Closed JSeggewiss closed 2 years ago
aakechin
commented
3 years ago @JSeggewiss Thank you for your question! Did use docker version with prepared hg19 or you downloaded version without it and downloaded hg19 separately and uploaded it into the docker container?
JSeggewiss
commented
3 years ago Hi!
Here comes the newbie... Yes, I downloaded the "latest" version incl. hg19. However, I was not able to choose the fasta file in the GUI. Therefore, I downloaded hg19 again and saved it on the HDD. However, it doesn´t seem to work.
How can I download the files "into the docker container"? And how can I choose those files in the GUI, where can I find them?
Thanks in advance!
Jochen
aakechin
commented
3 years ago @JSeggewiss If you downloaded the version with hg19, you can leave the corresponding field as default without any changes. Or, if you downloaded the hg19 reference genome. You need to make index files for it. Then the line "bwa index ucsc.hg19.fasta" is really incorrect. Because your reference genome file is ucsc.hg19.fa.
So, first of all try to use NGS-PrimerPlex with the default hg19 field.
JSeggewiss
commented
3 years ago Hi!
Ok, for that I have to "Prepare hg19 reference", correct? I click it - but it does not become grayed-out.
oem@Linux-SSD:~/Downloads/NGS-PrimerPlex$ python3 main.py
[INFO ] [Logger ] Record log in /home/oem/.kivy/logs/kivy_21-06-09_7.txt
[INFO ] [Kivy ] v2.0.0
[INFO ] [Kivy ] Installed at "/usr/local/lib/python3.8/dist-packages/kivy/init.py"
[INFO ] [Python ] v3.8.6 (default, May 27 2021, 13:28:02)
[GCC 10.2.0]
[INFO ] [Python ] Interpreter at "/usr/bin/python3"
[INFO ] [Factory ] 186 symbols loaded
[INFO ] [Image ] Providers: img_tex, img_dds, img_sdl2, img_pil (img_ffpyplayer ignored)
[INFO ] [Text ] Provider: sdl2
[INFO ] [Window ] Provider: sdl2
[INFO ] [GL ] Using the "OpenGL" graphics system
[INFO ] [GL ] Backend used
xsel - FileNotFoundError: [Errno 2] Datei oder Verzeichnis nicht gefunden: 'xsel'
File "/usr/local/lib/python3.8/dist-packages/kivy/core/init.py", line 58, in core_select_lib
mod = import(name='{2}.{0}.{1}'.format(
File "/usr/local/lib/python3.8/dist-packages/kivy/core/clipboard/clipboard_xsel.py", line 16, in
[INFO ] [GL ] NPOT texture support is available [INFO ] [Base ] Start application main loop Exception in thread Thread-1: Traceback (most recent call last): File "/usr/lib/python3.8/threading.py", line 932, in _bootstrap_inner self.run() File "/usr/lib/python3.8/threading.py", line 870, in run self._target(*self._args, **self._kwargs) File "main.py", line 122, in start_preparing_ref self.ids['prepare_ref_status'].text+='.' AttributeError: 'str' object has no attribute 'text'
What shall I do?
How can I use another genome like hg38? I did it the way described in the manual, but it does not work (see my message above).
Thanks for your patience and your support! It a great tool!
Best regards Jochen
aakechin
commented
3 years ago @JSeggewiss OK, I see that the problem is in the kivy version again... Could you uninstall the current version of kivy (2.0.0) and install 1.11.1 with two commands: pip3 uninstall kivy pip3 install kivy==1.11.1
JSeggewiss
commented
3 years ago Hi!
Next error message:
| em@Linux-SSD:~$ pip3 install kivy==1.11.1 Defaulting to user installation because normal site-packages is not writeable Collecting kivy==1.11.1 Downloading Kivy-1.11.1.tar.gz (23.6 MB) | ████████████████████████████████ | 23.6 MB 6.4 MB/s ERROR: Command errored out with exit status 1: command: /usr/bin/python3 -c 'import io, os, sys, setuptools, tokenize; sys.argv[0] = '"'"'/tmp/pip-install-xcz_ndw8/kivy_bf8f7e36d0b8493bb55274932837381f/setup.py'"'"'; file='"'"'/tmp/pip-install-xcz_ndw8/kivy_bf8f7e36d0b8493bb55274932837381f/setup.py'"'"';f = getattr(tokenize, '"'"'open'"'"', open)(file) if os.path.exists(file) else io.StringIO('"'"'from setuptools import setup; setup()'"'"');code = f.read().replace('"'"'\r\n'"'"', '"'"'\n'"'"');f.close();exec(compile(code, file, '"'"'exec'"'"'))' egg_info --egg-base /tmp/pip-pip-egg-info-chdi8z30 cwd: /tmp/pip-install-xcz_ndw8/kivy_bf8f7e36d0b8493bb55274932837381f/ Complete output (672 lines): fatal: Kein Git-Repository (oder irgendeines der Elternverzeichnisse): .git WARNING: Skipping page https://github.com/kivy-garden/garden/archive/master.zip because the HEAD request got Content-Type: application/zip.The only supported Content-Type is text/html ERROR: Command errored out with exit status 1: command: /usr/bin/python3 -u -c 'import io, os, sys, setuptools, tokenize; sys.argv[0] = '"'"'/tmp/pip-wheel-71rjsm60/cython_48fe37c869b94601bc9ef02b9802fd6f/setup.py'"'"'; file='"'"'/tmp/pip-wheel-71rjsm60/cython_48fe37c869b94601bc9ef02b9802fd6f/setup.py'"'"';f = getattr(tokenize, '"'"'open'"'"', open)(file) if os.path.exists(file) else io.StringIO('"'"'from setuptools import setup; setup()'"'"');code = f.read().replace('"'"'\r\n'"'"', '"'"'\n'"'"');f.close();exec(compile(code, file, '"'"'exec'"'"'))' bdist_wheel -d /tmp/pip-wheel-_8xf3cb7 cwd: /tmp/pip-wheel-71rjsm60/cython_48fe37c869b94601bc9ef02b9802fd6f/ Complete output (598 lines): Unable to find pgen, not compiling formal grammar. running bdist_wheel running build running build_py creating build creating build/lib.linux-x86_64-3.8 copying cython.py -> build/lib.linux-x86_64-3.8 creating build/lib.linux-x86_64-3.8/Cython copying Cython/Debugging.py -> build/lib.linux-x86_64-3.8/Cython copying Cython/init.py -> build/lib.linux-x86_64-3.8/Cython copying Cython/CodeWriter.py -> build/lib.linux-x86_64-3.8/Cython copying Cython/Shadow.py -> build/lib.linux-x86_64-3.8/Cython copying Cython/TestUtils.py -> build/lib.linux-x86_64-3.8/Cython copying Cython/Coverage.py -> build/lib.linux-x86_64-3.8/Cython copying Cython/StringIOTree.py -> build/lib.linux-x86_64-3.8/Cython copying Cython/Utils.py -> build/lib.linux-x86_64-3.8/Cython creating build/lib.linux-x86_64-3.8/Cython/Build copying Cython/Build/init.py -> build/lib.linux-x86_64-3.8/Cython/Build copying Cython/Build/Cythonize.py -> build/lib.linux-x86_64-3.8/Cython/Build copying Cython/Build/BuildExecutable.py -> build/lib.linux-x86_64-3.8/Cython/Build copying Cython/Build/Inline.py -> build/lib.linux-x86_64-3.8/Cython/Build copying Cython/Build/Dependencies.py -> build/lib.linux-x86_64-3.8/Cython/Build copying Cython/Build/Distutils.py -> build/lib.linux-x86_64-3.8/Cython/Build copying Cython/Build/IpythonMagic.py -> build/lib.linux-x86_64-3.8/Cython/Build creating build/lib.linux-x86_64-3.8/Cython/Compiler copying Cython/Compiler/Buffer.py -> build/lib.linux-x86_64-3.8/Cython/Compiler copying Cython/Compiler/Visitor.py -> build/lib.linux-x86_64-3.8/Cython/Compiler copying Cython/Compiler/AnalysedTreeTransforms.py -> build/lib.linux-x86_64-3.8/Cython/Compiler copying Cython/Compiler/Naming.py -> build/lib.linux-x86_64-3.8/Cython/Compiler copying Cython/Compiler/ParseTreeTransforms.py -> build/lib.linux-x86_64-3.8/Cython/Compiler copying Cython/Compiler/init.py -> build/lib.linux-x86_64-3.8/Cython/Compiler copying Cython/Compiler/Errors.py -> build/lib.linux-x86_64-3.8/Cython/Compiler copying Cython/Compiler/Lexicon.py -> build/lib.linux-x86_64-3.8/Cython/Compiler copying Cython/Compiler/FlowControl.py -> build/lib.linux-x86_64-3.8/Cython/Compiler copying Cython/Compiler/Scanning.py -> build/lib.linux-x86_64-3.8/Cython/Compiler copying Cython/Compiler/CodeGeneration.py -> build/lib.linux-x86_64-3.8/Cython/Compiler copying Cython/Compiler/Pythran.py -> build/lib.linux-x86_64-3.8/Cython/Compiler copying Cython/Compiler/MemoryView.py -> build/lib.linux-x86_64-3.8/Cython/Compiler copying Cython/Compiler/Main.py -> build/lib.linux-x86_64-3.8/Cython/Compiler copying Cython/Compiler/CmdLine.py -> build/lib.linux-x86_64-3.8/Cython/Compiler copying Cython/Compiler/StringEncoding.py -> build/lib.linux-x86_64-3.8/Cython/Compiler copying Cython/Compiler/UtilityCode.py -> build/lib.linux-x86_64-3.8/Cython/Compiler copying Cython/Compiler/UtilNodes.py -> build/lib.linux-x86_64-3.8/Cython/Compiler copying Cython/Compiler/TreePath.py -> build/lib.linux-x86_64-3.8/Cython/Compiler copying Cython/Compiler/AutoDocTransforms.py -> build/lib.linux-x86_64-3.8/Cython/Compiler copying Cython/Compiler/Options.py -> build/lib.linux-x86_64-3.8/Cython/Compiler copying Cython/Compiler/Code.py -> build/lib.linux-x86_64-3.8/Cython/Compiler copying Cython/Compiler/CythonScope.py -> build/lib.linux-x86_64-3.8/Cython/Compiler copying Cython/Compiler/TypeInference.py -> build/lib.linux-x86_64-3.8/Cython/Compiler copying Cython/Compiler/Annotate.py -> build/lib.linux-x86_64-3.8/Cython/Compiler copying Cython/Compiler/Optimize.py -> build/lib.linux-x86_64-3.8/Cython/Compiler copying Cython/Compiler/TreeFragment.py -> build/lib.linux-x86_64-3.8/Cython/Compiler copying Cython/Compiler/Parsing.py -> build/lib.linux-x86_64-3.8/Cython/Compiler copying Cython/Compiler/Version.py -> build/lib.linux-x86_64-3.8/Cython/Compiler copying Cython/Compiler/Pipeline.py -> build/lib.linux-x86_64-3.8/Cython/Compiler copying Cython/Compiler/DebugFlags.py -> build/lib.linux-x86_64-3.8/Cython/Compiler copying Cython/Compiler/Builtin.py -> build/lib.linux-x86_64-3.8/Cython/Compiler copying Cython/Compiler/ModuleNode.py -> build/lib.linux-x86_64-3.8/Cython/Compiler copying Cython/Compiler/Nodes.py -> build/lib.linux-x86_64-3.8/Cython/Compiler copying Cython/Compiler/FusedNode.py -> build/lib.linux-x86_64-3.8/Cython/Compiler copying Cython/Compiler/Symtab.py -> build/lib.linux-x86_64-3.8/Cython/Compiler copying Cython/Compiler/Future.py -> build/lib.linux-x86_64-3.8/Cython/Compiler copying Cython/Compiler/ExprNodes.py -> build/lib.linux-x86_64-3.8/Cython/Compiler copying Cython/Compiler/TypeSlots.py -> build/lib.linux-x86_64-3.8/Cython/Compiler copying Cython/Compiler/Interpreter.py -> build/lib.linux-x86_64-3.8/Cython/Compiler copying Cython/Compiler/PyrexTypes.py -> build/lib.linux-x86_64-3.8/Cython/Compiler creating build/lib.linux-x86_64-3.8/Cython/Runtime copying Cython/Runtime/init.py -> build/lib.linux-x86_64-3.8/Cython/Runtime creating build/lib.linux-x86_64-3.8/Cython/Distutils copying Cython/Distutils/init.py -> build/lib.linux-x86_64-3.8/Cython/Distutils copying Cython/Distutils/extension.py -> build/lib.linux-x86_64-3.8/Cython/Distutils copying Cython/Distutils/build_ext.py -> build/lib.linux-x86_64-3.8/Cython/Distutils copying Cython/Distutils/old_build_ext.py -> build/lib.linux-x86_64-3.8/Cython/Distutils creating build/lib.linux-x86_64-3.8/Cython/Debugger copying Cython/Debugger/libpython.py -> build/lib.linux-x86_64-3.8/Cython/Debugger copying Cython/Debugger/init.py -> build/lib.linux-x86_64-3.8/Cython/Debugger copying Cython/Debugger/libcython.py -> build/lib.linux-x86_64-3.8/Cython/Debugger copying Cython/Debugger/Cygdb.py -> build/lib.linux-x86_64-3.8/Cython/Debugger copying Cython/Debugger/DebugWriter.py -> build/lib.linux-x86_64-3.8/Cython/Debugger creating build/lib.linux-x86_64-3.8/Cython/Debugger/Tests copying Cython/Debugger/Tests/init.py -> build/lib.linux-x86_64-3.8/Cython/Debugger/Tests copying Cython/Debugger/Tests/test_libpython_in_gdb.py -> build/lib.linux-x86_64-3.8/Cython/Debugger/Tests copying Cython/Debugger/Tests/TestLibCython.py -> build/lib.linux-x86_64-3.8/Cython/Debugger/Tests copying Cython/Debugger/Tests/test_libcython_in_gdb.py -> build/lib.linux-x86_64-3.8/Cython/Debugger/Tests creating build/lib.linux-x86_64-3.8/Cython/Plex copying Cython/Plex/DFA.py -> build/lib.linux-x86_64-3.8/Cython/Plex copying Cython/Plex/Traditional.py -> build/lib.linux-x86_64-3.8/Cython/Plex copying Cython/Plex/init.py -> build/lib.linux-x86_64-3.8/Cython/Plex copying Cython/Plex/Errors.py -> build/lib.linux-x86_64-3.8/Cython/Plex copying Cython/Plex/Lexicons.py -> build/lib.linux-x86_64-3.8/Cython/Plex copying Cython/Plex/Machines.py -> build/lib.linux-x86_64-3.8/Cython/Plex copying Cython/Plex/Timing.py -> build/lib.linux-x86_64-3.8/Cython/Plex copying Cython/Plex/Transitions.py -> build/lib.linux-x86_64-3.8/Cython/Plex copying Cython/Plex/Regexps.py -> build/lib.linux-x86_64-3.8/Cython/Plex copying Cython/Plex/Scanners.py -> build/lib.linux-x86_64-3.8/Cython/Plex copying Cython/Plex/Actions.py -> build/lib.linux-x86_64-3.8/Cython/Plex creating build/lib.linux-x86_64-3.8/Cython/Tests copying Cython/Tests/init.py -> build/lib.linux-x86_64-3.8/Cython/Tests copying Cython/Tests/TestCodeWriter.py -> build/lib.linux-x86_64-3.8/Cython/Tests copying Cython/Tests/TestJediTyper.py -> build/lib.linux-x86_64-3.8/Cython/Tests copying Cython/Tests/TestStringIOTree.py -> build/lib.linux-x86_64-3.8/Cython/Tests copying Cython/Tests/TestCythonUtils.py -> build/lib.linux-x86_64-3.8/Cython/Tests copying Cython/Tests/xmlrunner.py -> build/lib.linux-x86_64-3.8/Cython/Tests creating build/lib.linux-x86_64-3.8/Cython/Build/Tests copying Cython/Build/Tests/TestCyCache.py -> build/lib.linux-x86_64-3.8/Cython/Build/Tests copying Cython/Build/Tests/init.py -> build/lib.linux-x86_64-3.8/Cython/Build/Tests copying Cython/Build/Tests/TestStripLiterals.py -> build/lib.linux-x86_64-3.8/Cython/Build/Tests copying Cython/Build/Tests/TestIpythonMagic.py -> build/lib.linux-x86_64-3.8/Cython/Build/Tests copying Cython/Build/Tests/TestInline.py -> build/lib.linux-x86_64-3.8/Cython/Build/Tests creating build/lib.linux-x86_64-3.8/Cython/Compiler/Tests copying Cython/Compiler/Tests/TestMemView.py -> build/lib.linux-x86_64-3.8/Cython/Compiler/Tests copying Cython/Compiler/Tests/init.py -> build/lib.linux-x86_64-3.8/Cython/Compiler/Tests copying Cython/Compiler/Tests/TestFlowControl.py -> build/lib.linux-x86_64-3.8/Cython/Compiler/Tests copying Cython/Compiler/Tests/TestTreeFragment.py -> build/lib.linux-x86_64-3.8/Cython/Compiler/Tests copying Cython/Compiler/Tests/TestSignatureMatching.py -> build/lib.linux-x86_64-3.8/Cython/Compiler/Tests copying Cython/Compiler/Tests/TestParseTreeTransforms.py -> build/lib.linux-x86_64-3.8/Cython/Compiler/Tests copying Cython/Compiler/Tests/TestCmdLine.py -> build/lib.linux-x86_64-3.8/Cython/Compiler/Tests copying Cython/Compiler/Tests/TestTreePath.py -> build/lib.linux-x86_64-3.8/Cython/Compiler/Tests copying Cython/Compiler/Tests/TestTypes.py -> build/lib.linux-x86_64-3.8/Cython/Compiler/Tests copying Cython/Compiler/Tests/TestBuffer.py -> build/lib.linux-x86_64-3.8/Cython/Compiler/Tests copying Cython/Compiler/Tests/TestGrammar.py -> build/lib.linux-x86_64-3.8/Cython/Compiler/Tests copying Cython/Compiler/Tests/TestUtilityLoad.py -> build/lib.linux-x86_64-3.8/Cython/Compiler/Tests copying Cython/Compiler/Tests/TestVisitor.py -> build/lib.linux-x86_64-3.8/Cython/Compiler/Tests creating build/lib.linux-x86_64-3.8/Cython/Utility copying Cython/Utility/init.py -> build/lib.linux-x86_64-3.8/Cython/Utility creating build/lib.linux-x86_64-3.8/Cython/Tempita copying Cython/Tempita/init.py -> build/lib.linux-x86_64-3.8/Cython/Tempita copying Cython/Tempita/_looper.py -> build/lib.linux-x86_64-3.8/Cython/Tempita copying Cython/Tempita/_tempita.py -> build/lib.linux-x86_64-3.8/Cython/Tempita copying Cython/Tempita/compat3.py -> build/lib.linux-x86_64-3.8/Cython/Tempita creating build/lib.linux-x86_64-3.8/pyximport copying pyximport/init.py -> build/lib.linux-x86_64-3.8/pyximport copying pyximport/pyximport.py -> build/lib.linux-x86_64-3.8/pyximport copying pyximport/pyxbuild.py -> build/lib.linux-x86_64-3.8/pyximport creating build/lib.linux-x86_64-3.8/Cython/Includes copying Cython/Includes/openmp.pxd -> build/lib.linux-x86_64-3.8/Cython/Includes creating build/lib.linux-x86_64-3.8/Cython/Includes/cpython copying Cython/Includes/cpython/set.pxd -> build/lib.linux-x86_64-3.8/Cython/Includes/cpython copying Cython/Includes/cpython/longintrepr.pxd -> build/lib.linux-x86_64-3.8/Cython/Includes/cpython copying Cython/Includes/cpython/pythread.pxd -> build/lib.linux-x86_64-3.8/Cython/Includes/cpython copying Cython/Includes/cpython/long.pxd -> build/lib.linux-x86_64-3.8/Cython/Includes/cpython copying Cython/Includes/cpython/pycapsule.pxd -> build/lib.linux-x86_64-3.8/Cython/Includes/cpython copying Cython/Includes/cpython/iterator.pxd -> build/lib.linux-x86_64-3.8/Cython/Includes/cpython copying Cython/Includes/cpython/int.pxd -> build/lib.linux-x86_64-3.8/Cython/Includes/cpython copying Cython/Includes/cpython/bool.pxd -> build/lib.linux-x86_64-3.8/Cython/Includes/cpython copying Cython/Includes/cpython/cobject.pxd -> build/lib.linux-x86_64-3.8/Cython/Includes/cpython copying Cython/Includes/cpython/ref.pxd -> build/lib.linux-x86_64-3.8/Cython/Includes/cpython copying Cython/Includes/cpython/tuple.pxd -> build/lib.linux-x86_64-3.8/Cython/Includes/cpython copying Cython/Includes/cpython/object.pxd -> build/lib.linux-x86_64-3.8/Cython/Includes/cpython copying Cython/Includes/cpython/instance.pxd -> build/lib.linux-x86_64-3.8/Cython/Includes/cpython copying Cython/Includes/cpython/string.pxd -> build/lib.linux-x86_64-3.8/Cython/Includes/cpython copying Cython/Includes/cpython/init.pxd -> build/lib.linux-x86_64-3.8/Cython/Includes/cpython copying Cython/Includes/cpython/float.pxd -> build/lib.linux-x86_64-3.8/Cython/Includes/cpython copying Cython/Includes/cpython/slice.pxd -> build/lib.linux-x86_64-3.8/Cython/Includes/cpython copying Cython/Includes/cpython/method.pxd -> build/lib.linux-x86_64-3.8/Cython/Includes/cpython copying Cython/Includes/cpython/getargs.pxd -> build/lib.linux-x86_64-3.8/Cython/Includes/cpython copying Cython/Includes/cpython/mem.pxd -> build/lib.linux-x86_64-3.8/Cython/Includes/cpython copying Cython/Includes/cpython/exc.pxd -> build/lib.linux-x86_64-3.8/Cython/Includes/cpython copying Cython/Includes/cpython/dict.pxd -> build/lib.linux-x86_64-3.8/Cython/Includes/cpython copying Cython/Includes/cpython/datetime.pxd -> build/lib.linux-x86_64-3.8/Cython/Includes/cpython copying Cython/Includes/cpython/type.pxd -> build/lib.linux-x86_64-3.8/Cython/Includes/cpython copying Cython/Includes/cpython/oldbuffer.pxd -> build/lib.linux-x86_64-3.8/Cython/Includes/cpython copying Cython/Includes/cpython/bytearray.pxd -> build/lib.linux-x86_64-3.8/Cython/Includes/cpython copying Cython/Includes/cpython/complex.pxd -> build/lib.linux-x86_64-3.8/Cython/Includes/cpython copying Cython/Includes/cpython/unicode.pxd -> build/lib.linux-x86_64-3.8/Cython/Includes/cpython copying Cython/Includes/cpython/array.pxd -> build/lib.linux-x86_64-3.8/Cython/Includes/cpython copying Cython/Includes/cpython/function.pxd -> build/lib.linux-x86_64-3.8/Cython/Includes/cpython copying Cython/Includes/cpython/pystate.pxd -> build/lib.linux-x86_64-3.8/Cython/Includes/cpython copying Cython/Includes/cpython/list.pxd -> build/lib.linux-x86_64-3.8/Cython/Includes/cpython copying Cython/Includes/cpython/buffer.pxd -> build/lib.linux-x86_64-3.8/Cython/Includes/cpython copying Cython/Includes/cpython/mapping.pxd -> build/lib.linux-x86_64-3.8/Cython/Includes/cpython copying Cython/Includes/cpython/version.pxd -> build/lib.linux-x86_64-3.8/Cython/Includes/cpython copying Cython/Includes/cpython/module.pxd -> build/lib.linux-x86_64-3.8/Cython/Includes/cpython copying Cython/Includes/cpython/number.pxd -> build/lib.linux-x86_64-3.8/Cython/Includes/cpython copying Cython/Includes/cpython/sequence.pxd -> build/lib.linux-x86_64-3.8/Cython/Includes/cpython copying Cython/Includes/cpython/pylifecycle.pxd -> build/lib.linux-x86_64-3.8/Cython/Includes/cpython copying Cython/Includes/cpython/bytes.pxd -> build/lib.linux-x86_64-3.8/Cython/Includes/cpython copying Cython/Includes/cpython/weakref.pxd -> build/lib.linux-x86_64-3.8/Cython/Includes/cpython copying Cython/Includes/cpython/ceval.pxd -> build/lib.linux-x86_64-3.8/Cython/Includes/cpython creating build/lib.linux-x86_64-3.8/Cython/Includes/libcpp copying Cython/Includes/libcpp/utility.pxd -> build/lib.linux-x86_64-3.8/Cython/Includes/libcpp copying Cython/Includes/libcpp/queue.pxd -> build/lib.linux-x86_64-3.8/Cython/Includes/libcpp copying Cython/Includes/libcpp/set.pxd -> build/lib.linux-x86_64-3.8/Cython/Includes/libcpp copying Cython/Includes/libcpp/map.pxd -> build/lib.linux-x86_64-3.8/Cython/Includes/libcpp copying Cython/Includes/libcpp/forward_list.pxd -> build/lib.linux-x86_64-3.8/Cython/Includes/libcpp copying Cython/Includes/libcpp/iterator.pxd -> build/lib.linux-x86_64-3.8/Cython/Includes/libcpp copying Cython/Includes/libcpp/pair.pxd -> build/lib.linux-x86_64-3.8/Cython/Includes/libcpp copying Cython/Includes/libcpp/unordered_set.pxd -> build/lib.linux-x86_64-3.8/Cython/Includes/libcpp copying Cython/Includes/libcpp/limits.pxd -> build/lib.linux-x86_64-3.8/Cython/Includes/libcpp copying Cython/Includes/libcpp/algorithm.pxd -> build/lib.linux-x86_64-3.8/Cython/Includes/libcpp copying Cython/Includes/libcpp/typeindex.pxd -> build/lib.linux-x86_64-3.8/Cython/Includes/libcpp copying Cython/Includes/libcpp/string.pxd -> build/lib.linux-x86_64-3.8/Cython/Includes/libcpp copying Cython/Includes/libcpp/init.pxd -> build/lib.linux-x86_64-3.8/Cython/Includes/libcpp copying Cython/Includes/libcpp/vector.pxd -> build/lib.linux-x86_64-3.8/Cython/Includes/libcpp copying Cython/Includes/libcpp/cast.pxd -> build/lib.linux-x86_64-3.8/Cython/Includes/libcpp copying Cython/Includes/libcpp/typeinfo.pxd -> build/lib.linux-x86_64-3.8/Cython/Includes/libcpp copying Cython/Includes/libcpp/memory.pxd -> build/lib.linux-x86_64-3.8/Cython/Includes/libcpp copying Cython/Includes/libcpp/deque.pxd -> build/lib.linux-x86_64-3.8/Cython/Includes/libcpp copying Cython/Includes/libcpp/complex.pxd -> build/lib.linux-x86_64-3.8/Cython/Includes/libcpp copying Cython/Includes/libcpp/unordered_map.pxd -> build/lib.linux-x86_64-3.8/Cython/Includes/libcpp copying Cython/Includes/libcpp/list.pxd -> build/lib.linux-x86_64-3.8/Cython/Includes/libcpp copying Cython/Includes/libcpp/stack.pxd -> build/lib.linux-x86_64-3.8/Cython/Includes/libcpp copying Cython/Includes/libcpp/functional.pxd -> build/lib.linux-x86_64-3.8/Cython/Includes/libcpp creating build/lib.linux-x86_64-3.8/Cython/Includes/numpy copying Cython/Includes/numpy/init.pxd -> build/lib.linux-x86_64-3.8/Cython/Includes/numpy copying Cython/Includes/numpy/math.pxd -> build/lib.linux-x86_64-3.8/Cython/Includes/numpy creating build/lib.linux-x86_64-3.8/Cython/Includes/Deprecated copying Cython/Includes/Deprecated/python_mem.pxd -> build/lib.linux-x86_64-3.8/Cython/Includes/Deprecated copying Cython/Includes/Deprecated/stdlib.pxd -> build/lib.linux-x86_64-3.8/Cython/Includes/Deprecated copying Cython/Includes/Deprecated/python_complex.pxd -> build/lib.linux-x86_64-3.8/Cython/Includes/Deprecated copying Cython/Includes/Deprecated/python_sequence.pxd -> build/lib.linux-x86_64-3.8/Cython/Includes/Deprecated copying Cython/Includes/Deprecated/python_bytes.pxd -> build/lib.linux-x86_64-3.8/Cython/Includes/Deprecated copying Cython/Includes/Deprecated/python_list.pxd -> build/lib.linux-x86_64-3.8/Cython/Includes/Deprecated copying Cython/Includes/Deprecated/python_version.pxd -> build/lib.linux-x86_64-3.8/Cython/Includes/Deprecated copying Cython/Includes/Deprecated/python_module.pxd -> build/lib.linux-x86_64-3.8/Cython/Includes/Deprecated copying Cython/Includes/Deprecated/python_oldbuffer.pxd -> build/lib.linux-x86_64-3.8/Cython/Includes/Deprecated copying Cython/Includes/Deprecated/python.pxd -> build/lib.linux-x86_64-3.8/Cython/Includes/Deprecated copying Cython/Includes/Deprecated/python_method.pxd -> build/lib.linux-x86_64-3.8/Cython/Includes/Deprecated copying Cython/Includes/Deprecated/python_instance.pxd -> build/lib.linux-x86_64-3.8/Cython/Includes/Deprecated copying Cython/Includes/Deprecated/stdio.pxd -> build/lib.linux-x86_64-3.8/Cython/Includes/Deprecated copying Cython/Includes/Deprecated/python_string.pxd -> build/lib.linux-x86_64-3.8/Cython/Includes/Deprecated copying Cython/Includes/Deprecated/stl.pxd -> build/lib.linux-x86_64-3.8/Cython/Includes/Deprecated copying Cython/Includes/Deprecated/python_getargs.pxd -> build/lib.linux-x86_64-3.8/Cython/Includes/Deprecated copying Cython/Includes/Deprecated/python_object.pxd -> build/lib.linux-x86_64-3.8/Cython/Includes/Deprecated copying Cython/Includes/Deprecated/python_iterator.pxd -> build/lib.linux-x86_64-3.8/Cython/Includes/Deprecated