Opened 3 years ago

Closed 3 years ago

#56501 closed defect (fixed)

Failed to fetch pymol: Subversion check out failed

Reported by: reddibharati Owned by: jwhowarth
Priority: Normal Milestone:
Component: ports Version:
Keywords: Cc: ryandesign (Ryan Schmidt)
Port: pymol

Description (last modified by jmroot (Joshua Root))

I am trying to install pymol from open source but it seems i am getting same error message. please give me suggestion to how to install pymol. here i am attaching commands i used.

Anthonys-iMac-2:~ aalab$ sudo port install tcl -corefoundation
--->  Cleaning tcl
--->  Scanning binaries for linking errors
--->  No broken files found.
Anthonys-iMac-2:~ aalab$ sudo port install tk -quartz
--->  Computing dependencies for tk
--->  Cleaning tk
--->  Scanning binaries for linking errors
--->  No broken files found.
Anthonys-iMac-2:~ aalab$ sudo port install pymol
--->  Computing dependencies for pymol
--->  Fetching archive for pymol
--->  Attempting to fetch pymol-2.1.0_1+python27.darwin_17.x86_64.tbz2 from http://jog.id.packages.macports.org/macports/packages/pymol
--->  Attempting to fetch pymol-2.1.0_1+python27.darwin_17.x86_64.tbz2 from http://kmq.jp.packages.macports.org/pymol
--->  Attempting to fetch pymol-2.1.0_1+python27.darwin_17.x86_64.tbz2 from http://lil.fr.packages.macports.org/pymol
--->  Fetching distfiles for pymol
Error: Failed to fetch pymol: Subversion check out failed
Error: See /opt/local/var/macports/logs/_opt_local_var_macports_sources_rsync.macports.org_macports_release_tarballs_ports_science_pymol/pymol/main.log for details.
Error: Follow https://guide.macports.org/#project.tickets to report a bug.
Error: Processing of port pymol failed
Anthonys-iMac-2:~ aalab$ sudo port clean pymol; sudo port install pymol
Password:
--->  Cleaning pymol
--->  Computing dependencies for pymol
--->  Fetching archive for pymol
--->  Attempting to fetch pymol-2.1.0_1+python27.darwin_17.x86_64.tbz2 from http://jog.id.packages.macports.org/macports/packages/pymol
--->  Attempting to fetch pymol-2.1.0_1+python27.darwin_17.x86_64.tbz2 from http://kmq.jp.packages.macports.org/pymol
--->  Attempting to fetch pymol-2.1.0_1+python27.darwin_17.x86_64.tbz2 from http://lil.fr.packages.macports.org/pymol
--->  Fetching distfiles for pymol
Error: Failed to fetch pymol: Subversion check out failed
Error: See /opt/local/var/macports/logs/_opt_local_var_macports_sources_rsync.macports.org_macports_release_tarballs_ports_science_pymol/pymol/main.log for details.
Error: Follow https://guide.macports.org/#project.tickets to report a bug.
Error: Processing of port pymol failed

Change History (11)

comment:1 Changed 3 years ago by reddibharati

Description: modified (diff)

comment:2 Changed 3 years ago by jmroot (Joshua Root)

Description: modified (diff)
Owner: set to jwhowarth
Port: pymol added
Status: newassigned

Please attach the main.log.

comment:3 Changed 3 years ago by mohrma

Hi Joshua, I think I have the same problem (very similar error). Here is my main.log: https://www.dropbox.com/s/czbuhz22i4sgrsx/main.log?dl=0 thanks, M

comment:4 Changed 3 years ago by jwhowarth

What happens if you execute the following from a Terminal window?

/usr/bin/svn --non-interactive --trust-server-cert export http://svn.code.sf.net/p/pymol/code/trunk/pymol@4187

I am seeing no problems with that command used by port here. Perhaps you are running into transient upstream svn down time.

Last edited 3 years ago by jwhowarth (previous) (diff)

comment:5 in reply to:  3 Changed 3 years ago by reddibharati

Replying to mohrma:

Hi Joshua,

Here is my main log
https://drive.google.com/open?id=1WDE2USkWc7UZoi2M1aqXInbiTKsFFbvD

Thanks

comment:6 Changed 3 years ago by jmroot (Joshua Root)

:debug:fetch system:  cd "/opt/local/var/macports/build/_opt_local_var_macports_sources_rsync.macports.org_macports_release_tarballs_ports_science_pymol/pymol/work" && /usr/bin/svn --non-interactive --trust-server-cert export http://svn.code.sf.net/p/pymol/code/trunk/pymol@4187 2>&1
:info:fetch svn: E170013: Unable to connect to a repository at URL 'http://svn.code.sf.net/p/pymol/code/trunk/pymol'
:info:fetch svn: E120108: Error running context: The server unexpectedly closed the connection.

Looks like a network problem, maybe a firewall interfering with svn? If it was sourceforge's server misbehaving then presumably it would affect everyone.

comment:7 in reply to:  6 Changed 3 years ago by reddibharati

Replying to jmroot: Hi Joshua, Thanks for reply, but still is there any other to install pymol from open source. If you know any other installization process for pymol please let me know. I will try to install by using it. Thank in advance

comment:8 Changed 3 years ago by ryandesign (Ryan Schmidt)

If the SourceForge svn servers are down or having problems, you'll have to wait until they're back up to be able to fetch and install this port.

But firewalls and proxies sometimes balk at the extended http verbs that Subversion needs to use to check out.

A workaround to that is to fetch via https instead of http. Firewalls and proxies cannot read the contents of the encrypted https connections, and therefore can't interfere with them.

pymol and other ports that fetch from SourceForge svn used to fetch via https, but I changed it to http in [23a487d670a45f85bf17635d5bdabc5caddfc134/macports-ports] because SourceForge began requiring newer https encryption methods than the version of Subversion included with El Capitan and earlier support.

MacPorts 2.4.4 has now been released, which uses MacPorts svn on earlier OS X versions, so fetching from SourceForge svn via https is no longer a problem. So my previous commit should be reverted.

comment:9 Changed 3 years ago by ryandesign (Ryan Schmidt)

Cc: ryandesign added

comment:10 in reply to:  8 Changed 3 years ago by ryandesign (Ryan Schmidt)

Replying to ryandesign:

So my previous commit should be reverted.

https://github.com/macports/macports-ports/pull/1833

comment:11 Changed 3 years ago by ryandesign (Ryan Schmidt)

Resolution: fixed
Status: assignedclosed

In ea104431bd80db717edb3b8b5e2433f9a70972d2/macports-ports (master):

Fetch from SourceForge SVN using https

Reverts 23a487d670a45f85bf17635d5bdabc5caddfc134

Closes: #56501

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