-
Notifications
You must be signed in to change notification settings - Fork 0
New issue
Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.
By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.
Already on GitHub? Sign in to your account
Install dependencies in Continuous Integration #63
Comments
Made some progress, after a
This gets us a bit further but the external dependency check now fails. Firstly the external dependencies aren't Building wheels for collected packages: isoslam, cgat, cgatcore
Building wheel for isoslam (pyproject.toml): started
Building wheel for isoslam (pyproject.toml): finished with status 'done'
Created wheel for isoslam: filename=isoslam-0.0.0-py3-none-any.whl size=13305 sha256=eb39d84b147ad37838bf94fe4d44ef8bfdf8404f83bda651ef9f4ea6aad2ede0
Stored in directory: /tmp/pip-ephem-wheel-cache-3khbcrg7/wheels/ea/01/86/084cbcdf45bb92deb6358e1d26242db9d6a4b1c671067ea0b8
Building wheel for cgat (setup.py): started
Building wheel for cgat (setup.py): finished with status 'error'
error: subprocess-exited-with-error
× python setup.py bdist_wheel did not run successfully.
│ exit code: 1
╰─> [460 lines of output]
/tmp/pip-install-vv2ffijk/cgat_e93847922c304a74975b9256a7624f1c/setup.py:52: DeprecationWarning: distutils Version classes are deprecated. Use packaging.version instead.
if LooseVersion(setuptools.__version__) < LooseVersion('1.1'):
WARNING: depency check for UCSC tools(wigToBigWig) failed, error 127
WARNING: depency check for bedtools(bedtools) failed, error 127
running bdist_wheel ...however the building of the C modules also fails... writing manifest file 'cgat.egg-info/SOURCES.txt'
/opt/hostedtoolcache/Python/3.11.10/x64/lib/python3.11/site-packages/setuptools/command/build_py.py:202: SetuptoolsDeprecationWarning: Installing 'cgat.BamTools' as data is deprecated, please list it in `packages`.
!!
############################
# Package would be ignored #
############################
Python recognizes 'cgat.BamTools' as an importable package,
but it is not listed in the `packages` configuration of setuptools.
'cgat.BamTools' has been automatically added to the distribution only
because it may contain data files, but this behavior is likely to change
in future versions of setuptools (and therefore is considered deprecated).
Please make sure that 'cgat.BamTools' is included as a package by using
the `packages` configuration field or the proper discovery methods
(for example by using `find_namespace_packages(...)`/`find_namespace:`
instead of `find_packages(...)`/`find:`).
You can read more about "package discovery" and "data files" on setuptools
documentation page.
!!
check.warn(importable)
/opt/hostedtoolcache/Python/3.11.10/x64/lib/python3.11/site-packages/setuptools/command/build_py.py:202: SetuptoolsDeprecationWarning: Installing 'cgat.Components' as data is deprecated, please list it in `packages`.
!!
############################
# Package would be ignored #
############################
Python recognizes 'cgat.Components' as an importable package,
but it is not listed in the `packages` configuration of setuptools.
'cgat.Components' has been automatically added to the distribution only
because it may contain data files, but this behavior is likely to change
in future versions of setuptools (and therefore is considered deprecated).
Please make sure that 'cgat.Components' is included as a package by using
the `packages` configuration field or the proper discovery methods
(for example by using `find_namespace_packages(...)`/`find_namespace:`
instead of `find_packages(...)`/`find:`).
You can read more about "package discovery" and "data files" on setuptools
documentation page.
!!
check.warn(importable)
/opt/hostedtoolcache/Python/3.11.10/x64/lib/python3.11/site-packages/setuptools/command/build_py.py:202: SetuptoolsDeprecationWarning: Installing 'cgat.FastqTools' as data is deprecated, please list it in `packages`.
!!
############################
# Package would be ignored #
############################
Python recognizes 'cgat.FastqTools' as an importable package,
but it is not listed in the `packages` configuration of setuptools.
