Closed omrison closed 4 years ago
2 additions:
looking forward to hearing your thoughts, thanks!
I’m having the same issue on my new win10 laptop. If I resolve I’ll post here.
These appear to be issues with installing spaCy. Please post an issue on their GitHub.
On Tue, May 7, 2019, 4:49 PM Andrew Bauman notifications@github.com wrote:
I’m having the same issue on my new win10 laptop. If I resolve I’ll post here.
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spacy actually installs just fine on its own, but fails on the medacy install. If I find a solution I'll post here.
so this is interesting. the latest spacy installs just fine, but the version in medacy setup has issues (independent of medacy). This issue can probably be closed out, the solution may lie here:
I will take a look and bump the requirements version if all tests pass and everything checks out.
In the mean time, you can clone down the repo, change the spaCy version in the setup.py locally, and installed the package from your altered clone.
You should have no issue utilizing the actual package with the different spaCy version as medaCy relies only on the core text processing functionality and API of spaCy. These should be invariant under minor releases.
Let me know if you run into any problems. Thanks!
On Tue, May 7, 2019, 7:10 PM Andrew Bauman notifications@github.com wrote:
so this is interesting. the latest spacy installs just fine, but the version in medacy setup has issues (independent of medacy). This issue can probably be closed out, the solution may lie here:
explosion/spaCy#2441 https://github.com/explosion/spaCy/issues/2441
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I'll give that a shot, thanks!
your suggestion worked. I might ultimately end up dockerizing this. If I do, I'll put the dockerfile and service stack in as a pull request.
I have solved the Microsoft Visual C++ build tools problem. Now I am getting this problem I have Windows 10 64 bit OS and Python 3.7.4-64 bit. I need this installed for my project but I am just stuck here. Anyone know what can be the problem? All other packages of python are installed nicely even spacy package but problem just happens with medaCy package. I don't know why..Help please!
Here is my output:
Microsoft Windows [Version 10.0.17763.107] (c) 2018 Microsoft Corporation. All rights reserved.
ERROR: Exception: Traceback (most recent call last): File "c:\users\marvi jokhio\appdata\local\programs\python\python37\lib\site-packages\pip_internal\commands\install.py", line 407, in run use_user_site=options.use_user_site, File "c:\users\marvi jokhio\appdata\local\programs\python\python37\lib\site-packages\pip_internal\req__init.py", line 58, in install_given_reqs **kwargs File "c:\users\marvi jokhio\appdata\local\programs\python\python37\lib\site-packages\pip_internal\req\req_install.py", line 959, in install spinner=spinner, File "c:\users\marvi jokhio\appdata\local\programs\python\python37\lib\site-packages\pip_internal\utils\misc.py", line 934, in call_subprocess raise InstallationError(exc_msg) pip._internal.exceptions.InstallationError: Command errored out with exit status 1: 'c:\users\marvi jokhio\appdata\local\programs\python\python37\python.exe' -u -c 'import sys, setuptools, tokenize; sys.argv[0] = '"'"'C:\Users\MARVIJ~1\AppData\Local\Temp\pip-install-c0asep64\nmslib\setup.py'"'"'; file='"'"'C:\Users\MARVIJ~1\AppData\Local\Temp\pip-install-c0asep64\nmslib\setup.py'"'"';f=getattr(tokenize, '"'"'open'"'"', open)(file);code=f.read().replace('"'"'\r\n'"'"', '"'"'\n'"'"');f.close();exec(compile(code, file__, '"'"'exec'"'"'))' install --record 'C:\Users\MARVIJ~1\AppData\Local\Temp\pip-record-v75x9l91\install-record.txt' --single-version-externally-managed --compile Check the logs for full command output.
