Dear All,
I am trying to install AMBERTOOLS16 on my Linux PC.
While following the standard procedure I am getting the following message,
but I am not sure is it is an error (in bold) which might cause problems
later.
Is it that an update failed to patch?
Please suggest.
Thank you.
[root.localhost Downloads]# cd amber16/
[root.localhost amber16]# ls -arlt
total 44
-rwxrwxr-x. 1 501 games 1336 Apr 15 05:55 update_amber
-rw-rw-r--. 1 501 games 1452 Apr 15 17:57 README
-rwxrwxr-x. 1 501 games 2509 Apr 15 17:57 configure
drwxrwxr-x. 2 501 games 4096 Apr 15 17:57 updateutils
-rw-rw-r--. 1 501 games 3033 Apr 27 21:41 Makefile
drwxr-xr-x. 14 vaibhav vaibhav 4096 Aug 11 16:31 ..
drwxr-xr-x. 6 root root 4096 Aug 11 16:33 AmberTools
drwxrwxr-x. 143 501 games 4096 Aug 11 16:33 test
drwxr-xr-x. 13 root root 4096 Aug 11 16:33 dat
drwxr-xr-x. 2 root root 4096 Aug 11 16:33 doc
drwxr-xr-x. 7 root root 4096 Aug 11 16:33 .
[root.localhost amber16]# export AMBERHOME=`pwd`
[root.localhost amber16]# ./configure gnu
Checking for updates...
Checking for available patches online. This may take a few seconds...
Checking for available patches online. This may take a few seconds...
Traceback (most recent call last):
File "./update_amber", line 23, in <module>
app.mainloop()
File "/home/vaibhav/Downloads/amber16/updateutils/main.py", line 479, in
mainloop
self.check_updates()
File "/home/vaibhav/Downloads/amber16/updateutils/main.py", line 171, in
check_updates
self.verbose) + '\n')
File "/home/vaibhav/Downloads/amber16/updateutils/repos.py", line 184, in
patch_details
self.fill_list()
File "/home/vaibhav/Downloads/amber16/updateutils/downloader.py", line
104, in new_fcn
return fcn(*args, **kwargs)
File "/home/vaibhav/Downloads/amber16/updateutils/repos.py", line 204, in
fill_list
p = urlopen(url)
File "/usr/lib64/python2.6/urllib2.py", line 126, in urlopen
return _opener.open(url, data, timeout)
File "/usr/lib64/python2.6/urllib2.py", line 391, in open
response = self._open(req, data)
File "/usr/lib64/python2.6/urllib2.py", line 409, in _open
'_open', req)
File "/usr/lib64/python2.6/urllib2.py", line 369, in _call_chain
result = func(*args)
File "/usr/lib64/python2.6/urllib2.py", line 1190, in http_open
return self.do_open(httplib.HTTPConnection, req)
* File "/usr/lib64/python2.6/urllib2.py", line 1165, in do_open raise
URLError(err)urllib2.URLError: <urlopen error timed out>Check for updates
failed.*
require Python version 2.7 or >= 3.4
No compatible Python installation found. I can download one from Continuum
via Miniconda with all prerequisites. This will only need to be done once.
This may take several minutes and will require Internet access.
(You can also install missing packages by yourself)
Should I do that? [y/n] y
Downloading an Amber-compatible Python version 2.7 via Miniconda
and installing it. This may take several minutes.
============================================================
====================
This script will download and install a version of Python compatible
with every component of AmberTools and install all required and optional
prerequisites. The Python distribution is downloaded for your operating
system from Miniconda.
Downloading Python 2.7 Miniconda
Detected Linux kernel. Downloading the Linux installer
Downloading the latest Miniconda distribution
Detected 64-bit Linux
--2016-08-11 16:34:32-- https://repo.continuum.io/
miniconda/Miniconda-latest-Linux-x86_64.sh
Resolving repo.continuum.io... 54.225.68.13, 50.16.198.140, 54.225.146.221,
...
Connecting to repo.continuum.io|54.225.68.13|:443... connected.
HTTP request sent, awaiting response... 200 OK
Length: 27208383 (26M) [application/octet-stream]
Saving to: “miniconda.sh”
100%[=======================================================
======================================================================>]
27,208,383 199K/s in 2m 14s
2016-08-11 16:36:48 (198 KB/s) - “miniconda.sh” saved [27208383/27208383]
Installing Miniconda Python.
