Just FYI,

With the recent version of cufflinks (at least 1.0.2), the developers added a 
'feature' of automatic version check.
While the idea is nice, the implications are not:
cufflinks,cuffcompare and cuffdiff will connect to host 
"cufflinks.cbcb.umd.edu" every time you run them.

I'm sure the intentions were good, but I don't like programs "calling home", 
basically reporting usage statistics and origins.

The "check_update" code is also not written with security in mind, and might be 
exploited (buffer overruns and such) - it's best to disable it.
This will also generate a message to STDERR, which is just annoying (and bad, 
with galaxy).

To disable it on the command line, add "--no-update-check" to every invocation.

If you compiled it from source code, edit the file "./src/common.cpp" and 
change the line:
   bool no_update_check = false;
   bool no_update_check = true;

Then recompile and re-install.


Jeremy Goecks wrote, On 05/10/2011 09:02 AM:
> We recently updated the Cufflinks/compare/diff wrappers to be compatible with 
> v1.0.* ; the wrappers are available in galaxy-central and should be available 
> in galaxy-dist in the next couple weeks as we're planning another release 
> soon.
> New features in v1.0.* have not been implemented in these updates (and, in 
> fact, there are features from 0.9.* that are still not available); the 
> changes we made were simply to ensure that the wrappers' current 
> functionality works with the new versions. 
> In the next couple months we plan to extend the current wrappers to include 
> new functionality. However, community contributions that extend the current 
> wrappers to include new functionality would be most welcome, and we can 
> integrate them into the galaxy code base if/when they are available.
> Best,
> J.
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