'cgat.FastqTools' has been automatically added to the distribution only
because it may contain data files, but this behavior is likely to change
in future versions of setuptools (and therefore is considered deprecated).
Please make sure that 'cgat.FastqTools' is included as a package by using
the `packages` configuration field or the proper discovery methods
(for example by using `find_namespace_packages(...)`/`find_namespace:`
instead of `find_packages(...)`/`find:`).
You can read more about "package discovery" and "data files" on setuptools
documentation page.
!!
check.warn(importable)
/opt/hostedtoolcache/Python/3.11.10/x64/lib/python3.11/site-packages/setuptools/command/build_py.py:202: SetuptoolsDeprecationWarning: Installing 'cgat.VCFTools' as data is deprecated, please list it in `packages`.
!!
############################
# Package would be ignored #
############################
Python recognizes 'cgat.VCFTools' as an importable package,
but it is not listed in the `packages` configuration of setuptools.
'cgat.VCFTools' has been automatically added to the distribution only
because it may contain data files, but this behavior is likely to change
in future versions of setuptools (and therefore is considered deprecated).
Please make sure that 'cgat.VCFTools' is included as a package by using
the `packages` configuration field or the proper discovery methods
(for example by using `find_namespace_packages(...)`/`find_namespace:`
instead of `find_packages(...)`/`find:`).
You can read more about "package discovery" and "data files" on setuptools
documentation page.
!!
check.warn(importable)
copying cgat/GeneModelAnalysis.pyx -> build/lib.linux-x86_64-cpython-311/cgat
creating build/lib.linux-x86_64-cpython-311/cgat/BamTools
copying cgat/BamTools/bamtools.pyx -> build/lib.linux-x86_64-cpython-311/cgat/BamTools
copying cgat/BamTools/geneprofile.pyx -> build/lib.linux-x86_64-cpython-311/cgat/BamTools
copying cgat/BamTools/peakshape.pyx -> build/lib.linux-x86_64-cpython-311/cgat/BamTools
creating build/lib.linux-x86_64-cpython-311/cgat/Components
copying cgat/Components/Components.pyx -> build/lib.linux-x86_64-cpython-311/cgat/Components
copying cgat/Components/connected_components.cpp -> build/lib.linux-x86_64-cpython-311/cgat/Components
copying cgat/Components/connected_components.h -> build/lib.linux-x86_64-cpython-311/cgat/Components
creating build/lib.linux-x86_64-cpython-311/cgat/FastqTools
copying cgat/FastqTools/fastqtools.pyx -> build/lib.linux-x86_64-cpython-311/cgat/FastqTools
creating build/lib.linux-x86_64-cpython-311/cgat/VCFTools
copying cgat/VCFTools/vcftools.pyx -> build/lib.linux-x86_64-cpython-311/cgat/VCFTools
copying cgat/NCL/_cnestedlist.pxd -> build/lib.linux-x86_64-cpython-311/cgat/NCL
copying cgat/NCL/cnestedlist.pyx -> build/lib.linux-x86_64-cpython-311/cgat/NCL
copying cgat/NCL/default.h -> build/lib.linux-x86_64-cpython-311/cgat/NCL
copying cgat/NCL/intervaldb.c -> build/lib.linux-x86_64-cpython-311/cgat/NCL
copying cgat/NCL/intervaldb.h -> build/lib.linux-x86_64-cpython-311/cgat/NCL
running build_ext
Compiling cgat/Components/Components.pyx because it changed.
