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bowang-lab / MedSAMSlicer

3D Slicer Plugin for Segment anything in medical images
https://www.nature.com/articles/s41467-024-44824-z
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cannot install dependencies. #19

Closed Ouyngh closed 3 months ago

Ouyngh commented 6 months ago

slicer 5.6.1 but cannot install dependencies. these is the errors: Installation will happen in F:/slicer5.6/dependencies Exception in thread Thread-7: Traceback (most recent call last): File "F:\slicer5.6\Slicer 5.6.1\lib\Python\Lib\threading.py", line 973, in _bootstrap_inner self.run() File "F:\slicer5.6\Slicer 5.6.1\lib\Python\Lib\threading.py", line 910, in run self._target(*self._args, *self._kwargs) File "F:/slicer5.6/MedSAMSlicer-0.05/MedSAMSlicer-0.05/MedSAM/MedSAMLite/MedSAMLite.py", line 518, in download_wrapper with urlopen(url) as r: File "F:\slicer5.6\Slicer 5.6.1\lib\Python\Lib\urllib\request.py", line 214, in urlopen return opener.open(url, data, timeout) File "F:\slicer5.6\Slicer 5.6.1\lib\Python\Lib\urllib\request.py", line 517, in open response = self._open(req, data) File "F:\slicer5.6\Slicer 5.6.1\lib\Python\Lib\urllib\request.py", line 534, in _open result = self._call_chain(self.handle_open, protocol, protocol + File "F:\slicer5.6\Slicer 5.6.1\lib\Python\Lib\urllib\request.py", line 494, in _call_chain result = func(args) File "F:\slicer5.6\Slicer 5.6.1\lib\Python\Lib\urllib\request.py", line 1389, in https_open return self.do_open(http.client.HTTPSConnection, req, File "F:\slicer5.6\Slicer 5.6.1\lib\Python\Lib\urllib\request.py", line 1350, in do_open r = h.getresponse() File "F:\slicer5.6\Slicer 5.6.1\lib\Python\Lib\http\client.py", line 1377, in getresponse response.begin() File "F:\slicer5.6\Slicer 5.6.1\lib\Python\Lib\http\client.py", line 320, in begin version, status, reason = self._read_status() File "F:\slicer5.6\Slicer 5.6.1\lib\Python\Lib\http\client.py", line 289, in _read_status raise RemoteDisconnected("Remote end closed connection without" http.client.RemoteDisconnected: Remote end closed connection without response Snipaste_2024-03-18_12-47-09

Ouyngh commented 6 months ago

Python 3.9.10 (main, Dec 12 2023, 02:25:18) [MSC v.1935 64 bit (AMD64)] on win32

Traceback (most recent call last): File "F:/slicer5.6/MedSAMSlicer-0.05/MedSAMSlicer-0.05/MedSAM/MedSAMLite/MedSAMLite.py", line 363, in enter self.initializeParameterNode() File "F:/slicer5.6/MedSAMSlicer-0.05/MedSAMSlicer-0.05/MedSAM/MedSAMLite/MedSAMLite.py", line 396, in initializeParameterNode self.setParameterNode(self.logic.getParameterNode()) File "F:/slicer5.6/MedSAMSlicer-0.05/MedSAMSlicer-0.05/MedSAM/MedSAMLite/MedSAMLite.py", line 416, in setParameterNode self._parameterNodeGuiTag = self._parameterNode.connectGui(self.ui) AttributeError: 'MedSAMLiteWidget' object has no attribute 'ui' Installation will happen in F:/slicer5.6/dependencies WARNING: Retrying (Retry(total=4, connect=None, read=None, redirect=None, status=None)) after connection broken by 'SSLError(SSLEOFError(8, 'EOF occurred in violation of protocol (_ssl.c:1129)'))': /simple/torch/ WARNING: Retrying (Retry(total=3, connect=None, read=None, redirect=None, status=None)) after connection broken by 'SSLError(SSLEOFError(8, 'EOF occurred in violation of protocol (_ssl.c:1129)'))': /simple/torch/ WARNING: Retrying (Retry(total=2, connect=None, read=None, redirect=None, status=None)) after connection broken by 'SSLError(SSLEOFError(8, 'EOF occurred in violation of protocol (_ssl.c:1129)'))': /simple/torch/ WARNING: Retrying (Retry(total=1, connect=None, read=None, redirect=None, status=None)) after connection broken by 'SSLError(SSLEOFError(8, 'EOF occurred in violation of protocol (_ssl.c:1129)'))': /simple/torch/ WARNING: Retrying (Retry(total=0, connect=None, read=None, redirect=None, status=None)) after connection broken by 'SSLError(SSLEOFError(8, 'EOF occurred in violation of protocol (_ssl.c:1129)'))': /simple/torch/ Could not fetch URL https://pypi.org/simple/torch/: There was a problem confirming the ssl certificate: HTTPSConnectionPool(host='pypi.org', port=443): Max retries exceeded with url: /simple/torch/ (Caused by SSLError(SSLEOFError(8, 'EOF occurred in violation of protocol (_ssl.c:1129)'))) - skipping ERROR: Could not find a version that satisfies the requirement torch==2.0.1 (from versions: none) ERROR: No matching distribution found for torch==2.0.1 Exception in thread Thread-2: Traceback (most recent call last): File "F:\slicer5.6\Slicer 5.6.1\lib\Python\Lib\threading.py", line 973, in _bootstrap_inner self.run() File "F:\slicer5.6\Slicer 5.6.1\lib\Python\Lib\threading.py", line 910, in run self._target(*self._args, **self._kwargs) File "F:/slicer5.6/MedSAMSlicer-0.05/MedSAMSlicer-0.05/MedSAM/MedSAMLite/MedSAMLite.py", line 513, in pip_install_wrapper slicer.util.pip_install(command) File "F:\slicer5.6\Slicer 5.6.1\bin\Python\slicer\util.py", line 3887, in pip_install _executePythonModule("pip", args) File "F:\slicer5.6\Slicer 5.6.1\bin\Python\slicer\util.py", line 3848, in _executePythonModule logProcessOutput(proc) File "F:\slicer5.6\Slicer 5.6.1\bin\Python\slicer\util.py", line 3814, in logProcessOutput raise CalledProcessError(retcode, proc.args, output=proc.stdout, stderr=proc.stderr) subprocess.CalledProcessError: Command '['F:/slicer5.6/Slicer 5.6.1/bin/../bin\PythonSlicer.EXE', '-m', 'pip', 'install', 'torch==2.0.1', 'torchvision==0.15.2']' returned non-zero exit status 1.

rasakereh commented 5 months ago

Seems like a connection issue. can you double check if you are using any proxy or behind any firewall and try with none in effect?