Re: [AMBER] patching problem amber12

From: Vaibhav Dixit <vaibhavadixit.gmail.com>
Date: Wed, 30 Jan 2013 10:57:54 +0530

Dear Daniel,
I have followed your suggestions and after making changes it is giving this
message below.
Did it apply patches correctly? I did not really understand the meaning of
the warning given below. It seems to have skipped some of the patchs, did
it? I have attached the patch_amber.py file, if check if it is according to
your expectation.
Please suggest. 

---
./patch_amber.py --update-tree
Error: No internet access!
Determining patches to download for AmberTools12
AmberTools12 is up to date. Nothing to download
Determining patches to download for Amber12
  Downloading bugfix.1
  Downloading bugfix.2
  Downloading bugfix.3
  Downloading bugfix.4
  Downloading bugfix.5
  Downloading bugfix.6
  Downloading bugfix.7
  Downloading bugfix.8
  Downloading bugfix.9
  Downloading bugfix.10
  Downloading bugfix.11
  Downloading bugfix.12
  Downloading bugfix.13
  Downloading bugfix.14
  Downloading bugfix.15
  Downloading bugfix.16
  Downloading bugfix.17
  Downloading bugfix.18
  Downloading bugfix.19
  Downloading bugfix.20
  Downloading bugfix.21
  Downloading bugfix.22
  Downloading bugfix.23
  Downloading bugfix.24
  Downloading bugfix.25
  Downloading bugfix.26
  Downloading bugfix.27
  Downloading bugfix.28
  Downloading bugfix.29
  Downloading bugfix.30
  Downloading bugfix.31
  Downloading bugfix.32
  Downloading bugfix.33
Applying AmberTools12 patches
Applying Amber12 patches
Error or warning during patching process for
.patches/Amber_Unapplied_Patches/bugfix.1:
Reversed (or previously applied) patch detected!  Skipping patch.
6 out of 6 hunks ignored -- saving rejects to file
AmberTools/src/parmed/ParmedTools/ParmedActions.py.rej
Reversed (or previously applied) patch detected!  Skipping patch.
1 out of 1 hunk ignored -- saving rejects to file
AmberTools/src/parmed/ParmedTools/exceptions.py.rej
Reversed (or previously applied) patch detected!  Skipping patch.
1 out of 1 hunk ignored -- saving rejects to file
AmberTools/src/parmed/ParmedTools/gui/_guiactions.py.rej
Reversed (or previously applied) patch detected!  Skipping patch.
2 out of 2 hunks ignored -- saving rejects to file
AmberTools/src/parmed/chemistry/amber/mask.py.rej
Reversed (or previously applied) patch detected!  Skipping patch.
1 out of 1 hunk ignored -- saving rejects to file
AmberTools/src/parmed/chemistry/amber/readparm.py.rej
Reversed (or previously applied) patch detected!  Skipping patch.
1 out of 1 hunk ignored -- saving rejects to file
AmberTools/src/parmed/chemistry/exceptions.py.rej
gm.linux-rfml:/usr/local/amber12>
On Wed, Jan 30, 2013 at 10:47 AM, Daniel Sindhikara <sindhikara.gmail.com>wrote:
> The line that exits due to lack of connection is "sys.exit(1)" around line
> number 865 in patch_amber.py as shown at the end of this message.
> But I don't know if it will run fine just because the exit line is
> commented out.
>
> According to the documentation of urllib.urlopen (which is what
> patch_amber.py is using):
>
> "Proxies which require authentication for use are not currently supported;
> this is considered an implementation limitation."
> This is probably why you cannot download the patches using your
> authentication-based proxy.
>
>
>
> Code below:
>
>    # Make sure we have internet access, since we'll need it from now on
>    try:
>       amberhome = urlopen('http://ambermd.org')
>       amberhome.close()
>       del amberhome
>    except IOError, err:
>       if 'timed out' in str(err):
>          print >> sys.stderr, \
>             'Error: Could not connect to http://ambermd.org in %.2f
> seconds' % (
>             opt.timeout)
>       else:
>          print >> sys.stderr, 'Error: No internet access!'
>       sys.exit(1)
>
>
>
>
> On Wed, Jan 30, 2013 at 1:55 PM, Vaibhav Dixit <vaibhavadixit.gmail.com
> >wrote:
>
> > Dear Daniel,
> > Thank for your reply.
> > Yes, wget works, using wget only I have downloaded the patches manually
> in
> > the folder as suggested by Jason here
> > http://archive.ambermd.org/201208/0427.html
> > But then I could not figure out myself which lines in the patch_amber.py
> > script to comment-out?
> > As far as I'm able to understand proxy setting are fine (I'm able to
> access
> > my email and use wget).
> > Please suggest.
> >