[1/1] Cythonizing cgat/Components/Components.pyx
building 'cgat.Components' extension
creating build/temp.linux-x86_64-cpython-311
creating build/temp.linux-x86_64-cpython-311/cgat
creating build/temp.linux-x86_64-cpython-311/cgat/Components
gcc -Wsign-compare -DNDEBUG -g -fwrapv -O3 -Wall -fPIC -I/opt/hostedtoolcache/Python/3.11.10/x64/include/python3.11 -c cgat/Components/Components.cpp -o build/temp.linux-x86_64-cpython-311/cgat/Components/Components.o
gcc -Wsign-compare -DNDEBUG -g -fwrapv -O3 -Wall -fPIC -I/opt/hostedtoolcache/Python/3.11.10/x64/include/python3.11 -c cgat/Components/connected_components.cpp -o build/temp.linux-x86_64-cpython-311/cgat/Components/connected_components.o
g++ -shared -Wl,--rpath=/opt/hostedtoolcache/Python/3.11.10/x64/lib -Wl,--rpath=/opt/hostedtoolcache/Python/3.11.10/x64/lib build/temp.linux-x86_64-cpython-311/cgat/Components/Components.o build/temp.linux-x86_64-cpython-311/cgat/Components/connected_components.o -L/opt/hostedtoolcache/Python/3.11.10/x64/lib -o build/lib.linux-x86_64-cpython-311/cgat/Components.cpython-311-x86_64-linux-gnu.so
Compiling cgat/NCL/cnestedlist.pyx because it changed.
[1/1] Cythonizing cgat/NCL/cnestedlist.pyx
warning: cgat/NCL/cnestedlist.pyx:106:24: Non-trivial type declarators in shared declaration (e.g. mix of pointers and values). Each pointer declaration should be on its own line.
warning: cgat/NCL/cnestedlist.pyx:106:28: Non-trivial type declarators in shared declaration (e.g. mix of pointers and values). Each pointer declaration should be on its own line.
warning: cgat/NCL/cnestedlist.pyx:389:24: Non-trivial type declarators in shared declaration (e.g. mix of pointers and values). Each pointer declaration should be on its own line.
warning: cgat/NCL/cnestedlist.pyx:389:28: Non-trivial type declarators in shared declaration (e.g. mix of pointers and values). Each pointer declaration should be on its own line.
warning: cgat/NCL/cnestedlist.pyx:265:26: Non-trivial type declarators in shared declaration (e.g. mix of pointers and values). Each pointer declaration should be on its own line.
warning: cgat/NCL/cnestedlist.pyx:265:30: Non-trivial type declarators in shared declaration (e.g. mix of pointers and values). Each pointer declaration should be on its own line.
warning: cgat/NCL/cnestedlist.pyx:353:26: Non-trivial type declarators in shared declaration (e.g. mix of pointers and values). Each pointer declaration should be on its own line.
warning: cgat/NCL/cnestedlist.pyx:353:30: Non-trivial type declarators in shared declaration (e.g. mix of pointers and values). Each pointer declaration should be on its own line.
building 'cgat.NCL.cnestedlist' extension
creating build/temp.linux-x86_64-cpython-311/cgat/NCL
gcc -Wsign-compare -DNDEBUG -g -fwrapv -O3 -Wall -fPIC -I/opt/hostedtoolcache/Python/3.11.10/x64/include/python3.11 -c cgat/NCL/cnestedlist.c -o build/temp.linux-x86_64-cpython-311/cgat/NCL/cnestedlist.o
gcc -Wsign-compare -DNDEBUG -g -fwrapv -O3 -Wall -fPIC -I/opt/hostedtoolcache/Python/3.11.10/x64/include/python3.11 -c cgat/NCL/intervaldb.c -o build/temp.linux-x86_64-cpython-311/cgat/NCL/intervaldb.o
cgat/NCL/intervaldb.c: In function ‘read_imdiv’:
cgat/NCL/intervaldb.c:486:3: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result]
486 | fread(imdiv,sizeof(IntervalMap),block,ifile);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cgat/NCL/intervaldb.c: In function ‘read_sublist’:
cgat/NCL/intervaldb.c:502:3: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result]
502 | fread(im,sizeof(IntervalMap),subheader->len,ifile);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cgat/NCL/intervaldb.c: In function ‘read_subheader_block’:
cgat/NCL/intervaldb.c:521:3: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result]
521 | fread(subheader,sizeof(SublistHeader),nblock,ifile);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cgat/NCL/intervaldb.c: In function ‘read_binary_files’:
cgat/NCL/intervaldb.c:829:3: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result]
829 | fscanf(ifile,"%d %d %d %d %d",&n,&ntop,&div,&nlists,&nii);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cgat/NCL/intervaldb.c:841:5: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result]
841 | fread(ii,sizeof(IntervalIndex),nii,ifile);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cgat/NCL/intervaldb.c: In function ‘write_binary_files’:
cgat/NCL/intervaldb.c:762:42: warning: ‘%s’ directive writing up to 2047 bytes into a region of size 1004 [-Wformat-overflow=]
762 | sprintf(err_msg,"unable to open file %s for writing",path);
| ^~ ~~~~
In file included from /usr/include/stdio.h:894,
from /opt/hostedtoolcache/Python/3.11.10/x64/include/python3.11/Python.h:24,
from cgat/NCL/default.h:13,
from cgat/NCL/intervaldb.h:4,
from cgat/NCL/intervaldb.c:2:
/usr/include/x86_64-linux-gnu/bits/stdio2.h:38:10: note: ‘__builtin___sprintf_chk’ output between 33 and 2080 bytes into a destination of size 1024
38 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1,
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
39 | __glibc_objsize (__s), __fmt,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
40 | __va_arg_pack ());
| ~~~~~~~~~~~~~~~~~
cgat/NCL/intervaldb.c: In function ‘text_file_to_binaries’:
cgat/NCL/intervaldb.c:1015:19: warning: ‘.size’ directive writing 5 bytes into a region of size between 1 and 2048 [-Wformat-overflow=]
1015 | sprintf(path,"%s.size",filestem); /* SAVE BASIC SIZE INFO*/
| ^~~~~
In file included from /usr/include/stdio.h:894,
from /opt/hostedtoolcache/Python/3.11.10/x64/include/python3.11/Python.h:24,
from cgat/NCL/default.h:13,
from cgat/NCL/intervaldb.h:4,
from cgat/NCL/intervaldb.c:2:
/usr/include/x86_64-linux-gnu/bits/stdio2.h:38:10: note: ‘__builtin___sprintf_chk’ output between 6 and 2053 bytes into a destination of size 2048
38 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1,
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
39 | __glibc_objsize (__s), __fmt,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
40 | __va_arg_pack ());
| ~~~~~~~~~~~~~~~~~
cgat/NCL/intervaldb.c:1029:21: warning: ‘.index’ directive writing 6 bytes into a region of size between 1 and 2048 [-Wformat-overflow=]
1029 | sprintf(path,"%s.index",filestem); /* SAVE INDEX INFO*/
| ^~~~~~
In file included from /usr/include/stdio.h:894,
from /opt/hostedtoolcache/Python/3.11.10/x64/include/python3.11/Python.h:24,
from cgat/NCL/default.h:13,
from cgat/NCL/intervaldb.h:4,
from cgat/NCL/intervaldb.c:2:
/usr/include/x86_64-linux-gnu/bits/stdio2.h:38:10: note: ‘__builtin___sprintf_chk’ output between 7 and 2054 bytes into a destination of size 2048
38 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1,
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
39 | __glibc_objsize (__s), __fmt,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
40 | __va_arg_pack ());
| ~~~~~~~~~~~~~~~~~
cgat/NCL/intervaldb.c:1045:21: warning: ‘.subhead’ directive writing 8 bytes into a region of size between 1 and 2048 [-Wformat-overflow=]
1045 | sprintf(path,"%s.subhead",filestem); /* SAVE THE SUBHEADER LIST */
| ^~~~~~~~
In file included from /usr/include/stdio.h:894,
from /opt/hostedtoolcache/Python/3.11.10/x64/include/python3.11/Python.h:24,
from cgat/NCL/default.h:13,
from cgat/NCL/intervaldb.h:4,
from cgat/NCL/intervaldb.c:2:
/usr/include/x86_64-linux-gnu/bits/stdio2.h:38:10: note: ‘__builtin___sprintf_chk’ output between 9 and 2056 bytes into a destination of size 2048
38 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1,
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
39 | __glibc_objsize (__s), __fmt,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
40 | __va_arg_pack ());
| ~~~~~~~~~~~~~~~~~
cgat/NCL/intervaldb.c:1061:19: warning: ‘.idb’ directive writing 4 bytes into a region of size between 1 and 2048 [-Wformat-overflow=]
1061 | sprintf(path,"%s.idb",filestem); /* SAVE THE ACTUAL INTERVAL DB*/
| ^~~~
In file included from /usr/include/stdio.h:894,
from /opt/hostedtoolcache/Python/3.11.10/x64/include/python3.11/Python.h:24,
from cgat/NCL/default.h:13,
from cgat/NCL/intervaldb.h:4,
from cgat/NCL/intervaldb.c:2:
/usr/include/x86_64-linux-gnu/bits/stdio2.h:38:10: note: ‘__builtin___sprintf_chk’ output between 5 and 2052 bytes into a destination of size 2048
38 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1,
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
39 | __glibc_objsize (__s), __fmt,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
40 | __va_arg_pack ());
| ~~~~~~~~~~~~~~~~~
gcc -shared -Wl,--rpath=/opt/hostedtoolcache/Python/3.11.10/x64/lib -Wl,--rpath=/opt/hostedtoolcache/Python/3.11.10/x64/lib build/temp.linux-x86_64-cpython-311/cgat/NCL/cnestedlist.o build/temp.linux-x86_64-cpython-311/cgat/NCL/intervaldb.o -L/opt/hostedtoolcache/Python/3.11.10/x64/lib -o build/lib.linux-x86_64-cpython-311/cgat/NCL/cnestedlist.cpython-311-x86_64-linux-gnu.so
Compiling cgat/GeneModelAnalysis.pyx because it changed.
[1/1] Cythonizing cgat/GeneModelAnalysis.pyx
Error compiling Cython file:
------------------------------------------------------------
...
utr5, utr3 = utr3, utr5
return utr5, utr3
cimport numpy
DTYPE_INT = numpy.int64
ctypedef numpy.int_t DTYPE_INT_t
^
------------------------------------------------------------
cgat/GeneModelAnalysis.pyx:311:9: 'int_t' is not a type identifier
Traceback (most recent call last):
File "<string>", line 2, in <module>
File "<pip-setuptools-caller>", line 34, in <module>
File "/tmp/pip-install-vv2ffijk/cgat_e93847922c304a74975b9256a7624f1c/setup.py", line 298, in <module>
setup(
File "/opt/hostedtoolcache/Python/3.11.10/x64/lib/python3.11/site-packages/setuptools/__init__.py", line 87, in setup
return distutils.core.setup(**attrs)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/opt/hostedtoolcache/Python/3.11.10/x64/lib/python3.11/site-packages/setuptools/_distutils/core.py", line 185, in setup
return run_commands(dist)
^^^^^^^^^^^^^^^^^^
File "/opt/hostedtoolcache/Python/3.11.10/x64/lib/python3.11/site-packages/setuptools/_distutils/core.py", line 201, in run_commands
dist.run_commands()
File "/opt/hostedtoolcache/Python/3.11.10/x64/lib/python3.11/site-packages/setuptools/_distutils/dist.py", line 968, in run_commands
self.run_command(cmd)
File "/opt/hostedtoolcache/Python/3.11.10/x64/lib/python3.11/site-packages/setuptools/dist.py", line 1217, in run_command
super().run_command(command)
File "/opt/hostedtoolcache/Python/3.11.10/x64/lib/python3.11/site-packages/setuptools/_distutils/dist.py", line 987, in run_command
cmd_obj.run()
File "/opt/hostedtoolcache/Python/3.11.10/x64/lib/python3.11/site-packages/wheel/_bdist_wheel.py", line 387, in run
self.run_command("build")
File "/opt/hostedtoolcache/Python/3.11.10/x64/lib/python3.11/site-packages/setuptools/_distutils/cmd.py", line 319, in run_command
self.distribution.run_command(command)
File "/opt/hostedtoolcache/Python/3.11.10/x64/lib/python3.11/site-packages/setuptools/dist.py", line 1217, in run_command
super().run_command(command)
File "/opt/hostedtoolcache/Python/3.11.10/x64/lib/python3.11/site-packages/setuptools/_distutils/dist.py", line 987, in run_command
cmd_obj.run()
File "/opt/hostedtoolcache/Python/3.11.10/x64/lib/python3.11/site-packages/setuptools/_distutils/command/build.py", line 132, in run
self.run_command(cmd_name)
File "/opt/hostedtoolcache/Python/3.11.10/x64/lib/python3.11/site-packages/setuptools/_distutils/cmd.py", line 319, in run_command
self.distribution.run_command(command)
File "/opt/hostedtoolcache/Python/3.11.10/x64/lib/python3.11/site-packages/setuptools/dist.py", line 1217, in run_command
super().run_command(command)
File "/opt/hostedtoolcache/Python/3.11.10/x64/lib/python3.11/site-packages/setuptools/_distutils/dist.py", line 987, in run_command
cmd_obj.run()
File "/opt/hostedtoolcache/Python/3.11.10/x64/lib/python3.11/site-packages/setuptools/_distutils/command/build_ext.py", line 346, in run
self.build_extensions()
File "/opt/hostedtoolcache/Python/3.11.10/x64/lib/python3.11/site-packages/setuptools/_distutils/command/build_ext.py", line 466, in build_extensions
self._build_extensions_serial()
File "/opt/hostedtoolcache/Python/3.11.10/x64/lib/python3.11/site-packages/setuptools/_distutils/command/build_ext.py", line 492, in _build_extensions_serial
self.build_extension(ext)
File "/opt/hostedtoolcache/Python/3.11.10/x64/lib/python3.11/site-packages/Cython/Distutils/build_ext.py", line 130, in build_extension
new_ext = cythonize(
^^^^^^^^^^
File "/opt/hostedtoolcache/Python/3.11.10/x64/lib/python3.11/site-packages/Cython/Build/Dependencies.py", line 1154, in cythonize
cythonize_one(*args)
File "/opt/hostedtoolcache/Python/3.11.10/x64/lib/python3.11/site-packages/Cython/Build/Dependencies.py", line 1321, in cythonize_one
raise CompileError(None, pyx_file)
Cython.Compiler.Errors.CompileError: cgat/GeneModelAnalysis.pyx
[end of output]
note: This error originates from a subprocess, and is likely not a problem with pip.
ERROR: Failed building wheel for cgat
Running setup.py clean for cgat
Building wheel for cgatcore (setup.py): started
Building wheel for cgatcore (setup.py): finished with status 'done'
Created wheel for cgatcore: filename=cgatcore-0.6.16-py3-none-any.whl size=119476 sha256=e55b56915d6e53eb0caaabcd4dc18d8f9bb6d3ffa0db777a008bb0fd0ac3f377
Stored in directory: /home/runner/.cache/pip/wheels/29/9b/6d/b62a62fcfeb6c07a516b2e5c79c7300b93b7c21e39a36021b8
Successfully built isoslam cgatcore
Failed to build cgat
ERROR: ERROR: Failed to build installable wheels for some pyproject.toml based projects (cgat)
Error: Process completed with exit code 1. It might be related to the deprecation warnings... /opt/hostedtoolcache/Python/3.11.10/x64/lib/python3.11/site-packages/setuptools/command/build_py.py:202: SetuptoolsDeprecationWarning: Installing 'cgat.Components' as data is deprecated, please list it in `packages`.
|
Currently
.github/workflows/test.yaml
does not run because one of the dependencies that is importedcgat
fails to correctly detectnumpy
even though this is explicitly installed before hand.This needs fixing so that we can have Continuous Integration tests run on each merge to
main
to ensure changes to the code base do not break things.For the minimal reproducible example in #62 has been merged so that refactoring can begin but we will need to fix this soon.
The text was updated successfully, but these errors were encountered: