Comments (15)
Hi,
Are you using virtual env to install it ?. Can you please check if, after installation, you get the help message when you type HOME-pairwise or HOME-timeseries.
from home.
Thank you very much! I didn't use virtual env to install HOME. Since I also use python 2.7. Is it necessary to use virtual env to install? Why? I will try 'virtual env' again. And I didn't get the help messages after the type of HOME-pairwise or HOME-timeseries.
from home.
Sorry, after I retry to install HOME follow the instructions (use the virtual env to install ) completely. It gives me another error. As following:
Traceback (most recent call last):
File "/data1/linhua/QIANLAB/PROJECT/TEST_PY/hh/bin/HOME-pairwise", line 4, in <module>
__import__('pkg_resources').run_script('HOME==0.4', 'HOME-pairwise')
File "/data1/linhua/QIANLAB/PROJECT/TEST_PY/hh/lib/python2.7/site-packages/pkg_resources/__init__.py", line 750, in run_script
self.require(requires)[0].run_script(script_name, ns)
File "/data1/linhua/QIANLAB/PROJECT/TEST_PY/hh/lib/python2.7/site-packages/pkg_resources/__init__.py", line 1518, in run_script
.format(**locals()),
pkg_resources.ResolutionError: Script 'scripts/HOME-pairwise' not found in metadata at '/data1/linhua/QIANLAB/PROJECT/TEST_PY/HOME/HOME.egg-info'
Thank you very much!
from home.
Hi, seems like the package is not installed successfully. Did you get any error message after running python setup.py install
?. Also please make sure you cd in the HOME directory before starting the run.
from home.
Hi, you can see it seems that the installation is successful. I didn't see any error messages duing installation. And sure, I cd into the HOME dir.
(hh) [linhua@localhost /data1/linhua/QIANLAB/PROJECT/TEST_PY/HOME]$python setup.py install
running install
running bdist_egg
running egg_info
writing requirements to HOME.egg-info/requires.txt
writing HOME.egg-info/PKG-INFO
writing top-level names to HOME.egg-info/top_level.txt
writing dependency_links to HOME.egg-info/dependency_links.txt
reading manifest file 'HOME.egg-info/SOURCES.txt'
writing manifest file 'HOME.egg-info/SOURCES.txt'
installing library code to build/bdist.linux-x86_64/egg
running install_lib
running build_py
creating build/bdist.linux-x86_64/egg
creating build/bdist.linux-x86_64/egg/HOME
copying build/lib/HOME/__init__.py -> build/bdist.linux-x86_64/egg/HOME
copying build/lib/HOME/HOME_functions.py -> build/bdist.linux-x86_64/egg/HOME
copying build/lib/HOME/HOME_timeseries_functions.py -> build/bdist.linux-x86_64/egg/HOME
byte-compiling build/bdist.linux-x86_64/egg/HOME/__init__.py to __init__.pyc
byte-compiling build/bdist.linux-x86_64/egg/HOME/HOME_functions.py to HOME_functions.pyc
byte-compiling build/bdist.linux-x86_64/egg/HOME/HOME_timeseries_functions.py to HOME_timeseries_functions.pyc
creating build/bdist.linux-x86_64/egg/EGG-INFO
installing scripts to build/bdist.linux-x86_64/egg/EGG-INFO/scripts
running install_scripts
running build_scripts
creating build/bdist.linux-x86_64/egg/EGG-INFO/scripts
copying build/scripts-2.7/HOME-timeseries -> build/bdist.linux-x86_64/egg/EGG-INFO/scripts
copying build/scripts-2.7/HOME-pairwise -> build/bdist.linux-x86_64/egg/EGG-INFO/scripts
changing mode of build/bdist.linux-x86_64/egg/EGG-INFO/scripts/HOME-timeseries to 775
changing mode of build/bdist.linux-x86_64/egg/EGG-INFO/scripts/HOME-pairwise to 775
copying HOME.egg-info/PKG-INFO -> build/bdist.linux-x86_64/egg/EGG-INFO
copying HOME.egg-info/SOURCES.txt -> build/bdist.linux-x86_64/egg/EGG-INFO
copying HOME.egg-info/dependency_links.txt -> build/bdist.linux-x86_64/egg/EGG-INFO
copying HOME.egg-info/requires.txt -> build/bdist.linux-x86_64/egg/EGG-INFO
copying HOME.egg-info/top_level.txt -> build/bdist.linux-x86_64/egg/EGG-INFO
zip_safe flag not set; analyzing archive contents...
