* [PATCH] Fix pbtranscript-tofu runtime errors.
@ 2015-03-31 11:51 Ricardo Wurmus
2015-03-31 17:38 ` Mark H Weaver
2015-04-01 9:10 ` Ludovic Courtès
0 siblings, 2 replies; 5+ messages in thread
From: Ricardo Wurmus @ 2015-03-31 11:51 UTC (permalink / raw
To: Guix-devel
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Hi Guix,
pbtranscript-tofu has a few more dependencies that the install script
didn't check for. The four patches add packages for as yet unpackaged
dependencies (python-decorator and python-networkx), remove even more
pre-built stuff from the pbtranscript-tofu tarball, and finally add all
missing inputs.
~~ Ricardo
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[-- Attachment #2: 0001-gnu-Add-python-decorator.patch --]
[-- Type: text/x-patch, Size: 1866 bytes --]
From 1e18e4a855659f674203777b454035cbee1a8da6 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <ricardo.wurmus@mdc-berlin.de>
Date: Tue, 31 Mar 2015 12:34:37 +0200
Subject: [PATCH 1/4] gnu: Add python-decorator.
* gnu/packages/python.scm (python-decorator, python2-decorator): New
variables.
---
gnu/packages/python.scm | 28 ++++++++++++++++++++++++++++
1 file changed, 28 insertions(+)
diff --git a/gnu/packages/python.scm b/gnu/packages/python.scm
index 23afec7..f7eb478 100644
--- a/gnu/packages/python.scm
+++ b/gnu/packages/python.scm
@@ -2837,6 +2837,34 @@ PNG, PostScript, PDF, and SVG file output.")
(define-public python2-cairocffi
(package-with-python2 python-cairocffi))
+(define-public python-decorator
+ (package
+ (name "python-decorator")
+ (version "3.4.2")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (string-append
+ "https://pypi.python.org/packages/source/d/decorator/decorator-"
+ version ".tar.gz"))
+ (sha256
+ (base32 "0i2bnlkh0p9gs76hb28mafandcrig2fmv56w9ai6mshxwqn0083k"))))
+ (build-system python-build-system)
+ (arguments '(#:tests? #f)) ; no test target
+ (native-inputs
+ `(("python-setuptools" ,python-setuptools)))
+ (home-page "http://pypi.python.org/pypi/decorator/")
+ (synopsis "Python module to simplify usage of decorators")
+ (description
+ "The aim of the decorator module is to simplify the usage of decorators
+for the average programmer, and to popularize decorators usage giving examples
+of useful decorators, such as memoize, tracing, redirecting_stdout, locked,
+etc. The core of this module is a decorator factory.")
+ (license license:expat)))
+
+(define-public python2-decorator
+ (package-with-python2 python-decorator))
+
(define-public python-ipython
(package
(name "python-ipython")
--
2.1.0
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[-- Attachment #3: 0002-gnu-Add-python-networkx.patch --]
[-- Type: text/x-patch, Size: 1803 bytes --]
From cebbfa900aaba3468654f173cda38bbeb2df31a6 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <ricardo.wurmus@mdc-berlin.de>
Date: Tue, 31 Mar 2015 12:35:09 +0200
Subject: [PATCH 2/4] gnu: Add python-networkx.
* gnu/packages/python.scm (python-networkx, python2-networkx): New variables.
---
gnu/packages/python.scm | 29 +++++++++++++++++++++++++++++
1 file changed, 29 insertions(+)
diff --git a/gnu/packages/python.scm b/gnu/packages/python.scm
index f7eb478..c5cae6d 100644
--- a/gnu/packages/python.scm
+++ b/gnu/packages/python.scm
@@ -3335,6 +3335,35 @@ interfaces in an easy and portable manner.")
(define-public python2-netifaces
(package-with-python2 python-netifaces))
+(define-public python-networkx
+ (package
+ (name "python-networkx")
+ (version "1.9.1")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (string-append
+ "https://pypi.python.org/packages/source/n/networkx/networkx-"
+ version ".tar.gz"))
+ (sha256
+ (base32 "0n8wy0yq1kmdq4wh68mlhwhkndvwzx48lg41a1z0sxxms0wfp033"))))
+ (build-system python-build-system)
+ ;; python-decorator is needed at runtime
+ (propagated-inputs
+ `(("python-decorator" ,python-decorator)))
+ (native-inputs
+ `(("python-setuptools" ,python-setuptools)
+ ("python-nose" ,python-nose)))
+ (home-page "http://networkx.github.io/")
+ (synopsis "Python module for creating and manipulating graphs and networks")
+ (description
+ "NetworkX is a Python package for the creation, manipulation, and study
+of the structure, dynamics, and functions of complex networks.")
