The New Plan

ebuild branch has old ebuilds.  profiles dir still has CFLAGS.

Everything else is removed or modified for changing of upstream to
Alpine.

1 files changed, 0 insertions, 89 deletions

diff --git a/licenses/psipred b/licenses/psipred
deleted file mode 100644
index 7f797d17d..000000000
--- a/licenses/psipred
+++ /dev/null
@@ -1,89 +0,0 @@
-PLEASE READ THE FOLLOWING LICENSE AGREEMENT. BY USING THE PROGRAM YOU ARE
-ACKNOWLEDGING THE FACT THAT YOU AGREE TO THE TERMS OUTLINED IN THIS
-AGREEMENT. USERS WISHING TO USE THE SOFTWARE FOR COMMERCIAL ACTIVITIES
-NOT COVERED BY THIS AGREEMENT SHOULD SEND E-MAIL TO: dtj@cs.ucl.ac.uk
-
-* NOTE RECENT CHANGES TO PARAGRAPH 8 *
-
-
-
- PSIPRED2 - PROTEIN SECONDARY STRUCTURE PREDICTION PROGRAM BY D.T.JONES
- ----------------------------------------------------------------------
-
-                          GENERAL LICENSE &
-                          -----------------
-
-		     CONFIDENTIALITY AGREEMENT
-		     -------------------------
-
-
-
-In regard to the protein structure prediction program (PSIPRED2)
-herewith (the Software) the copyright and other intellectual property
-rights to which belong to the Author(s).
-
-Any user (the User) of the program undertakes to the Copyright holder that he
-or she shall be bound by the following terms and conditions:-
-
-1. The User will receive the Software and any related documentation in
-confidence and will not use the same except for the purpose of their own 
-research. The Software will be used only by such of the User's officers or
-employees to whom it must reasonably be communicated to enable them to
-undertake their research and who agree to be bound by the same confidence.
-The User shall procure and enforce such agreement from his or her staff for
-the benefit of the Copyright holder.
-
-2. The publication of research using the Software must include an
-appropriate citation to the method:
-
-Jones, D.T. (1999) Protein secondary structure prediction based on
-position-specific scoring matrices. J. Mol. Biol. 292:195-202.
-
-3. All forms of the Software will be kept in a reasonably secure place to
-prevent unauthorised access.
-
-4. Each copy of the Software or, if not practicable then, any package
-associated therewith shall be suitably marked (and such marking maintained) 
-with the following copyright notice: "Copyright 2000 D.T.Jones. All Rights
-Reserved.".
-
-5. The Software may be modified, but any changes made shall be communicated
-to the Author(s) and made freely available.
-
-6. The Software may not be sold as a standalone package, or incorporated into
-a commercial software package without the written permission of the Copyright
-holder. The Software may be used freely for individual academic or commercial
-research. The Software may also be made freely available for training or
-teaching purposes.
-
-7. The results produced by the Software may not be incorporated into any
-data banks or databases which are subject to the payment of access or
-license fees without the written permission of the Copyright holder.
-
-8. The Software may be made available to users over a local network or
-wide area network (including the Internet), but only if access is granted
-free of charge to all authorised users. Incorporation of the Software into
-a commercial Web site or other fee paying service is not allowed without
-the written permission of the Copyright holder. If PSIPRED results are
-returned to the user via such a network service, then a suitable
-acknowledgement of the PSIPRED method must be returned somewhere in the
-output text.
-
-9. The confidentiality obligation in paragraph one shall not apply:
-
-   (i)  to information and data known to the User at the time of
-	receipt hereunder (as evidenced by its written records);
-
-  (ii)	to information and data which was at the time of receipt in the 
-	public domain or thereafter becomes so through no wrongful act of
-	the User;
-
- (iii)	to information and data which the User receives from a third
-	party not in breach of any obligation of confidentiality owed to
-	the Author(s).
-
-10. The User understands that the Software is supplied "as is". No warranty
-   as to its fitness or suitability for any purpose whatsoever is made or
-   implied. In no event shall the Author(s) or Copyright holder be held
-   responsible for any direct or indirect damages arising through the use
-   of the Software.