creating 'dist/HOME-0.4-py2.7.egg' and adding 'build/bdist.linux-x86_64/egg' to it
removing 'build/bdist.linux-x86_64/egg' (and everything under it)
Processing HOME-0.4-py2.7.egg
Removing /data1/linhua/QIANLAB/PROJECT/TEST_PY/hh/lib/python2.7/site-packages/HOME-0.4-py2.7.egg
Copying HOME-0.4-py2.7.egg to /data1/linhua/QIANLAB/PROJECT/TEST_PY/hh/lib/python2.7/site-packages
HOME 0.4 is already the active version in easy-install.pth
Installing HOME-pairwise script to /data1/linhua/QIANLAB/PROJECT/TEST_PY/hh/bin
Installing HOME-timeseries script to /data1/linhua/QIANLAB/PROJECT/TEST_PY/hh/bin
Installed /data1/linhua/QIANLAB/PROJECT/TEST_PY/hh/lib/python2.7/site-packages/HOME-0.4-py2.7.egg
Processing dependencies for HOME==0.4
Searching for statsmodels==0.6.1
Best match: statsmodels 0.6.1
Adding statsmodels 0.6.1 to easy-install.pth file
Using /data1/linhua/QIANLAB/PROJECT/TEST_PY/hh/lib/python2.7/site-packages
Searching for scikit-learn==0.16.1
Best match: scikit-learn 0.16.1
Adding scikit-learn 0.16.1 to easy-install.pth file
Using /data1/linhua/QIANLAB/PROJECT/TEST_PY/hh/lib/python2.7/site-packages
Searching for scipy==0.16.0
Best match: scipy 0.16.0
Adding scipy 0.16.0 to easy-install.pth file
Using /data1/linhua/QIANLAB/PROJECT/TEST_PY/hh/lib/python2.7/site-packages
Searching for pandas==0.17.1
Best match: pandas 0.17.1
Adding pandas 0.17.1 to easy-install.pth file
Using /data1/linhua/QIANLAB/PROJECT/TEST_PY/hh/lib/python2.7/site-packages
Searching for numpy==1.13.3
Best match: numpy 1.13.3
Adding numpy 1.13.3 to easy-install.pth file
Using /data1/linhua/QIANLAB/PROJECT/TEST_PY/hh/lib/python2.7/site-packages
Searching for python-dateutil==2.6.1
Best match: python-dateutil 2.6.1
Adding python-dateutil 2.6.1 to easy-install.pth file
Using /data1/linhua/QIANLAB/PROJECT/TEST_PY/hh/lib/python2.7/site-packages
Searching for pytz==2017.3
Best match: pytz 2017.3
Adding pytz 2017.3 to easy-install.pth file
Using /data1/linhua/QIANLAB/PROJECT/TEST_PY/hh/lib/python2.7/site-packages
Searching for six==1.11.0
Best match: six 1.11.0
Adding six 1.11.0 to easy-install.pth file
Using /data1/linhua/QIANLAB/PROJECT/TEST_PY/hh/lib/python2.7/site-packages
Finished processing dependencies for HOME==0.4
from home.
Hi, the installation looks fine. Can you please check if your virtual environment (hh) bin contains HOME-pairwise and HOME-timeseries binaries, something like below:
from home.
Yes, you can see it is there:
(hh) [linhua@localhost /data1/linhua/QIANLAB/PROJECT/TEST_PY/hh/bin]$pwd
/data1/linhua/QIANLAB/PROJECT/TEST_PY/hh/bin
(hh) [linhua@localhost /data1/linhua/QIANLAB/PROJECT/TEST_PY/hh/bin]$l
total 68K
-rwxrwxr-x 1 linhua linhua 9.9K Dec 13 17:22 python
lrwxrwxrwx 1 linhua linhua 6 Dec 13 17:22 python2.7 -> python
lrwxrwxrwx 1 linhua linhua 6 Dec 13 17:22 python2 -> python
-rwxrwxr-x 1 linhua linhua 269 Dec 13 17:22 easy_install-2.7
-rwxrwxr-x 1 linhua linhua 269 Dec 13 17:22 easy_install
-rwxrwxr-x 1 linhua linhua 241 Dec 13 17:22 pip2.7
-rwxrwxr-x 1 linhua linhua 241 Dec 13 17:22 pip2
-rwxrwxr-x 1 linhua linhua 241 Dec 13 17:22 pip
-rwxrwxr-x 1 linhua linhua 248 Dec 13 17:22 wheel
-rw-rw-r-- 1 linhua linhua 1.2K Dec 13 17:22 activate_this.py
-rw-rw-r-- 1 linhua linhua 2.2K Dec 13 17:22 activate.fish
-rw-rw-r-- 1 linhua linhua 1.1K Dec 13 17:22 activate.csh
-rw-rw-r-- 1 linhua linhua 2.1K Dec 13 17:22 activate
-rwxrwxr-x 1 linhua linhua 2.4K Dec 13 17:22 python-config
-rwxrwxr-x 1 linhua linhua 793 Dec 13 17:27 f2py
-rwxrwxr-x 1 linhua linhua 201 Dec 13 20:07 HOME-pairwise
-rwxrwxr-x 1 linhua linhua 205 Dec 13 20:07 HOME-timeseries
(hh) [linhua@localhost /data1/linhua/QIANLAB/PROJECT/TEST_PY/hh/bin]$
from home.