PREFIX=/home/vaibhav/Downloads/amber16/miniconda
installing: _cache-0.0-py27_x0 ...
installing: python-2.7.11-0 ...
installing: conda-env-2.4.5-py27_0 ...
installing: openssl-1.0.2g-0 ...
installing: pycosat-0.6.1-py27_0 ...
installing: pyyaml-3.11-py27_1 ...
installing: readline-6.2-2 ...
installing: requests-2.9.1-py27_0 ...
installing: sqlite-3.9.2-0 ...
installing: tk-8.5.18-0 ...
installing: yaml-0.1.6-0 ...
installing: zlib-1.2.8-0 ...
installing: conda-4.0.5-py27_0 ...
installing: pycrypto-2.6.1-py27_0 ...
installing: pip-8.1.1-py27_1 ...
installing: wheel-0.29.0-py27_0 ...
installing: setuptools-20.3-py27_0 ...
Python 2.7.11 :: Continuum Analytics, Inc.
creating default environment...
installation finished.
Updating and installing required and optional packages...
Fetching package metadata: ....
Solving package specifications: .........
Package plan for installation in environment /home/vaibhav/Downloads/
amber16/miniconda:
The following packages will be downloaded:
package | build
---------------------------|-----------------
nomkl-1.0 | 0 402 B
sqlite-3.13.0 | 0 4.0 MB
python-2.7.12 | 1 12.1 MB
conda-env-2.5.1 | py27_0 26 KB
ruamel_yaml-0.11.14 | py27_0 352 KB
conda-4.1.11 | py27_0 201 KB
------------------------------------------------------------
Total: 16.6 MB
The following NEW packages will be INSTALLED:
nomkl: 1.0-0
ruamel_yaml: 0.11.14-py27_0
The following packages will be UPDATED:
conda: 4.0.5-py27_0 --> 4.1.11-py27_0
conda-env: 2.4.5-py27_0 --> 2.5.1-py27_0
python: 2.7.11-0 --> 2.7.12-1
sqlite: 3.9.2-0 --> 3.13.0-0
Fetching packages ...
nomkl-1.0-0.ta 100% |#############################
############################################################
##############################| Time: 0:00:00 351.71 kB/s
sqlite-3.13.0- 100% |#############################
############################################################
##############################| Time: 0:00:40 101.75 kB/s
python-2.7.12- 100% |#############################
############################################################
##############################| Time: 0:01:14 170.23 kB/s
conda-env-2.5. 100% |#############################
############################################################
##############################| Time: 0:00:00 63.07 kB/s
ruamel_yaml-0. 100% |#############################
############################################################
##############################| Time: 0:00:03 101.73 kB/s
conda-4.1.11-p 100% |#############################
############################################################
##############################| Time: 0:00:01 140.04 kB/s
Extracting packages ...
[ COMPLETE ]|############################
############################################################
##################################################| 100%
Unlinking packages ...
[ COMPLETE ]|############################
############################################################
##################################################| 100%
Linking packages ...
[ COMPLETE ]|############################
############################################################
##################################################| 100%
Fetching package metadata .......
Solving package specifications: ..........
Package plan for installation in environment /home/vaibhav/Downloads/
amber16/miniconda:
The following packages will be downloaded:
package | build
---------------------------|-----------------
libgfortran-3.0.0 | 1 281 KB
libsodium-1.0.10 | 0 1.2 MB
openblas-0.2.14 | 4 3.6 MB
zeromq-4.1.4 | 0 4.1 MB
backports-1.0 | py27_0 1 KB
backports_abc-0.4 | py27_0 5 KB
conda-env-2.5.2 | py27_0 26 KB