copying Cython/Includes/Deprecated/python_mapping.pxd -> build/lib.linux-x86_64-3.8/Cython/Includes/Deprecated copying Cython/Includes/Deprecated/python_weakref.pxd -> build/lib.linux-x86_64-3.8/Cython/Includes/Deprecated copying Cython/Includes/Deprecated/python_exc.pxd -> build/lib.linux-x86_64-3.8/Cython/Includes/Deprecated copying Cython/Includes/Deprecated/python_function.pxd -> build/lib.linux-x86_64-3.8/Cython/Includes/Deprecated copying Cython/Includes/Deprecated/python_buffer.pxd -> build/lib.linux-x86_64-3.8/Cython/Includes/Deprecated copying Cython/Includes/Deprecated/python_tuple.pxd -> build/lib.linux-x86_64-3.8/Cython/Includes/Deprecated copying Cython/Includes/Deprecated/python_ref.pxd -> build/lib.linux-x86_64-3.8/Cython/Includes/Deprecated copying Cython/Includes/Deprecated/python_type.pxd -> build/lib.linux-x86_64-3.8/Cython/Includes/Deprecated copying Cython/Includes/Deprecated/python_dict.pxd -> build/lib.linux-x86_64-3.8/Cython/Includes/Deprecated copying Cython/Includes/Deprecated/python_cobject.pxd -> build/lib.linux-x86_64-3.8/Cython/Includes/Deprecated copying Cython/Includes/Deprecated/python_set.pxd -> build/lib.linux-x86_64-3.8/Cython/Includes/Deprecated copying Cython/Includes/Deprecated/python_pycapsule.pxd -> build/lib.linux-x86_64-3.8/Cython/Includes/Deprecated copying Cython/Includes/Deprecated/python_float.pxd -> build/lib.linux-x86_64-3.8/Cython/Includes/Deprecated copying Cython/Includes/Deprecated/python_number.pxd -> build/lib.linux-x86_64-3.8/Cython/Includes/Deprecated copying Cython/Includes/Deprecated/python_int.pxd -> build/lib.linux-x86_64-3.8/Cython/Includes/Deprecated copying Cython/Includes/Deprecated/python_long.pxd -> build/lib.linux-x86_64-3.8/Cython/Includes/Deprecated copying Cython/Includes/Deprecated/python_bool.pxd -> build/lib.linux-x86_64-3.8/Cython/Includes/Deprecated copying Cython/Includes/Deprecated/python_unicode.pxd -> build/lib.linux-x86_64-3.8/Cython/Includes/Deprecated creating build/lib.linux-x86_64-3.8/Cython/Includes/posix copying Cython/Includes/posix/fcntl.pxd -> build/lib.linux-x86_64-3.8/Cython/Includes/posix copying Cython/Includes/posix/stdlib.pxd -> build/lib.linux-x86_64-3.8/Cython/Includes/posix copying Cython/Includes/posix/types.pxd -> build/lib.linux-x86_64-3.8/Cython/Includes/posix copying Cython/Includes/posix/signal.pxd -> build/lib.linux-x86_64-3.8/Cython/Includes/posix copying Cython/Includes/posix/select.pxd -> build/lib.linux-x86_64-3.8/Cython/Includes/posix copying Cython/Includes/posix/stdio.pxd -> build/lib.linux-x86_64-3.8/Cython/Includes/posix copying Cython/Includes/posix/wait.pxd -> build/lib.linux-x86_64-3.8/Cython/Includes/posix copying Cython/Includes/posix/strings.pxd -> build/lib.linux-x86_64-3.8/Cython/Includes/posix copying Cython/Includes/posix/ioctl.pxd -> build/lib.linux-x86_64-3.8/Cython/Includes/posix copying Cython/Includes/posix/init.pxd -> build/lib.linux-x86_64-3.8/Cython/Includes/posix copying Cython/Includes/posix/unistd.pxd -> build/lib.linux-x86_64-3.8/Cython/Includes/posix copying Cython/Includes/posix/stat.pxd -> build/lib.linux-x86_64-3.8/Cython/Includes/posix copying Cython/Includes/posix/time.pxd -> build/lib.linux-x86_64-3.8/Cython/Includes/posix copying Cython/Includes/posix/mman.pxd -> build/lib.linux-x86_64-3.8/Cython/Includes/posix copying Cython/Includes/posix/dlfcn.pxd -> build/lib.linux-x86_64-3.8/Cython/Includes/posix copying Cython/Includes/posix/resource.pxd -> build/lib.linux-x86_64-3.8/Cython/Includes/posix creating build/lib.linux-x86_64-3.8/Cython/Includes/libc copying Cython/Includes/libc/stdint.pxd -> build/lib.linux-x86_64-3.8/Cython/Includes/libc copying Cython/Includes/libc/stdlib.pxd -> build/lib.linux-x86_64-3.8/Cython/Includes/libc copying Cython/Includes/libc/signal.pxd -> build/lib.linux-x86_64-3.8/Cython/Includes/libc copying Cython/Includes/libc/stdio.pxd -> build/lib.linux-x86_64-3.8/Cython/Includes/libc copying Cython/Includes/libc/limits.pxd -> build/lib.linux-x86_64-3.8/Cython/Includes/libc copying Cython/Includes/libc/errno.pxd -> build/lib.linux-x86_64-3.8/Cython/Includes/libc copying Cython/Includes/libc/string.pxd -> build/lib.linux-x86_64-3.8/Cython/Includes/libc copying Cython/Includes/libc/init.pxd -> build/lib.linux-x86_64-3.8/Cython/Includes/libc copying Cython/Includes/libc/float.pxd -> build/lib.linux-x86_64-3.8/Cython/Includes/libc copying Cython/Includes/libc/math.pxd -> build/lib.linux-x86_64-3.8/Cython/Includes/libc copying Cython/Includes/libc/stddef.pxd -> build/lib.linux-x86_64-3.8/Cython/Includes/libc copying Cython/Includes/libc/time.pxd -> build/lib.linux-x86_64-3.8/Cython/Includes/libc copying Cython/Includes/libc/setjmp.pxd -> build/lib.linux-x86_64-3.8/Cython/Includes/libc copying Cython/Includes/libc/locale.pxd -> build/lib.linux-x86_64-3.8/Cython/Includes/libc copying Cython/Compiler/FlowControl.pxd -> build/lib.linux-x86_64-3.8/Cython/Compiler copying Cython/Compiler/Parsing.pxd -> build/lib.linux-x86_64-3.8/Cython/Compiler copying Cython/Compiler/ParseTreeTransforms.pxd -> build/lib.linux-x86_64-3.8/Cython/Compiler copying Cython/Compiler/Visitor.pxd -> build/lib.linux-x86_64-3.8/Cython/Compiler copying Cython/Compiler/Code.pxd -> build/lib.linux-x86_64-3.8/Cython/Compiler copying Cython/Compiler/Scanning.pxd -> build/lib.linux-x86_64-3.8/Cython/Compiler copying Cython/Runtime/refnanny.pyx -> build/lib.linux-x86_64-3.8/Cython/Runtime copying Cython/Debugger/Tests/codefile -> build/lib.linux-x86_64-3.8/Cython/Debugger/Tests copying Cython/Debugger/Tests/cfuncs.c -> build/lib.linux-x86_64-3.8/Cython/Debugger/Tests copying Cython/Plex/Actions.pxd -> build/lib.linux-x86_64-3.8/Cython/Plex copying Cython/Plex/Scanners.pxd -> build/lib.linux-x86_64-3.8/Cython/Plex copying Cython/Utility/TestCyUtilityLoader.pyx -> build/lib.linux-x86_64-3.8/Cython/Utility copying Cython/Utility/CConvert.pyx -> build/lib.linux-x86_64-3.8/Cython/Utility copying Cython/Utility/CppConvert.pyx -> build/lib.linux-x86_64-3.8/Cython/Utility copying Cython/Utility/TestCythonScope.pyx -> build/lib.linux-x86_64-3.8/Cython/Utility copying Cython/Utility/CpdefEnums.pyx -> build/lib.linux-x86_64-3.8/Cython/Utility copying Cython/Utility/MemoryView.pyx -> build/lib.linux-x86_64-3.8/Cython/Utility copying Cython/Utility/FunctionArguments.c -> build/lib.linux-x86_64-3.8/Cython/Utility copying Cython/Utility/CythonFunction.c -> build/lib.linux-x86_64-3.8/Cython/Utility copying Cython/Utility/CMath.c -> build/lib.linux-x86_64-3.8/Cython/Utility copying Cython/Utility/Printing.c -> build/lib.linux-x86_64-3.8/Cython/Utility copying Cython/Utility/Builtins.c -> build/lib.linux-x86_64-3.8/Cython/Utility copying Cython/Utility/ImportExport.c -> build/lib.linux-x86_64-3.8/Cython/Utility copying Cython/Utility/Capsule.c -> build/lib.linux-x86_64-3.8/Cython/Utility copying Cython/Utility/Exceptions.c -> build/lib.linux-x86_64-3.8/Cython/Utility copying Cython/Utility/Embed.c -> build/lib.linux-x86_64-3.8/Cython/Utility copying Cython/Utility/Optimize.c -> build/lib.linux-x86_64-3.8/Cython/Utility copying Cython/Utility/ObjectHandling.c -> build/lib.linux-x86_64-3.8/Cython/Utility copying Cython/Utility/TypeConversion.c -> build/lib.linux-x86_64-3.8/Cython/Utility copying Cython/Utility/MemoryView_C.c -> build/lib.linux-x86_64-3.8/Cython/Utility copying Cython/Utility/StringTools.c -> build/lib.linux-x86_64-3.8/Cython/Utility copying Cython/Utility/ModuleSetupCode.c -> build/lib.linux-x86_64-3.8/Cython/Utility copying Cython/Utility/Buffer.c -> build/lib.linux-x86_64-3.8/Cython/Utility copying Cython/Utility/Overflow.c -> build/lib.linux-x86_64-3.8/Cython/Utility copying Cython/Utility/TestUtilityLoader.c -> build/lib.linux-x86_64-3.8/Cython/Utility copying Cython/Utility/Coroutine.c -> build/lib.linux-x86_64-3.8/Cython/Utility copying Cython/Utility/CommonStructures.c -> build/lib.linux-x86_64-3.8/Cython/Utility copying Cython/Utility/Complex.c -> build/lib.linux-x86_64-3.8/Cython/Utility copying Cython/Utility/ExtensionTypes.c -> build/lib.linux-x86_64-3.8/Cython/Utility copying Cython/Utility/AsyncGen.c -> build/lib.linux-x86_64-3.8/Cython/Utility copying Cython/Utility/Profile.c -> build/lib.linux-x86_64-3.8/Cython/Utility copying Cython/Utility/arrayarray.h -> build/lib.linux-x86_64-3.8/Cython/Utility copying Cython/Utility/CppSupport.cpp -> build/lib.linux-x86_64-3.8/Cython/Utility running build_ext building 'Cython.Plex.Scanners' extension creating build/temp.linux-x86_64-3.8 creating build/temp.linux-x86_64-3.8/tmp creating build/temp.linux-x86_64-3.8/tmp/pip-wheel-71rjsm60 creating build/temp.linux-x86_64-3.8/tmp/pip-wheel-71rjsm60/cython_48fe37c869b94601bc9ef02b9802fd6f creating build/temp.linux-x86_64-3.8/tmp/pip-wheel-71rjsm60/cython_48fe37c869b94601bc9ef02b9802fd6f/Cython creating build/temp.linux-x86_64-3.8/tmp/pip-wheel-71rjsm60/cython_48fe37c869b94601bc9ef02b9802fd6f/Cython/Plex x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include/python3.8 -c /tmp/pip-wheel-71rjsm60/cython_48fe37c869b94601bc9ef02b9802fd6f/Cython/Plex/Scanners.c -o build/temp.linux-x86_64-3.8/tmp/pip-wheel-71rjsm60/cython_48fe37c869b94601bc9ef02b9802fd6f/Cython/Plex/Scanners.o /tmp/pip-wheel-71rjsm60/cython_48fe37c869b94601bc9ef02b9802fd6f/Cython/Plex/Scanners.c: In function ‘__Pyx_InitCachedConstants’: /usr/include/python3.8/code.h:72:25: warning: passing argument 6 of ‘PyCode_New’ makes pointer from integer without a cast [-Wint-conversion] 72 | #define CO_OPTIMIZED 0x0001 | ^ |
|---|---|---|---|---|
| int |
/tmp/pip-wheel-71rjsm60/cython_48fe37c869b94601bc9ef02b9802fd6f/Cython/Plex/Scanners.c:333:37: note: in definition of macro ‘__Pyx_PyCode_New’
333 | PyCode_New(a, 0, k, l, s, f, code, c, n, v, fv, cell, fn, name, fline, lnos)
| ^
/tmp/pip-wheel-71rjsm60/cython_48fe37c869b94601bc9ef02b9802fd6f/Cython/Plex/Scanners.c:7241:62: note: in expansion of macro ‘CO_OPTIMIZED’
7241 | __pyx_codeobj__6 = (PyObject*)__Pyx_PyCode_New(1, 0, 1, 0, CO_OPTIMIZED|CO_NEWLOCALS, __pyx_empty_bytes, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_tuple__5, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_kp_s_Cython_Plex_Scanners_py, __pyx_n_s_read, 113, __pyx_empty_bytes); if (unlikely(!__pyx_codeobj__6)) __PYX_ERR(0, 113, __pyx_L1_error)
| ^~~~~~~~~~~~
In file included from /usr/include/python3.8/compile.h:5,
from /usr/include/python3.8/Python.h:138,
from /tmp/pip-wheel-71rjsm60/cython_48fe37c869b94601bc9ef02b9802fd6f/Cython/Plex/Scanners.c:19:
/usr/include/python3.8/code.h:123:34: note: expected ‘PyObject *’ {aka ‘struct _object *’} but argument is of type ‘int’
123 | int, int, int, int, int, PyObject *, PyObject *,
| ^~~~~~~~~~
/tmp/pip-wheel-71rjsm60/cython_48fe37c869b94601bc9ef02b9802fd6f/Cython/Plex/Scanners.c:7241:236: warning: passing argument 14 of ‘PyCode_New’ makes integer from pointer without a cast [-Wint-conversion]
7241 | __pyx_codeobj__6 = (PyObject*)__Pyx_PyCode_New(1, 0, 1, 0, CO_OPTIMIZED|CO_NEWLOCALS, __pyx_empty_bytes, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_tuple__5, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_kp_s_Cython_Plex_Scanners_py, __pyx_n_s_read, 113, __pyx_empty_bytes); if (unlikely(!__pyx_codeobj__6)) __PYX_ERR(0, 113, __pyx_L1_error)
| ^~~~~~~~~~~~~~
| |
| PyObject * {aka struct _object *}
/tmp/pip-wheel-71rjsm60/cython_48fe37c869b94601bc9ef02b9802fd6f/Cython/Plex/Scanners.c:333:69: note: in definition of macro ‘__Pyx_PyCode_New’
333 | PyCode_New(a, 0, k, l, s, f, code, c, n, v, fv, cell, fn, name, fline, lnos)
| ^~~~
In file included from /usr/include/python3.8/compile.h:5,
from /usr/include/python3.8/Python.h:138,
from /tmp/pip-wheel-71rjsm60/cython_48fe37c869b94601bc9ef02b9802fd6f/Cython/Plex/Scanners.c:19:
/usr/include/python3.8/code.h:125:33: note: expected ‘int’ but argument is of type ‘PyObject *’ {aka ‘struct _object *’}
125 | PyObject *, PyObject *, int, PyObject *);
| ^~~
/tmp/pip-wheel-71rjsm60/cython_48fe37c869b94601bc9ef02b9802fd6f/Cython/Plex/Scanners.c:7241:252: warning: passing argument 15 of ‘PyCode_New’ makes pointer from integer without a cast [-Wint-conversion]
7241 | __pyx_codeobj__6 = (PyObject*)__Pyx_PyCode_New(1, 0, 1, 0, CO_OPTIMIZED|CO_NEWLOCALS, __pyx_empty_bytes, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_tuple__5, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_kp_s_Cython_Plex_Scanners_py, __pyx_n_s_read, 113, __pyx_empty_bytes); if (unlikely(!__pyx_codeobj__6)) __PYX_ERR(0, 113, __pyx_L1_error)
| ^~~
| |
| int
/tmp/pip-wheel-71rjsm60/cython_48fe37c869b94601bc9ef02b9802fd6f/Cython/Plex/Scanners.c:333:75: note: in definition of macro ‘__Pyx_PyCode_New’
333 | PyCode_New(a, 0, k, l, s, f, code, c, n, v, fv, cell, fn, name, fline, lnos)
| ^~~~~
In file included from /usr/include/python3.8/compile.h:5,
from /usr/include/python3.8/Python.h:138,
from /tmp/pip-wheel-71rjsm60/cython_48fe37c869b94601bc9ef02b9802fd6f/Cython/Plex/Scanners.c:19:
/usr/include/python3.8/code.h:125:38: note: expected ‘PyObject *’ {aka ‘struct _object *’} but argument is of type ‘int’
125 | PyObject *, PyObject *, int, PyObject *);
| ^~~~~~~~~~
/tmp/pip-wheel-71rjsm60/cython_48fe37c869b94601bc9ef02b9802fd6f/Cython/Plex/Scanners.c:333:11: error: too many arguments to function ‘PyCode_New’
333 | PyCode_New(a, 0, k, l, s, f, code, c, n, v, fv, cell, fn, name, fline, lnos)
| ^~~~~~~~~~
/tmp/pip-wheel-71rjsm60/cython_48fe37c869b94601bc9ef02b9802fd6f/Cython/Plex/Scanners.c:7241:33: note: in expansion of macro ‘__Pyx_PyCode_New’
7241 | __pyx_codeobj__6 = (PyObject*)__Pyx_PyCode_New(1, 0, 1, 0, CO_OPTIMIZED|CO_NEWLOCALS, __pyx_empty_bytes, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_tuple__5, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_kp_s_Cython_Plex_Scanners_py, __pyx_n_s_read, 113, __pyx_empty_bytes); if (unlikely(!__pyx_codeobj__6)) __PYX_ERR(0, 113, __pyx_L1_error)
| ^~~~~~~~~~~~~~~~
In file included from /usr/include/python3.8/compile.h:5,
from /usr/include/python3.8/Python.h:138,
from /tmp/pip-wheel-71rjsm60/cython_48fe37c869b94601bc9ef02b9802fd6f/Cython/Plex/Scanners.c:19:
/usr/include/python3.8/code.h:122:28: note: declared here
122 | PyAPI_FUNC(PyCodeObject *) PyCode_New(
| ^~~~~~~~~~
/usr/include/python3.8/code.h:72:25: warning: passing argument 6 of ‘PyCode_New’ makes pointer from integer without a cast [-Wint-conversion]
72 | #define CO_OPTIMIZED 0x0001
| ^
| |
| int
/tmp/pip-wheel-71rjsm60/cython_48fe37c869b94601bc9ef02b9802fd6f/Cython/Plex/Scanners.c:333:37: note: in definition of macro ‘__Pyx_PyCode_New’
333 | PyCode_New(a, 0, k, l, s, f, code, c, n, v, fv, cell, fn, name, fline, lnos)
| ^
/tmp/pip-wheel-71rjsm60/cython_48fe37c869b94601bc9ef02b9802fd6f/Cython/Plex/Scanners.c:7253:62: note: in expansion of macro ‘CO_OPTIMIZED’
7253 | __pyx_codeobj__8 = (PyObject*)__Pyx_PyCode_New(1, 0, 1, 0, CO_OPTIMIZED|CO_NEWLOCALS, __pyx_empty_bytes, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_tuple__7, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_kp_s_Cython_Plex_Scanners_py, __pyx_n_s_position, 297, __pyx_empty_bytes); if (unlikely(!__pyx_codeobj__8)) __PYX_ERR(0, 297, __pyx_L1_error)
| ^~~~~~~~~~~~
In file included from /usr/include/python3.8/compile.h:5,
from /usr/include/python3.8/Python.h:138,
from /tmp/pip-wheel-71rjsm60/cython_48fe37c869b94601bc9ef02b9802fd6f/Cython/Plex/Scanners.c:19:
/usr/include/python3.8/code.h:123:34: note: expected ‘PyObject *’ {aka ‘struct _object *’} but argument is of type ‘int’
123 | int, int, int, int, int, PyObject *, PyObject *,
| ^~~~~~~~~~
/tmp/pip-wheel-71rjsm60/cython_48fe37c869b94601bc9ef02b9802fd6f/Cython/Plex/Scanners.c:7253:236: warning: passing argument 14 of ‘PyCode_New’ makes integer from pointer without a cast [-Wint-conversion]
7253 | __pyx_codeobj__8 = (PyObject*)__Pyx_PyCode_New(1, 0, 1, 0, CO_OPTIMIZED|CO_NEWLOCALS, __pyx_empty_bytes, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_tuple__7, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_kp_s_Cython_Plex_Scanners_py, __pyx_n_s_position, 297, __pyx_empty_bytes); if (unlikely(!__pyx_codeobj__8)) __PYX_ERR(0, 297, __pyx_L1_error)
| ^~~~~~~~~~~~~~~~~~
| |
| PyObject * {aka struct _object *}
/tmp/pip-wheel-71rjsm60/cython_48fe37c869b94601bc9ef02b9802fd6f/Cython/Plex/Scanners.c:333:69: note: in definition of macro ‘__Pyx_PyCode_New’
333 | PyCode_New(a, 0, k, l, s, f, code, c, n, v, fv, cell, fn, name, fline, lnos)
| ^~~~
In file included from /usr/include/python3.8/compile.h:5,
from /usr/include/python3.8/Python.h:138,
from /tmp/pip-wheel-71rjsm60/cython_48fe37c869b94601bc9ef02b9802fd6f/Cython/Plex/Scanners.c:19:
/usr/include/python3.8/code.h:125:33: note: expected ‘int’ but argument is of type ‘PyObject *’ {aka ‘struct _object *’}
125 | PyObject *, PyObject *, int, PyObject *);
| ^~~
/tmp/pip-wheel-71rjsm60/cython_48fe37c869b94601bc9ef02b9802fd6f/Cython/Plex/Scanners.c:7253:256: warning: passing argument 15 of ‘PyCode_New’ makes pointer from integer without a cast [-Wint-conversion]
7253 | __pyx_codeobj__8 = (PyObject*)__Pyx_PyCode_New(1, 0, 1, 0, CO_OPTIMIZED|CO_NEWLOCALS, __pyx_empty_bytes, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_tuple__7, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_kp_s_Cython_Plex_Scanners_py, __pyx_n_s_position, 297, __pyx_empty_bytes); if (unlikely(!__pyx_codeobj__8)) __PYX_ERR(0, 297, __pyx_L1_error)
| ^~~
| |
| int
/tmp/pip-wheel-71rjsm60/cython_48fe37c869b94601bc9ef02b9802fd6f/Cython/Plex/Scanners.c:333:75: note: in definition of macro ‘__Pyx_PyCode_New’
333 | PyCode_New(a, 0, k, l, s, f, code, c, n, v, fv, cell, fn, name, fline, lnos)
| ^~~~~
In file included from /usr/include/python3.8/compile.h:5,
from /usr/include/python3.8/Python.h:138,
from /tmp/pip-wheel-71rjsm60/cython_48fe37c869b94601bc9ef02b9802fd6f/Cython/Plex/Scanners.c:19:
/usr/include/python3.8/code.h:125:38: note: expected ‘PyObject *’ {aka ‘struct _object *’} but argument is of type ‘int’
125 | PyObject *, PyObject *, int, PyObject *);
| ^~~~~~~~~~
/tmp/pip-wheel-71rjsm60/cython_48fe37c869b94601bc9ef02b9802fd6f/Cython/Plex/Scanners.c:333:11: error: too many arguments to function ‘PyCode_New’
333 | PyCode_New(a, 0, k, l, s, f, code, c, n, v, fv, cell, fn, name, fline, lnos)
| ^~~~~~~~~~
/tmp/pip-wheel-71rjsm60/cython_48fe37c869b94601bc9ef02b9802fd6f/Cython/Plex/Scanners.c:7253:33: note: in expansion of macro ‘__Pyx_PyCode_New’
7253 | __pyx_codeobj__8 = (PyObject*)__Pyx_PyCode_New(1, 0, 1, 0, CO_OPTIMIZED|CO_NEWLOCALS, __pyx_empty_bytes, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_tuple__7, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_kp_s_Cython_Plex_Scanners_py, __pyx_n_s_position, 297, __pyx_empty_bytes); if (unlikely(!__pyx_codeobj__8)) __PYX_ERR(0, 297, __pyx_L1_error)
| ^~~~~~~~~~~~~~~~
In file included from /usr/include/python3.8/compile.h:5,
from /usr/include/python3.8/Python.h:138,
from /tmp/pip-wheel-71rjsm60/cython_48fe37c869b94601bc9ef02b9802fd6f/Cython/Plex/Scanners.c:19:
/usr/include/python3.8/code.h:122:28: note: declared here
122 | PyAPI_FUNC(PyCodeObject *) PyCode_New(
| ^~~~~~~~~~
/usr/include/python3.8/code.h:72:25: warning: passing argument 6 of ‘PyCode_New’ makes pointer from integer without a cast [-Wint-conversion]
72 | #define CO_OPTIMIZED 0x0001
| ^
| |
| int
/tmp/pip-wheel-71rjsm60/cython_48fe37c869b94601bc9ef02b9802fd6f/Cython/Plex/Scanners.c:333:37: note: in definition of macro ‘__Pyx_PyCode_New’
333 | PyCode_New(a, 0, k, l, s, f, code, c, n, v, fv, cell, fn, name, fline, lnos)
| ^
/tmp/pip-wheel-71rjsm60/cython_48fe37c869b94601bc9ef02b9802fd6f/Cython/Plex/Scanners.c:7265:63: note: in expansion of macro ‘CO_OPTIMIZED’
7265 | __pyx_codeobj__10 = (PyObject*)__Pyx_PyCode_New(1, 0, 1, 0, CO_OPTIMIZED|CO_NEWLOCALS, __pyx_empty_bytes, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_tuple__9, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_kp_s_Cython_Plex_Scanners_py, __pyx_n_s_get_position, 308, __pyx_empty_bytes); if (unlikely(!__pyx_codeobj__10)) __PYX_ERR(0, 308, __pyx_L1_error)
| ^~~~~~~~~~~~
In file included from /usr/include/python3.8/compile.h:5,
from /usr/include/python3.8/Python.h:138,
from /tmp/pip-wheel-71rjsm60/cython_48fe37c869b94601bc9ef02b9802fd6f/Cython/Plex/Scanners.c:19:
/usr/include/python3.8/code.h:123:34: note: expected ‘PyObject *’ {aka ‘struct _object *’} but argument is of type ‘int’
123 | int, int, int, int, int, PyObject *, PyObject *,
| ^~~~~~~~~~
/tmp/pip-wheel-71rjsm60/cython_48fe37c869b94601bc9ef02b9802fd6f/Cython/Plex/Scanners.c:7265:237: warning: passing argument 14 of ‘PyCode_New’ makes integer from pointer without a cast [-Wint-conversion]
7265 | __pyx_codeobj__10 = (PyObject*)__Pyx_PyCode_New(1, 0, 1, 0, CO_OPTIMIZED|CO_NEWLOCALS, __pyx_empty_bytes, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_tuple__9, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_kp_s_Cython_Plex_Scanners_py, __pyx_n_s_get_position, 308, __pyx_empty_bytes); if (unlikely(!__pyx_codeobj__10)) __PYX_ERR(0, 308, __pyx_L1_error)
| ^~~~~~~~~~~~~~~~~~~~~~
| |
| PyObject * {aka struct _object *}
/tmp/pip-wheel-71rjsm60/cython_48fe37c869b94601bc9ef02b9802fd6f/Cython/Plex/Scanners.c:333:69: note: in definition of macro ‘__Pyx_PyCode_New’
333 | PyCode_New(a, 0, k, l, s, f, code, c, n, v, fv, cell, fn, name, fline, lnos)
| ^~~~
In file included from /usr/include/python3.8/compile.h:5,
from /usr/include/python3.8/Python.h:138,
from /tmp/pip-wheel-71rjsm60/cython_48fe37c869b94601bc9ef02b9802fd6f/Cython/Plex/Scanners.c:19:
/usr/include/python3.8/code.h:125:33: note: expected ‘int’ but argument is of type ‘PyObject *’ {aka ‘struct _object *’}
125 | PyObject *, PyObject *, int, PyObject *);
| ^~~
/tmp/pip-wheel-71rjsm60/cython_48fe37c869b94601bc9ef02b9802fd6f/Cython/Plex/Scanners.c:7265:261: warning: passing argument 15 of ‘PyCode_New’ makes pointer from integer without a cast [-Wint-conversion]
7265 | __pyx_codeobj__10 = (PyObject*)__Pyx_PyCode_New(1, 0, 1, 0, CO_OPTIMIZED|CO_NEWLOCALS, __pyx_empty_bytes, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_tuple__9, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_kp_s_Cython_Plex_Scanners_py, __pyx_n_s_get_position, 308, __pyx_empty_bytes); if (unlikely(!__pyx_codeobj__10)) __PYX_ERR(0, 308, __pyx_L1_error)
| ^~~
| |
| int
/tmp/pip-wheel-71rjsm60/cython_48fe37c869b94601bc9ef02b9802fd6f/Cython/Plex/Scanners.c:333:75: note: in definition of macro ‘__Pyx_PyCode_New’
333 | PyCode_New(a, 0, k, l, s, f, code, c, n, v, fv, cell, fn, name, fline, lnos)
| ^~~~~
In file included from /usr/include/python3.8/compile.h:5,
from /usr/include/python3.8/Python.h:138,
from /tmp/pip-wheel-71rjsm60/cython_48fe37c869b94601bc9ef02b9802fd6f/Cython/Plex/Scanners.c:19:
/usr/include/python3.8/code.h:125:38: note: expected ‘PyObject *’ {aka ‘struct _object *’} but argument is of type ‘int’
125 | PyObject *, PyObject *, int, PyObject *);
| ^~~~~~~~~~
/tmp/pip-wheel-71rjsm60/cython_48fe37c869b94601bc9ef02b9802fd6f/Cython/Plex/Scanners.c:333:11: error: too many arguments to function ‘PyCode_New’
333 | PyCode_New(a, 0, k, l, s, f, code, c, n, v, fv, cell, fn, name, fline, lnos)
| ^~~~~~~~~~
/tmp/pip-wheel-71rjsm60/cython_48fe37c869b94601bc9ef02b9802fd6f/Cython/Plex/Scanners.c:7265:34: note: in expansion of macro ‘__Pyx_PyCode_New’
7265 | __pyx_codeobj__10 = (PyObject*)__Pyx_PyCode_New(1, 0, 1, 0, CO_OPTIMIZED|CO_NEWLOCALS, __pyx_empty_bytes, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_tuple__9, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_kp_s_Cython_Plex_Scanners_py, __pyx_n_s_get_position, 308, __pyx_empty_bytes); if (unlikely(!__pyx_codeobj__10)) __PYX_ERR(0, 308, __pyx_L1_error)
| ^~~~~~~~~~~~~~~~
In file included from /usr/include/python3.8/compile.h:5,
from /usr/include/python3.8/Python.h:138,
from /tmp/pip-wheel-71rjsm60/cython_48fe37c869b94601bc9ef02b9802fd6f/Cython/Plex/Scanners.c:19:
/usr/include/python3.8/code.h:122:28: note: declared here
122 | PyAPI_FUNC(PyCodeObject *) PyCode_New(
| ^~~~~~~~~~
/usr/include/python3.8/code.h:72:25: warning: passing argument 6 of ‘PyCode_New’ makes pointer from integer without a cast [-Wint-conversion]
72 | #define CO_OPTIMIZED 0x0001
| ^
| |
| int