Can you please send me what you get by following commands :
(hh) [linhua@localhost /data1/linhua/QIANLAB/PROJECT/TEST_PY/HOME]$ ls
(hh) [linhua@localhost /data1/linhua/QIANLAB/PROJECT/TEST_PY/HOME]$ HOME-pairwise
from home.
Thank you so much:
(hh) [linhua@localhost /data1/linhua/QIANLAB/PROJECT/TEST_PY/hh/bin]$cd /data1/linhua/QIANLAB/PROJECT/TEST_PY/HOME
(hh) [linhua@localhost /data1/linhua/QIANLAB/PROJECT/TEST_PY/HOME]$ls
HOME HOME.egg-info README.md build dist environment.yml requirements.txt saved_model scripts setup.py testcase training_data
(hh) [linhua@localhost /data1/linhua/QIANLAB/PROJECT/TEST_PY/HOME]$HOME-pairwise
Traceback (most recent call last):
File "/data1/linhua/QIANLAB/PROJECT/TEST_PY/hh/bin/HOME-pairwise", line 4, in <module>
__import__('pkg_resources').run_script('HOME==0.4', 'HOME-pairwise')
File "/data1/linhua/QIANLAB/PROJECT/TEST_PY/hh/lib/python2.7/site-packages/pkg_resources/__init__.py", line 750, in run_script
self.require(requires)[0].run_script(script_name, ns)
File "/data1/linhua/QIANLAB/PROJECT/TEST_PY/hh/lib/python2.7/site-packages/pkg_resources/__init__.py", line 1518, in run_script
.format(**locals()),
pkg_resources.ResolutionError: Script 'scripts/HOME-pairwise' not found in metadata at '/data1/linhua/QIANLAB/PROJECT/TEST_PY/HOME/HOME.egg-info'
(hh) [linhua@localhost /data1/linhua/QIANLAB/PROJECT/TEST_PY/HOME]$
from home.
The issue is it's not able to find HOME-pairwise
in scripts. Can you please do the following to check if the binaries are present in script:
(hh) [linhua@localhost /data1/linhua/QIANLAB/PROJECT/TEST_PY/HOME]$ cd ./scripts/
and then ls
Also, please just try deactivating and reactivatiing your virtual env.
from home.
You can see there are those binaries files.
(hh) [linhua@localhost /data1/linhua/QIANLAB/PROJECT/TEST_PY/HOME/scripts]$l
total 56K
-rwxrwxrwx 1 linhua linhua 1.3K Dec 13 17:24 HOME_R_time.R
-rwxrwxrwx 1 linhua linhua 1.4K Dec 13 17:24 HOME_R.R
-rwxrwxrwx 1 linhua linhua 23K Dec 13 17:24 HOME-timeseries
-rwxrwxrwx 1 linhua linhua 22K Dec 13 17:24 HOME-pairwise
And I exit the shell and login in again, then reactivate my virtual env. But it still not works. And new errors generated after I chmod 777 the HOME-pairwise and other files. I see that they don't have run permission.
