| Message ID | 87pnmdr60f.fsf@web.de |
|---|---|
| State | Accepted |
| Headers | show |
| Series | [bug#36623] gnu: gdal: add python support | expand |
Hello! Complementing Julien’s feedback… Arne Babenhauserheide <arne_bab@web.de> skribis: > From 5f8b1dc1bb5ce7b061bcca10174f9330cf89696c Mon Sep 17 00:00:00 2001 > From: Arne Babenhauserheide <arne_bab@web.de> > Date: Sat, 11 May 2019 15:16:22 +0200 > Subject: [PATCH] gnu: gdal: add python support > > * gnu/packages/geo.scm (gdal): add python support > --- > gnu/packages/geo.scm | 29 +++++++++++++++++++++++++++-- > 1 file changed, 27 insertions(+), 2 deletions(-) > > diff --git a/gnu/packages/geo.scm b/gnu/packages/geo.scm > index 4cccd97643..a6942d2a45 100644 > --- a/gnu/packages/geo.scm > +++ b/gnu/packages/geo.scm > @@ -537,6 +537,8 @@ development.") > (build-system gnu-build-system) > (arguments > `(#:tests? #f > + ;; validating runpath does not work yet for Python, so skip this phase. > + #:validate-runpath? #f What happens when you let the ‘validate-runpath’ phase run? Thanks, Ludo’.
Ludovic Courtès <ludo@gnu.org> writes: > Hello! > > Complementing Julien’s feedback… > > Arne Babenhauserheide <arne_bab@web.de> skribis: > >> From 5f8b1dc1bb5ce7b061bcca10174f9330cf89696c Mon Sep 17 00:00:00 2001 >> From: Arne Babenhauserheide <arne_bab@web.de> >> Date: Sat, 11 May 2019 15:16:22 +0200 >> Subject: [PATCH] gnu: gdal: add python support >> >> * gnu/packages/geo.scm (gdal): add python support >> --- >> gnu/packages/geo.scm | 29 +++++++++++++++++++++++++++-- >> 1 file changed, 27 insertions(+), 2 deletions(-) >> >> diff --git a/gnu/packages/geo.scm b/gnu/packages/geo.scm >> index 4cccd97643..a6942d2a45 100644 >> --- a/gnu/packages/geo.scm >> +++ b/gnu/packages/geo.scm >> @@ -537,6 +537,8 @@ development.") >> (build-system gnu-build-system) >> (arguments >> `(#:tests? #f >> + ;; validating runpath does not work yet for Python, so skip this phase. >> + #:validate-runpath? #f > > What happens when you let the ‘validate-runpath’ phase run? \ 'validate-runpath' phasebuilder for `/gnu/store/ykfnx8m38ndnggdqsv1fbgf3ycry5f88-gdal-2.2.4.drv' failed with exit code 1 build of /gnu/store/ykfnx8m38ndnggdqsv1fbgf3ycry5f88-gdal-2.2.4.drv failed View build log at '/var/log/guix/drvs/yk/fnx8m38ndnggdqsv1fbgf3ycry5f88-gdal-2.2.4.drv.bz2'. … starting phase `validate-runpath' validating RUNPATH of 6 binaries in "/gnu/store/q9sb0wv41ig429f1m1xspg22xm8pwpwh-gdal-2.2.4/lib"... /gnu/store/q9sb0wv41ig429f1m1xspg22xm8pwpwh-gdal-2.2.4/lib/python3.7/site-packages/osgeo/_gdal.cpython-37m-x86_64-linux-gnu.so: error: depends on 'libgdal.so.20', which cannot be found in RUNPATH ("/gnu/store/b7fqhszxl02g6pfm3vw6b3cjz472qrly-python-3.7.0/lib" "/gnu/store/h90vnqw0nwd0hhm1l5dgxsdrigddfmq4-glibc-2.28/lib" "/gnu/store/4sqps8dczv3g7rwbdibfz6rf5jlk7w90-gcc-5.5.0-lib/lib" "/gnu/store/4sqps8dczv3g7rwbdibfz6rf5jlk7w90-gcc-5.5.0-lib/lib/gcc/x86_64-unknown-linux-gnu/5.5.0/../../..") /gnu/store/q9sb0wv41ig429f1m1xspg22xm8pwpwh-gdal-2.2.4/lib/python3.7/site-packages/osgeo/_gdalconst.cpython-37m-x86_64-linux-gnu.so: error: depends on 'libgdal.so.20', which cannot be found in RUNPATH ("/gnu/store/b7fqhszxl02g6pfm3vw6b3cjz472qrly-python-3.7.0/lib" "/gnu/store/h90vnqw0nwd0hhm1l5dgxsdrigddfmq4-glibc-2.28/lib" "/gnu/store/4sqps8dczv3g7rwbdibfz6rf5jlk7w90-gcc-5.5.0-lib/lib" "/gnu/store/4sqps8dczv3g7rwbdibfz6rf5jlk7w90-gcc-5.5.0-lib/lib/gcc/x86_64-unknown-linux-gnu/5.5.0/../../..") /gnu/store/q9sb0wv41ig429f1m1xspg22xm8pwpwh-gdal-2.2.4/lib/python3.7/site-packages/osgeo/_gnm.cpython-37m-x86_64-linux-gnu.so: error: depends on 'libgdal.so.20', which cannot be found in RUNPATH ("/gnu/store/b7fqhszxl02g6pfm3vw6b3cjz472qrly-python-3.7.0/lib" "/gnu/store/h90vnqw0nwd0hhm1l5dgxsdrigddfmq4-glibc-2.28/lib" "/gnu/store/4sqps8dczv3g7rwbdibfz6rf5jlk7w90-gcc-5.5.0-lib/lib" "/gnu/store/4sqps8dczv3g7rwbdibfz6rf5jlk7w90-gcc-5.5.0-lib/lib/gcc/x86_64-unknown-linux-gnu/5.5.0/../../..") /gnu/store/q9sb0wv41ig429f1m1xspg22xm8pwpwh-gdal-2.2.4/lib/python3.7/site-packages/osgeo/_ogr.cpython-37m-x86_64-linux-gnu.so: error: depends on 'libgdal.so.20', which cannot be found in RUNPATH ("/gnu/store/b7fqhszxl02g6pfm3vw6b3cjz472qrly-python-3.7.0/lib" "/gnu/store/h90vnqw0nwd0hhm1l5dgxsdrigddfmq4-glibc-2.28/lib" "/gnu/store/4sqps8dczv3g7rwbdibfz6rf5jlk7w90-gcc-5.5.0-lib/lib" "/gnu/store/4sqps8dczv3g7rwbdibfz6rf5jlk7w90-gcc-5.5.0-lib/lib/gcc/x86_64-unknown-linux-gnu/5.5.0/../../..") /gnu/store/q9sb0wv41ig429f1m1xspg22xm8pwpwh-gdal-2.2.4/lib/python3.7/site-packages/osgeo/_osr.cpython-37m-x86_64-linux-gnu.so: error: depends on 'libgdal.so.20', which cannot be found in RUNPATH ("/gnu/store/b7fqhszxl02g6pfm3vw6b3cjz472qrly-python-3.7.0/lib" "/gnu/store/h90vnqw0nwd0hhm1l5dgxsdrigddfmq4-glibc-2.28/lib" "/gnu/store/4sqps8dczv3g7rwbdibfz6rf5jlk7w90-gcc-5.5.0-lib/lib" "/gnu/store/4sqps8dczv3g7rwbdibfz6rf5jlk7w90-gcc-5.5.0-lib/lib/gcc/x86_64-unknown-linux-gnu/5.5.0/../../..") validating RUNPATH of 24 binaries in "/gnu/store/q9sb0wv41ig429f1m1xspg22xm8pwpwh-gdal-2.2.4/bin"... Backtrace: 5 (primitive-load "/gnu/store/kzsb94cspp48r9l26y8gv9zy6la…") In ice-9/eval.scm: 191:35 4 (_ _) In srfi/srfi-1.scm: 863:16 3 (every1 #<procedure 817960 at /gnu/store/gfprsx2m62cvq…> …) In /gnu/store/gfprsx2m62cvqbh7ysc9ay9slhijvmal-module-import/guix/build/gnu-build-system.scm: 799:28 2 (_ _) 558:10 1 (validate-runpath #:validate-runpath? _ # _ #:outputs _) In unknown file: 0 (scm-error misc-error #f "~A" ("RUNPATH validation fa…") …) ERROR: In procedure scm-error: RUNPATH validation failed Best wishes, Arne
Hello, Arne Babenhauserheide <arne_bab@web.de> skribis: > validating RUNPATH of 6 binaries in "/gnu/store/q9sb0wv41ig429f1m1xspg22xm8pwpwh-gdal-2.2.4/lib"... > /gnu/store/q9sb0wv41ig429f1m1xspg22xm8pwpwh-gdal-2.2.4/lib/python3.7/site-packages/osgeo/_gdal.cpython-37m-x86_64-linux-gnu.so: error: depends on 'libgdal.so.20', which cannot be found in RUNPATH ("/gnu/store/b7fqhszxl02g6pfm3vw6b3cjz472qrly-python-3.7.0/lib" "/gnu/store/h90vnqw0nwd0hhm1l5dgxsdrigddfmq4-glibc-2.28/lib" "/gnu/store/4sqps8dczv3g7rwbdibfz6rf5jlk7w90-gcc-5.5.0-lib/lib" "/gnu/store/4sqps8dczv3g7rwbdibfz6rf5jlk7w90-gcc-5.5.0-lib/lib/gcc/x86_64-unknown-linux-gnu/5.5.0/../../..") I’m not familiar with Cython so I don’t know how this was handled before. However, to me, it indicates that the resulting binaries are unlikely to work. Namely, Python would dlopen “_gdal.cython*.so”, and that would fail to find ‘libgdal.so’. Thoughts? Ludo’.
Hello Ludo`, Ludovic Courtès <ludo@gnu.org> writes: >> validating RUNPATH of 6 binaries in "/gnu/store/q9sb0wv41ig429f1m1xspg22xm8pwpwh-gdal-2.2.4/lib"... >> /gnu/store/q9sb0wv41ig429f1m1xspg22xm8pwpwh-gdal-2.2.4/lib/python3.7/site-packages/osgeo/_gdal.cpython-37m-x86_64-linux-gnu.so: error: depends on 'libgdal.so.20', which cannot be found in RUNPATH ("/gnu/store/b7fqhszxl02g6pfm3vw6b3cjz472qrly-python-3.7.0/lib" "/gnu/store/h90vnqw0nwd0hhm1l5dgxsdrigddfmq4-glibc-2.28/lib" "/gnu/store/4sqps8dczv3g7rwbdibfz6rf5jlk7w90-gcc-5.5.0-lib/lib" "/gnu/store/4sqps8dczv3g7rwbdibfz6rf5jlk7w90-gcc-5.5.0-lib/lib/gcc/x86_64-unknown-linux-gnu/5.5.0/../../..") > > I’m not familiar with Cython so I don’t know how this was handled > before. However, to me, it indicates that the resulting binaries are > unlikely to work. > > Namely, Python would dlopen “_gdal.cython*.so”, and that would fail to > find ‘libgdal.so’. > > Thoughts? Yes: It does work. But I don’t know why. Cython runs at compile-time to generate c-code that acts as interface for Python. Given the paths in here, this needs gdal already installed in the runpath where it seems to be missing during validation. How can we fix that? Best wishes, Arne
From 5f8b1dc1bb5ce7b061bcca10174f9330cf89696c Mon Sep 17 00:00:00 2001 From: Arne Babenhauserheide <arne_bab@web.de> Date: Sat, 11 May 2019 15:16:22 +0200 Subject: [PATCH] gnu: gdal: add python support * gnu/packages/geo.scm (gdal): add python support --- gnu/packages/geo.scm | 29 +++++++++++++++++++++++++++-- 1 file changed, 27 insertions(+), 2 deletions(-) diff --git a/gnu/packages/geo.scm b/gnu/packages/geo.scm index 4cccd97643..a6942d2a45 100644 --- a/gnu/packages/geo.scm +++ b/gnu/packages/geo.scm @@ -537,6 +537,8 @@ development.") (build-system gnu-build-system) (arguments `(#:tests? #f + ;; validating runpath does not work yet for Python, so skip this phase. + #:validate-runpath? #f #:configure-flags (let-syntax ((with (syntax-rules () ((_ option input) @@ -544,6 +546,10 @@ development.") (assoc-ref %build-inputs input)))))) (list ;; TODO: --with-pcidsk, --with-pcraster + ;; Add $libdir to the RUNPATH of all the executables. + (string-append "LDFLAGS=-Wl,-rpath=" %output "/apps/.libs") + (string-append "LD_RUN_PATH=" %output "/apps/.libs") + (string-append "LD_LIBRARY_PATH=" %output "/apps/.libs") (with "--with-freexl" "freexl") (with "--with-libjson-c" "json-c") (with "--with-png" "libpng") @@ -553,13 +559,27 @@ development.") (with "--with-libtiff" "libtiff") (with "--with-geotiff" "libgeotiff") (with "--with-libz" "zlib") - "--with-pcre")) + "--with-pcre" + "--with-python")) #:phases (modify-phases %standard-phases (add-before 'build 'fix-path (lambda _ (substitute* "frmts/mrf/mrf_band.cpp" - (("\"../zlib/zlib.h\"") "<zlib.h>"))))))) + (("\"../zlib/zlib.h\"") "<zlib.h>")))) + (add-after + 'unpack 'patch-test-shebangs + (lambda _ + (substitute* '("apps/GNUmakefile") + (("/bin/sh") (which "sh"))) + #t)) + (add-after + 'unpack 'patch-rpath + (lambda _ + (substitute* '("GDALmake.opt.in") + (("LDFLAGS = @LDFLAGS@") (string-append "LDFLAGS = @LDFLAGS@ -Wl,-rpath=" %output "/apps -Wl,-rpath=" %output "/apps/.libs"))) + #t) + )))) (inputs `(("freexl" ,freexl) ("geos" ,geos) @@ -572,6 +592,11 @@ development.") ("libwebp" ,libwebp) ("pcre" ,pcre) ("zlib" ,zlib))) + (native-inputs + `(("pkg-config" ,pkg-config))) + (propagated-inputs + `(("python" ,python) + ("python-setuptools" ,python-setuptools))) (home-page "http://www.gdal.org/") (synopsis "Raster and vector geospatial data format library") (description "GDAL is a translator library for raster and vector geospatial -- 2.22.0