/tmp/pip-wheel-71rjsm60/cython_48fe37c869b94601bc9ef02b9802fd6f/Cython/Plex/Scanners.c:333:37: note: in definition of macro ‘__Pyx_PyCode_New’
333 | PyCode_New(a, 0, k, l, s, f, code, c, n, v, fv, cell, fn, name, fline, lnos)
| ^
/tmp/pip-wheel-71rjsm60/cython_48fe37c869b94601bc9ef02b9802fd6f/Cython/Plex/Scanners.c:7277:63: note: in expansion of macro ‘CO_OPTIMIZED’
7277 | __pyx_codeobj__12 = (PyObject*)__Pyx_PyCode_New(1, 0, 1, 0, CO_OPTIMIZED|CO_NEWLOCALS, __pyx_empty_bytes, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_tuple__11, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_kp_s_Cython_Plex_Scanners_py, __pyx_n_s_eof, 334, __pyx_empty_bytes); if (unlikely(!__pyx_codeobj__12)) __PYX_ERR(0, 334, __pyx_L1_error)
| ^~~~~~~~~~~~
In file included from /usr/include/python3.8/compile.h:5,
from /usr/include/python3.8/Python.h:138,
from /tmp/pip-wheel-71rjsm60/cython_48fe37c869b94601bc9ef02b9802fd6f/Cython/Plex/Scanners.c:19:
/usr/include/python3.8/code.h:123:34: note: expected ‘PyObject *’ {aka ‘struct _object *’} but argument is of type ‘int’
123 | int, int, int, int, int, PyObject *, PyObject *,
| ^~~~~~~~~~
/tmp/pip-wheel-71rjsm60/cython_48fe37c869b94601bc9ef02b9802fd6f/Cython/Plex/Scanners.c:7277:238: warning: passing argument 14 of ‘PyCode_New’ makes integer from pointer without a cast [-Wint-conversion]
7277 | __pyx_codeobj__12 = (PyObject*)__Pyx_PyCode_New(1, 0, 1, 0, CO_OPTIMIZED|CO_NEWLOCALS, __pyx_empty_bytes, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_tuple__11, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_kp_s_Cython_Plex_Scanners_py, __pyx_n_s_eof, 334, __pyx_empty_bytes); if (unlikely(!__pyx_codeobj__12)) __PYX_ERR(0, 334, __pyx_L1_error)
| ^~~~~~~~~~~~~
| |
| PyObject * {aka struct _object *}
/tmp/pip-wheel-71rjsm60/cython_48fe37c869b94601bc9ef02b9802fd6f/Cython/Plex/Scanners.c:333:69: note: in definition of macro ‘__Pyx_PyCode_New’
333 | PyCode_New(a, 0, k, l, s, f, code, c, n, v, fv, cell, fn, name, fline, lnos)
| ^~~~
In file included from /usr/include/python3.8/compile.h:5,
from /usr/include/python3.8/Python.h:138,
from /tmp/pip-wheel-71rjsm60/cython_48fe37c869b94601bc9ef02b9802fd6f/Cython/Plex/Scanners.c:19:
/usr/include/python3.8/code.h:125:33: note: expected ‘int’ but argument is of type ‘PyObject *’ {aka ‘struct _object *’}
125 | PyObject *, PyObject *, int, PyObject *);
| ^~~
/tmp/pip-wheel-71rjsm60/cython_48fe37c869b94601bc9ef02b9802fd6f/Cython/Plex/Scanners.c:7277:253: warning: passing argument 15 of ‘PyCode_New’ makes pointer from integer without a cast [-Wint-conversion]
7277 | __pyx_codeobj__12 = (PyObject*)__Pyx_PyCode_New(1, 0, 1, 0, CO_OPTIMIZED|CO_NEWLOCALS, __pyx_empty_bytes, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_tuple__11, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_kp_s_Cython_Plex_Scanners_py, __pyx_n_s_eof, 334, __pyx_empty_bytes); if (unlikely(!__pyx_codeobj__12)) __PYX_ERR(0, 334, __pyx_L1_error)
| ^~~
| |
| int
/tmp/pip-wheel-71rjsm60/cython_48fe37c869b94601bc9ef02b9802fd6f/Cython/Plex/Scanners.c:333:75: note: in definition of macro ‘__Pyx_PyCode_New’
333 | PyCode_New(a, 0, k, l, s, f, code, c, n, v, fv, cell, fn, name, fline, lnos)
| ^~~~~
In file included from /usr/include/python3.8/compile.h:5,
from /usr/include/python3.8/Python.h:138,
from /tmp/pip-wheel-71rjsm60/cython_48fe37c869b94601bc9ef02b9802fd6f/Cython/Plex/Scanners.c:19:
/usr/include/python3.8/code.h:125:38: note: expected ‘PyObject *’ {aka ‘struct _object *’} but argument is of type ‘int’
125 | PyObject *, PyObject *, int, PyObject *);
| ^~~~~~~~~~
/tmp/pip-wheel-71rjsm60/cython_48fe37c869b94601bc9ef02b9802fd6f/Cython/Plex/Scanners.c:333:11: error: too many arguments to function ‘PyCode_New’
333 | PyCode_New(a, 0, k, l, s, f, code, c, n, v, fv, cell, fn, name, fline, lnos)
| ^~~~~~~~~~
/tmp/pip-wheel-71rjsm60/cython_48fe37c869b94601bc9ef02b9802fd6f/Cython/Plex/Scanners.c:7277:34: note: in expansion of macro ‘__Pyx_PyCode_New’
7277 | __pyx_codeobj__12 = (PyObject*)__Pyx_PyCode_New(1, 0, 1, 0, CO_OPTIMIZED|CO_NEWLOCALS, __pyx_empty_bytes, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_tuple__11, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_kp_s_Cython_Plex_Scanners_py, __pyx_n_s_eof, 334, __pyx_empty_bytes); if (unlikely(!__pyx_codeobj__12)) __PYX_ERR(0, 334, __pyx_L1_error)
| ^~~~~~~~~~~~~~~~
In file included from /usr/include/python3.8/compile.h:5,
from /usr/include/python3.8/Python.h:138,
from /tmp/pip-wheel-71rjsm60/cython_48fe37c869b94601bc9ef02b9802fd6f/Cython/Plex/Scanners.c:19:
/usr/include/python3.8/code.h:122:28: note: declared here
122 | PyAPI_FUNC(PyCodeObject *) PyCode_New(
| ^~~~~~~~~~
/tmp/pip-wheel-71rjsm60/cython_48fe37c869b94601bc9ef02b9802fd6f/Cython/Plex/Scanners.c: In function ‘__Pyx_CreateCodeObjectForTraceback’:
/tmp/pip-wheel-71rjsm60/cython_48fe37c869b94601bc9ef02b9802fd6f/Cython/Plex/Scanners.c:10051:9: warning: passing argument 14 of ‘PyCode_New’ makes integer from pointer without a cast [-Wint-conversion]
10051 | py_funcname, /*PyObject *name,*/
| ^~~~~~~~~~~
| |
| PyObject * {aka struct _object *}
/tmp/pip-wheel-71rjsm60/cython_48fe37c869b94601bc9ef02b9802fd6f/Cython/Plex/Scanners.c:333:69: note: in definition of macro ‘__Pyx_PyCode_New’
333 | PyCode_New(a, 0, k, l, s, f, code, c, n, v, fv, cell, fn, name, fline, lnos)
| ^~~~
In file included from /usr/include/python3.8/compile.h:5,
from /usr/include/python3.8/Python.h:138,
from /tmp/pip-wheel-71rjsm60/cython_48fe37c869b94601bc9ef02b9802fd6f/Cython/Plex/Scanners.c:19:
/usr/include/python3.8/code.h:125:33: note: expected ‘int’ but argument is of type ‘PyObject *’ {aka ‘struct _object *’}
125 | PyObject *, PyObject *, int, PyObject *);
| ^~~
/tmp/pip-wheel-71rjsm60/cython_48fe37c869b94601bc9ef02b9802fd6f/Cython/Plex/Scanners.c:10052:9: warning: passing argument 15 of ‘PyCode_New’ makes pointer from integer without a cast [-Wint-conversion]
10052 | py_line,
| ^~~~~~~
| |
| int
/tmp/pip-wheel-71rjsm60/cython_48fe37c869b94601bc9ef02b9802fd6f/Cython/Plex/Scanners.c:333:75: note: in definition of macro ‘__Pyx_PyCode_New’
333 | PyCode_New(a, 0, k, l, s, f, code, c, n, v, fv, cell, fn, name, fline, lnos)
| ^~~~~
In file included from /usr/include/python3.8/compile.h:5,
from /usr/include/python3.8/Python.h:138,
from /tmp/pip-wheel-71rjsm60/cython_48fe37c869b94601bc9ef02b9802fd6f/Cython/Plex/Scanners.c:19:
/usr/include/python3.8/code.h:125:38: note: expected ‘PyObject *’ {aka ‘struct _object *’} but argument is of type ‘int’
125 | PyObject *, PyObject *, int, PyObject *);
| ^~~~~~~~~~
/tmp/pip-wheel-71rjsm60/cython_48fe37c869b94601bc9ef02b9802fd6f/Cython/Plex/Scanners.c:333:11: error: too many arguments to function ‘PyCode_New’
333 | PyCode_New(a, 0, k, l, s, f, code, c, n, v, fv, cell, fn, name, fline, lnos)
| ^~~~~~~~~~
/tmp/pip-wheel-71rjsm60/cython_48fe37c869b94601bc9ef02b9802fd6f/Cython/Plex/Scanners.c:10038:15: note: in expansion of macro ‘__Pyx_PyCode_New’
10038 | py_code = __Pyx_PyCode_New(
| ^~~~~~~~~~~~~~~~
In file included from /usr/include/python3.8/compile.h:5,
from /usr/include/python3.8/Python.h:138,
from /tmp/pip-wheel-71rjsm60/cython_48fe37c869b94601bc9ef02b9802fd6f/Cython/Plex/Scanners.c:19:
/usr/include/python3.8/code.h:122:28: note: declared here
122 | PyAPI_FUNC(PyCodeObject *) PyCode_New(
| ^~~~~~~~~~
error: command 'x86_64-linux-gnu-gcc' failed with exit status 1
----------------------------------------
ERROR: Failed building wheel for cython
ERROR: Failed to build one or more wheels
Traceback (most recent call last):
File "/usr/lib/python3/dist-packages/setuptools/installer.py", line 128, in fetch_build_egg
subprocess.check_call(cmd)
File "/usr/lib/python3.8/subprocess.py", line 364, in check_call
raise CalledProcessError(retcode, cmd)
subprocess.CalledProcessError: Command '['/usr/bin/python3', '-m', 'pip', '--disable-pip-version-check', 'wheel', '--no-deps', '-w', '/tmp/tmpme5ed_b9', '--quiet', '--find-links', 'https://github.com/kivy-garden/garden/archive/master.zip', 'cython!=0.27,!=0.27.2,<=0.29.10,>=0.24']' returned non-zero exit status 1.
