issue when installing from yaml file #50
Comments
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Thanks for reporting. I’ll have a look in less than a week.
Endre
…On Wed, 10 May 2023 at 19:36, Vince Buffalo ***@***.***> wrote:
Hey ncls folks,
I really like ncls but am having a very odd issue when installing it from
an environment YAML file, which I need to use to include it as a dependency
for a software package. I have created an MRE. Here is the test.yml file:
name: testdependencies:
- pip:
- ncls
Note that it does work when I use:
$ pip install ncls
Collecting ncls
Using cached ncls-0.0.66-cp310-cp310-macosx_11_0_arm64.whl
Requirement already satisfied: numpy in /Users/vsb/miniconda3/lib/python3.10/site-packages (from ncls) (1.24.2)
Installing collected packages: ncls
Successfully installed ncls-0.0.66
but when I create a new conda environment using this test.yml and mamba
(I tried with conda too, but same problem), it compiles and hits an error:
$ mamba env create -n test -f test.yml
Warning: you have pip-installed dependencies in your environment file, but you do not list pip itself as one of your conda dependencies. Conda may not use the correct pip to install your packages, and they may end up in the wrong place. Please add an explicit pip dependency. I'm adding one for you, but still nagging you.
conda-forge/osx-arm64 Using cache
conda-forge/noarch Using cache
bioconda/osx-arm64 Using cache
bioconda/noarch Using cache
pkgs/r/osx-arm64 No change
pkgs/r/noarch No change
pkgs/main/noarch No change
pkgs/main/osx-arm64 No change
Looking for: ['pip']
Transaction
Prefix: /Users/vsb/miniconda3/envs/test
Updating specs:
- pip
Package Version Build Channel Size
─────────────────────────────────────────────────────────────────────────────────────
Install:
─────────────────────────────────────────────────────────────────────────────────────
+ bzip2 1.0.8 h3422bc3_4 conda-forge/osx-arm64 Cached
+ ca-certificates 2023.5.7 hf0a4a13_0 conda-forge/osx-arm64 Cached
+ libexpat 2.5.0 hb7217d7_1 conda-forge/osx-arm64 Cached
+ libffi 3.4.2 h3422bc3_5 conda-forge/osx-arm64 Cached
+ libsqlite 3.41.2 hb31c410_1 conda-forge/osx-arm64 Cached
+ libzlib 1.2.13 h03a7124_4 conda-forge/osx-arm64 Cached
+ ncurses 6.3 h07bb92c_1 conda-forge/osx-arm64 Cached
+ openssl 3.1.0 h53f4e23_3 conda-forge/osx-arm64 Cached
+ pip 23.1.2 pyhd8ed1ab_0 conda-forge/noarch Cached
+ python 3.11.3 h1456518_0_cpython conda-forge/osx-arm64 Cached
+ readline 8.2 h92ec313_1 conda-forge/osx-arm64 Cached
+ setuptools 67.7.2 pyhd8ed1ab_0 conda-forge/noarch Cached
+ tk 8.6.12 he1e0b03_0 conda-forge/osx-arm64 Cached
+ tzdata 2023c h71feb2d_0 conda-forge/noarch Cached
+ wheel 0.40.0 pyhd8ed1ab_0 conda-forge/noarch Cached
+ xz 5.2.6 h57fd34a_0 conda-forge/osx-arm64 Cached
Summary:
Install: 16 packages
Total download: 0 B
─────────────────────────────────────────────────────────────────────────────────────
Downloading and Extracting Packages
Preparing transaction: done
Verifying transaction: done
Executing transaction: done
Installing pip dependencies: - Ran pip subprocess with arguments:
['/Users/vsb/miniconda3/envs/test/bin/python', '-m', 'pip', 'install', '-U', '-r', '/Users/vsb/src/cod_temp_cov/condaenv.y8g_6009.requirements.txt', '--exists-action=b']
Pip subprocess output:
Collecting ncls (from -r /Users/vsb/src/cod_temp_cov/condaenv.y8g_6009.requirements.txt (line 1))
Using cached ncls-0.0.66.tar.gz (494 kB)
Preparing metadata (setup.py): started
Preparing metadata (setup.py): finished with status 'done'
Collecting numpy (from ncls->-r /Users/vsb/src/cod_temp_cov/condaenv.y8g_6009.requirements.txt (line 1))
Using cached numpy-1.24.3-cp311-cp311-macosx_11_0_arm64.whl (13.8 MB)
Building wheels for collected packages: ncls
Building wheel for ncls (setup.py): started
Building wheel for ncls (setup.py): finished with status 'error'
Running setup.py clean for ncls
Failed to build ncls
Pip subprocess error:
error: subprocess-exited-with-error
× python setup.py bdist_wheel did not run successfully.
│ exit code: 1
╰─> [87 lines of output]
Warning: Cannot compile with Cython. Using legacy build.
