installation error
Closed this issue · 10 comments
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.
@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.
(base) Jiangs-MacBook-Pro-2:~ jiangxu$ export C_INCLUDE_PATH="/usr/local/lib:/usr/local/include/libpng16:/usr/local/opt/openssl/include"
(base) Jiangs-MacBook-Pro-2:~ jiangxu$ export LIBRARY_PATH="/usr/local/lib:/usr/local/include/libpng:/usr/local/opt/openssl/include"
(base) Jiangs-MacBook-Pro-2:~ jiangxu$ pip install pybbi
Collecting pybbi
Using cached https://files.pythonhosted.org/packages/ef/39/d1dab1bd79e118237a8de87c12b7a8c99964c005de5ca31ee4f60683099e/pybbi-0.2.0.tar.gz
Requirement already satisfied: six in ./anaconda3/lib/python3.7/site-packages (from pybbi) (1.12.0)
Requirement already satisfied: numpy in ./anaconda3/lib/python3.7/site-packages (from pybbi) (1.17.2)
Building wheels for collected packages: pybbi
Building wheel for pybbi (setup.py) ... error
ERROR: Command errored out with exit status 1:
Hey guys, I forgot to mention that I used mac oxs 10.14.6.
I successfully installed clodius in Ubuntu 18.04. Hope you guys can solve the problem
Thanks a lot!
Best!
Jiang
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:
jiangxu$ pip install pybbi
Collecting pybbi
Using cached https://files.pythonhosted.org/packages/ef/39/d1dab1bd79e118237a8de87c12b7a8c99964c005de5ca31ee4f60683099e/pybbi-0.2.0.tar.gz
Requirement already satisfied: six in /Users/jiangxu/anaconda3/lib/python3.7/site-packages (from pybbi) (1.12.0)
Requirement already satisfied: numpy in /Users/jiangxu/anaconda3/lib/python3.7/site-packages (from pybbi) (1.17.2)
Building wheels for collected packages: pybbi
Building wheel for pybbi (setup.py) ... error
@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:
https://pastebin.com/60VKjYZm
@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.
Looks like the headers for openssl are missing:
udc.c:39:10: fatal error: 'openssl/sha.h' file not found
#include <openssl/sha.h>
Were you able to brew install openssl (not libressl), and if so, did you export the C_INCLUDE_PATH environment variable before installing?
export C_INCLUDE_PATH="/usr/local/lib:/usr/local/include/libpng16:/usr/local/opt/openssl/include"
It's possible that the location of the headers has changed or is different for you. Check if /usr/local/opt/openssl/include exists.
Hey nvictus
Thank you so much for your hint. I solve the problem.
The openssl that I use is a little bit different:
(base) vpn-052-085:include jiangxu$ cd /usr/local/opt
(base) vpn-052-085:opt jiangxu$ ls -lah
total 0
drwxrwxr-x 32 jiangxu admin 1.0K Nov 23 17:35 .
drwxr-xr-x 16 root wheel 512B Nov 13 23:25 ..
-rw-r--r-- 1 jiangxu admin 0B Nov 9 17:11 .keepme
lrwxr-xr-x 1 jiangxu admin 24B Nov 9 17:14 freeglut -> ../Cellar/freeglut/3.0.0
lrwxr-xr-x 1 jiangxu admin 25B Nov 9 17:14 freetype -> ../Cellar/freetype/2.10.1
lrwxr-xr-x 1 jiangxu admin 21B Nov 9 17:15 gdbm -> ../Cellar/gdbm/1.18.1
lrwxr-xr-x 1 jiangxu admin 24B Nov 14 09:38 gettext -> ../Cellar/gettext/0.20.1
lrwxr-xr-x 1 jiangxu admin 20B Nov 9 17:14 glew -> ../Cellar/glew/2.1.0
lrwxr-xr-x 1 jiangxu admin 21B Nov 9 17:14 glm -> ../Cellar/glm/0.9.9.5
lrwxr-xr-x 1 jiangxu admin 22B Nov 11 18:45 htop -> ../Cellar/htop/2.2.0_1
lrwxr-xr-x 1 jiangxu admin 22B Nov 11 18:45 htop-osx -> ../Cellar/htop/2.2.0_1
lrwxr-xr-x 1 jiangxu admin 25B Nov 14 09:38 libidn2 -> ../Cellar/libidn2/2.2.0_1
lrwxr-xr-x 1 jiangxu admin 23B Nov 23 17:35 libpng -> ../Cellar/libpng/1.6.37
lrwxr-xr-x 1 jiangxu admin 29B Nov 14 09:38 libunistring -> ../Cellar/libunistring/0.9.10
lrwxr-xr-x 1 jiangxu admin 24B Nov 9 17:14 mmtf-cpp -> ../Cellar/mmtf-cpp/1.0.0
lrwxr-xr-x 1 jiangxu admin 23B Nov 9 17:14 msgpack -> ../Cellar/msgpack/3.2.0
lrwxr-xr-x 1 jiangxu admin 21B Nov 11 18:45 ncurses -> ../Cellar/ncurses/6.1
lrwxr-xr-x 1 jiangxu admin 28B Nov 9 17:15 openssl@1.1 -> ../Cellar/openssl@1.1/1.1.1d
lrwxr-xr-x 1 jiangxu admin 21B Nov 9 17:18 pymol -> ../Cellar/pymol/2.3.0
lrwxr-xr-x 1 jiangxu admin 23B Nov 9 17:15 pyqt -> ../Cellar/pyqt/5.10.1_2
lrwxr-xr-x 1 jiangxu admin 23B Nov 9 17:15 pyqt5 -> ../Cellar/pyqt/5.10.1_2
lrwxr-xr-x 1 jiangxu admin 22B Nov 9 17:15 python -> ../Cellar/python/3.7.5
lrwxr-xr-x 1 jiangxu admin 22B Nov 9 17:15 python3 -> ../Cellar/python/3.7.5
lrwxr-xr-x 1 jiangxu admin 22B Nov 9 17:15 python@3 -> ../Cellar/python/3.7.5
lrwxr-xr-x 1 jiangxu admin 19B Nov 9 17:15 qt -> ../Cellar/qt/5.13.2
lrwxr-xr-x 1 jiangxu admin 19B Nov 9 17:15 qt5 -> ../Cellar/qt/5.13.2
lrwxr-xr-x 1 jiangxu admin 24B Nov 9 17:15 readline -> ../Cellar/readline/8.0.1
lrwxr-xr-x 1 jiangxu admin 23B Nov 9 17:15 sip -> ../Cellar/sip/4.19.19_2
lrwxr-xr-x 1 jiangxu admin 23B Nov 9 17:15 sqlite -> ../Cellar/sqlite/3.30.1
lrwxr-xr-x 1 jiangxu admin 23B Nov 9 17:15 sqlite3 -> ../Cellar/sqlite/3.30.1
lrwxr-xr-x 1 jiangxu admin 23B Nov 14 09:38 wget -> ../Cellar/wget/1.20.3_1
lrwxr-xr-x 1 jiangxu admin 18B Nov 9 17:15 xz -> ../Cellar/xz/5.2.4
From above I found that the directory is a little bit diffrent and so I changed path to the following and it worked.
export C_INCLUDE_PATH="/usr/local/lib:/usr/local/include/libpng16:/usr/local/opt/openssl@1.1/include"
Glad to hear it! :)