The above exception was the direct cause of the following exception:
Traceback (most recent call last):
File "<string>", line 1, in <module>
File "/tmp/pip-install-xcz_ndw8/kivy_bf8f7e36d0b8493bb55274932837381f/setup.py", line 1073, in <module>
setup(
File "/usr/lib/python3/dist-packages/setuptools/__init__.py", line 162, in setup
_install_setup_requires(attrs)
File "/usr/lib/python3/dist-packages/setuptools/__init__.py", line 157, in _install_setup_requires
dist.fetch_build_eggs(dist.setup_requires)
File "/usr/lib/python3/dist-packages/setuptools/dist.py", line 699, in fetch_build_eggs
resolved_dists = pkg_resources.working_set.resolve(
File "/usr/lib/python3/dist-packages/pkg_resources/__init__.py", line 779, in resolve
dist = best[req.key] = env.best_match(
File "/usr/lib/python3/dist-packages/pkg_resources/__init__.py", line 1064, in best_match
return self.obtain(req, installer)
File "/usr/lib/python3/dist-packages/pkg_resources/__init__.py", line 1076, in obtain
return installer(requirement)
File "/usr/lib/python3/dist-packages/setuptools/dist.py", line 758, in fetch_build_egg
return fetch_build_egg(self, req)
File "/usr/lib/python3/dist-packages/setuptools/installer.py", line 130, in fetch_build_egg
raise DistutilsError(str(e)) from e
distutils.errors.DistutilsError: Command '['/usr/bin/python3', '-m', 'pip', '--disable-pip-version-check', 'wheel', '--no-deps', '-w', '/tmp/tmpme5ed_b9', '--quiet', '--find-links', 'https://github.com/kivy-garden/garden/archive/master.zip', 'cython!=0.27,!=0.27.2,<=0.29.10,>=0.24']' returned non-zero exit status 1.
Using setuptools
Using this graphics system: OpenGL
WARNING: A problem occurred while running pkg-config --libs --cflags gstreamer-1.0 (code 1)
b"Package gstreamer-1.0 was not found in the pkg-config search path.\nPerhaps you should add the directory containing `gstreamer-1.0.pc'\nto the PKG_CONFIG_PATH environment variable\nNo package 'gstreamer-1.0' found\n"
WARNING: A problem occurred while running pkg-config --libs --cflags sdl2 SDL2_ttf SDL2_image SDL2_mixer (code 1)
b"Package sdl2 was not found in the pkg-config search path.\nPerhaps you should add the directory containing `sdl2.pc'\nto the PKG_CONFIG_PATH environment variable\nNo package 'sdl2' found\nPackage SDL2_ttf was not found in the pkg-config search path.\nPerhaps you should add the directory containing `SDL2_ttf.pc'\nto the PKG_CONFIG_PATH environment variable\nNo package 'SDL2_ttf' found\nPackage SDL2_image was not found in the pkg-config search path.\nPerhaps you should add the directory containing `SDL2_image.pc'\nto the PKG_CONFIG_PATH environment variable\nNo package 'SDL2_image' found\nPackage SDL2_mixer was not found in the pkg-config search path.\nPerhaps you should add the directory containing `SDL2_mixer.pc'\nto the PKG_CONFIG_PATH environment variable\nNo package 'SDL2_mixer' found\n"
WARNING: A problem occurred while running pkg-config --libs --cflags pangoft2 (code 1)
b"Package pangoft2 was not found in the pkg-config search path.\nPerhaps you should add the directory containing `pangoft2.pc'\nto the PKG_CONFIG_PATH environment variable\nNo package 'pangoft2' found\n"
ERROR: Dependency for context.pyx not resolved: config.pxi
ERROR: Dependency for compiler.pyx not resolved: config.pxi
ERROR: Dependency for context_instructions.pyx not resolved: config.pxi
ERROR: Dependency for fbo.pyx not resolved: config.pxi
ERROR: Dependency for gl_instructions.pyx not resolved: config.pxi
ERROR: Dependency for instructions.pyx not resolved: config.pxi
ERROR: Dependency for opengl.pyx not resolved: config.pxi
ERROR: Dependency for opengl_utils.pyx not resolved: config.pxi
ERROR: Dependency for shader.pyx not resolved: config.pxi
ERROR: Dependency for stencil_instructions.pyx not resolved: config.pxi
ERROR: Dependency for scissor_instructions.pyx not resolved: config.pxi
ERROR: Dependency for texture.pyx not resolved: config.pxi
ERROR: Dependency for vbo.pyx not resolved: config.pxi
ERROR: Dependency for vertex.pyx not resolved: config.pxi
ERROR: Dependency for vertex_instructions.pyx not resolved: config.pxi
ERROR: Dependency for cgl.pyx not resolved: config.pxi
ERROR: Dependency for cgl_mock.pyx not resolved: config.pxi
ERROR: Dependency for cgl_gl.pyx not resolved: config.pxi
ERROR: Dependency for cgl_glew.pyx not resolved: config.pxi
ERROR: Dependency for cgl_sdl2.pyx not resolved: config.pxi
ERROR: Dependency for svg.pyx not resolved: config.pxi
----------------------------------------WARNING: Discarding https://files.pythonhosted.org/packages/1b/4d/3f8a720f561dc1eabe036c0d87c6ce9d02823275391265538e606f45e37a/Kivy-1.11.1.tar.gz#sha256=4d0e596f74271e901b551f77661dde238df4765484fce9f5d1c72e8022984e84 (from https://pypi.org/simple/kivy/). Command errored out with exit status 1: python setup.py egg_info Check the logs for full command output. ERROR: Could not find a version that satisfies the requirement kivy==1.11.1 (from versions: 1.0.1a0, 1.0.2a0, 1.0.3a0, 1.0.4b0, 1.0.5, 1.0.6, 1.0.7, 1.0.8, 1.0.9, 1.1.0, 1.1.1, 1.2.0, 1.3.0, 1.4.0, 1.4.1, 1.5.0, 1.5.1, 1.6.0, 1.7.0, 1.7.1, 1.7.2, 1.8.0, 1.9.0, 1.9.1, 1.10.0, 1.10.1, 1.11.0rc1, 1.11.0rc2, 1.11.0, 1.11.1, 2.0.0rc1, 2.0.0rc2, 2.0.0rc3, 2.0.0rc4, 2.0.0) ERROR: No matching distribution found for kivy==1.11.1
Same message with "sudo pip3 install kivy==1.11.1".
Jochen
aakechin
commented
3 years ago @JSeggewiss Maybe installation and use of python3.5 could resolve this problem? Then you will have to run all romands as e.g. python3.5 NGS-Primerplex.py... Or if you use Ubuntu, could you run the NGS-PrimerPlex in the command-line? I understood already that kivy is a bad package for GUI due to such a big difference between kivy and python versions. I'll try to replace it with PyQt in the future...
Hi!
After a lot of work (for me a Linux & Docker & Python newbie), it works almost fine. It's running under UBUNTU, GUI mode
I downloaded hg19 as describes in the manual. twoBitToFa hg19.2bit ucsc.hg19.fa bwa index ucsc.hg19.fasta
Is "ucsc.hg19.fasta" in the second line wrong? Shouldn't it be "ucsc.hg19.fa"?
Only when I use "Check for non-target hybridisation", I get the following error message:
Analyzing primers for their specificity... Running BWA... Traceback (most recent call last): File "/NGS-PrimerPlex/NGS_primerplex.py", line 3291, in
args.maxNonSpecLen,args.maxPrimerNonspec,False,'',args.blastNum)
File "/NGS-PrimerPlex/NGS_primerplex.py", line 1297, in checkPrimersSpecificity samFile=pysam.AlignmentFile(bwaResultFileName+'.sam') File "pysam/libcalignmentfile.pyx", line 737, in pysam.libcalignmentfile.AlignmentFile.cinit File "pysam/libcalignmentfile.pyx", line 986, in pysam.libcalignmentfile.AlignmentFile._open ValueError: file has no sequences defined (mode='r') - is it SAM/BAM format? Consider opening with check_sq=False
Whatś wrong?
Best regards Jochen