ncls/src/ncls.c:28981:43: warning: 'ob_shash' is deprecated [-Wdeprecated-declarations]
hash1 = ((PyBytesObject*)s1)->ob_shash;
^
/Users/vsb/miniconda3/envs/test/include/python3.11/cpython/bytesobject.h:7:5: note: 'ob_shash' has been explicitly marked deprecated here
Py_DEPRECATED(3.11) Py_hash_t ob_shash;
^
/Users/vsb/miniconda3/envs/test/include/python3.11/pyport.h:336:54: note: expanded from macro 'Py_DEPRECATED'
#define Py_DEPRECATED(VERSION_UNUSED) __attribute__((__deprecated__))
^
ncls/src/ncls.c:28982:43: warning: 'ob_shash' is deprecated [-Wdeprecated-declarations]
hash2 = ((PyBytesObject*)s2)->ob_shash;
^
/Users/vsb/miniconda3/envs/test/include/python3.11/cpython/bytesobject.h:7:5: note: 'ob_shash' has been explicitly marked deprecated here
Py_DEPRECATED(3.11) Py_hash_t ob_shash;
^
/Users/vsb/miniconda3/envs/test/include/python3.11/pyport.h:336:54: note: expanded from macro 'Py_DEPRECATED'
#define Py_DEPRECATED(VERSION_UNUSED) __attribute__((__deprecated__))
^
ncls/src/ncls.c:29355:23: error: no member named 'exc_type' in 'struct _err_stackitem'
while ((exc_info->exc_type == NULL || exc_info->exc_type == Py_None) &&
~~~~~~~~ ^
ncls/src/ncls.c:29355:53: error: no member named 'exc_type' in 'struct _err_stackitem'
while ((exc_info->exc_type == NULL || exc_info->exc_type == Py_None) &&
~~~~~~~~ ^
ncls/src/ncls.c:29369:23: error: no member named 'exc_type' in 'struct _err_stackitem'
*type = exc_info->exc_type;
~~~~~~~~ ^
ncls/src/ncls.c:29371:21: error: no member named 'exc_traceback' in 'struct _err_stackitem'
*tb = exc_info->exc_traceback;
~~~~~~~~ ^
ncls/src/ncls.c:29385:26: error: no member named 'exc_type' in 'struct _err_stackitem'
tmp_type = exc_info->exc_type;
~~~~~~~~ ^
ncls/src/ncls.c:29387:24: error: no member named 'exc_traceback' in 'struct _err_stackitem'
tmp_tb = exc_info->exc_traceback;
~~~~~~~~ ^
ncls/src/ncls.c:29388:15: error: no member named 'exc_type' in 'struct _err_stackitem'
exc_info->exc_type = type;
~~~~~~~~ ^
ncls/src/ncls.c:29390:15: error: no member named 'exc_traceback' in 'struct _err_stackitem'
exc_info->exc_traceback = tb;
~~~~~~~~ ^
ncls/src/ncls.c:29447:30: error: no member named 'exc_type' in 'struct _err_stackitem'
tmp_type = exc_info->exc_type;
~~~~~~~~ ^
ncls/src/ncls.c:29449:28: error: no member named 'exc_traceback' in 'struct _err_stackitem'
tmp_tb = exc_info->exc_traceback;
~~~~~~~~ ^
ncls/src/ncls.c:29450:19: error: no member named 'exc_type' in 'struct _err_stackitem'
exc_info->exc_type = local_type;
~~~~~~~~ ^
ncls/src/ncls.c:29452:19: error: no member named 'exc_traceback' in 'struct _err_stackitem'
exc_info->exc_traceback = local_tb;
~~~~~~~~ ^
ncls/src/ncls.c:29485:26: error: no member named 'exc_type' in 'struct _err_stackitem'
tmp_type = exc_info->exc_type;
~~~~~~~~ ^
ncls/src/ncls.c:29487:24: error: no member named 'exc_traceback' in 'struct _err_stackitem'
tmp_tb = exc_info->exc_traceback;
~~~~~~~~ ^
ncls/src/ncls.c:29488:15: error: no member named 'exc_type' in 'struct _err_stackitem'
exc_info->exc_type = *type;
~~~~~~~~ ^
ncls/src/ncls.c:29490:15: error: no member named 'exc_traceback' in 'struct _err_stackitem'
exc_info->exc_traceback = *tb;
~~~~~~~~ ^
ncls/src/ncls.c:30888:5: error: incomplete definition of type 'struct _frame'
__Pyx_PyFrame_SetLineNumber(py_frame, py_line);
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
ncls/src/ncls.c:432:62: note: expanded from macro '__Pyx_PyFrame_SetLineNumber'
#define __Pyx_PyFrame_SetLineNumber(frame, lineno) (frame)->f_lineno = (lineno)
~~~~~~~^
/Users/vsb/miniconda3/envs/test/include/python3.11/pytypedefs.h:22:16: note: forward declaration of 'struct _frame'
typedef struct _frame PyFrameObject;
^
ncls/src/ncls.c:32961:20: error: no member named 'exc_type' in 'struct _err_stackitem'
t = exc_state->exc_type;
~~~~~~~~~ ^
ncls/src/ncls.c:32963:21: error: no member named 'exc_traceback' in 'struct _err_stackitem'
tb = exc_state->exc_traceback;
~~~~~~~~~ ^
fatal error: too many errors emitted, stopping now [-ferror-limit=]
2 warnings and 20 errors generated.
error: command '/usr/bin/clang' failed with exit code 1
[end of output]
note: This error originates from a subprocess, and is likely not a problem with pip.
ERROR: Failed building wheel for ncls
ERROR: Could not build wheels for ncls, which is required to install pyproject.toml-based projects
failed
CondaEnvException: Pip failed
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Seems like the specific errors you are getting is due to https://bugs.python.org/issue45711 |
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(I deleted some red herring replies in this thread). I have no solution now, but I think this will be fixed when we are able to build wheels. |
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@vsbuffalo After we started building wheels, it works on my end. Does it work for you too? If not, what wheels are you missing? |
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Hey ncls folks,
I really like ncls but am having a very odd issue when installing it from an environment YAML file, which I need to use to include it as a dependency for a software package. I have created an MRE. Here is the
test.ymlfile:Note that it does work when I use:
but when I create a new conda environment using this
test.ymland mamba (I tried with conda too, but same problem), it compiles and hits an error:The text was updated successfully, but these errors were encountered: