error during prefix substitution of text file
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Jeremy McCormick
May 18, 2016, 6:47:26 PM5/18/16
to conda - Public
Hi,
I'm attempting to build this external package with conda.
This is a large C++ framework used in particle physics. It has a Python binding which I'm trying to integrate into my build system.
My meta.yaml looks like this:
--
package:
name: root
version: "6.06.02"
source:
fn: root_v6.06.02.source.tar.gz
requirements:
build:
- python
--
The build.sh is pretty simple and just consists of the following:
--
./configure --prefix=$PREFIX
make install
--
The download and compilation step seems to work fine.
But I'm having some trouble at the step where conda tries to replace the build prefix with the installation dir.
I get this cryptic traceback from the build:
updating shebang: bin/rootbrowse
[...]
Traceback (most recent call last):
File "/work/conda-build/miniconda/bin/conda-build", line 5, in <module>
sys.exit(main())
File "/work/conda-build/miniconda/lib/python2.7/site-packages/conda_build/main_build.py", line 208, in main
args_func(args, p)
File "/work/conda-build/miniconda/lib/python2.7/site-packages/conda_build/main_build.py", line 493, in args_func
args.func(args, p)
File "/work/conda-build/miniconda/lib/python2.7/site-packages/conda_build/main_build.py", line 438, in execute
include_recipe=args.include_recipe)
File "/work/conda-build/miniconda/lib/python2.7/site-packages/conda_build/build.py", line 515, in build
post_build(m, sorted(files2 - files1))
File "/work/conda-build/miniconda/lib/python2.7/site-packages/conda_build/post.py", line 332, in post_build
fix_shebang(f, osx_is_app=osx_is_app)
File "/work/conda-build/miniconda/lib/python2.7/site-packages/conda_build/post.py", line 76, in fix_shebang
fo.write(new_data)
TypeError: must be unicode, not str
When installed normally outside of conda the 'bin/rootbrowse' file is just a short Python script. But here when I look in the build directory, 'bin/rootbrowse' ends up as an empty file with size 0, presumably because conda has clobbered its contents somehow.
Now I'm not sure this is problem with Conda itself (probably not), but I'm unable to determine here what is happening such that this file cannot be processed correctly. There's nothing really special about it. In fact, the file doesn't even contain the build prefix, so it could be skipped entirely! (something which I don't know how to do)
Here's my relevant conda env:
[1019 $] conda info
Using Anaconda Cloud api site https://api.anaconda.org
Current conda install:
platform : linux-64
conda version : 4.0.5
conda-build version : 1.20.1
python version : 2.7.11.final.0
requests version : 2.9.1
[..]
channel URLs : https://repo.continuum.io/pkgs/free/linux-64/
config file : None
is foreign system : False
Can anyone give me some clues here as to what might be going on so that Conda chokes on this file during the substitution of the install prefix into text files?
Is there any way to skip certain files during this step? If so I could not find it in the docs.
Any way to turn on extra debugging info so I can get more details about what conda is doing here?
Thanks.
--Jeremy
Chris Barker
May 18, 2016, 6:56:50 PM5/18/16
to Jeremy McCormick, conda - Public
On Wed, May 18, 2016 at 3:47 PM, Jeremy McCormick <jermcc...@gmail.com> wrote:
updating shebang: bin/rootbrowse
not sure if this will help, but does rootbrowse HAVE a #! line? maybe there is something wrong with it. Or, if it doesn't maybe try adding one...
-CHB
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Jeremy McCormick
May 18, 2016, 7:02:40 PM5/18/16
to Chris Barker, conda - Public
Hi, Chris.
Yes, it does. First line is....
#!/usr/bin/env python
The 'file' command seems to understand it okay....
[1092 $] file /work/sw/root/root-6.06.02/bin/rootbrowse
/work/sw/root/root-6.06.02/bin/rootbrowse: a /usr/bin/env python script text executable
I'm not sure what conda is trying to do here though....shouldn't this be left as is or will conda's actual python install location be substituted here instead? (Forgive the basic questions...I'm just starting to use this tool so I don't fully understand all its conventions.)
Thanks.
--Jeremy
Charles Doutriaux
May 18, 2016, 7:19:20 PM5/18/16
to co...@continuum.io
I don't know if it helps but I ran into the same error, then I
updated my conda-build and it now works happily.
C.
C.
Kale Franz
May 19, 2016, 5:34:10 AM5/19/16
to Charles Doutriaux, conda - Public
conda-build is now (today) at release 1.20.3. If you still encounter the error, go ahead an file it here: https://github.com/conda/conda-build/issues/new
Jeremy McCormick
May 19, 2016, 6:29:38 PM5/19/16
to Kale Franz, Charles Doutriaux, conda - Public
Hi,
The error has now gone away after doing a 'conda update conda-build' to get the latest release.
Thanks!
--Jeremy
conda-build is now (today) at release 1.20.3. If you still encounter the error, go ahead an file it here: https://github.com/conda/conda-build/issues/new
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