-
Notifications
You must be signed in to change notification settings - Fork 21
New issue
Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.
By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.
Already on GitHub? Sign in to your account
installation error #114
Comments
@nvictus Does this ring any bells to you? Looks like something to do with pybbi. |
Hey guys, I tried to pip install pybbi, the system also report error, and I tried the way @nvictus suggested but still not being able to solve the problem. |
Hey guys, I forgot to mention that I used mac oxs 10.14.6. |
Is there any more information? It looks like you've already seen nvictus/pybbi#2 and installed libpng and openssl? |
Yes. I did tried that. All the packages I tried installed to mac oxs 10.14.6 so far, including higlass-manage, clodius were stucked at the pybbi. Also, I tried to "pip install pybbi", and it showed similar error message: |
@JiangXu123, could you put the full error log in a pastebin (https://pastebin.com/)? The tail of the log will be more relevant, because all I see above is output from the compiler, which looks fine. |
hey thanks for your attention. Please check the following:
|
Looks like the headers for openssl are missing:
Were you able to brew install openssl (not libressl), and if so, did you export the
It's possible that the location of the headers has changed or is different for you. Check if |
Hey nvictus From above I found that the directory is a little bit diffrent and so I changed path to the following and it worked. |
Glad to hear it! :) |
Hey guys, I tried to install clodius on my computer using pip and could not finish the installation. Could you help to solve the problem? Thanks! Here is the error messages:
pip install clodius
Collecting clodius
Requirement already satisfied: cooler>=0.8.5 in /Users/jiangxu/anaconda3/lib/python3.7/site-packages (from clodius) (0.8.6.post0)
Requirement already satisfied: slugid in /Users/jiangxu/anaconda3/lib/python3.7/site-packages (from clodius) (2.0.0)
Requirement already satisfied: numpy in /Users/jiangxu/anaconda3/lib/python3.7/site-packages (from clodius) (1.17.2)
Requirement already satisfied: pandas in /Users/jiangxu/anaconda3/lib/python3.7/site-packages (from clodius) (0.25.1)
Requirement already satisfied: dask in /Users/jiangxu/anaconda3/lib/python3.7/site-packages (from clodius) (2.5.2)
Requirement already satisfied: nose in /Users/jiangxu/anaconda3/lib/python3.7/site-packages (from clodius) (1.3.7)
Requirement already satisfied: Click>=7 in /Users/jiangxu/anaconda3/lib/python3.7/site-packages (from clodius) (7.0)
Requirement already satisfied: h5py in /Users/jiangxu/anaconda3/lib/python3.7/site-packages (from clodius) (2.9.0)
Requirement already satisfied: negspy in /Users/jiangxu/anaconda3/lib/python3.7/site-packages (from clodius) (0.2.23)
Collecting pybbi>=0.2.0 (from clodius)
Using cached https://files.pythonhosted.org/packages/ef/39/d1dab1bd79e118237a8de87c12b7a8c99964c005de5ca31ee4f60683099e/pybbi-0.2.0.tar.gz
Requirement already satisfied: sortedcontainers in /Users/jiangxu/anaconda3/lib/python3.7/site-packages (from clodius) (2.1.0)
Requirement already satisfied: pysam in /Users/jiangxu/anaconda3/lib/python3.7/site-packages (from clodius) (0.15.3)
Requirement already satisfied: requests in /Users/jiangxu/anaconda3/lib/python3.7/site-packages (from clodius) (2.22.0)
Requirement already satisfied: asciitree in /Users/jiangxu/anaconda3/lib/python3.7/site-packages (from cooler>=0.8.5->clodius) (0.3.3)
Requirement already satisfied: pypairix in /Users/jiangxu/anaconda3/lib/python3.7/site-packages (from cooler>=0.8.5->clodius) (0.3.7)
Requirement already satisfied: scipy>=0.16 in /Users/jiangxu/anaconda3/lib/python3.7/site-packages (from cooler>=0.8.5->clodius) (1.3.1)
Requirement already satisfied: pyyaml in /Users/jiangxu/anaconda3/lib/python3.7/site-packages (from cooler>=0.8.5->clodius) (5.1.2)
Requirement already satisfied: pyfaidx in /Users/jiangxu/anaconda3/lib/python3.7/site-packages (from cooler>=0.8.5->clodius) (0.5.5.2)
Requirement already satisfied: biopython in /Users/jiangxu/anaconda3/lib/python3.7/site-packages (from cooler>=0.8.5->clodius) (1.75)
Requirement already satisfied: six in /Users/jiangxu/anaconda3/lib/python3.7/site-packages (from cooler>=0.8.5->clodius) (1.12.0)
Requirement already satisfied: cytoolz in /Users/jiangxu/anaconda3/lib/python3.7/site-packages (from cooler>=0.8.5->clodius) (0.10.0)
Requirement already satisfied: multiprocess in /Users/jiangxu/anaconda3/lib/python3.7/site-packages (from cooler>=0.8.5->clodius) (0.70.9)
Requirement already satisfied: pytz>=2017.2 in /Users/jiangxu/anaconda3/lib/python3.7/site-packages (from pandas->clodius) (2019.3)