During handling of the above exception, another exception occurred:
Traceback (most recent call last): File "c:\users\marvi jokhio\appdata\local\programs\python\python37\lib\site-packages\pip_internal\cli\base_command.py", line 188, in main status = self.run(options, args) File "c:\users\marvi jokhio\appdata\local\programs\python\python37\lib\site-packages\pip_internal\commands\install.py", line 450, in run requirement_set.cleanup_files() File "c:\users\marvi jokhio\appdata\local\programs\python\python37\lib\site-packages\pip_internal\req\req_set.py", line 193, in cleanup_files req.remove_temporary_source() File "c:\users\marvi jokhio\appdata\local\programs\python\python37\lib\site-packages\pip_internal\req\req_install.py", line 387, in remove_temporary_source rmtree(self.source_dir) File "c:\users\marvi jokhio\appdata\local\programs\python\python37\lib\site-packages\pip_vendor\retrying.py", line 49, in wrapped_f return Retrying(*dargs, dkw).call(f, *args, *kw) File "c:\users\marvi jokhio\appdata\local\programs\python\python37\lib\site-packages\pip_vendor\retrying.py", line 212, in call raise attempt.get() File "c:\users\marvi jokhio\appdata\local\programs\python\python37\lib\site-packages\pip_vendor\retrying.py", line 247, in get six.reraise(self.value[0], self.value[1], self.value[2]) File "c:\users\marvi jokhio\appdata\local\programs\python\python37\lib\site-packages\pip_vendor\six.py", line 693, in reraise raise value File "c:\users\marvi jokhio\appdata\local\programs\python\python37\lib\site-packages\pip_vendor\retrying.py", line 200, in call attempt = Attempt(fn(args, kwargs), attempt_number, False) File "c:\users\marvi jokhio\appdata\local\programs\python\python37\lib\site-packages\pip_internal\utils\misc.py", line 169, in rmtree onerror=rmtree_errorhandler) File "c:\users\marvi jokhio\appdata\local\programs\python\python37\lib\shutil.py", line 516, in rmtree return _rmtree_unsafe(path, onerror) File "c:\users\marvi jokhio\appdata\local\programs\python\python37\lib\shutil.py", line 395, in _rmtree_unsafe _rmtree_unsafe(fullname, onerror) File "c:\users\marvi jokhio\appdata\local\programs\python\python37\lib\shutil.py", line 395, in _rmtree_unsafe _rmtree_unsafe(fullname, onerror) File "c:\users\marvi jokhio\appdata\local\programs\python\python37\lib\shutil.py", line 395, in _rmtree_unsafe _rmtree_unsafe(fullname, onerror) [Previous line repeated 4 more times] File "c:\users\marvi jokhio\appdata\local\programs\python\python37\lib\shutil.py", line 400, in _rmtree_unsafe onerror(os.unlink, fullname, sys.exc_info()) File "c:\users\marvi jokhio\appdata\local\programs\python\python37\lib\site-packages\pip_internal\utils\misc.py", line 179, in rmtree_errorhandler os.chmod(path, stat.S_IWRITE) PermissionError: [WinError 5] Access is denied: 'C:\Users\MARVIJ~1\AppData\Local\Temp\pip-install-c0asep64\nmslib\build\temp.win-amd64-3.7\Release\nmslib\similarity_search\src\method\perm_index_incr_bin.obj'
C:\Users\Marvi Jokhio>
Did anything happen with this error? I'm having the same error
Hi,
Thank you for bringing up this issue. We do not plan to provide immediate support to windows users at this time.
Best, Andriy
On Fri, Aug 2, 2019, 11:35 AM moalkawi notifications@github.com wrote:
Did anything happen with this error? I'm having the same error
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On Fri, Aug 2, 2019, 11:35 AM moalkawi notifications@github.com wrote:
Did anything happen with this error? I'm having the same error
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Hi, I could install medacy but while running following from medacy.ner.model import Model
model = Model.load_external('medacy_model_clinical_notes') annotation = model.predict("The patient was prescribed 1 capsule of Advil for 5 days.") print(annotation)
I am getting this error ......................................... Traceback (most recent call last):
File "
File "C:\Users\lenovo\Anaconda3\lib\site-packages\spyder\utils\site\sitecustomize.py", line 866, in runfile execfile(filename, namespace)
File "C:\Users\lenovo\Anaconda3\lib\site-packages\spyder\utils\site\sitecustomize.py", line 102, in execfile exec(compile(f.read(), filename, 'exec'), namespace)
File "C:/Users/lenovo/.spyder-py3/temp.py", line 10, in
File "C:\Users\lenovo\Anaconda3\lib\site-packages\medacy-0.1.1-py3.6.egg\medacy\ner\model\model.py", line 461, in load_external return importlib.import_module(package_name).load()
File "C:\Users\lenovo\Anaconda3\lib\site-packages\medacy_model_clinical_notes-1.0.1-py3.6.egg\medacy_model_clinical_notes\medacy_model_clinical_notes.py", line 8, in load pipeline = ClinicalPipeline(entities=entities)
File "C:\Users\lenovo\Anaconda3\lib\site-packages\medacy-0.1.1-py3.6.egg\medacy\ner\pipelines\clinical_pipeline.py", line 24, in init spacy_pipeline=spacy.load("en_core_web_sm"),
File "C:\Users\lenovo\Anaconda3\lib\site-packages\spacy__init__.py", line 27, in load return util.load_model(name, **overrides)
File "C:\Users\lenovo\Anaconda3\lib\site-packages\spacy\util.py", line 134, in load_model return load_model_from_package(name, **overrides)
File "C:\Users\lenovo\Anaconda3\lib\site-packages\spacy\util.py", line 155, in load_model_from_package return cls.load(**overrides)
File "C:\Users\lenovo\Anaconda3\lib\site-packages\en_core_web_sm-2.0.0-py3.6.egg\en_core_web_sm__init.py", line 12, in load return load_model_from_init_py(file__, **overrides)
File "C:\Users\lenovo\Anaconda3\lib\site-packages\spacy\util.py", line 196, in load_model_from_init_py return load_model_from_path(data_path, meta, **overrides)
File "C:\Users\lenovo\Anaconda3\lib\site-packages\spacy\util.py", line 179, in load_model_from_path return nlp.from_disk(model_path)
File "C:\Users\lenovo\Anaconda3\lib\site-packages\spacy\language.py", line 832, in from_disk util.from_disk(path, deserializers, exclude)
File "C:\Users\lenovo\Anaconda3\lib\site-packages\spacy\util.py", line 636, in from_disk reader(path / key)
File "C:\Users\lenovo\Anaconda3\lib\site-packages\spacy\language.py", line 819, in
File "tokenizer.pyx", line 391, in spacy.tokenizer.Tokenizer.from_disk
File "tokenizer.pyx", line 437, in spacy.tokenizer.Tokenizer.from_bytes
File "C:\Users\lenovo\Anaconda3\lib\re.py", line 233, in compile return _compile(pattern, flags)
File "C:\Users\lenovo\Anaconda3\lib\re.py", line 301, in _compile p = sre_compile.compile(pattern, flags)
File "C:\Users\lenovo\Anaconda3\lib\sre_compile.py", line 562, in compile p = sre_parse.parse(p, flags)
File "C:\Users\lenovo\Anaconda3\lib\sre_parse.py", line 856, in parse p = _parse_sub(source, pattern, flags & SRE_FLAG_VERBOSE, False)
File "C:\Users\lenovo\Anaconda3\lib\sre_parse.py", line 415, in _parse_sub itemsappend(_parse(source, state, verbose))
File "C:\Users\lenovo\Anaconda3\lib\sre_parse.py", line 526, in _parse code1 = _class_escape(source, this)
File "C:\Users\lenovo\Anaconda3\lib\sre_parse.py", line 336, in _class_escape raise source.error('bad escape %s' % escape, len(escape))
error: bad escape \p
I upgraded my spacy with python -m spacy download en_core_web_sm and now medacy is working fine
Hi, I could install medacy but while running following from medacy.ner.model import Model
model = Model.load_external('medacy_model_clinical_notes') annotation = model.predict("The patient was prescribed 1 capsule of Advil for 5 days.") print(annotation)
I am getting this error ......................................... Traceback (most recent call last):
File "", line 1, in runfile('C:/Users/lenovo/.spyder-py3/temp.py', wdir='C:/Users/lenovo/.spyder-py3')
File "C:\Users\lenovo\Anaconda3\lib\site-packages\spyder\utils\site\sitecustomize.py", line 866, in runfile execfile(filename, namespace)
File "C:\Users\lenovo\Anaconda3\lib\site-packages\spyder\utils\site\sitecustomize.py", line 102, in execfile exec(compile(f.read(), filename, 'exec'), namespace)
File "C:/Users/lenovo/.spyder-py3/temp.py", line 10, in model = Model.load_external('medacy_model_clinical_notes')
File "C:\Users\lenovo\Anaconda3\lib\site-packages\medacy-0.1.1-py3.6.egg\medacy\ner\model\model.py", line 461, in load_external return importlib.import_module(package_name).load()
File "C:\Users\lenovo\Anaconda3\lib\site-packages\medacy_model_clinical_notes-1.0.1-py3.6.egg\medacy_model_clinical_notes\medacy_model_clinical_notes.py", line 8, in load pipeline = ClinicalPipeline(entities=entities)
File "C:\Users\lenovo\Anaconda3\lib\site-packages\medacy-0.1.1-py3.6.egg\medacy\ner\pipelines\clinical_pipeline.py", line 24, in init spacy_pipeline=spacy.load("en_core_web_sm"),
File "C:\Users\lenovo\Anaconda3\lib\site-packages\spacyinit.py", line 27, in load return util.load_model(name, **overrides)
File "C:\Users\lenovo\Anaconda3\lib\site-packages\spacy\util.py", line 134, in load_model return load_model_from_package(name, **overrides)
File "C:\Users\lenovo\Anaconda3\lib\site-packages\spacy\util.py", line 155, in load_model_from_package return cls.load(**overrides)
File "C:\Users\lenovo\Anaconda3\lib\site-packages\en_core_web_sm-2.0.0-py3.6.egg\en_core_web_sminit.py", line 12, in load return load_model_from_init_py(file, **overrides)
File "C:\Users\lenovo\Anaconda3\lib\site-packages\spacy\util.py", line 196, in load_model_from_init_py return load_model_from_path(data_path, meta, **overrides)
File "C:\Users\lenovo\Anaconda3\lib\site-packages\spacy\util.py", line 179, in load_model_from_path return nlp.from_disk(model_path)
File "C:\Users\lenovo\Anaconda3\lib\site-packages\spacy\language.py", line 832, in from_disk util.from_disk(path, deserializers, exclude)
File "C:\Users\lenovo\Anaconda3\lib\site-packages\spacy\util.py", line 636, in from_disk reader(path / key)
File "C:\Users\lenovo\Anaconda3\lib\site-packages\spacy\language.py", line 819, in p, exclude=["vocab"]
File "tokenizer.pyx", line 391, in spacy.tokenizer.Tokenizer.from_disk
File "tokenizer.pyx", line 437, in spacy.tokenizer.Tokenizer.from_bytes
File "C:\Users\lenovo\Anaconda3\lib\re.py", line 233, in compile return _compile(pattern, flags)
File "C:\Users\lenovo\Anaconda3\lib\re.py", line 301, in _compile p = sre_compile.compile(pattern, flags)
File "C:\Users\lenovo\Anaconda3\lib\sre_compile.py", line 562, in compile p = sre_parse.parse(p, flags)
File "C:\Users\lenovo\Anaconda3\lib\sre_parse.py", line 856, in parse p = _parse_sub(source, pattern, flags & SRE_FLAG_VERBOSE, False)
File "C:\Users\lenovo\Anaconda3\lib\sre_parse.py", line 415, in _parse_sub itemsappend(_parse(source, state, verbose))
File "C:\Users\lenovo\Anaconda3\lib\sre_parse.py", line 526, in _parse code1 = _class_escape(source, this)
File "C:\Users\lenovo\Anaconda3\lib\sre_parse.py", line 336, in _class_escape raise source.error('bad escape %s' % escape, len(escape))
error: bad escape \p
How did you install it on your side? May I know what is your system and the way you tried to install?
Hi, I could install it now but whenever I am trying to run the examples from help PDF it is asking for more dependent packages.
On Wed, 21 Aug, 2019, 7:05 PM marvijokhio, notifications@github.com wrote:
Hi, I could install medacy but while running following from medacy.ner.model import Model
model = Model.load_external('medacy_model_clinical_notes') annotation = model.predict("The patient was prescribed 1 capsule of Advil for 5 days.") print(annotation)
I am getting this error ......................................... Traceback (most recent call last):
File "", line 1, in runfile('C:/Users/lenovo/.spyder-py3/temp.py', wdir='C:/Users/lenovo/.spyder-py3')
File "C:\Users\lenovo\Anaconda3\lib\site-packages\spyder\utils\site\sitecustomize.py", line 866, in runfile execfile(filename, namespace)
File "C:\Users\lenovo\Anaconda3\lib\site-packages\spyder\utils\site\sitecustomize.py", line 102, in execfile exec(compile(f.read(), filename, 'exec'), namespace)
File "C:/Users/lenovo/.spyder-py3/temp.py", line 10, in model = Model.load_external('medacy_model_clinical_notes')
File "C:\Users\lenovo\Anaconda3\lib\site-packages\medacy-0.1.1-py3.6.egg\medacy\ner\model\model.py", line 461, in load_external return importlib.import_module(package_name).load()
File "C:\Users\lenovo\Anaconda3\lib\site-packages\medacy_model_clinical_notes-1.0.1-py3.6.egg\medacy_model_clinical_notes\medacy_model_clinical_notes.py", line 8, in load pipeline = ClinicalPipeline(entities=entities)
File "C:\Users\lenovo\Anaconda3\lib\site-packages\medacy-0.1.1-py3.6.egg\medacy\ner\pipelines\clinical_pipeline.py", line 24, in init spacy_pipeline=spacy.load("en_core_web_sm"),
File "C:\Users\lenovo\Anaconda3\lib\site-packages\spacyinit.py", line 27, in load return util.load_model(name, **overrides)
File "C:\Users\lenovo\Anaconda3\lib\site-packages\spacy\util.py", line 134, in load_model return load_model_from_package(name, **overrides)
File "C:\Users\lenovo\Anaconda3\lib\site-packages\spacy\util.py", line 155, in load_model_from_package return cls.load(**overrides)
File "C:\Users\lenovo\Anaconda3\lib\site-packages\en_core_web_sm-2.0.0-py3.6.egg\en_core_web_sminit.py", line 12, in load return load_model_from_init_py(file, **overrides)
File "C:\Users\lenovo\Anaconda3\lib\site-packages\spacy\util.py", line 196, in load_model_from_init_py return load_model_from_path(data_path, meta, **overrides)
File "C:\Users\lenovo\Anaconda3\lib\site-packages\spacy\util.py", line 179, in load_model_from_path return nlp.from_disk(model_path)
File "C:\Users\lenovo\Anaconda3\lib\site-packages\spacy\language.py", line 832, in from_disk util.from_disk(path, deserializers, exclude)
File "C:\Users\lenovo\Anaconda3\lib\site-packages\spacy\util.py", line 636, in from_disk reader(path / key)
File "C:\Users\lenovo\Anaconda3\lib\site-packages\spacy\language.py", line 819, in p, exclude=["vocab"]
File "tokenizer.pyx", line 391, in spacy.tokenizer.Tokenizer.from_disk
File "tokenizer.pyx", line 437, in spacy.tokenizer.Tokenizer.from_bytes
File "C:\Users\lenovo\Anaconda3\lib\re.py", line 233, in compile return _compile(pattern, flags)
File "C:\Users\lenovo\Anaconda3\lib\re.py", line 301, in _compile p = sre_compile.compile(pattern, flags)
File "C:\Users\lenovo\Anaconda3\lib\sre_compile.py", line 562, in compile p = sre_parse.parse(p, flags)
File "C:\Users\lenovo\Anaconda3\lib\sre_parse.py", line 856, in parse p = _parse_sub(source, pattern, flags & SRE_FLAG_VERBOSE, False)
File "C:\Users\lenovo\Anaconda3\lib\sre_parse.py", line 415, in _parse_sub itemsappend(_parse(source, state, verbose))
File "C:\Users\lenovo\Anaconda3\lib\sre_parse.py", line 526, in _parse code1 = _class_escape(source, this)
File "C:\Users\lenovo\Anaconda3\lib\sre_parse.py", line 336, in _class_escape raise source.error('bad escape %s' % escape, len(escape))
error: bad escape \p
How did you install it on your side? May I know what is your system and the way you tried to install?