cython-0.24.1 | py27_0 5.3 MB
decorator-4.0.10 | py27_0 12 KB
functools32-3.2.3.2 | py27_0 15 KB
ipython_genutils-0.1.0 | py27_0 32 KB
markupsafe-0.23 | py27_2 31 KB
mistune-0.7.2 | py27_0 570 KB
numpy-1.11.1 | py27_nomkl_0 6.2 MB
path.py-8.2.1 | py27_0 45 KB
ptyprocess-0.5.1 | py27_0 19 KB
pygments-2.1.3 | py27_0 1.2 MB
pyzmq-15.4.0 | py27_0 705 KB
simplegeneric-0.8.1 | py27_1 7 KB
six-1.10.0 | py27_0 16 KB
wcwidth-0.1.7 | py27_0 21 KB
configparser-3.5.0 | py27_0 31 KB
get_terminal_size-1.0.0 | py27_0 4 KB
jinja2-2.8 | py27_1 264 KB
jsonschema-2.5.1 | py27_0 55 KB
pathlib2-2.1.0 | py27_0 26 KB
pexpect-4.0.1 | py27_0 63 KB
prompt_toolkit-1.0.3 | py27_0 295 KB
scipy-0.18.0 |np111py27_nomkl_0 31.0 MB
singledispatch-3.4.0.3 | py27_0 12 KB
ssl_match_hostname-3.4.0.2 | py27_1 6 KB
traitlets-4.2.2 | py27_0 108 KB
entrypoints-0.2.2 | py27_0 6 KB
jupyter_core-4.1.0 | py27_0 51 KB
pickleshare-0.7.3 | py27_0 8 KB
tornado-4.4.1 | py27_0 552 KB
ipython-5.0.0 | py27_0 933 KB
jupyter_client-4.3.0 | py27_0 96 KB
nbformat-4.0.1 | py27_0 112 KB
terminado-0.6 | py27_0 18 KB
ipykernel-4.3.1 | py27_0 117 KB
nbconvert-4.2.0 | py27_0 310 KB
notebook-4.2.2 | py27_0 5.0 MB
------------------------------------------------------------
Total: 62.3 MB
The following NEW packages will be INSTALLED:
backports: 1.0-py27_0
backports_abc: 0.4-py27_0
configparser: 3.5.0-py27_0
cython: 0.24.1-py27_0
decorator: 4.0.10-py27_0
entrypoints: 0.2.2-py27_0
functools32: 3.2.3.2-py27_0
get_terminal_size: 1.0.0-py27_0
ipykernel: 4.3.1-py27_0
ipython: 5.0.0-py27_0
ipython_genutils: 0.1.0-py27_0
jinja2: 2.8-py27_1
jsonschema: 2.5.1-py27_0
jupyter_client: 4.3.0-py27_0
jupyter_core: 4.1.0-py27_0
libgfortran: 3.0.0-1
libsodium: 1.0.10-0
markupsafe: 0.23-py27_2
mistune: 0.7.2-py27_0
nbconvert: 4.2.0-py27_0
nbformat: 4.0.1-py27_0
notebook: 4.2.2-py27_0
numpy: 1.11.1-py27_nomkl_0 [nomkl]
openblas: 0.2.14-4
path.py: 8.2.1-py27_0
pathlib2: 2.1.0-py27_0
pexpect: 4.0.1-py27_0
pickleshare: 0.7.3-py27_0
prompt_toolkit: 1.0.3-py27_0
ptyprocess: 0.5.1-py27_0
pygments: 2.1.3-py27_0
pyzmq: 15.4.0-py27_0
scipy: 0.18.0-np111py27_nomkl_0 [nomkl]
simplegeneric: 0.8.1-py27_1
singledispatch: 3.4.0.3-py27_0
six: 1.10.0-py27_0
ssl_match_hostname: 3.4.0.2-py27_1
terminado: 0.6-py27_0
tornado: 4.4.1-py27_0
traitlets: 4.2.2-py27_0
wcwidth: 0.1.7-py27_0
zeromq: 4.1.4-0
The following packages will be UPDATED:
conda-env: 2.5.1-py27_0 --> 2.5.2-py27_0
Fetching packages ...
libgfortran-3. 100% |#############################
############################################################
##############################| Time: 0:00:03 93.87 kB/s
libsodium-1.0. 100% |#############################
############################################################
##############################| Time: 0:00:15 79.69 kB/s
openblas-0.2.1 100% |#############################
############################################################
##############################| Time: 0:00:23 161.98 kB/s
--
With Regards.
Dr. Vaibhav A. Dixit, (M.S. and Ph.D.: NIPER, Postdoc: AstraZeneca, UK and
IISc, Bangalore)
Associate Professor,
Department of Pharmaceutical Chemistry,
School of Pharmacy & Technology Management,
SVKM's NMIMS,
Mukesh Patel Technology Park
Babulde, Bank of Tapi River,
Mumbai-Agra Road,
Shirpur, Dist. Dhule -425405
India.
Email: vaibhav.dixit.nmims.edu
www.nmims.edu
http://pharmacy-shirpur.nmims.edu/faculty-and-research/
faculty/dr-vaibhav-dixit/
+91-7709129400.
http://scholar.google.co.in/citations?user=X876BKcAAAAJ&hl=en&oi=sra
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Received on Thu Aug 11 2016 - 21:00:03 PDT