+ (license bsd-3)))
+
+(define-public python2-networkx
+ (package-with-python2 python-networkx))
+
(define-public snakemake
(package
(name "snakemake")
--
2.1.0
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[-- Attachment #4: 0003-gnu-pbtranscript-tofu-delete-pre-built-libraries.patch --]
[-- Type: text/x-patch, Size: 1499 bytes --]
From aad74ddc7c66fdb1c58dc89afa7078288ebeb918 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <ricardo.wurmus@mdc-berlin.de>
Date: Tue, 31 Mar 2015 12:37:31 +0200
Subject: [PATCH 3/4] gnu: pbtranscript-tofu: delete pre-built libraries.
* gnu/packages/bioinformatics.scm (pbtranscript-tofu)[arguments]: Delete
"build" directory and any shared objects after unpacking.
---
gnu/packages/bioinformatics.scm | 3 +++
1 file changed, 3 insertions(+)
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 93dc542..f124732 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -830,12 +830,15 @@ files and writing bioinformatics applications.")
(chdir "pbtranscript-tofu/pbtranscript/")
;; Delete clutter
(delete-file-recursively "dist/")
+ (delete-file-recursively "build/")
(delete-file-recursively "setuptools_cython-0.2.1-py2.6.egg/")
(delete-file-recursively "pbtools.pbtranscript.egg-info")
(delete-file "Cython-0.20.1.tar.gz")
(delete-file "setuptools_cython-0.2.1-py2.7.egg")
(delete-file "setuptools_cython-0.2.1.tar.gz")
(delete-file "setup.cfg")
+ (for-each delete-file
+ (find-files "." "\\.so"))
;; files should be writable for install phase
(for-each (lambda (f) (chmod f #o755))
(find-files "." "\\.py")))
--
2.1.0
[-- Warning: decoded text below may be mangled, UTF-8 assumed --]
[-- Attachment #5: 0004-gnu-pbtranscript-tofu-add-missing-inputs.patch --]
[-- Type: text/x-patch, Size: 997 bytes --]
From 8c6999e039048e9dd5063cc1fa4c76b59e5263c0 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <ricardo.wurmus@mdc-berlin.de>
Date: Tue, 31 Mar 2015 13:46:27 +0200
Subject: [PATCH 4/4] gnu: pbtranscript-tofu: add missing inputs.
* gnu/packages/bioinformatics.scm (pbtranscript-tofu)[inputs]: Add missing
runtime inputs.
---
gnu/packages/bioinformatics.scm | 2 ++
1 file changed, 2 insertions(+)
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index f124732..76dd2cd 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -847,6 +847,8 @@ files and writing bioinformatics applications.")
`(("python-cython" ,python2-cython)
("python-numpy" ,python2-numpy)
("python-bx-python" ,python2-bx-python)
+ ("python-networkx" ,python2-networkx)
+ ("python-scipy" ,python2-scipy)
("python-pbcore" ,python2-pbcore)))
(native-inputs
`(("python-nose" ,python2-nose)
--
2.1.0
^ permalink raw reply related [flat|nested] 5+ messages in thread
* Re: [PATCH] Fix pbtranscript-tofu runtime errors.
2015-03-31 11:51 [PATCH] Fix pbtranscript-tofu runtime errors Ricardo Wurmus
@ 2015-03-31 17:38 ` Mark H Weaver
2015-03-31 18:06 ` Ricardo Wurmus
2015-04-01 9:10 ` Ludovic Courtès
1 sibling, 1 reply; 5+ messages in thread
From: Mark H Weaver @ 2015-03-31 17:38 UTC (permalink / raw
To: Ricardo Wurmus; +Cc: Guix-devel
Ricardo Wurmus <ricardo.wurmus@mdc-berlin.de> writes:
> From 1e18e4a855659f674203777b454035cbee1a8da6 Mon Sep 17 00:00:00 2001
> From: Ricardo Wurmus <ricardo.wurmus@mdc-berlin.de>
> Date: Tue, 31 Mar 2015 12:34:37 +0200
> Subject: [PATCH 1/4] gnu: Add python-decorator.
Looks good.
> From cebbfa900aaba3468654f173cda38bbeb2df31a6 Mon Sep 17 00:00:00 2001
> From: Ricardo Wurmus <ricardo.wurmus@mdc-berlin.de>
> Date: Tue, 31 Mar 2015 12:35:09 +0200
> Subject: [PATCH 2/4] gnu: Add python-networkx.
Looks good.
> From aad74ddc7c66fdb1c58dc89afa7078288ebeb918 Mon Sep 17 00:00:00 2001
> From: Ricardo Wurmus <ricardo.wurmus@mdc-berlin.de>
> Date: Tue, 31 Mar 2015 12:37:31 +0200
> Subject: [PATCH 3/4] gnu: pbtranscript-tofu: delete pre-built libraries.
Please capitalize "Delete".
> diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
> index 93dc542..f124732 100644
> --- a/gnu/packages/bioinformatics.scm
> +++ b/gnu/packages/bioinformatics.scm
> @@ -830,12 +830,15 @@ files and writing bioinformatics applications.")
> (chdir "pbtranscript-tofu/pbtranscript/")
> ;; Delete clutter
> (delete-file-recursively "dist/")
> + (delete-file-recursively "build/")
> (delete-file-recursively "setuptools_cython-0.2.1-py2.6.egg/")
> (delete-file-recursively "pbtools.pbtranscript.egg-info")
> (delete-file "Cython-0.20.1.tar.gz")
> (delete-file "setuptools_cython-0.2.1-py2.7.egg")
> (delete-file "setuptools_cython-0.2.1.tar.gz")
> (delete-file "setup.cfg")
> + (for-each delete-file
> + (find-files "." "\\.so"))
> ;; files should be writable for install phase
> (for-each (lambda (f) (chmod f #o755))
> (find-files "." "\\.py")))
In the calls to 'find-files', the patterns should be "\\.so$" and
"\\.py$", respectively.
> From 8c6999e039048e9dd5063cc1fa4c76b59e5263c0 Mon Sep 17 00:00:00 2001
> From: Ricardo Wurmus <ricardo.wurmus@mdc-berlin.de>
> Date: Tue, 31 Mar 2015 13:46:27 +0200
> Subject: [PATCH 4/4] gnu: pbtranscript-tofu: add missing inputs.
Please capitalize "Add".
Otherwise these patches look good to me. Okay to push with these
changes.
Thanks!
Mark
^ permalink raw reply [flat|nested] 5+ messages in thread
* Re: [PATCH] Fix pbtranscript-tofu runtime errors.
2015-03-31 17:38 ` Mark H Weaver
@ 2015-03-31 18:06 ` Ricardo Wurmus
0 siblings, 0 replies; 5+ messages in thread
From: Ricardo Wurmus @ 2015-03-31 18:06 UTC (permalink / raw
To: Mark H Weaver; +Cc: Guix-devel
Mark H Weaver writes:
> Ricardo Wurmus <ricardo.wurmus@mdc-berlin.de> writes:
>
>> From 1e18e4a855659f674203777b454035cbee1a8da6 Mon Sep 17 00:00:00 2001
>> From: Ricardo Wurmus <ricardo.wurmus@mdc-berlin.de>
>> Date: Tue, 31 Mar 2015 12:34:37 +0200
>> Subject: [PATCH 1/4] gnu: Add python-decorator.
>
> Looks good.
>
>> From cebbfa900aaba3468654f173cda38bbeb2df31a6 Mon Sep 17 00:00:00 2001
>> From: Ricardo Wurmus <ricardo.wurmus@mdc-berlin.de>
>> Date: Tue, 31 Mar 2015 12:35:09 +0200
>> Subject: [PATCH 2/4] gnu: Add python-networkx.
>
> Looks good.
>
>> From aad74ddc7c66fdb1c58dc89afa7078288ebeb918 Mon Sep 17 00:00:00 2001
>> From: Ricardo Wurmus <ricardo.wurmus@mdc-berlin.de>
>> Date: Tue, 31 Mar 2015 12:37:31 +0200
>> Subject: [PATCH 3/4] gnu: pbtranscript-tofu: delete pre-built libraries.
>
> Please capitalize "Delete".
>
>> diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
>> index 93dc542..f124732 100644
>> --- a/gnu/packages/bioinformatics.scm
>> +++ b/gnu/packages/bioinformatics.scm
>> @@ -830,12 +830,15 @@ files and writing bioinformatics applications.")
>> (chdir "pbtranscript-tofu/pbtranscript/")
>> ;; Delete clutter
>> (delete-file-recursively "dist/")
>> + (delete-file-recursively "build/")
>> (delete-file-recursively "setuptools_cython-0.2.1-py2.6.egg/")
>> (delete-file-recursively "pbtools.pbtranscript.egg-info")
>> (delete-file "Cython-0.20.1.tar.gz")
>> (delete-file "setuptools_cython-0.2.1-py2.7.egg")
>> (delete-file "setuptools_cython-0.2.1.tar.gz")
>> (delete-file "setup.cfg")
>> + (for-each delete-file
>> + (find-files "." "\\.so"))
>> ;; files should be writable for install phase
>> (for-each (lambda (f) (chmod f #o755))
>> (find-files "." "\\.py")))
>
> In the calls to 'find-files', the patterns should be "\\.so$" and
> "\\.py$", respectively.