> > On Wed, Jan 30, 2013 at 10:01 AM, Daniel Sindhikara <
> sindhikara.gmail.com
> > >wrote:
> >
> > > Does wget or curl work for you in the terminal? If not you should
> contact
> > > your sysadmin to help you with the proxy settings.
> > >
> > > -Dan
> > >
> > >
> > > On Wed, Jan 30, 2013 at 1:03 PM, Vaibhav Dixit <
> vaibhavadixit.gmail.com
> > > >wrote:
> > >
> > > > Please suggest on this patching problem, I'm unable to install
> Amber12.
> > > > Thanks in advance.
> > > >
> > > > On Tue, Jan 29, 2013 at 9:49 AM, Vaibhav Dixit <
> > vaibhavadixit.gmail.com
> > > > >wrote:
> > > >
> > > > > Dear Amber community members,
> > > > > I'm facing a problem while patching amber12 updates using the
> command
> > > > > ---------
> > > > > gm.linux-rfml:/usr/local/amber12> ./patch_amber.py --update-tree
> > > > > Error: No internet access!
> > > > > -----------
> > > > > I tried suggestions given here,
> > > > > http://archive.ambermd.org/201208/0427.html
> > > > >
> > > > > My proxy setting are correct (I'm able to use internet on the same
> PC
> > > and
> > > > > I have set the path with proper user name and password (export
> > > > http_proxy="
> > > > > http://username:password.proxy.iisc.ernet.in:3128"). But this did
> > not
> > > > > work, then I tried *./patch_amber.py --update-tree --timeout 20,
> but
> > > this
> > > > > also gave the same result*
> > > > >
> > > > > After downloading all the patches, I have made following changes to
> > the
> > > > > patch_amber.py file, *but I'm unable to understand which line in
> this
> > > > > file should I comment out*, so that the patch file are used
> directly
> > > from
> > > > > the folder specified.
> > > > > -----------
> > > > > BUGFIX_PREFIX = 'bugfix'
> > > > > patch_locs = ['file:///home/gm/bugfixes/AmberTools/12.0/',
> > > > >               'file:///home/gm/bugfixes/12.0/']
> > > > > -----------
> > > > >
> > > > > --
> > > > > With regards
> > > > >
> > > > > Dr. Dixit Vaibhav Anil (Dr. D.S.Kothari Fellow)
> > > > > Department of Inogranic and Physical Chemistry
> > > > > Indian Institute of Science (IISc), Bangalore-560012
> > > > > Karnataka.
> > > > > Phone (Mobile): +919915214408, +91-7709129400.
> > > > > E-mail: vaibhavadixit.gmail.com, vaibhavadixit.ipc.iisc.ernet.in
> > > > > http://www.iisc.ernet.in/
> > > > >  <http://www.niper.nic.in>
> > > >
> > > >
> > > >
> > > >
> > > > --
> > > > With regards
> > > >
> > > > Vaibhav A. Dixit
> > > > Ph.D.
> > > > Department of Medicinal Chemistry
> > > > Natl. Inst. Pharm. Edu. & Res. (NIPER)
> > > > Sector 67, Phase X,  S.A.S. Nagar (Mohali)
> > > > Punjab -160 062 INDIA
> > > > Phone (Mobile): +919915214408, +91-7709129400.
> > > > E-mail: vaibhavadixit.gmail.com
> > > > www.niper.nic.in
> > > > _______________________________________________
> > > > AMBER mailing list
> > > > AMBER.ambermd.org
> > > > http://lists.ambermd.org/mailman/listinfo/amber
> > > >
> > >
> > >
> > >
> > > --
> > > Dr. Daniel J. Sindhikara <
> http://www.dansindhikara.com/Information.html>
> > > Ritsumeikan University <http://www.ritsumei.ac.jp/eng/>
> > > sindhikara.gmail.com <http://www.dansindhikara.com>
> > > --
> > > _______________________________________________
> > > AMBER mailing list
> > > AMBER.ambermd.org
> > > http://lists.ambermd.org/mailman/listinfo/amber
> > >
> >
> >
> >
> > --
> > With regards
> >
> > Vaibhav A. Dixit
> > Ph.D.
> > Department of Medicinal Chemistry
> > Natl. Inst. Pharm. Edu. & Res. (NIPER)
> > Sector 67, Phase X,  S.A.S. Nagar (Mohali)
> > Punjab -160 062 INDIA
> > Phone (Mobile): +919915214408, +91-7709129400.
> > E-mail: vaibhavadixit.gmail.com
> > www.niper.nic.in
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
>
>
>
> --
> Dr. Daniel J. Sindhikara <http://www.dansindhikara.com/Information.html>
> Ritsumeikan University <http://www.ritsumei.ac.jp/eng/>
> sindhikara.gmail.com <http://www.dansindhikara.com>
> --
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
-- 
With regards
Vaibhav A. Dixit
Ph.D.
Department of Medicinal Chemistry
Natl. Inst. Pharm. Edu. & Res. (NIPER)
Sector 67, Phase X,  S.A.S. Nagar (Mohali)
Punjab -160 062 INDIA
Phone (Mobile): +919915214408, +91-7709129400.
E-mail: vaibhavadixit.gmail.com
www.niper.nic.in

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Received on Tue Jan 29 2013 - 22:00:02 PST
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