Requirement already satisfied: python-dateutil>=2.6.1 in /Users/jiangxu/anaconda3/lib/python3.7/site-packages (from pandas->clodius) (2.8.0)
Requirement already satisfied: certifi>=2017.4.17 in /Users/jiangxu/anaconda3/lib/python3.7/site-packages (from requests->clodius) (2019.9.11)
Requirement already satisfied: chardet<3.1.0,>=3.0.2 in /Users/jiangxu/anaconda3/lib/python3.7/site-packages (from requests->clodius) (3.0.4)
Requirement already satisfied: urllib3!=1.25.0,!=1.25.1,<1.26,>=1.21.1 in /Users/jiangxu/anaconda3/lib/python3.7/site-packages (from requests->clodius) (1.24.2)
Requirement already satisfied: idna<2.9,>=2.5 in /Users/jiangxu/anaconda3/lib/python3.7/site-packages (from requests->clodius) (2.8)
Requirement already satisfied: setuptools>=0.7 in /Users/jiangxu/anaconda3/lib/python3.7/site-packages (from pyfaidx->cooler>=0.8.5->clodius) (41.4.0)
Requirement already satisfied: toolz>=0.8.0 in /Users/jiangxu/anaconda3/lib/python3.7/site-packages (from cytoolz->cooler>=0.8.5->clodius) (0.10.0)
Requirement already satisfied: dill>=0.3.1 in /Users/jiangxu/anaconda3/lib/python3.7/site-packages (from multiprocess->cooler>=0.8.5->clodius) (0.3.1.1)
Building wheels for collected packages: pybbi
Building wheel for pybbi (setup.py) ... error
ERROR: Command errored out with exit status 1:
command: /Users/jiangxu/anaconda3/bin/python -u -c 'import sys, setuptools, tokenize; sys.argv[0] = '"'"'/private/var/folders/yy/87g5h_vd1s51f7ghkv2y9bnw0000gn/T/pip-install-wuedhxyq/pybbi/setup.py'"'"'; file='"'"'/private/var/folders/yy/87g5h_vd1s51f7ghkv2y9bnw0000gn/T/pip-install-wuedhxyq/pybbi/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 /private/var/folders/yy/87g5h_vd1s51f7ghkv2y9bnw0000gn/T/pip-wheel-4i3t_8eq --python-tag cp37
cwd: /private/var/folders/yy/87g5h_vd1s51f7ghkv2y9bnw0000gn/T/pip-install-wuedhxyq/pybbi/
...
1 error generated.
make[1]: *** [udc.o] Error 1
make: *** [src/x86_64/libkent.a] Error 2
Traceback (most recent call last):
File "", line 1, in
File "/private/var/folders/yy/87g5h_vd1s51f7ghkv2y9bnw0000gn/T/pip-install-wuedhxyq/pybbi/setup.py", line 152, in
'build_ext': build_ext
File "/Users/jiangxu/anaconda3/lib/python3.7/site-packages/setuptools/init.py", line 145, in setup
return distutils.core.setup(**attrs)
File "/Users/jiangxu/anaconda3/lib/python3.7/distutils/core.py", line 148, in setup
dist.run_commands()
File "/Users/jiangxu/anaconda3/lib/python3.7/distutils/dist.py", line 966, in run_commands
self.run_command(cmd)
File "/Users/jiangxu/anaconda3/lib/python3.7/distutils/dist.py", line 985, in run_command
cmd_obj.run()
File "/Users/jiangxu/anaconda3/lib/python3.7/site-packages/setuptools/command/install.py", line 61, in run
return orig.install.run(self)
File "/Users/jiangxu/anaconda3/lib/python3.7/distutils/command/install.py", line 545, in run
self.run_command('build')
File "/Users/jiangxu/anaconda3/lib/python3.7/distutils/cmd.py", line 313, in run_command
self.distribution.run_command(command)
File "/Users/jiangxu/anaconda3/lib/python3.7/distutils/dist.py", line 985, in run_command
cmd_obj.run()
File "/Users/jiangxu/anaconda3/lib/python3.7/distutils/command/build.py", line 135, in run
self.run_command(cmd_name)
File "/Users/jiangxu/anaconda3/lib/python3.7/distutils/cmd.py", line 313, in run_command
self.distribution.run_command(command)
File "/Users/jiangxu/anaconda3/lib/python3.7/distutils/dist.py", line 985, in run_command
cmd_obj.run()
File "/private/var/folders/yy/87g5h_vd1s51f7ghkv2y9bnw0000gn/T/pip-install-wuedhxyq/pybbi/setup.py", line 86, in run
check_call(['make', 'build-c'])
File "/Users/jiangxu/anaconda3/lib/python3.7/subprocess.py", line 347, in check_call
raise CalledProcessError(retcode, cmd)
subprocess.CalledProcessError: Command '['make', 'build-c']' returned non-zero exit status 2.
----------------------------------------
ERROR: Command errored out with exit status 1: /Users/jiangxu/anaconda3/bin/python -u -c 'import sys, setuptools, tokenize; sys.argv[0] = '"'"'/private/var/folders/yy/87g5h_vd1s51f7ghkv2y9bnw0000gn/T/pip-install-wuedhxyq/pybbi/setup.py'"'"'; file='"'"'/private/var/folders/yy/87g5h_vd1s51f7ghkv2y9bnw0000gn/T/pip-install-wuedhxyq/pybbi/setup.py'"'"';f=getattr(tokenize, '"'"'open'"'"', open)(file);code=f.read().replace('"'"'\r\n'"'"', '"'"'\n'"'"');f.close();exec(compile(code, file, '"'"'exec'"'"'))' install --record /private/var/folders/yy/87g5h_vd1s51f7ghkv2y9bnw0000gn/T/pip-record-a7uczv4x/install-record.txt --single-version-externally-managed --compile Check the logs for full command output.
The text was updated successfully, but these errors were encountered: