC = clang + CFLAGS = -O3 -mavx2 -pthread + LDFLAGS = -pthread + TARGET = my_program + +diff --git a/Makefile.AVX.PTHREADS.mac b/Makefile.AVX.PTHREADS.mac +--- a/Makefile.AVX.PTHREADS.mac ++++ b/Makefile.AVX.PTHREADS.mac +@@ -1,7 +1,6 @@ + # Makefile for AVX with Pthreads on Mac + # + +-CC = clang + CFLAGS = -O3 -mavx -pthread + LDFLAGS = -pthread + TARGET = my_program + +diff --git a/Makefile.gcc b/Makefile.gcc +--- a/Makefile.gcc ++++ b/Makefile.gcc +@@ -1,7 +1,6 @@ + # Makefile for GCC + # + +-CC = gcc + CFLAGS = -O3 + LDFLAGS = + TARGET = my_program + +diff --git a/Makefile.PTHREADS.gcc b/Makefile.PTHREADS.gcc +--- a/Makefile.PTHREADS.gcc ++++ b/Makefile.PTHREADS.gcc +@@ -1,7 +1,6 @@ + # Makefile for Pthreads with GCC + # + +-CC = gcc + CFLAGS = -O3 -pthread + LDFLAGS = -pthread + TARGET = my_program + +diff --git a/Makefile.AVX2.PTHREADS.gcc b/Makefile.AVX2.PTHREADS.gcc +--- a/Makefile.AVX2.PTHREADS.gcc ++++ b/Makefile.AVX2.PTHREADS.gcc +@@ -1,7 +1,6 @@ + # Makefile for AVX2 with Pthreads on GCC + # + +-CC = gcc + CFLAGS = -O3 -mavx2 -pthread + LDFLAGS = -pthread + TARGET = my_program + +diff --git a/Makefile.AVX2.gcc b/Makefile.AVX2.gcc +--- a/Makefile.AVX2.gcc ++++ b/Makefile.AVX2.gcc +@@ -1,7 +1,6 @@ + # Makefile for AVX2 on GCC + # + +-CC = gcc + CFLAGS = -O3 -mavx2 + LDFLAGS = + TARGET = my_program + +diff --git a/Makefile.SSE3.PTHREADS.gcc b/Makefile.SSE3.PTHREADS.gcc +--- a/Makefile.SSE3.PTHREADS.gcc ++++ b/Makefile.SSE3.PTHREADS.gcc +@@ -1,7 +1,6 @@ + # Makefile for SSE3 with Pthreads on GCC + # + +-CC = gcc + CFLAGS = -O3 -msse3 -pthread + LDFLAGS = -pthread + TARGET = my_program + +diff --git a/Makefile.SSE3.gcc b/Makefile.SSE3.gcc +--- a/Makefile.SSE3.gcc ++++ b/Makefile.SSE3.gcc +@@ -1,7 +1,6 @@ + # Makefile for SSE3 on GCC + # + +-CC = gcc + CFLAGS = -O3 -msse3 + LDFLAGS = + TARGET = my_program + +diff --git a/Makefile.AVX.PTHREADS.gcc b/Makefile.AVX.PTHREADS.gcc +--- a/Makefile.AVX.PTHREADS.gcc ++++ b/Makefile.AVX.PTHREADS.gcc +@@ -1,7 +1,6 @@ + # Makefile for AVX with Pthreads on GCC + # + +-CC = gcc + CFLAGS = -O3 -mavx -pthread + LDFLAGS = -pthread + TARGET = my_program + +diff --git a/Makefile.AVX.gcc b/Makefile.AVX.gcc +--- a/Makefile.AVX.gcc ++++ b/Makefile.AVX.gcc +@@ -1,7 +1,6 @@ + # Makefile for AVX on GCC + # + +-CC = gcc + CFLAGS = -O3 -mavx + LDFLAGS = + TARGET = my_program \ No newline at end of file From 3bf8943a8b2c45ef0779d4800b4b2e815cf88ee8 Mon Sep 17 00:00:00 2001 From: Cornelius Roemer Date: Thu, 11 Jul 2024 01:23:18 +0200 Subject: [PATCH 5/8] try again, with better patch --- recipes/raxml/patch | 387 ++++++++++++++++++++++++++++---------------- 1 file changed, 245 insertions(+), 142 deletions(-) diff --git a/recipes/raxml/patch b/recipes/raxml/patch index 4b62d04b52139..700a4b0a1927a 100644 --- a/recipes/raxml/patch +++ b/recipes/raxml/patch @@ -1,179 +1,282 @@ -diff --git a/Makefile.SSE3.PTHREADS.mac b/Makefile.SSE3.PTHREADS.mac ---- a/Makefile.SSE3.PTHREADS.mac -+++ b/Makefile.SSE3.PTHREADS.mac +diff --git a/Makefile.AVX.PTHREADS.gcc b/Makefile.AVX.PTHREADS.gcc +index 7fd619e..22a07e0 100644 +--- a/Makefile.AVX.PTHREADS.gcc ++++ b/Makefile.AVX.PTHREADS.gcc @@ -1,7 +1,6 @@ - # Makefile for SSE3 with Pthreads on Mac - # + # Makefile August 2006 by Alexandros Stamatakis + # Makefile cleanup October 2006, Courtesy of Peter Cordes --CC = clang - CFLAGS = -O3 -msse3 -pthread - LDFLAGS = -pthread - TARGET = my_program - -diff --git a/Makefile.AVX2.mac b/Makefile.AVX2.mac ---- a/Makefile.AVX2.mac -+++ b/Makefile.AVX2.mac +-CC = gcc + + CFLAGS = -D_USE_PTHREADS -D__SIM_SSE3 -O2 -D_GNU_SOURCE -msse3 -fomit-frame-pointer -funroll-loops -D__AVX #-Wall -pedantic -Wunused-parameter -Wredundant-decls -Wreturn-type -Wswitch-default -Wunused-value -Wimplicit -Wimplicit-function-declaration -Wimplicit-int -Wimport -Wunused -Wunused-function -Wunused-label -Wno-int-to-pointer-cast -Wbad-function-cast -Wmissing-declarations -Wmissing-prototypes -Wnested-externs -Wold-style-definition -Wstrict-prototypes -Wdeclaration-after-statement -Wpointer-sign -Wextra -Wredundant-decls -Wunused -Wunused-function -Wunused-parameter -Wunused-value -Wunused-variable -Wformat -Wformat-nonliteral -Wparentheses -Wsequence-point -Wuninitialized -Wundef -Wbad-function-cast + +diff --git a/Makefile.AVX.PTHREADS.mac b/Makefile.AVX.PTHREADS.mac +index b993bae..a5cd801 100644 +--- a/Makefile.AVX.PTHREADS.mac ++++ b/Makefile.AVX.PTHREADS.mac @@ -1,7 +1,6 @@ - # Makefile for AVX2 on Mac - # + # Makefile August 2006 by Alexandros Stamatakis + # Makefile cleanup October 2006, Courtesy of Peter Cordes + +-CC = clang + + CFLAGS = -D_USE_PTHREADS -D__SIM_SSE3 -O2 -D_GNU_SOURCE -msse3 -fomit-frame-pointer -funroll-loops -D__AVX #-Wall -pedantic -Wunused-parameter -Wredundant-decls -Wreturn-type -Wswitch-default -Wunused-value -Wimplicit -Wimplicit-function-declaration -Wimplicit-int -Wimport -Wunused -Wunused-function -Wunused-label -Wno-int-to-pointer-cast -Wbad-function-cast -Wmissing-declarations -Wmissing-prototypes -Wnested-externs -Wold-style-definition -Wstrict-prototypes -Wdeclaration-after-statement -Wpointer-sign -Wextra -Wredundant-decls -Wunused -Wunused-function -Wunused-parameter -Wunused-value -Wunused-variable -Wformat -Wformat-nonliteral -Wparentheses -Wsequence-point -Wuninitialized -Wundef -Wbad-function-cast + +diff --git a/Makefile.AVX.gcc b/Makefile.AVX.gcc +index e9d7dbe..f2ccdc2 100644 +--- a/Makefile.AVX.gcc ++++ b/Makefile.AVX.gcc +@@ -1,7 +1,6 @@ + # Makefile August 2006 by Alexandros Stamatakis + # Makefile cleanup October 2006, Courtesy of Peter Cordes + +-CC = gcc + + CFLAGS = -D__SIM_SSE3 -msse3 -D_GNU_SOURCE -O2 -fomit-frame-pointer -funroll-loops -D__AVX #-Wall -Wunused-parameter -Wredundant-decls -Wreturn-type -Wswitch-default -Wunused-value -Wimplicit -Wimplicit-function-declaration -Wimplicit-int -Wimport -Wunused -Wunused-function -Wunused-label -Wno-int-to-pointer-cast -Wbad-function-cast -Wmissing-declarations -Wmissing-prototypes -Wnested-externs -Wold-style-definition -Wstrict-prototypes -Wpointer-sign -Wextra -Wredundant-decls -Wunused -Wunused-function -Wunused-parameter -Wunused-value -Wunused-variable -Wformat -Wformat-nonliteral -Wparentheses -Wsequence-point -Wuninitialized -Wundef -Wbad-function-cast --CC = clang - CFLAGS = -O3 -mavx2 - LDFLAGS = - TARGET = my_program - diff --git a/Makefile.AVX.mac b/Makefile.AVX.mac +index 6d72f5d..e8d4ff5 100644 --- a/Makefile.AVX.mac +++ b/Makefile.AVX.mac @@ -1,7 +1,6 @@ - # Makefile for AVX on Mac - # + # Makefile August 2006 by Alexandros Stamatakis + # Makefile cleanup October 2006, Courtesy of Peter Cordes -CC = clang - CFLAGS = -O3 -mavx - LDFLAGS = - TARGET = my_program - -diff --git a/Makefile.PTHREADS.mac b/Makefile.PTHREADS.mac ---- a/Makefile.PTHREADS.mac -+++ b/Makefile.PTHREADS.mac -@@ -1,7 +1,6 @@ - # Makefile for Pthreads on Mac - # --CC = clang - CFLAGS = -O3 -pthread - LDFLAGS = -pthread - TARGET = my_program - -diff --git a/Makefile.SSE3.mac b/Makefile.SSE3.mac ---- a/Makefile.SSE3.mac -+++ b/Makefile.SSE3.mac + CFLAGS = -D__SIM_SSE3 -msse3 -D_GNU_SOURCE -O2 -fomit-frame-pointer -funroll-loops -D__AVX #-Weverything -Wno-padded # -Wall -pedantic -Wunused-parameter -Wredundant-decls -Wreturn-type -Wswitch-default -Wunused-value -Wimplicit -Wimplicit-function-declaration -Wimplicit-int -Wimport -Wunused -Wunused-function -Wunused-label -Wno-int-to-pointer-cast -Wbad-function-cast -Wmissing-declarations -Wmissing-prototypes -Wnested-externs -Wold-style-definition -Wstrict-prototypes -Wdeclaration-after-statement -Wpointer-sign -Wextra -Wredundant-decls -Wunused -Wunused-function -Wunused-parameter -Wunused-value -Wunused-variable -Wformat -Wformat-nonliteral -Wparentheses -Wsequence-point -Wuninitialized -Wundef -Wbad-function-cast + +diff --git a/Makefile.AVX2.PTHREADS.gcc b/Makefile.AVX2.PTHREADS.gcc +index 44ac3c0..fdf9e45 100644 +--- a/Makefile.AVX2.PTHREADS.gcc ++++ b/Makefile.AVX2.PTHREADS.gcc @@ -1,7 +1,6 @@ - # Makefile for SSE3 on Mac - # + # Makefile August 2006 by Alexandros Stamatakis + # Makefile cleanup October 2006, Courtesy of Peter Cordes + +-CC = gcc + + CFLAGS = -D_USE_PTHREADS -D__SIM_SSE3 -O2 -D_GNU_SOURCE -msse3 -fomit-frame-pointer -funroll-loops -D__AVX #-Wall -pedantic -Wunused-parameter -Wredundant-decls -Wreturn-type -Wswitch-default -Wunused-value -Wimplicit -Wimplicit-function-declaration -Wimplicit-int -Wimport -Wunused -Wunused-function -Wunused-label -Wno-int-to-pointer-cast -Wbad-function-cast -Wmissing-declarations -Wmissing-prototypes -Wnested-externs -Wold-style-definition -Wstrict-prototypes -Wdeclaration-after-statement -Wpointer-sign -Wextra -Wredundant-decls -Wunused -Wunused-function -Wunused-parameter -Wunused-value -Wunused-variable -Wformat -Wformat-nonliteral -Wparentheses -Wsequence-point -Wuninitialized -Wundef -Wbad-function-cast --CC = clang - CFLAGS = -O3 -msse3 - LDFLAGS = - TARGET = my_program - diff --git a/Makefile.AVX2.PTHREADS.mac b/Makefile.AVX2.PTHREADS.mac +index a76a993..9934be0 100644 --- a/Makefile.AVX2.PTHREADS.mac +++ b/Makefile.AVX2.PTHREADS.mac @@ -1,7 +1,6 @@ - # Makefile for AVX2 with Pthreads on Mac - # + # Makefile August 2006 by Alexandros Stamatakis + # Makefile cleanup October 2006, Courtesy of Peter Cordes --CC = clang - CFLAGS = -O3 -mavx2 -pthread - LDFLAGS = -pthread - TARGET = my_program - -diff --git a/Makefile.AVX.PTHREADS.mac b/Makefile.AVX.PTHREADS.mac ---- a/Makefile.AVX.PTHREADS.mac -+++ b/Makefile.AVX.PTHREADS.mac +-CC = clang + + CFLAGS = -D_USE_PTHREADS -D__SIM_SSE3 -O2 -D_GNU_SOURCE -msse3 -fomit-frame-pointer -funroll-loops -D__AVX #-Wall -pedantic -Wunused-parameter -Wredundant-decls -Wreturn-type -Wswitch-default -Wunused-value -Wimplicit -Wimplicit-function-declaration -Wimplicit-int -Wimport -Wunused -Wunused-function -Wunused-label -Wno-int-to-pointer-cast -Wbad-function-cast -Wmissing-declarations -Wmissing-prototypes -Wnested-externs -Wold-style-definition -Wstrict-prototypes -Wdeclaration-after-statement -Wpointer-sign -Wextra -Wredundant-decls -Wunused -Wunused-function -Wunused-parameter -Wunused-value -Wunused-variable -Wformat -Wformat-nonliteral -Wparentheses -Wsequence-point -Wuninitialized -Wundef -Wbad-function-cast + +diff --git a/Makefile.AVX2.gcc b/Makefile.AVX2.gcc +index 85390a1..7085db5 100644 +--- a/Makefile.AVX2.gcc ++++ b/Makefile.AVX2.gcc @@ -1,7 +1,6 @@ - # Makefile for AVX with Pthreads on Mac - # + # Makefile August 2006 by Alexandros Stamatakis + # Makefile cleanup October 2006, Courtesy of Peter Cordes --CC = clang - CFLAGS = -O3 -mavx -pthread - LDFLAGS = -pthread - TARGET = my_program - -diff --git a/Makefile.gcc b/Makefile.gcc ---- a/Makefile.gcc -+++ b/Makefile.gcc +-CC = gcc + + CFLAGS = -D__SIM_SSE3 -msse3 -D_GNU_SOURCE -O2 -fomit-frame-pointer -funroll-loops -D__AVX #-Wall -Wunused-parameter -Wredundant-decls -Wreturn-type -Wswitch-default -Wunused-value -Wimplicit -Wimplicit-function-declaration -Wimplicit-int -Wimport -Wunused -Wunused-function -Wunused-label -Wno-int-to-pointer-cast -Wbad-function-cast -Wmissing-declarations -Wmissing-prototypes -Wnested-externs -Wold-style-definition -Wstrict-prototypes -Wpointer-sign -Wextra -Wredundant-decls -Wunused -Wunused-function -Wunused-parameter -Wunused-value -Wunused-variable -Wformat -Wformat-nonliteral -Wparentheses -Wsequence-point -Wuninitialized -Wundef -Wbad-function-cast + +diff --git a/Makefile.AVX2.mac b/Makefile.AVX2.mac +index b66f807..14b2336 100644 +--- a/Makefile.AVX2.mac ++++ b/Makefile.AVX2.mac @@ -1,7 +1,6 @@ - # Makefile for GCC - # - --CC = gcc - CFLAGS = -O3 - LDFLAGS = - TARGET = my_program - + # Makefile August 2006 by Alexandros Stamatakis + # Makefile cleanup October 2006, Courtesy of Peter Cordes + +-CC = clang + + CFLAGS = -D__SIM_SSE3 -msse3 -D_GNU_SOURCE -O2 -fomit-frame-pointer -funroll-loops -D__AVX #-Wall -pedantic -Wunused-parameter -Wredundant-decls -Wreturn-type -Wswitch-default -Wunused-value -Wimplicit -Wimplicit-function-declaration -Wimplicit-int -Wimport -Wunused -Wunused-function -Wunused-label -Wno-int-to-pointer-cast -Wbad-function-cast -Wmissing-declarations -Wmissing-prototypes -Wnested-externs -Wold-style-definition -Wstrict-prototypes -Wdeclaration-after-statement -Wpointer-sign -Wextra -Wredundant-decls -Wunused -Wunused-function -Wunused-parameter -Wunused-value -Wunused-variable -Wformat -Wformat-nonliteral -Wparentheses -Wsequence-point -Wuninitialized -Wundef -Wbad-function-cast + diff --git a/Makefile.PTHREADS.gcc b/Makefile.PTHREADS.gcc +index e5bcb2b..b532b30 100644 --- a/Makefile.PTHREADS.gcc +++ b/Makefile.PTHREADS.gcc @@ -1,7 +1,6 @@ - # Makefile for Pthreads with GCC - # - --CC = gcc - CFLAGS = -O3 -pthread - LDFLAGS = -pthread - TARGET = my_program - -diff --git a/Makefile.AVX2.PTHREADS.gcc b/Makefile.AVX2.PTHREADS.gcc ---- a/Makefile.AVX2.PTHREADS.gcc -+++ b/Makefile.AVX2.PTHREADS.gcc -@@ -1,7 +1,6 @@ - # Makefile for AVX2 with Pthreads on GCC - # - --CC = gcc - CFLAGS = -O3 -mavx2 -pthread - LDFLAGS = -pthread - TARGET = my_program - -diff --git a/Makefile.AVX2.gcc b/Makefile.AVX2.gcc ---- a/Makefile.AVX2.gcc -+++ b/Makefile.AVX2.gcc + # Makefile August 2006 by Alexandros Stamatakis + # Makefile cleanup October 2006, Courtesy of Peter Cordes + +-CC = gcc + + ARCH := $(shell uname -m) + ifeq ($(ARCH), x86_64) +diff --git a/Makefile.PTHREADS.mac b/Makefile.PTHREADS.mac +index 83efe92..49ed80b 100644 +--- a/Makefile.PTHREADS.mac ++++ b/Makefile.PTHREADS.mac @@ -1,7 +1,6 @@ - # Makefile for AVX2 on GCC - # - --CC = gcc - CFLAGS = -O3 -mavx2 - LDFLAGS = - TARGET = my_program - + # Makefile August 2006 by Alexandros Stamatakis + # Makefile cleanup October 2006, Courtesy of Peter Cordes + +-CC = clang + + + CFLAGS = -D_GNU_SOURCE -fomit-frame-pointer -funroll-loops -O2 -D_USE_PTHREADS -msse #-Wall -Wunused-parameter -Wredundant-decls -Wreturn-type -Wswitch-default -Wunused-value -Wimplicit -Wimplicit-function-declaration -Wimplicit-int -Wimport -Wunused -Wunused-function -Wunused-label -Wno-int-to-pointer-cast -Wbad-function-cast -Wmissing-declarations -Wmissing-prototypes -Wnested-externs -Wold-style-definition -Wstrict-prototypes -Wpointer-sign -Wextra -Wredundant-decls -Wunused -Wunused-function -Wunused-parameter -Wunused-value -Wunused-variable -Wformat -Wformat-nonliteral -Wparentheses -Wsequence-point -Wuninitialized -Wundef -Wbad-function-cast diff --git a/Makefile.SSE3.PTHREADS.gcc b/Makefile.SSE3.PTHREADS.gcc +index 507cba7..a1c0802 100644 --- a/Makefile.SSE3.PTHREADS.gcc +++ b/Makefile.SSE3.PTHREADS.gcc @@ -1,7 +1,6 @@ - # Makefile for SSE3 with Pthreads on GCC - # - --CC = gcc - CFLAGS = -O3 -msse3 -pthread - LDFLAGS = -pthread - TARGET = my_program - + # Makefile August 2006 by Alexandros Stamatakis + # Makefile cleanup October 2006, Courtesy of Peter Cordes + +-CC = gcc + + ARCH := $(shell uname -m) + ifeq ($(ARCH), x86_64) +diff --git a/Makefile.SSE3.PTHREADS.mac b/Makefile.SSE3.PTHREADS.mac +index f90dfd4..bf025f3 100644 +--- a/Makefile.SSE3.PTHREADS.mac ++++ b/Makefile.SSE3.PTHREADS.mac +@@ -1,7 +1,6 @@ + # Makefile August 2006 by Alexandros Stamatakis + # Makefile cleanup October 2006, Courtesy of Peter Cordes + +-CC = clang + + CFLAGS = -D_USE_PTHREADS -D__SIM_SSE3 -O2 -D_GNU_SOURCE -msse3 -fomit-frame-pointer -funroll-loops #-Wall -pedantic -Wunused-parameter -Wredundant-decls -Wreturn-type -Wswitch-default -Wunused-value -Wimplicit -Wimplicit-function-declaration -Wimplicit-int -Wimport -Wunused -Wunused-function -Wunused-label -Wno-int-to-pointer-cast -Wbad-function-cast -Wmissing-declarations -Wmissing-prototypes -Wnested-externs -Wold-style-definition -Wstrict-prototypes -Wdeclaration-after-statement -Wpointer-sign -Wextra -Wredundant-decls -Wunused -Wunused-function -Wunused-parameter -Wunused-value -Wunused-variable -Wformat -Wformat-nonliteral -Wparentheses -Wsequence-point -Wuninitialized -Wundef -Wbad-function-cast + diff --git a/Makefile.SSE3.gcc b/Makefile.SSE3.gcc +index 3749317..d769645 100644 --- a/Makefile.SSE3.gcc +++ b/Makefile.SSE3.gcc @@ -1,7 +1,6 @@ - # Makefile for SSE3 on GCC - # - --CC = gcc - CFLAGS = -O3 -msse3 - LDFLAGS = - TARGET = my_program - -diff --git a/Makefile.AVX.PTHREADS.gcc b/Makefile.AVX.PTHREADS.gcc ---- a/Makefile.AVX.PTHREADS.gcc -+++ b/Makefile.AVX.PTHREADS.gcc + # Makefile August 2006 by Alexandros Stamatakis + # Makefile cleanup October 2006, Courtesy of Peter Cordes + +-CC = gcc + + ARCH := $(shell uname -m) + ifeq ($(ARCH), x86_64) +diff --git a/Makefile.SSE3.mac b/Makefile.SSE3.mac +index ae39ec3..8387421 100644 +--- a/Makefile.SSE3.mac ++++ b/Makefile.SSE3.mac @@ -1,7 +1,6 @@ - # Makefile for AVX with Pthreads on GCC - # - --CC = gcc - CFLAGS = -O3 -mavx -pthread - LDFLAGS = -pthread - TARGET = my_program - -diff --git a/Makefile.AVX.gcc b/Makefile.AVX.gcc ---- a/Makefile.AVX.gcc -+++ b/Makefile.AVX.gcc + # Makefile August 2006 by Alexandros Stamatakis + # Makefile cleanup October 2006, Courtesy of Peter Cordes + +-CC = clang + + CFLAGS = -D__SIM_SSE3 -msse3 -D_GNU_SOURCE -O2 -fomit-frame-pointer -funroll-loops #-Weverything -Wno-padded #-Wall -pedantic -Wunused-parameter -Wredundant-decls -Wreturn-type -Wswitch-default -Wunused-value -Wimplicit -Wimplicit-function-declaration -Wimplicit-int -Wimport -Wunused -Wunused-function -Wunused-label -Wno-int-to-pointer-cast -Wbad-function-cast -Wmissing-declarations -Wmissing-prototypes -Wnested-externs -Wold-style-definition -Wstrict-prototypes -Wdeclaration-after-statement -Wpointer-sign -Wextra -Wredundant-decls -Wunused -Wunused-function -Wunused-parameter -Wunused-value -Wunused-variable -Wformat -Wformat-nonliteral -Wparentheses -Wsequence-point -Wuninitialized -Wundef -Wbad-function-cast + +diff --git a/Makefile.gcc b/Makefile.gcc +index 85a9cab..1a8f032 100644 +--- a/Makefile.gcc ++++ b/Makefile.gcc @@ -1,7 +1,6 @@ - # Makefile for AVX on GCC - # + # Makefile August 2006 by Alexandros Stamatakis + # Makefile cleanup October 2006, Courtesy of Peter Cordes + +-CC = gcc --CC = gcc - CFLAGS = -O3 -mavx - LDFLAGS = - TARGET = my_program \ No newline at end of file + ARCH := $(shell uname -m) + ifeq ($(ARCH), x86_64) +diff --git a/my_changes.patch b/my_changes.patch +new file mode 100644 +index 0000000..6fdaf38 +--- /dev/null ++++ b/my_changes.patch +@@ -0,0 +1,96 @@ ++diff --git a/Makefile.AVX.PTHREADS.gcc b/Makefile.AVX.PTHREADS.gcc ++index 7fd619e..22a07e0 100644 ++--- a/Makefile.AVX.PTHREADS.gcc +++++ b/Makefile.AVX.PTHREADS.gcc ++@@ -1,7 +1,6 @@ ++ # Makefile August 2006 by Alexandros Stamatakis ++ # Makefile cleanup October 2006, Courtesy of Peter Cordes ++ ++-CC = gcc ++ ++ CFLAGS = -D_USE_PTHREADS -D__SIM_SSE3 -O2 -D_GNU_SOURCE -msse3 -fomit-frame-pointer -funroll-loops -D__AVX #-Wall -pedantic -Wunused-parameter -Wredundant-decls -Wreturn-type -Wswitch-default -Wunused-value -Wimplicit -Wimplicit-function-declaration -Wimplicit-int -Wimport -Wunused -Wunused-function -Wunused-label -Wno-int-to-pointer-cast -Wbad-function-cast -Wmissing-declarations -Wmissing-prototypes -Wnested-externs -Wold-style-definition -Wstrict-prototypes -Wdeclaration-after-statement -Wpointer-sign -Wextra -Wredundant-decls -Wunused -Wunused-function -Wunused-parameter -Wunused-value -Wunused-variable -Wformat -Wformat-nonliteral -Wparentheses -Wsequence-point -Wuninitialized -Wundef -Wbad-function-cast ++ ++diff --git a/Makefile.AVX.gcc b/Makefile.AVX.gcc ++index e9d7dbe..f2ccdc2 100644 ++--- a/Makefile.AVX.gcc +++++ b/Makefile.AVX.gcc ++@@ -1,7 +1,6 @@ ++ # Makefile August 2006 by Alexandros Stamatakis ++ # Makefile cleanup October 2006, Courtesy of Peter Cordes ++ ++-CC = gcc ++ ++ CFLAGS = -D__SIM_SSE3 -msse3 -D_GNU_SOURCE -O2 -fomit-frame-pointer -funroll-loops -D__AVX #-Wall -Wunused-parameter -Wredundant-decls -Wreturn-type -Wswitch-default -Wunused-value -Wimplicit -Wimplicit-function-declaration -Wimplicit-int -Wimport -Wunused -Wunused-function -Wunused-label -Wno-int-to-pointer-cast -Wbad-function-cast -Wmissing-declarations -Wmissing-prototypes -Wnested-externs -Wold-style-definition -Wstrict-prototypes -Wpointer-sign -Wextra -Wredundant-decls -Wunused -Wunused-function -Wunused-parameter -Wunused-value -Wunused-variable -Wformat -Wformat-nonliteral -Wparentheses -Wsequence-point -Wuninitialized -Wundef -Wbad-function-cast ++ ++diff --git a/Makefile.AVX2.PTHREADS.gcc b/Makefile.AVX2.PTHREADS.gcc ++index 44ac3c0..fdf9e45 100644 ++--- a/Makefile.AVX2.PTHREADS.gcc +++++ b/Makefile.AVX2.PTHREADS.gcc ++@@ -1,7 +1,6 @@ ++ # Makefile August 2006 by Alexandros Stamatakis ++ # Makefile cleanup October 2006, Courtesy of Peter Cordes ++ ++-CC = gcc ++ ++ CFLAGS = -D_USE_PTHREADS -D__SIM_SSE3 -O2 -D_GNU_SOURCE -msse3 -fomit-frame-pointer -funroll-loops -D__AVX #-Wall -pedantic -Wunused-parameter -Wredundant-decls -Wreturn-type -Wswitch-default -Wunused-value -Wimplicit -Wimplicit-function-declaration -Wimplicit-int -Wimport -Wunused -Wunused-function -Wunused-label -Wno-int-to-pointer-cast -Wbad-function-cast -Wmissing-declarations -Wmissing-prototypes -Wnested-externs -Wold-style-definition -Wstrict-prototypes -Wdeclaration-after-statement -Wpointer-sign -Wextra -Wredundant-decls -Wunused -Wunused-function -Wunused-parameter -Wunused-value -Wunused-variable -Wformat -Wformat-nonliteral -Wparentheses -Wsequence-point -Wuninitialized -Wundef -Wbad-function-cast ++ ++diff --git a/Makefile.AVX2.gcc b/Makefile.AVX2.gcc ++index 85390a1..7085db5 100644 ++--- a/Makefile.AVX2.gcc +++++ b/Makefile.AVX2.gcc ++@@ -1,7 +1,6 @@ ++ # Makefile August 2006 by Alexandros Stamatakis ++ # Makefile cleanup October 2006, Courtesy of Peter Cordes ++ ++-CC = gcc ++ ++ CFLAGS = -D__SIM_SSE3 -msse3 -D_GNU_SOURCE -O2 -fomit-frame-pointer -funroll-loops -D__AVX #-Wall -Wunused-parameter -Wredundant-decls -Wreturn-type -Wswitch-default -Wunused-value -Wimplicit -Wimplicit-function-declaration -Wimplicit-int -Wimport -Wunused -Wunused-function -Wunused-label -Wno-int-to-pointer-cast -Wbad-function-cast -Wmissing-declarations -Wmissing-prototypes -Wnested-externs -Wold-style-definition -Wstrict-prototypes -Wpointer-sign -Wextra -Wredundant-decls -Wunused -Wunused-function -Wunused-parameter -Wunused-value -Wunused-variable -Wformat -Wformat-nonliteral -Wparentheses -Wsequence-point -Wuninitialized -Wundef -Wbad-function-cast ++ ++diff --git a/Makefile.PTHREADS.gcc b/Makefile.PTHREADS.gcc ++index e5bcb2b..b532b30 100644 ++--- a/Makefile.PTHREADS.gcc +++++ b/Makefile.PTHREADS.gcc ++@@ -1,7 +1,6 @@ ++ # Makefile August 2006 by Alexandros Stamatakis ++ # Makefile cleanup October 2006, Courtesy of Peter Cordes ++ ++-CC = gcc ++ ++ ARCH := $(shell uname -m) ++ ifeq ($(ARCH), x86_64) ++diff --git a/Makefile.SSE3.PTHREADS.gcc b/Makefile.SSE3.PTHREADS.gcc ++index 507cba7..a1c0802 100644 ++--- a/Makefile.SSE3.PTHREADS.gcc +++++ b/Makefile.SSE3.PTHREADS.gcc ++@@ -1,7 +1,6 @@ ++ # Makefile August 2006 by Alexandros Stamatakis ++ # Makefile cleanup October 2006, Courtesy of Peter Cordes ++ ++-CC = gcc ++ ++ ARCH := $(shell uname -m) ++ ifeq ($(ARCH), x86_64) ++diff --git a/Makefile.SSE3.gcc b/Makefile.SSE3.gcc ++index 3749317..d769645 100644 ++--- a/Makefile.SSE3.gcc +++++ b/Makefile.SSE3.gcc ++@@ -1,7 +1,6 @@ ++ # Makefile August 2006 by Alexandros Stamatakis ++ # Makefile cleanup October 2006, Courtesy of Peter Cordes ++ ++-CC = gcc ++ ++ ARCH := $(shell uname -m) ++ ifeq ($(ARCH), x86_64) ++diff --git a/Makefile.gcc b/Makefile.gcc ++index 85a9cab..1a8f032 100644 ++--- a/Makefile.gcc +++++ b/Makefile.gcc ++@@ -1,7 +1,6 @@ ++ # Makefile August 2006 by Alexandros Stamatakis ++ # Makefile cleanup October 2006, Courtesy of Peter Cordes ++ ++-CC = gcc ++ ++ ARCH := $(shell uname -m) ++ ifeq ($(ARCH), x86_64) From 4eee658d716b0684e9211bbcc9efe3836f1998f0 Mon Sep 17 00:00:00 2001 From: Cornelius Roemer Date: Thu, 11 Jul 2024 11:50:14 +0200 Subject: [PATCH 6/8] fix: thanks @martin-g --- recipes/raxml/build.sh | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/recipes/raxml/build.sh b/recipes/raxml/build.sh index ca76f01c78408..92f87d162d35e 100644 --- a/recipes/raxml/build.sh +++ b/recipes/raxml/build.sh @@ -33,7 +33,7 @@ for PTHREADS in "" .PTHREADS; do else MAKEFILE=${MAKEFILE}.gcc fi - make -f ${MAKEFILE} + make -f ${MAKEFILE} CC=$CC mv raxmlHPC* "$PREFIX"/bin make -f ${MAKEFILE} clean done From 53508deb8861796a6f83198115ab149976e7738f Mon Sep 17 00:00:00 2001 From: Cornelius Roemer Date: Thu, 11 Jul 2024 11:50:28 +0200 Subject: [PATCH 7/8] Delete recipes/raxml/patch --- recipes/raxml/patch | 282 -------------------------------------------- 1 file changed, 282 deletions(-) delete mode 100644 recipes/raxml/patch diff --git a/recipes/raxml/patch b/recipes/raxml/patch deleted file mode 100644 index 700a4b0a1927a..0000000000000 --- a/recipes/raxml/patch +++ /dev/null @@ -1,282 +0,0 @@ -diff --git a/Makefile.AVX.PTHREADS.gcc b/Makefile.AVX.PTHREADS.gcc -index 7fd619e..22a07e0 100644 ---- a/Makefile.AVX.PTHREADS.gcc -+++ b/Makefile.AVX.PTHREADS.gcc -@@ -1,7 +1,6 @@ - # Makefile August 2006 by Alexandros Stamatakis - # Makefile cleanup October 2006, Courtesy of Peter Cordes - --CC = gcc - - CFLAGS = -D_USE_PTHREADS -D__SIM_SSE3 -O2 -D_GNU_SOURCE -msse3 -fomit-frame-pointer -funroll-loops -D__AVX #-Wall -pedantic -Wunused-parameter -Wredundant-decls -Wreturn-type -Wswitch-default -Wunused-value -Wimplicit -Wimplicit-function-declaration -Wimplicit-int -Wimport -Wunused -Wunused-function -Wunused-label -Wno-int-to-pointer-cast -Wbad-function-cast -Wmissing-declarations -Wmissing-prototypes -Wnested-externs -Wold-style-definition -Wstrict-prototypes -Wdeclaration-after-statement -Wpointer-sign -Wextra -Wredundant-decls -Wunused -Wunused-function -Wunused-parameter -Wunused-value -Wunused-variable -Wformat -Wformat-nonliteral -Wparentheses -Wsequence-point -Wuninitialized -Wundef -Wbad-function-cast - -diff --git a/Makefile.AVX.PTHREADS.mac b/Makefile.AVX.PTHREADS.mac -index b993bae..a5cd801 100644 ---- a/Makefile.AVX.PTHREADS.mac -+++ b/Makefile.AVX.PTHREADS.mac -@@ -1,7 +1,6 @@ - # Makefile August 2006 by Alexandros Stamatakis - # Makefile cleanup October 2006, Courtesy of Peter Cordes - --CC = clang - - CFLAGS = -D_USE_PTHREADS -D__SIM_SSE3 -O2 -D_GNU_SOURCE -msse3 -fomit-frame-pointer -funroll-loops -D__AVX #-Wall -pedantic -Wunused-parameter -Wredundant-decls -Wreturn-type -Wswitch-default -Wunused-value -Wimplicit -Wimplicit-function-declaration -Wimplicit-int -Wimport -Wunused -Wunused-function -Wunused-label -Wno-int-to-pointer-cast -Wbad-function-cast -Wmissing-declarations -Wmissing-prototypes -Wnested-externs -Wold-style-definition -Wstrict-prototypes -Wdeclaration-after-statement -Wpointer-sign -Wextra -Wredundant-decls -Wunused -Wunused-function -Wunused-parameter -Wunused-value -Wunused-variable -Wformat -Wformat-nonliteral -Wparentheses -Wsequence-point -Wuninitialized -Wundef -Wbad-function-cast - -diff --git a/Makefile.AVX.gcc b/Makefile.AVX.gcc -index e9d7dbe..f2ccdc2 100644 ---- a/Makefile.AVX.gcc -+++ b/Makefile.AVX.gcc -@@ -1,7 +1,6 @@ - # Makefile August 2006 by Alexandros Stamatakis - # Makefile cleanup October 2006, Courtesy of Peter Cordes - --CC = gcc - - CFLAGS = -D__SIM_SSE3 -msse3 -D_GNU_SOURCE -O2 -fomit-frame-pointer -funroll-loops -D__AVX #-Wall -Wunused-parameter -Wredundant-decls -Wreturn-type -Wswitch-default -Wunused-value -Wimplicit -Wimplicit-function-declaration -Wimplicit-int -Wimport -Wunused -Wunused-function -Wunused-label -Wno-int-to-pointer-cast -Wbad-function-cast -Wmissing-declarations -Wmissing-prototypes -Wnested-externs -Wold-style-definition -Wstrict-prototypes -Wpointer-sign -Wextra -Wredundant-decls -Wunused -Wunused-function -Wunused-parameter -Wunused-value -Wunused-variable -Wformat -Wformat-nonliteral -Wparentheses -Wsequence-point -Wuninitialized -Wundef -Wbad-function-cast - -diff --git a/Makefile.AVX.mac b/Makefile.AVX.mac -index 6d72f5d..e8d4ff5 100644 ---- a/Makefile.AVX.mac -+++ b/Makefile.AVX.mac -@@ -1,7 +1,6 @@ - # Makefile August 2006 by Alexandros Stamatakis - # Makefile cleanup October 2006, Courtesy of Peter Cordes - --CC = clang - - CFLAGS = -D__SIM_SSE3 -msse3 -D_GNU_SOURCE -O2 -fomit-frame-pointer -funroll-loops -D__AVX #-Weverything -Wno-padded # -Wall -pedantic -Wunused-parameter -Wredundant-decls -Wreturn-type -Wswitch-default -Wunused-value -Wimplicit -Wimplicit-function-declaration -Wimplicit-int -Wimport -Wunused -Wunused-function -Wunused-label -Wno-int-to-pointer-cast -Wbad-function-cast -Wmissing-declarations -Wmissing-prototypes -Wnested-externs -Wold-style-definition -Wstrict-prototypes -Wdeclaration-after-statement -Wpointer-sign -Wextra -Wredundant-decls -Wunused -Wunused-function -Wunused-parameter -Wunused-value -Wunused-variable -Wformat -Wformat-nonliteral -Wparentheses -Wsequence-point -Wuninitialized -Wundef -Wbad-function-cast - -diff --git a/Makefile.AVX2.PTHREADS.gcc b/Makefile.AVX2.PTHREADS.gcc -index 44ac3c0..fdf9e45 100644 ---- a/Makefile.AVX2.PTHREADS.gcc -+++ b/Makefile.AVX2.PTHREADS.gcc -@@ -1,7 +1,6 @@ - # Makefile August 2006 by Alexandros Stamatakis - # Makefile cleanup October 2006, Courtesy of Peter Cordes - --CC = gcc - - CFLAGS = -D_USE_PTHREADS -D__SIM_SSE3 -O2 -D_GNU_SOURCE -msse3 -fomit-frame-pointer -funroll-loops -D__AVX #-Wall -pedantic -Wunused-parameter -Wredundant-decls -Wreturn-type -Wswitch-default -Wunused-value -Wimplicit -Wimplicit-function-declaration -Wimplicit-int -Wimport -Wunused -Wunused-function -Wunused-label -Wno-int-to-pointer-cast -Wbad-function-cast -Wmissing-declarations -Wmissing-prototypes -Wnested-externs -Wold-style-definition -Wstrict-prototypes -Wdeclaration-after-statement -Wpointer-sign -Wextra -Wredundant-decls -Wunused -Wunused-function -Wunused-parameter -Wunused-value -Wunused-variable -Wformat -Wformat-nonliteral -Wparentheses -Wsequence-point -Wuninitialized -Wundef -Wbad-function-cast - -diff --git a/Makefile.AVX2.PTHREADS.mac b/Makefile.AVX2.PTHREADS.mac -index a76a993..9934be0 100644 ---- a/Makefile.AVX2.PTHREADS.mac -+++ b/Makefile.AVX2.PTHREADS.mac -@@ -1,7 +1,6 @@ - # Makefile August 2006 by Alexandros Stamatakis - # Makefile cleanup October 2006, Courtesy of Peter Cordes - --CC = clang - - CFLAGS = -D_USE_PTHREADS -D__SIM_SSE3 -O2 -D_GNU_SOURCE -msse3 -fomit-frame-pointer -funroll-loops -D__AVX #-Wall -pedantic -Wunused-parameter -Wredundant-decls -Wreturn-type -Wswitch-default -Wunused-value -Wimplicit -Wimplicit-function-declaration -Wimplicit-int -Wimport -Wunused -Wunused-function -Wunused-label -Wno-int-to-pointer-cast -Wbad-function-cast -Wmissing-declarations -Wmissing-prototypes -Wnested-externs -Wold-style-definition -Wstrict-prototypes -Wdeclaration-after-statement -Wpointer-sign -Wextra -Wredundant-decls -Wunused -Wunused-function -Wunused-parameter -Wunused-value -Wunused-variable -Wformat -Wformat-nonliteral -Wparentheses -Wsequence-point -Wuninitialized -Wundef -Wbad-function-cast - -diff --git a/Makefile.AVX2.gcc b/Makefile.AVX2.gcc -index 85390a1..7085db5 100644 ---- a/Makefile.AVX2.gcc -+++ b/Makefile.AVX2.gcc -@@ -1,7 +1,6 @@ - # Makefile August 2006 by Alexandros Stamatakis - # Makefile cleanup October 2006, Courtesy of Peter Cordes - --CC = gcc - - CFLAGS = -D__SIM_SSE3 -msse3 -D_GNU_SOURCE -O2 -fomit-frame-pointer -funroll-loops -D__AVX #-Wall -Wunused-parameter -Wredundant-decls -Wreturn-type -Wswitch-default -Wunused-value -Wimplicit -Wimplicit-function-declaration -Wimplicit-int -Wimport -Wunused -Wunused-function -Wunused-label -Wno-int-to-pointer-cast -Wbad-function-cast -Wmissing-declarations -Wmissing-prototypes -Wnested-externs -Wold-style-definition -Wstrict-prototypes -Wpointer-sign -Wextra -Wredundant-decls -Wunused -Wunused-function -Wunused-parameter -Wunused-value -Wunused-variable -Wformat -Wformat-nonliteral -Wparentheses -Wsequence-point -Wuninitialized -Wundef -Wbad-function-cast - -diff --git a/Makefile.AVX2.mac b/Makefile.AVX2.mac -index b66f807..14b2336 100644 ---- a/Makefile.AVX2.mac -+++ b/Makefile.AVX2.mac -@@ -1,7 +1,6 @@ - # Makefile August 2006 by Alexandros Stamatakis - # Makefile cleanup October 2006, Courtesy of Peter Cordes - --CC = clang - - CFLAGS = -D__SIM_SSE3 -msse3 -D_GNU_SOURCE -O2 -fomit-frame-pointer -funroll-loops -D__AVX #-Wall -pedantic -Wunused-parameter -Wredundant-decls -Wreturn-type -Wswitch-default -Wunused-value -Wimplicit -Wimplicit-function-declaration -Wimplicit-int -Wimport -Wunused -Wunused-function -Wunused-label -Wno-int-to-pointer-cast -Wbad-function-cast -Wmissing-declarations -Wmissing-prototypes -Wnested-externs -Wold-style-definition -Wstrict-prototypes -Wdeclaration-after-statement -Wpointer-sign -Wextra -Wredundant-decls -Wunused -Wunused-function -Wunused-parameter -Wunused-value -Wunused-variable -Wformat -Wformat-nonliteral -Wparentheses -Wsequence-point -Wuninitialized -Wundef -Wbad-function-cast - -diff --git a/Makefile.PTHREADS.gcc b/Makefile.PTHREADS.gcc -index e5bcb2b..b532b30 100644 ---- a/Makefile.PTHREADS.gcc -+++ b/Makefile.PTHREADS.gcc -@@ -1,7 +1,6 @@ - # Makefile August 2006 by Alexandros Stamatakis - # Makefile cleanup October 2006, Courtesy of Peter Cordes - --CC = gcc - - ARCH := $(shell uname -m) - ifeq ($(ARCH), x86_64) -diff --git a/Makefile.PTHREADS.mac b/Makefile.PTHREADS.mac -index 83efe92..49ed80b 100644 ---- a/Makefile.PTHREADS.mac -+++ b/Makefile.PTHREADS.mac -@@ -1,7 +1,6 @@ - # Makefile August 2006 by Alexandros Stamatakis - # Makefile cleanup October 2006, Courtesy of Peter Cordes - --CC = clang - - - CFLAGS = -D_GNU_SOURCE -fomit-frame-pointer -funroll-loops -O2 -D_USE_PTHREADS -msse #-Wall -Wunused-parameter -Wredundant-decls -Wreturn-type -Wswitch-default -Wunused-value -Wimplicit -Wimplicit-function-declaration -Wimplicit-int -Wimport -Wunused -Wunused-function -Wunused-label -Wno-int-to-pointer-cast -Wbad-function-cast -Wmissing-declarations -Wmissing-prototypes -Wnested-externs -Wold-style-definition -Wstrict-prototypes -Wpointer-sign -Wextra -Wredundant-decls -Wunused -Wunused-function -Wunused-parameter -Wunused-value -Wunused-variable -Wformat -Wformat-nonliteral -Wparentheses -Wsequence-point -Wuninitialized -Wundef -Wbad-function-cast -diff --git a/Makefile.SSE3.PTHREADS.gcc b/Makefile.SSE3.PTHREADS.gcc -index 507cba7..a1c0802 100644 ---- a/Makefile.SSE3.PTHREADS.gcc -+++ b/Makefile.SSE3.PTHREADS.gcc -@@ -1,7 +1,6 @@ - # Makefile August 2006 by Alexandros Stamatakis - # Makefile cleanup October 2006, Courtesy of Peter Cordes - --CC = gcc - - ARCH := $(shell uname -m) - ifeq ($(ARCH), x86_64) -diff --git a/Makefile.SSE3.PTHREADS.mac b/Makefile.SSE3.PTHREADS.mac -index f90dfd4..bf025f3 100644 ---- a/Makefile.SSE3.PTHREADS.mac -+++ b/Makefile.SSE3.PTHREADS.mac -@@ -1,7 +1,6 @@ - # Makefile August 2006 by Alexandros Stamatakis - # Makefile cleanup October 2006, Courtesy of Peter Cordes - --CC = clang - - CFLAGS = -D_USE_PTHREADS -D__SIM_SSE3 -O2 -D_GNU_SOURCE -msse3 -fomit-frame-pointer -funroll-loops #-Wall -pedantic -Wunused-parameter -Wredundant-decls -Wreturn-type -Wswitch-default -Wunused-value -Wimplicit -Wimplicit-function-declaration -Wimplicit-int -Wimport -Wunused -Wunused-function -Wunused-label -Wno-int-to-pointer-cast -Wbad-function-cast -Wmissing-declarations -Wmissing-prototypes -Wnested-externs -Wold-style-definition -Wstrict-prototypes -Wdeclaration-after-statement -Wpointer-sign -Wextra -Wredundant-decls -Wunused -Wunused-function -Wunused-parameter -Wunused-value -Wunused-variable -Wformat -Wformat-nonliteral -Wparentheses -Wsequence-point -Wuninitialized -Wundef -Wbad-function-cast - -diff --git a/Makefile.SSE3.gcc b/Makefile.SSE3.gcc -index 3749317..d769645 100644 ---- a/Makefile.SSE3.gcc -+++ b/Makefile.SSE3.gcc -@@ -1,7 +1,6 @@ - # Makefile August 2006 by Alexandros Stamatakis - # Makefile cleanup October 2006, Courtesy of Peter Cordes - --CC = gcc - - ARCH := $(shell uname -m) - ifeq ($(ARCH), x86_64) -diff --git a/Makefile.SSE3.mac b/Makefile.SSE3.mac -index ae39ec3..8387421 100644 ---- a/Makefile.SSE3.mac -+++ b/Makefile.SSE3.mac -@@ -1,7 +1,6 @@ - # Makefile August 2006 by Alexandros Stamatakis - # Makefile cleanup October 2006, Courtesy of Peter Cordes - --CC = clang - - CFLAGS = -D__SIM_SSE3 -msse3 -D_GNU_SOURCE -O2 -fomit-frame-pointer -funroll-loops #-Weverything -Wno-padded #-Wall -pedantic -Wunused-parameter -Wredundant-decls -Wreturn-type -Wswitch-default -Wunused-value -Wimplicit -Wimplicit-function-declaration -Wimplicit-int -Wimport -Wunused -Wunused-function -Wunused-label -Wno-int-to-pointer-cast -Wbad-function-cast -Wmissing-declarations -Wmissing-prototypes -Wnested-externs -Wold-style-definition -Wstrict-prototypes -Wdeclaration-after-statement -Wpointer-sign -Wextra -Wredundant-decls -Wunused -Wunused-function -Wunused-parameter -Wunused-value -Wunused-variable -Wformat -Wformat-nonliteral -Wparentheses -Wsequence-point -Wuninitialized -Wundef -Wbad-function-cast - -diff --git a/Makefile.gcc b/Makefile.gcc -index 85a9cab..1a8f032 100644 ---- a/Makefile.gcc -+++ b/Makefile.gcc -@@ -1,7 +1,6 @@ - # Makefile August 2006 by Alexandros Stamatakis - # Makefile cleanup October 2006, Courtesy of Peter Cordes - --CC = gcc - - ARCH := $(shell uname -m) - ifeq ($(ARCH), x86_64) -diff --git a/my_changes.patch b/my_changes.patch -new file mode 100644 -index 0000000..6fdaf38 ---- /dev/null -+++ b/my_changes.patch -@@ -0,0 +1,96 @@ -+diff --git a/Makefile.AVX.PTHREADS.gcc b/Makefile.AVX.PTHREADS.gcc -+index 7fd619e..22a07e0 100644 -+--- a/Makefile.AVX.PTHREADS.gcc -++++ b/Makefile.AVX.PTHREADS.gcc -+@@ -1,7 +1,6 @@ -+ # Makefile August 2006 by Alexandros Stamatakis -+ # Makefile cleanup October 2006, Courtesy of Peter Cordes -+ -+-CC = gcc -+ -+ CFLAGS = -D_USE_PTHREADS -D__SIM_SSE3 -O2 -D_GNU_SOURCE -msse3 -fomit-frame-pointer -funroll-loops -D__AVX #-Wall -pedantic -Wunused-parameter -Wredundant-decls -Wreturn-type -Wswitch-default -Wunused-value -Wimplicit -Wimplicit-function-declaration -Wimplicit-int -Wimport -Wunused -Wunused-function -Wunused-label -Wno-int-to-pointer-cast -Wbad-function-cast -Wmissing-declarations -Wmissing-prototypes -Wnested-externs -Wold-style-definition -Wstrict-prototypes -Wdeclaration-after-statement -Wpointer-sign -Wextra -Wredundant-decls -Wunused -Wunused-function -Wunused-parameter -Wunused-value -Wunused-variable -Wformat -Wformat-nonliteral -Wparentheses -Wsequence-point -Wuninitialized -Wundef -Wbad-function-cast -+ -+diff --git a/Makefile.AVX.gcc b/Makefile.AVX.gcc -+index e9d7dbe..f2ccdc2 100644 -+--- a/Makefile.AVX.gcc -++++ b/Makefile.AVX.gcc -+@@ -1,7 +1,6 @@ -+ # Makefile August 2006 by Alexandros Stamatakis -+ # Makefile cleanup October 2006, Courtesy of Peter Cordes -+ -+-CC = gcc -+ -+ CFLAGS = -D__SIM_SSE3 -msse3 -D_GNU_SOURCE -O2 -fomit-frame-pointer -funroll-loops -D__AVX #-Wall -Wunused-parameter -Wredundant-decls -Wreturn-type -Wswitch-default -Wunused-value -Wimplicit -Wimplicit-function-declaration -Wimplicit-int -Wimport -Wunused -Wunused-function -Wunused-label -Wno-int-to-pointer-cast -Wbad-function-cast -Wmissing-declarations -Wmissing-prototypes -Wnested-externs -Wold-style-definition -Wstrict-prototypes -Wpointer-sign -Wextra -Wredundant-decls -Wunused -Wunused-function -Wunused-parameter -Wunused-value -Wunused-variable -Wformat -Wformat-nonliteral -Wparentheses -Wsequence-point -Wuninitialized -Wundef -Wbad-function-cast -+ -+diff --git a/Makefile.AVX2.PTHREADS.gcc b/Makefile.AVX2.PTHREADS.gcc -+index 44ac3c0..fdf9e45 100644 -+--- a/Makefile.AVX2.PTHREADS.gcc -++++ b/Makefile.AVX2.PTHREADS.gcc -+@@ -1,7 +1,6 @@ -+ # Makefile August 2006 by Alexandros Stamatakis -+ # Makefile cleanup October 2006, Courtesy of Peter Cordes -+ -+-CC = gcc -+ -+ CFLAGS = -D_USE_PTHREADS -D__SIM_SSE3 -O2 -D_GNU_SOURCE -msse3 -fomit-frame-pointer -funroll-loops -D__AVX #-Wall -pedantic -Wunused-parameter -Wredundant-decls -Wreturn-type -Wswitch-default -Wunused-value -Wimplicit -Wimplicit-function-declaration -Wimplicit-int -Wimport -Wunused -Wunused-function -Wunused-label -Wno-int-to-pointer-cast -Wbad-function-cast -Wmissing-declarations -Wmissing-prototypes -Wnested-externs -Wold-style-definition -Wstrict-prototypes -Wdeclaration-after-statement -Wpointer-sign -Wextra -Wredundant-decls -Wunused -Wunused-function -Wunused-parameter -Wunused-value -Wunused-variable -Wformat -Wformat-nonliteral -Wparentheses -Wsequence-point -Wuninitialized -Wundef -Wbad-function-cast -+ -+diff --git a/Makefile.AVX2.gcc b/Makefile.AVX2.gcc -+index 85390a1..7085db5 100644 -+--- a/Makefile.AVX2.gcc -++++ b/Makefile.AVX2.gcc -+@@ -1,7 +1,6 @@ -+ # Makefile August 2006 by Alexandros Stamatakis -+ # Makefile cleanup October 2006, Courtesy of Peter Cordes -+ -+-CC = gcc -+ -+ CFLAGS = -D__SIM_SSE3 -msse3 -D_GNU_SOURCE -O2 -fomit-frame-pointer -funroll-loops -D__AVX #-Wall -Wunused-parameter -Wredundant-decls -Wreturn-type -Wswitch-default -Wunused-value -Wimplicit -Wimplicit-function-declaration -Wimplicit-int -Wimport -Wunused -Wunused-function -Wunused-label -Wno-int-to-pointer-cast -Wbad-function-cast -Wmissing-declarations -Wmissing-prototypes -Wnested-externs -Wold-style-definition -Wstrict-prototypes -Wpointer-sign -Wextra -Wredundant-decls -Wunused -Wunused-function -Wunused-parameter -Wunused-value -Wunused-variable -Wformat -Wformat-nonliteral -Wparentheses -Wsequence-point -Wuninitialized -Wundef -Wbad-function-cast -+ -+diff --git a/Makefile.PTHREADS.gcc b/Makefile.PTHREADS.gcc -+index e5bcb2b..b532b30 100644 -+--- a/Makefile.PTHREADS.gcc -++++ b/Makefile.PTHREADS.gcc -+@@ -1,7 +1,6 @@ -+ # Makefile August 2006 by Alexandros Stamatakis -+ # Makefile cleanup October 2006, Courtesy of Peter Cordes -+ -+-CC = gcc -+ -+ ARCH := $(shell uname -m) -+ ifeq ($(ARCH), x86_64) -+diff --git a/Makefile.SSE3.PTHREADS.gcc b/Makefile.SSE3.PTHREADS.gcc -+index 507cba7..a1c0802 100644 -+--- a/Makefile.SSE3.PTHREADS.gcc -++++ b/Makefile.SSE3.PTHREADS.gcc -+@@ -1,7 +1,6 @@ -+ # Makefile August 2006 by Alexandros Stamatakis -+ # Makefile cleanup October 2006, Courtesy of Peter Cordes -+ -+-CC = gcc -+ -+ ARCH := $(shell uname -m) -+ ifeq ($(ARCH), x86_64) -+diff --git a/Makefile.SSE3.gcc b/Makefile.SSE3.gcc -+index 3749317..d769645 100644 -+--- a/Makefile.SSE3.gcc -++++ b/Makefile.SSE3.gcc -+@@ -1,7 +1,6 @@ -+ # Makefile August 2006 by Alexandros Stamatakis -+ # Makefile cleanup October 2006, Courtesy of Peter Cordes -+ -+-CC = gcc -+ -+ ARCH := $(shell uname -m) -+ ifeq ($(ARCH), x86_64) -+diff --git a/Makefile.gcc b/Makefile.gcc -+index 85a9cab..1a8f032 100644 -+--- a/Makefile.gcc -++++ b/Makefile.gcc -+@@ -1,7 +1,6 @@ -+ # Makefile August 2006 by Alexandros Stamatakis -+ # Makefile cleanup October 2006, Courtesy of Peter Cordes -+ -+-CC = gcc -+ -+ ARCH := $(shell uname -m) -+ ifeq ($(ARCH), x86_64) From f10ff37170ff1b08941dfb02e80faaea150bb405 Mon Sep 17 00:00:00 2001 From: Cornelius Roemer Date: Thu, 11 Jul 2024 11:50:44 +0200 Subject: [PATCH 8/8] Update meta.yaml --- recipes/raxml/meta.yaml | 2 -- 1 file changed, 2 deletions(-) diff --git a/recipes/raxml/meta.yaml b/recipes/raxml/meta.yaml index 72587490ca912..b7e8de64fbd89 100644 --- a/recipes/raxml/meta.yaml +++ b/recipes/raxml/meta.yaml @@ -10,8 +10,6 @@ build: source: url: https://github.com/stamatak/standard-RAxML/archive/refs/tags/v8.2.13.tar.gz sha256: 28e500793324bd7d330b396ef27ea49c9186fa5e1edb3d5439036dc6c33e6067 - patches: - - patch requirements: build: