zhangyiss/spack
1
0
Fork 0
Code Issues Pull Requests Actions Packages Projects Releases Wiki Activity

R: cleanup recipe and fix linking to lapack libraries (#41040)

Browse Source
This commit is contained in:
Harmen Stoppels 2023-11-14 14:44:36 +01:00 committed by GitHub
parent 6fc8679fb4
commit 18ebef60aa
No known key found for this signature in database
GPG Key ID: 4AEE18F83AFDEB23
1 changed files with 36 additions and 34 deletions
Show Stats Download Patch File Download Diff File Expand all files Collapse all files

70
var/spack/repos/builtin/packages/r/package.py
View File

@ -4,7 +4,6 @@
# SPDX-License-Identifier: (Apache-2.0 OR MIT) # SPDX-License-Identifier: (Apache-2.0 OR MIT)
import os import os
import re
from spack.package import * from spack.package import *
@ -60,21 +59,20 @@ class R(AutotoolsPackage):
version("3.1.3", sha256="07e98323935baa38079204bfb9414a029704bb9c0ca5ab317020ae521a377312") version("3.1.3", sha256="07e98323935baa38079204bfb9414a029704bb9c0ca5ab317020ae521a377312")
version("3.1.2", sha256="bcd150afcae0e02f6efb5f35a6ab72432be82e849ec52ce0bb89d8c342a8fa7a") version("3.1.2", sha256="bcd150afcae0e02f6efb5f35a6ab72432be82e849ec52ce0bb89d8c342a8fa7a")
variant(
"external-lapack", default=False, description="Links to externally installed BLAS/LAPACK"
)
variant("X", default=False, description="Enable X11 support (TCLTK, PNG, JPEG, TIFF, CAIRO)") variant("X", default=False, description="Enable X11 support (TCLTK, PNG, JPEG, TIFF, CAIRO)")
variant("memory_profiling", default=False, description="Enable memory profiling") variant("memory_profiling", default=False, description="Enable memory profiling")
variant("rmath", default=False, description="Build standalone Rmath library") variant("rmath", default=False, description="Build standalone Rmath library")
depends_on("blas", when="+external-lapack") depends_on("blas")
depends_on("lapack", when="+external-lapack") depends_on("lapack")
depends_on("bzip2") depends_on("bzip2")
depends_on("curl+libidn2") depends_on("curl+libidn2")
# R didn't anticipate the celebratory non-breaking major version bump of curl 8. # R didn't anticipate the celebratory non-breaking major version bump of curl 8.
depends_on("curl@:7", when="@:4.2") depends_on("curl@:7", when="@:4.2")
depends_on("icu4c") depends_on("icu4c")
depends_on("java") depends_on("java")
depends_on("libtirpc")
depends_on("ncurses") depends_on("ncurses")
depends_on("pcre", when="@:3.6.3") depends_on("pcre", when="@:3.6.3")
depends_on("pcre2", when="@4:") depends_on("pcre2", when="@4:")
@ -84,16 +82,18 @@ class R(AutotoolsPackage):
depends_on("zlib-api") depends_on("zlib-api")
depends_on("zlib@1.2.5:", when="^zlib") depends_on("zlib@1.2.5:", when="^zlib")
depends_on("texinfo", type="build") depends_on("texinfo", type="build")
depends_on("cairo+X+gobject+pdf", when="+X")
depends_on("pango+X", when="+X") with when("+X"):
depends_on("harfbuzz+graphite2", when="+X") depends_on("cairo+X+gobject+pdf")
depends_on("jpeg", when="+X") depends_on("pango+X")
depends_on("libpng", when="+X") depends_on("harfbuzz+graphite2")
depends_on("libtiff", when="+X") depends_on("jpeg")
depends_on("libx11", when="+X") depends_on("libpng")
depends_on("libxmu", when="+X") depends_on("libtiff")
depends_on("libxt", when="+X") depends_on("libx11")
depends_on("tk", when="+X") depends_on("libxmu")
depends_on("libxt")
depends_on("tk")
patch("zlib.patch", when="@:3.3.2") patch("zlib.patch", when="@:3.3.2")
@ -126,32 +126,34 @@ def configure_args(self):
spec = self.spec spec = self.spec
prefix = self.prefix prefix = self.prefix
extra_rpath = join_path(prefix, "rlib", "R", "lib")
blas_flags: str = spec["blas"].libs.ld_flags
lapack_flags: str = spec["lapack"].libs.ld_flags
# R uses LAPACK in Fortran, which requires libmkl_gf_* when gfortran is used.
# TODO: cleaning this up seem to require both compilers as dependencies and use variants.
if spec["lapack"].name in INTEL_MATH_LIBRARIES and "gfortran" in self.compiler.fc:
xlp64 = "ilp64" if spec["lapack"].satisfies("+ilp64") else "lp64"
blas_flags = blas_flags.replace(f"mkl_intel_{xlp64}", f"mkl_gf_{xlp64}")
lapack_flags = lapack_flags.replace(f"mkl_intel_{xlp64}", f"mkl_gf_{xlp64}")
config_args = [ config_args = [
"--with-internal-tzcode", "--with-internal-tzcode",
"--libdir={0}".format(join_path(prefix, "rlib")), "--libdir={0}".format(join_path(prefix, "rlib")),
"--enable-R-shlib", "--enable-R-shlib",
"--enable-BLAS-shlib",
"--enable-R-framework=no", "--enable-R-framework=no",
"--without-recommended-packages", "--without-recommended-packages",
"LDFLAGS=-L{0} -Wl,-rpath,{0}".format(join_path(prefix, "rlib", "R", "lib")), f"LDFLAGS=-Wl,-rpath,{extra_rpath}",
f"--with-blas={blas_flags}",
f"--with-lapack={lapack_flags}",
# cannot disable docs with a normal configure option
"ac_cv_path_PDFLATEX=",
"ac_cv_path_PDFTEX=",
"ac_cv_path_TEX=",
"ac_cv_path_TEXI2DVI=",
] ]
if "+external-lapack" in spec:
if spec["lapack"].name in INTEL_MATH_LIBRARIES and "gfortran" in self.compiler.fc:
mkl_re = re.compile(r"(mkl_)intel(_i?lp64\b)")
config_args.extend(
[
mkl_re.sub(
r"\g<1>gf\g<2>", "--with-blas={0}".format(spec["blas"].libs.ld_flags)
),
"--with-lapack",
]
)
else:
config_args.extend(
["--with-blas={0}".format(spec["blas"].libs.ld_flags), "--with-lapack"]
)
if "+X" in spec: if "+X" in spec:
config_args.append("--with-cairo") config_args.append("--with-cairo")
config_args.append("--with-jpeglib") config_args.append("--with-jpeglib")