>
>> From 8c6999e039048e9dd5063cc1fa4c76b59e5263c0 Mon Sep 17 00:00:00 2001
>> From: Ricardo Wurmus <ricardo.wurmus@mdc-berlin.de>
>> Date: Tue, 31 Mar 2015 13:46:27 +0200
>> Subject: [PATCH 4/4] gnu: pbtranscript-tofu: add missing inputs.
>
> Please capitalize "Add".
>
> Otherwise these patches look good to me. Okay to push with these
> changes.
Thank you for the fast review. I pushed the commits with the suggested
changes.
~~ Ricardo
^ permalink raw reply [flat|nested] 5+ messages in thread
* Re: [PATCH] Fix pbtranscript-tofu runtime errors.
2015-03-31 11:51 [PATCH] Fix pbtranscript-tofu runtime errors Ricardo Wurmus
2015-03-31 17:38 ` Mark H Weaver
@ 2015-04-01 9:10 ` Ludovic Courtès
2015-04-01 20:07 ` Ludovic Courtès
1 sibling, 1 reply; 5+ messages in thread
From: Ludovic Courtès @ 2015-04-01 9:10 UTC (permalink / raw
To: Ricardo Wurmus; +Cc: Guix-devel
Ricardo Wurmus <ricardo.wurmus@mdc-berlin.de> skribis:
> From 1e18e4a855659f674203777b454035cbee1a8da6 Mon Sep 17 00:00:00 2001
> From: Ricardo Wurmus <ricardo.wurmus@mdc-berlin.de>
> Date: Tue, 31 Mar 2015 12:34:37 +0200
> Subject: [PATCH 1/4] gnu: Add python-decorator.
>
> * gnu/packages/python.scm (python-decorator, python2-decorator): New
> variables.
OK.
> From cebbfa900aaba3468654f173cda38bbeb2df31a6 Mon Sep 17 00:00:00 2001
> From: Ricardo Wurmus <ricardo.wurmus@mdc-berlin.de>
> Date: Tue, 31 Mar 2015 12:35:09 +0200
> Subject: [PATCH 2/4] gnu: Add python-networkx.
>
> * gnu/packages/python.scm (python-networkx, python2-networkx): New variables.
OK.
> From aad74ddc7c66fdb1c58dc89afa7078288ebeb918 Mon Sep 17 00:00:00 2001
> From: Ricardo Wurmus <ricardo.wurmus@mdc-berlin.de>
> Date: Tue, 31 Mar 2015 12:37:31 +0200
> Subject: [PATCH 3/4] gnu: pbtranscript-tofu: delete pre-built libraries.
>
> * gnu/packages/bioinformatics.scm (pbtranscript-tofu)[arguments]: Delete
> "build" directory and any shared objects after unpacking.
OK. (So the tarball also contained .so files, bah!)
> From 8c6999e039048e9dd5063cc1fa4c76b59e5263c0 Mon Sep 17 00:00:00 2001
> From: Ricardo Wurmus <ricardo.wurmus@mdc-berlin.de>
> Date: Tue, 31 Mar 2015 13:46:27 +0200
> Subject: [PATCH 4/4] gnu: pbtranscript-tofu: add missing inputs.
>
> * gnu/packages/bioinformatics.scm (pbtranscript-tofu)[inputs]: Add missing
> runtime inputs.
OK!
Thanks,
Ludo’.
^ permalink raw reply [flat|nested] 5+ messages in thread
* Re: [PATCH] Fix pbtranscript-tofu runtime errors.
2015-04-01 9:10 ` Ludovic Courtès
@ 2015-04-01 20:07 ` Ludovic Courtès
0 siblings, 0 replies; 5+ messages in thread
From: Ludovic Courtès @ 2015-04-01 20:07 UTC (permalink / raw
To: Ricardo Wurmus; +Cc: Guix-devel
Somehow I hadn’t seen Mark’s message. Sorry for the noise!
Ludo’.
^ permalink raw reply [flat|nested] 5+ messages in thread
end of thread, other threads:[~2015-04-01 20:07 UTC | newest]
Thread overview: 5+ messages (download: mbox.gz follow: Atom feed
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2015-03-31 11:51 [PATCH] Fix pbtranscript-tofu runtime errors Ricardo Wurmus
2015-03-31 17:38 ` Mark H Weaver
2015-03-31 18:06 ` Ricardo Wurmus
2015-04-01 9:10 ` Ludovic Courtès
2015-04-01 20:07 ` Ludovic Courtès
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