— You are receiving this because you commented. Reply to this email directly, view it on GitHub https://github.com/NLPatVCU/medaCy/issues/124?email_source=notifications&email_token=AICBFNJ3FKK5RC4FIA4ZXMDQFVABHA5CNFSM4HKIRTUKYY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGOD4ZVYLY#issuecomment-523459631, or mute the thread https://github.com/notifications/unsubscribe-auth/AICBFNIUNSCXLZ65VR4BPS3QFVABHANCNFSM4HKIRTUA .
Hi, you need to install the spacy small model. Thanks!
On Sun, Aug 25, 2019, 9:12 AM Pranita Mahajan notifications@github.com wrote:
Hi, I could install it now but whenever I am trying to run the examples from help PDF it is asking for more dependent packages.
On Wed, 21 Aug, 2019, 7:05 PM marvijokhio, notifications@github.com wrote:
Hi, I could install medacy but while running following from medacy.ner.model import Model
model = Model.load_external('medacy_model_clinical_notes') annotation = model.predict("The patient was prescribed 1 capsule of Advil for 5 days.") print(annotation)
I am getting this error ......................................... Traceback (most recent call last):
File "", line 1, in runfile('C:/Users/lenovo/.spyder-py3/temp.py', wdir='C:/Users/lenovo/.spyder-py3')
File
"C:\Users\lenovo\Anaconda3\lib\site-packages\spyder\utils\site\sitecustomize.py", line 866, in runfile execfile(filename, namespace)
File
"C:\Users\lenovo\Anaconda3\lib\site-packages\spyder\utils\site\sitecustomize.py", line 102, in execfile exec(compile(f.read(), filename, 'exec'), namespace)
File "C:/Users/lenovo/.spyder-py3/temp.py", line 10, in model = Model.load_external('medacy_model_clinical_notes')
File
"C:\Users\lenovo\Anaconda3\lib\site-packages\medacy-0.1.1-py3.6.egg\medacy\ner\model\model.py", line 461, in load_external return importlib.import_module(package_name).load()
File
"C:\Users\lenovo\Anaconda3\lib\site-packages\medacy_model_clinical_notes-1.0.1-py3.6.egg\medacy_model_clinical_notes\medacy_model_clinical_notes.py", line 8, in load pipeline = ClinicalPipeline(entities=entities)
File
"C:\Users\lenovo\Anaconda3\lib\site-packages\medacy-0.1.1-py3.6.egg\medacy\ner\pipelines\clinical_pipeline.py", line 24, in init spacy_pipeline=spacy.load("en_core_web_sm"),
File "C:\Users\lenovo\Anaconda3\lib\site-packages\spacyinit.py", line 27, in load return util.load_model(name, **overrides)
File "C:\Users\lenovo\Anaconda3\lib\site-packages\spacy\util.py", line 134, in load_model return load_model_from_package(name, **overrides)
File "C:\Users\lenovo\Anaconda3\lib\site-packages\spacy\util.py", line 155, in load_model_from_package return cls.load(**overrides)
File
"C:\Users\lenovo\Anaconda3\lib\site-packages\en_core_web_sm-2.0.0-py3.6.egg\en_core_web_sminit.py", line 12, in load return load_model_from_init_py(file, **overrides)
File "C:\Users\lenovo\Anaconda3\lib\site-packages\spacy\util.py", line 196, in load_model_from_init_py return load_model_from_path(data_path, meta, **overrides)
File "C:\Users\lenovo\Anaconda3\lib\site-packages\spacy\util.py", line 179, in load_model_from_path return nlp.from_disk(model_path)
File "C:\Users\lenovo\Anaconda3\lib\site-packages\spacy\language.py", line 832, in from_disk util.from_disk(path, deserializers, exclude)
File "C:\Users\lenovo\Anaconda3\lib\site-packages\spacy\util.py", line 636, in from_disk reader(path / key)
File "C:\Users\lenovo\Anaconda3\lib\site-packages\spacy\language.py", line 819, in p, exclude=["vocab"]
File "tokenizer.pyx", line 391, in spacy.tokenizer.Tokenizer.from_disk
File "tokenizer.pyx", line 437, in spacy.tokenizer.Tokenizer.from_bytes
File "C:\Users\lenovo\Anaconda3\lib\re.py", line 233, in compile return _compile(pattern, flags)
File "C:\Users\lenovo\Anaconda3\lib\re.py", line 301, in _compile p = sre_compile.compile(pattern, flags)
File "C:\Users\lenovo\Anaconda3\lib\sre_compile.py", line 562, in compile p = sre_parse.parse(p, flags)
File "C:\Users\lenovo\Anaconda3\lib\sre_parse.py", line 856, in parse p = _parse_sub(source, pattern, flags & SRE_FLAG_VERBOSE, False)
File "C:\Users\lenovo\Anaconda3\lib\sre_parse.py", line 415, in _parse_sub itemsappend(_parse(source, state, verbose))
File "C:\Users\lenovo\Anaconda3\lib\sre_parse.py", line 526, in _parse code1 = _class_escape(source, this)
File "C:\Users\lenovo\Anaconda3\lib\sre_parse.py", line 336, in _class_escape raise source.error('bad escape %s' % escape, len(escape))
error: bad escape \p
How did you install it on your side? May I know what is your system and the way you tried to install?
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Hi, Thanks a lot for your reply. I will try installing it and let you know the updates. It's a great help for me. Regards Pranita Mahajan
On Sun, 25 Aug, 2019, 9:04 PM Andriy Mulyar, notifications@github.com wrote:
Hi, you need to install the spacy small model. Thanks!
On Sun, Aug 25, 2019, 9:12 AM Pranita Mahajan notifications@github.com wrote:
Hi, I could install it now but whenever I am trying to run the examples from help PDF it is asking for more dependent packages.
On Wed, 21 Aug, 2019, 7:05 PM marvijokhio, notifications@github.com wrote:
Hi, I could install medacy but while running following from medacy.ner.model import Model
model = Model.load_external('medacy_model_clinical_notes') annotation = model.predict("The patient was prescribed 1 capsule of Advil for 5 days.") print(annotation)
I am getting this error ......................................... Traceback (most recent call last):
File "", line 1, in runfile('C:/Users/lenovo/.spyder-py3/temp.py', wdir='C:/Users/lenovo/.spyder-py3')
File
"C:\Users\lenovo\Anaconda3\lib\site-packages\spyder\utils\site\sitecustomize.py",
line 866, in runfile execfile(filename, namespace)
File
"C:\Users\lenovo\Anaconda3\lib\site-packages\spyder\utils\site\sitecustomize.py",
line 102, in execfile exec(compile(f.read(), filename, 'exec'), namespace)
File "C:/Users/lenovo/.spyder-py3/temp.py", line 10, in model = Model.load_external('medacy_model_clinical_notes')
File
"C:\Users\lenovo\Anaconda3\lib\site-packages\medacy-0.1.1-py3.6.egg\medacy\ner\model\model.py",
line 461, in load_external return importlib.import_module(package_name).load()
File
"C:\Users\lenovo\Anaconda3\lib\site-packages\medacy_model_clinical_notes-1.0.1-py3.6.egg\medacy_model_clinical_notes\medacy_model_clinical_notes.py",
line 8, in load pipeline = ClinicalPipeline(entities=entities)
File
"C:\Users\lenovo\Anaconda3\lib\site-packages\medacy-0.1.1-py3.6.egg\medacy\ner\pipelines\clinical_pipeline.py",
line 24, in init spacy_pipeline=spacy.load("en_core_web_sm"),
File "C:\Users\lenovo\Anaconda3\lib\site-packages\spacyinit.py", line 27, in load return util.load_model(name, **overrides)
File "C:\Users\lenovo\Anaconda3\lib\site-packages\spacy\util.py", line 134, in load_model return load_model_from_package(name, **overrides)
File "C:\Users\lenovo\Anaconda3\lib\site-packages\spacy\util.py", line 155, in load_model_from_package return cls.load(**overrides)
File
"C:\Users\lenovo\Anaconda3\lib\site-packages\en_core_web_sm-2.0.0-py3.6.egg\en_core_web_sminit.py",
line 12, in load return load_model_from_init_py(file, **overrides)
File "C:\Users\lenovo\Anaconda3\lib\site-packages\spacy\util.py", line 196, in load_model_from_init_py return load_model_from_path(data_path, meta, **overrides)
File "C:\Users\lenovo\Anaconda3\lib\site-packages\spacy\util.py", line 179, in load_model_from_path return nlp.from_disk(model_path)
File "C:\Users\lenovo\Anaconda3\lib\site-packages\spacy\language.py", line 832, in from_disk util.from_disk(path, deserializers, exclude)
File "C:\Users\lenovo\Anaconda3\lib\site-packages\spacy\util.py", line 636, in from_disk reader(path / key)
File "C:\Users\lenovo\Anaconda3\lib\site-packages\spacy\language.py", line 819, in p, exclude=["vocab"]
File "tokenizer.pyx", line 391, in spacy.tokenizer.Tokenizer.from_disk
File "tokenizer.pyx", line 437, in spacy.tokenizer.Tokenizer.from_bytes
File "C:\Users\lenovo\Anaconda3\lib\re.py", line 233, in compile return _compile(pattern, flags)
File "C:\Users\lenovo\Anaconda3\lib\re.py", line 301, in _compile p = sre_compile.compile(pattern, flags)
File "C:\Users\lenovo\Anaconda3\lib\sre_compile.py", line 562, in compile p = sre_parse.parse(p, flags)
File "C:\Users\lenovo\Anaconda3\lib\sre_parse.py", line 856, in parse p = _parse_sub(source, pattern, flags & SRE_FLAG_VERBOSE, False)
File "C:\Users\lenovo\Anaconda3\lib\sre_parse.py", line 415, in _parse_sub itemsappend(_parse(source, state, verbose))
File "C:\Users\lenovo\Anaconda3\lib\sre_parse.py", line 526, in _parse code1 = _class_escape(source, this)
File "C:\Users\lenovo\Anaconda3\lib\sre_parse.py", line 336, in _class_escape raise source.error('bad escape %s' % escape, len(escape))
error: bad escape \p
How did you install it on your side? May I know what is your system and the way you tried to install?
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, or mute the thread <
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hi, Do I need to install medacy.pipelines as well? is there any link for where I can install all dependent packages ? thanks
Description
issues when trying to install medacy on windows.
Steps/Code to Reproduce
on cmd i am running: pip install git+https://github.com/NLPatVCU/medaCy.git
Expected Results
medacy installed
Actual Results
Building wheel for ujson (setup.py) ... error ERROR: Complete output from command 'c:\python\python37\python.exe' -u -c 'import setuptools, tokenize;file='"'"'C:\Users\om\AppData\Local\Temp\pip-install-5k7yz4al\ujson\setup.py'"'"';f=getattr(tokenize, '"'"'open'"'"', open)(file);code=f.read().replace('"'"'\r\n'"'"', '"'"'\n'"'"');f.close();exec(compile(code, file, '"'"'exec'"'"'))' bdist_wheel -d 'C:\Users\om\AppData\Local\Temp\pip-wheel-572h8xdt' --python-tag cp37: ERROR: Warning: 'classifiers' should be a list, got type 'filter' running bdist_wheel running build running build_ext building 'ujson' extension error: Microsoft Visual C++ 14.0 is required. Get it with "Microsoft Visual C++ Build Tools": https://visualstudio.microsoft.com/downloads/
ERROR: Failed building wheel for ujson
Versions
Windows-10-10.0.17763-SP0 Python 3.7.2 (tags/v3.7.2:9a3ffc0492, Dec 23 2018, 23:09:28) [MSC v.1916 64 bit (AMD64)] NumPy 1.16.2 ModuleNotFoundError: No module named 'scipy' ModuleNotFoundError: No module named 'medacy'