Hi Vaibhav,
I don't see anything highlighted in bold here but I also don't see any error. It is complaining that your don't have python installed but then you say yes to download one which should fix it - does configure finish? If yes you should then be good do type 'make'.
All the best
Ross
> On Aug 11, 2016, at 8:44 PM, Vaibhav Dixit <vaibhavadixit.gmail.com> wrote:
>
> 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
>
> Please consider the environment before printing this e-mail
> _______________________________________________
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Received on Thu Aug 11 2016 - 22:00:02 PDT
