* bug#43855: gnu: python-shapely fails to build
@ 2020-10-07 21:32 Malte Frank Gerdes
2020-10-08 6:44 ` Efraim Flashner
2020-10-08 18:25 ` bug#43855: [PATCH] gnu: python-shapely: Update to 1.7.1 Malte Frank Gerdes
0 siblings, 2 replies; 6+ messages in thread
From: Malte Frank Gerdes @ 2020-10-07 21:32 UTC (permalink / raw)
To: 43855
Hi,
python-shapely fails to build, because it can't find the c libary,
the package definition was not complete (patch at the end).
Now the package finds a C libary but the Test Suite fails with the
follwoing error:
--8<---------------cut here---------------start------------->8---
======================================================================
FAIL: test_operations (tests.test_operations.OperationsTestCase)
----------------------------------------------------------------------
Traceback (most recent call last):
File "/tmp/guix-build-python-shapely-1.6.4.post2.drv-0/Shapely-1.6.4.post2/tests/test_operations.py", line 25, in test_operations
self.assertIsInstance(point.intersection(Point(-1, -1)),
AssertionError: <shapely.geometry.point.Point object at 0x7fffe1544f70> is not an instance of <class 'shapely.geometry.collection.GeometryCollection'>
--8<---------------cut here---------------end--------------->8---
This package was last successfully built on 13th September.
Malte
--8<---------------cut here---------------start------------->8---
diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm
index 459526941b..02744bfc6d 100644
--- a/gnu/packages/python-xyz.scm
+++ b/gnu/packages/python-xyz.scm
@@ -533,13 +533,16 @@ pidof, tty, taskset, pmap.")
(let ((geos (assoc-ref inputs "geos"))
(glibc (assoc-ref inputs ,(if (%current-target-system)
"cross-libc" "libc"))))
- (substitute* "shapely/geos.py"
- (("_lgeos = load_dll\\('geos_c', fallbacks=.*\\)")
- (string-append "_lgeos = load_dll('geos_c', fallbacks=['"
- geos "/lib/libgeos_c.so'])"))
- (("free = load_dll\\('c'\\)\\.free")
- (string-append "free = load_dll('c', fallbacks=['"
- glibc "/lib/libc.so.6']).free"))))
+ (map
+ (lambda (file)
+ (substitute* file
+ (("_lgeos = load_dll\\('geos_c', fallbacks=.*\\)")
+ (string-append "_lgeos = load_dll('geos_c', fallbacks=['"
+ geos "/lib/libgeos_c.so'])"))
+ (("free = load_dll\\('c'\\)\\.free")
+ (string-append "free = load_dll('c', fallbacks=['"
+ glibc "/lib/libc.so.6']).free"))))
+ '("shapely/geos.py" "shapely/_buildcfg.py")))
#t)))))
(home-page "https://github.com/Toblerity/Shapely")
(synopsis "Library for the manipulation and analysis of geometric objects")
--8<---------------cut here---------------end--------------->8---
^ permalink raw reply related [flat|nested] 6+ messages in thread* bug#43855: gnu: python-shapely fails to build
2020-10-07 21:32 bug#43855: gnu: python-shapely fails to build Malte Frank Gerdes
@ 2020-10-08 6:44 ` Efraim Flashner
2020-10-08 12:05 ` Malte Frank Gerdes
2020-10-08 18:25 ` bug#43855: [PATCH] gnu: python-shapely: Update to 1.7.1 Malte Frank Gerdes
1 sibling, 1 reply; 6+ messages in thread
From: Efraim Flashner @ 2020-10-08 6:44 UTC (permalink / raw)
To: Malte Frank Gerdes; +Cc: 43855
[-- Attachment #1: Type: text/plain, Size: 5164 bytes --]
On Wed, Oct 07, 2020 at 11:32:01PM +0200, Malte Frank Gerdes wrote:
> Hi,
>
> python-shapely fails to build, because it can't find the c libary,
> the package definition was not complete (patch at the end).
>
> Now the package finds a C libary but the Test Suite fails with the
> follwoing error:
>
> --8<---------------cut here---------------start------------->8---
> ======================================================================
> FAIL: test_operations (tests.test_operations.OperationsTestCase)
> ----------------------------------------------------------------------
> Traceback (most recent call last):
> File "/tmp/guix-build-python-shapely-1.6.4.post2.drv-0/Shapely-1.6.4.post2/tests/test_operations.py", line 25, in test_operations
> self.assertIsInstance(point.intersection(Point(-1, -1)),
> AssertionError: <shapely.geometry.point.Point object at 0x7fffe1544f70> is not an instance of <class 'shapely.geometry.collection.GeometryCollection'>
> --8<---------------cut here---------------end--------------->8---
>
> This package was last successfully built on 13th September.
>
It turns out this is due to a change in geos with 3.8
https://github.com/Toblerity/Shapely/issues/799
If I cherry-pick the patch to fix it then it passes the test suite. If I
upgrade python-shapely to 1.7.1 the fix is already included but there's
a new build error:
gcc -pthread -shared -Wl,-rpath=/gnu/store/q9rm8h9imazsq2c4qiv2yjpvlvliywqb-python-3.8.2/lib build/temp.linux-x86_64-3.8/shapely/vectorized/_vectorized.o -L/gnu/store/pinvpk9w6izxcwci4ghiwgvykmgsfy2c-geos-3.8.1/lib -L/gnu/store/q9rm8h9imazsq2c4qiv2yjpvlvliywqb-python-3.8.2/lib -lgeos_c -o /tmp/guix-build-python-shapely-1.7.1.drv-0/Shapely-1.7.1/shapely/vectorized/_vectorized.cpython-38-x86_64-linux-gnu.so
warning: no library file corresponding to '/gnu/store/603imkkh2bqs01z8ik0b2ndgpdz0jghk-python-numpy-1.17.3/lib/python3.8/site-packages/numpy/core/include' found (skipping)
warning: no library file corresponding to '/gnu/store/603imkkh2bqs01z8ik0b2ndgpdz0jghk-python-numpy-1.17.3/lib/python3.8/site-packages/numpy/core/include' found (skipping)
error: Could not find lib c or load any of its variants ['libc.musl-x86_64.so.1'].
command "python" "-c" "import setuptools, tokenize;__file__='setup.py';f=getattr(tokenize, 'open', open)(__file__);code=f.read().replace('\\r\\n', '\\n');f.close();exec(compile(code, __file__, 'exec'))" "test" failed with status 1
builder for `/gnu/store/2yz1ybl0156canhfz4vhay0g473c5nwv-python-shapely-1.7.1.drv' failed with exit code 1
build of /gnu/store/2yz1ybl0156canhfz4vhay0g473c5nwv-python-shapely-1.7.1.drv failed
View build log at '/var/log/guix/drvs/2y/z1ybl0156canhfz4vhay0g473c5nwv-python-shapely-1.7.1.drv.bz2'.
guix build: error: build of `/gnu/store/2yz1ybl0156canhfz4vhay0g473c5nwv-python-shapely-1.7.1.drv' failed
Do you want to take a stab at updating python-shapely to 1.7.1?
>
> Malte
>
> --8<---------------cut here---------------start------------->8---
> diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm
> index 459526941b..02744bfc6d 100644
> --- a/gnu/packages/python-xyz.scm
> +++ b/gnu/packages/python-xyz.scm
> @@ -533,13 +533,16 @@ pidof, tty, taskset, pmap.")
> (let ((geos (assoc-ref inputs "geos"))
> (glibc (assoc-ref inputs ,(if (%current-target-system)
> "cross-libc" "libc"))))
> - (substitute* "shapely/geos.py"
> - (("_lgeos = load_dll\\('geos_c', fallbacks=.*\\)")
> - (string-append "_lgeos = load_dll('geos_c', fallbacks=['"
> - geos "/lib/libgeos_c.so'])"))
> - (("free = load_dll\\('c'\\)\\.free")
> - (string-append "free = load_dll('c', fallbacks=['"
> - glibc "/lib/libc.so.6']).free"))))
> + (map
> + (lambda (file)
> + (substitute* file
> + (("_lgeos = load_dll\\('geos_c', fallbacks=.*\\)")
> + (string-append "_lgeos = load_dll('geos_c', fallbacks=['"
> + geos "/lib/libgeos_c.so'])"))
> + (("free = load_dll\\('c'\\)\\.free")
> + (string-append "free = load_dll('c', fallbacks=['"
> + glibc "/lib/libc.so.6']).free"))))
> + '("shapely/geos.py" "shapely/_buildcfg.py")))
> #t)))))
> (home-page "https://github.com/Toblerity/Shapely")
> (synopsis "Library for the manipulation and analysis of geometric objects")
> --8<---------------cut here---------------end--------------->8---
>
substitute* can take a list, so it would be simpler to write this as:
substitute* '("shapely/geos.py"
"shapely/_buildcfg.py")
--
Efraim Flashner <efraim@flashner.co.il> אפרים פלשנר
GPG key = A28B F40C 3E55 1372 662D 14F7 41AA E7DC CA3D 8351
Confidentiality cannot be guaranteed on emails sent or received unencrypted
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^ permalink raw reply [flat|nested] 6+ messages in thread* bug#43855: gnu: python-shapely fails to build
2020-10-08 6:44 ` Efraim Flashner
@ 2020-10-08 12:05 ` Malte Frank Gerdes
2020-10-09 4:59 ` Efraim Flashner
0 siblings, 1 reply; 6+ messages in thread
From: Malte Frank Gerdes @ 2020-10-08 12:05 UTC (permalink / raw)
To: 43855
Efraim Flashner <efraim@flashner.co.il> writes:
> It turns out this is due to a change in geos with 3.8
> https://github.com/Toblerity/Shapely/issues/799
>
> If I cherry-pick the patch to fix it then it passes the test suite. If I
> upgrade python-shapely to 1.7.1 the fix is already included but there's
> a new build error:
>
> gcc -pthread -shared
> -Wl,-rpath=/gnu/store/q9rm8h9imazsq2c4qiv2yjpvlvliywqb-python-3.8.2/lib
> build/temp.linux-x86_64-3.8/shapely/vectorized/_vectorized.o
> -L/gnu/store/pinvpk9w6izxcwci4ghiwgvykmgsfy2c-geos-3.8.1/lib
> -L/gnu/store/q9rm8h9imazsq2c4qiv2yjpvlvliywqb-python-3.8.2/lib -lgeos_c -o
> /tmp/guix-build-python-shapely-1.7.1.drv-0/Shapely-1.7.1/shapely/vectorized/_vectorized.cpython-38-x86_64-linux-gnu.so
> warning: no library file corresponding to
> '/gnu/store/603imkkh2bqs01z8ik0b2ndgpdz0jghk-python-numpy-1.17.3/lib/python3.8/site-packages/numpy/core/include'
> found (skipping)
> warning: no library file corresponding to
> '/gnu/store/603imkkh2bqs01z8ik0b2ndgpdz0jghk-python-numpy-1.17.3/lib/python3.8/site-packages/numpy/core/include'
> found (skipping)
> error: Could not find lib c or load any of its variants ['libc.musl-x86_64.so.1'].
> command "python" "-c" "import setuptools,
> tokenize;__file__='setup.py';f=getattr(tokenize, 'open',
> open)(__file__);code=f.read().replace('\\r\\n',
> '\\n');f.close();exec(compile(code, __file__, 'exec'))" "test" failed with
> status 1
> builder for `/gnu/store/2yz1ybl0156canhfz4vhay0g473c5nwv-python-shapely-1.7.1.drv' failed with exit code 1
> build of /gnu/store/2yz1ybl0156canhfz4vhay0g473c5nwv-python-shapely-1.7.1.drv failed
> View build log at '/var/log/guix/drvs/2y/z1ybl0156canhfz4vhay0g473c5nwv-python-shapely-1.7.1.drv.bz2'.
> guix build: error: build of `/gnu/store/2yz1ybl0156canhfz4vhay0g473c5nwv-python-shapely-1.7.1.drv' failed
>
> Do you want to take a stab at updating python-shapely to 1.7.1?
I can certainly try to fix this. I will look into it in the evening.
BTW: Are you using musl libc as your primary libc? If so, that's cool,
how did you do that? :)
> substitute* can take a list, so it would be simpler to write this as:
> substitute* '("shapely/geos.py"
> "shapely/_buildcfg.py")
One more thing i've learned :)
Malte
^ permalink raw reply [flat|nested] 6+ messages in thread* bug#43855: gnu: python-shapely fails to build
2020-10-08 12:05 ` Malte Frank Gerdes
@ 2020-10-09 4:59 ` Efraim Flashner
0 siblings, 0 replies; 6+ messages in thread
From: Efraim Flashner @ 2020-10-09 4:59 UTC (permalink / raw)
To: Malte Frank Gerdes; +Cc: 43855
[-- Attachment #1: Type: text/plain, Size: 2840 bytes --]
On Thu, Oct 08, 2020 at 02:05:50PM +0200, Malte Frank Gerdes wrote:
> Efraim Flashner <efraim@flashner.co.il> writes:
>
> > It turns out this is due to a change in geos with 3.8
> > https://github.com/Toblerity/Shapely/issues/799
> >
> > If I cherry-pick the patch to fix it then it passes the test suite. If I
> > upgrade python-shapely to 1.7.1 the fix is already included but there's
> > a new build error:
> >
> > gcc -pthread -shared
> > -Wl,-rpath=/gnu/store/q9rm8h9imazsq2c4qiv2yjpvlvliywqb-python-3.8.2/lib
> > build/temp.linux-x86_64-3.8/shapely/vectorized/_vectorized.o
> > -L/gnu/store/pinvpk9w6izxcwci4ghiwgvykmgsfy2c-geos-3.8.1/lib
> > -L/gnu/store/q9rm8h9imazsq2c4qiv2yjpvlvliywqb-python-3.8.2/lib -lgeos_c -o
> > /tmp/guix-build-python-shapely-1.7.1.drv-0/Shapely-1.7.1/shapely/vectorized/_vectorized.cpython-38-x86_64-linux-gnu.so
> > warning: no library file corresponding to
> > '/gnu/store/603imkkh2bqs01z8ik0b2ndgpdz0jghk-python-numpy-1.17.3/lib/python3.8/site-packages/numpy/core/include'
> > found (skipping)
> > warning: no library file corresponding to
> > '/gnu/store/603imkkh2bqs01z8ik0b2ndgpdz0jghk-python-numpy-1.17.3/lib/python3.8/site-packages/numpy/core/include'
> > found (skipping)
> > error: Could not find lib c or load any of its variants ['libc.musl-x86_64.so.1'].
> > command "python" "-c" "import setuptools,
> > tokenize;__file__='setup.py';f=getattr(tokenize, 'open',
> > open)(__file__);code=f.read().replace('\\r\\n',
> > '\\n');f.close();exec(compile(code, __file__, 'exec'))" "test" failed with
> > status 1
> > builder for `/gnu/store/2yz1ybl0156canhfz4vhay0g473c5nwv-python-shapely-1.7.1.drv' failed with exit code 1
> > build of /gnu/store/2yz1ybl0156canhfz4vhay0g473c5nwv-python-shapely-1.7.1.drv failed
> > View build log at '/var/log/guix/drvs/2y/z1ybl0156canhfz4vhay0g473c5nwv-python-shapely-1.7.1.drv.bz2'.
> > guix build: error: build of `/gnu/store/2yz1ybl0156canhfz4vhay0g473c5nwv-python-shapely-1.7.1.drv' failed
> >
> > Do you want to take a stab at updating python-shapely to 1.7.1?
>
> I can certainly try to fix this. I will look into it in the evening.
> BTW: Are you using musl libc as your primary libc? If so, that's cool,
> how did you do that? :)
Ah, no. It comes from the code. I suppose it would be possible to tell
Guix to use musl instead of glibc but I don't think the build system is
set up for that.
> > substitute* can take a list, so it would be simpler to write this as:
> > substitute* '("shapely/geos.py"
> > "shapely/_buildcfg.py")
>
> One more thing i've learned :)
>
> Malte
--
Efraim Flashner <efraim@flashner.co.il> אפרים פלשנר
GPG key = A28B F40C 3E55 1372 662D 14F7 41AA E7DC CA3D 8351
Confidentiality cannot be guaranteed on emails sent or received unencrypted
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^ permalink raw reply [flat|nested] 6+ messages in thread
* bug#43855: [PATCH] gnu: python-shapely: Update to 1.7.1.
2020-10-07 21:32 bug#43855: gnu: python-shapely fails to build Malte Frank Gerdes
2020-10-08 6:44 ` Efraim Flashner
@ 2020-10-08 18:25 ` Malte Frank Gerdes
2020-10-09 5:01 ` Efraim Flashner
1 sibling, 1 reply; 6+ messages in thread
From: Malte Frank Gerdes @ 2020-10-08 18:25 UTC (permalink / raw)
To: 43855
[-- Attachment #1: Type: text/plain, Size: 150 bytes --]
It seems python-shapely assumes musl libc, because the store path of
glibc was missing in one place. Now the Test suite runs without failure.
Malte
[-- Warning: decoded text below may be mangled, UTF-8 assumed --]
[-- Attachment #2: 0001-gnu-python-shapely-Update-to-1.7.1.patch --]
[-- Type: text/x-patch, Size: 2114 bytes --]
From a320ab014d60f5401f409eb37ccb16aa23c32cf1 Mon Sep 17 00:00:00 2001
From: Malte Frank Gerdes <malte.f.gerdes@gmail.com>
Date: Thu, 8 Oct 2020 20:20:12 +0200
Subject: [PATCH] gnu: python-shapely: Update to 1.7.1.
* gnu/packages/python-xyz.scm (python-shapely): Update to 1.7.1.
---
gnu/packages/python-xyz.scm | 9 ++++++---
1 file changed, 6 insertions(+), 3 deletions(-)
diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm
index 459526941b..fa4a4f4954 100644
--- a/gnu/packages/python-xyz.scm
+++ b/gnu/packages/python-xyz.scm
@@ -507,14 +507,14 @@ pidof, tty, taskset, pmap.")
(define-public python-shapely
(package
(name "python-shapely")
- (version "1.6.4.post2")
+ (version "1.7.1")
(source
(origin
(method url-fetch)
(uri (pypi-uri "Shapely" version))
(sha256
(base32
- "03r42fmd9alp6r3q95ad6rldq2f7n1wimrw53zy5kpn33yv7pf64"))))
+ "0adiz4jwmwxk7k1awqifb1a9bj5x4nx4gglb5dz9liam21674h8n"))))
(build-system python-build-system)
(native-inputs
`(("python-cython" ,python-cython)
@@ -533,11 +533,14 @@ pidof, tty, taskset, pmap.")
(let ((geos (assoc-ref inputs "geos"))
(glibc (assoc-ref inputs ,(if (%current-target-system)
"cross-libc" "libc"))))
- (substitute* "shapely/geos.py"
+ (substitute* '("shapely/geos.py" "shapely/_buildcfg.py")
(("_lgeos = load_dll\\('geos_c', fallbacks=.*\\)")
(string-append "_lgeos = load_dll('geos_c', fallbacks=['"
geos "/lib/libgeos_c.so'])"))
(("free = load_dll\\('c'\\)\\.free")
+ (string-append "free = load_dll('c', fallbacks=['"
+ glibc "/lib/libc.so.6']).free"))
+ (("free = load_dll\\('c', fallbacks=.*\\)\\.free")
(string-append "free = load_dll('c', fallbacks=['"
glibc "/lib/libc.so.6']).free"))))
#t)))))
--
2.28.0
^ permalink raw reply related [flat|nested] 6+ messages in thread
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Thread overview: 6+ messages (download: mbox.gz follow: Atom feed
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2020-10-07 21:32 bug#43855: gnu: python-shapely fails to build Malte Frank Gerdes
2020-10-08 6:44 ` Efraim Flashner
2020-10-08 12:05 ` Malte Frank Gerdes
2020-10-09 4:59 ` Efraim Flashner
2020-10-08 18:25 ` bug#43855: [PATCH] gnu: python-shapely: Update to 1.7.1 Malte Frank Gerdes
2020-10-09 5:01 ` Efraim Flashner
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