Traceback (most recent call last):
File "/data1/linhua/QIANLAB/PROJECT/TEST_PY/hh/bin/HOME-pairwise", line 4, in <module>
__import__('pkg_resources').run_script('HOME==0.4', 'HOME-pairwise')
File "/data1/linhua/QIANLAB/PROJECT/TEST_PY/hh/lib/python2.7/site-packages/pkg_resources/__init__.py", line 750, in run_script
self.require(requires)[0].run_script(script_name, ns)
File "/data1/linhua/QIANLAB/PROJECT/TEST_PY/hh/lib/python2.7/site-packages/pkg_resources/__init__.py", line 1534, in run_script
exec(script_code, namespace, namespace)
File "/data1/linhua/QIANLAB/PROJECT/TEST_PY/hh/lib/python2.7/site-packages/HOME-0.4-py2.7.egg/EGG-INFO/scripts/HOME-pairwise", line 18, in <module>
File "/data1/linhua/QIANLAB/PROJECT/TEST_PY/hh/lib/python2.7/site-packages/pandas/__init__.py", line 48, in <module>
from pandas.io.api import *
File "/data1/linhua/QIANLAB/PROJECT/TEST_PY/hh/lib/python2.7/site-packages/pandas/io/api.py", line 15, in <module>
from pandas.io.packers import read_msgpack, to_msgpack
File "/data1/linhua/QIANLAB/PROJECT/TEST_PY/hh/lib/python2.7/site-packages/pandas/io/packers.py", line 63, in <module>
from pandas.msgpack import Unpacker as _Unpacker, Packer as _Packer, ExtType
File "/data1/linhua/QIANLAB/PROJECT/TEST_PY/hh/lib/python2.7/site-packages/pandas/msgpack/__init__.py", line 21, in <module>
from pandas.msgpack._packer import Packer
ImportError: /lib64/libc.so.6: version `GLIBC_2.18' not found (required by /home/linhua/.linuxbrew/lib/libstdc++.so.6)
Thank you very much!
from home.
I guess you have installed HOME inside your virtual environment and that's why you are getting permission issue. Can you please make sure HOME directory is installed "outside" the virtual env as below.
HOME_env is the virtual env name. In your case it will be hh.
from home.
Wow, it seems to be the key point. I will have a try immediately.
from home.
Sorry for the wrong reply. I am sure that HOME directory is installed "outside" the virtual env. You can see following:
(hh) [linhua@localhost /data1/linhua/QIANLAB/PROJECT/TEST_PY]$l
total 8.0K
drwxrwxr-x 5 linhua linhua 4.0K Dec 13 17:22 hh
drwxrwxr-x 11 linhua linhua 4.0K Dec 13 17:27 HOME
(hh) [linhua@localhost /data1/linhua/QIANLAB/PROJECT/TEST_PY]$l *
hh:
total 16K
drwxrwxr-x 2 linhua linhua 4.0K Dec 13 17:22 include
drwxrwxr-x 3 linhua linhua 4.0K Dec 13 17:22 lib
-rw-rw-r-- 1 linhua linhua 60 Dec 13 17:22 pip-selfcheck.json
drwxrwxr-x 2 linhua linhua 4.0K Dec 13 20:07 bin
HOME:
total 60K
-rw-rw-r-- 1 linhua linhua 74 Dec 13 17:24 requirements.txt
-rw-rw-r-- 1 linhua linhua 146 Dec 13 17:24 environment.yml
-rw-rw-r-- 1 linhua linhua 13K Dec 13 17:24 README.md
drwxrwxr-x 2 linhua linhua 4.0K Dec 13 17:24 HOME
drwxrwxr-x 2 linhua linhua 4.0K Dec 13 17:24 saved_model
-rw-rw-r-- 1 linhua linhua 511 Dec 13 17:24 setup.py
drwxrwxr-x 2 linhua linhua 4.0K Dec 13 17:24 scripts
drwxrwxr-x 4 linhua linhua 4.0K Dec 13 17:24 testcase
drwxrwxr-x 2 linhua linhua 4.0K Dec 13 17:24 training_data
drwxrwxr-x 2 linhua linhua 4.0K Dec 13 17:27 HOME.egg-info
drwxrwxr-x 5 linhua linhua 4.0K Dec 13 17:27 build
drwxrwxr-x 2 linhua linhua 4.0K Dec 13 17:27 dist
from home.
Hi, your virtual environment doesn't seem to have local and share directory as in the example I sent earlier. Also, it has an extra include directory. Can you please make sure you follow the steps for setting up the virtual environment correctly. Thanks
from home.
Related Issues (20)
- training data CG and non-CG for arabidopsis HOT 1
- HOME-timeseries error HOT 2
- sample path HOT 1
- cannot open file './scripts/HOME_R.R': No such file or directory HOT 1
- HOME-pairwise script is missing HOT 1
- HOME run does not end HOT 6
- Error when finding DMR's with scaffolded genome HOT 4
- multiprocessing range parameter HOT 3
- double scalar error HOT 5
- Issue 20# Home run doesnโt end HOT 6
- HOME-pairwise for different numbers of replicate HOT 4
- HOME ubale to open X server HOT 1
- HOME_DMR error HOT 1
- All Comb1-n "NA" for most DMRs in CHH HOT 8
- Push more
- Nanopore data? HOT 2
- NameError: name 'status' is not defined HOT 2
- HOME-timeseries Exception HOT 4
- Exception: reduce() of empty sequence with no initial value
- Installation Error
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from home.