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Upstream-Name: rtracklayer
Upstream-Contact: Michael Lawrence <michafla@gene.com>
Source: https://bioconductor.org/packages/rtracklayer/
Files: *
Copyright: © 2006-2016 Michael Lawrence, Vince Carey, Robert Gentleman
License: Artistic-2.0
Files: src/ucsc/*
Copyright: 2011-2014 The Regents of the University of California
License: all_use_kentlib
*** TEXT FROM ORIGINAL KENT SOURCE LIB README ***
This directory contains general purpose, web oriented,
and computational biology oriented modules, as well
as some less general stuff associated with the Intronerator
web site. Initially this library was created by Jim
Kent from 1999 to 2001. Since then other programmers have
also added to it. Jim continues to make substantial
contributions.
.
With the exception of the gifcomp.c module, all
modules here are free for all use - public, private,
or commercial. The gifcomp.c module contains code
originally distributed by CompuServe under a similar
"free for all" license. However this uses the LZW
patented by UniSys, which UniSys started enforcing
several years after CompuServe released this module.
The last I heard UniSys did not require a license
for non-commercial purposes, but did require a
license for commercial purposes. This may change
in the future, though the patent is nearing it's
expiration date in any case. Commercial users
are advised to either get a license for LZW, or
to switch from GIF to PNG.
Files: src/ucsc/bits.*
src/ucsc/common.*
src/ucsc/dlist.*
src/ucsc/dnaseq.*
src/ucsc/dnautil.*
src/ucsc/dystring.*
src/ucsc/errAbort.*
src/ucsc/hash.*
src/ucsc/hmmstats.c
src/ucsc/htmshell.h
src/ucsc/linefile.*
src/ucsc/localmem.*
src/ucsc/memalloc.*
src/ucsc/net.*
src/ucsc/obscure.*
src/ucsc/options.h
src/ucsc/os*x.c
src/ucsc/portable.h
src/ucsc/sqlNum.*
src/ucsc/wildcmp.c
src/ucsc/cheapcgi.h
src/ucsc/hmmstats.h
src/ucsc/portimpl.h
src/ucsc/sig.h
Copyright: 2000-2005 Jim Kent
License: all_use
license is hereby granted for all use - public, private or commercial
Comment: The files
src/ucsc/cheapcgi.h
src/ucsc/hmmstats.h
src/ucsc/portimpl.h
src/ucsc/sig.h
in this source download do contain the statement:
Source code may be freely used
for personal, academic, and non-profit purposes. Commercial use
permitted only by explicit agreement with Jim Kent (jim_kent@pacbell.net)
but the author Jim Kent declared publicly here
https://lists.alioth.debian.org/pipermail/debian-med-packaging/2016-May/042035.html
that this is not the proper license but the license above applies.
Files: debian/*
Copyright: 2013-2016 Andreas Tille <tille@debian.org>
License: Artistic-2.0
License: Artistic-2.0
The "Artistic License"
.
Preamble
.
1. You may make and give away verbatim copies of the source form of the
Standard Version of this Package without restriction, provided that
you duplicate all of the original copyright notices and associated
disclaimers.
.
2. You may apply bug fixes, portability fixes and other modifications
derived from the Public Domain or from the Copyright Holder. A
Package modified in such a way shall still be considered the Standard
Version.
.
3. You may otherwise modify your copy of this Package in any way,
provided that you insert a prominent notice in each changed file stating
how and when you changed that file, and provided that you do at least
ONE of the following:
.
a) place your modifications in the Public Domain or otherwise make them
Freely Available, such as by posting said modifications to Usenet or
an equivalent medium, or placing the modifications on a major archive
site such as uunet.uu.net, or by allowing the Copyright Holder to include
your modifications in the Standard Version of the Package.
.
b) use the modified Package only within your corporation or organization.
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c) rename any non-standard executables so the names do not conflict
with standard executables, which must also be provided, and provide
a separate manual page for each non-standard executable that clearly
documents how it differs from the Standard Version.
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d) make other distribution arrangements with the Copyright Holder.
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4. You may distribute the programs of this Package in object code or
executable form, provided that you do at least ONE of the following:
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a) distribute a Standard Version of the executables and library files,
together with instructions (in the manual page or equivalent) on where
to get the Standard Version.
.
b) accompany the distribution with the machine-readable source of
the Package with your modifications.
.
c) give non-standard executables non-standard names, and clearly
document the differences in manual pages (or equivalent), together
with instructions on where to get the Standard Version.
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d) make other distribution arrangements with the Copyright Holder.
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5. You may charge a reasonable copying fee for any distribution of this
Package. You may charge any fee you choose for support of this Package.
You may not charge a fee for this Package itself. However, you may
distribute this Package in aggregate with other (possibly commercial)
programs as part of a larger (possibly commercial) software distribution
provided that you do not advertise this Package as a product of your
own. You may embed this Package's interpreter within an executable of
yours (by linking); this shall be construed as a mere form of
aggregation, provided that the complete Standard Version of the
interpreter is so embedded.
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6. The scripts and library files supplied as input to or produced as
output from the programs of this Package do not automatically fall under
the copyright of this Package, but belong to whoever generated them, and
may be sold commercially, and may be aggregated with this Package. If
such scripts or library files are aggregated with this Package via the
so-called "undump" or "unexec" methods of producing a binary executable
image, then distribution of such an image shall neither be construed as
a distribution of this Package nor shall it fall under the restrictions
of Paragraphs 3 and 4, provided that you do not represent such an
executable image as a Standard Version of this Package.
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7. C subroutines (or comparably compiled subroutines in other
languages) supplied by you and linked into this Package in order to
emulate subroutines and variables of the language defined by this
Package shall not be considered part of this Package, but are the
equivalent of input as in Paragraph 6, provided these subroutines do
not change the language in any way that would cause it to fail the
regression tests for the language.
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8. Aggregation of this Package with a commercial distribution is always
permitted provided that the use of this Package is embedded; that is,
when no overt attempt is made to make this Package's interfaces visible
to the end user of the commercial distribution. Such use shall not be
construed as a distribution of this Package.
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9. The name of the Copyright Holder may not be used to endorse or promote
products derived from this software without specific prior written permission.
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10. THIS PACKAGE IS PROVIDED "AS IS" AND WITHOUT ANY EXPRESS OR
IMPLIED WARRANTIES, INCLUDING, WITHOUT LIMITATION, THE IMPLIED
WARRANTIES OF MERCHANTIBILITY AND FITNESS FOR A PARTICULAR PURPOSE.
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