Added script front-end for primer-design code

[htsworkflow.git] / htswanalysis / MACS / lib / gsl / gsl-1.11 / doc / gpl.texi

@center Version 3, 29 June 2007
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@c This file is intended to be included in another file.

@display
Copyright @copyright{} 2007 Free Software Foundation, Inc. @url{http://fsf.org/}

Everyone is permitted to copy and distribute verbatim copies of this
license document, but changing it is not allowed.
@end display

@heading Preamble

The GNU General Public License is a free, copyleft license for
software and other kinds of works.

The licenses for most software and other practical works are designed
to take away your freedom to share and change the works.  By contrast,
the GNU General Public License is intended to guarantee your freedom
to share and change all versions of a program--to make sure it remains
free software for all its users.  We, the Free Software Foundation,
use the GNU General Public License for most of our software; it
applies also to any other work released this way by its authors.  You
can apply it to your programs, too.

When we speak of free software, we are referring to freedom, not
price.  Our General Public Licenses are designed to make sure that you
have the freedom to distribute copies of free software (and charge for
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want it, that you can change the software or use pieces of it in new
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To protect your rights, we need to prevent others from denying you
these rights or asking you to surrender the rights.  Therefore, you
have certain responsibilities if you distribute copies of the
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of others.

For example, if you distribute copies of such a program, whether
gratis or for a fee, you must pass on to the recipients the same
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Developers that use the GNU GPL protect your rights with two steps:
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For the developers' and authors' protection, the GPL clearly explains
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Some devices are designed to deny users access to install or run
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The precise terms and conditions for copying, distribution and
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@heading TERMS AND CONDITIONS

@enumerate 0
@item Definitions.

``This License'' refers to version 3 of the GNU General Public License.

``Copyright'' also means copyright-like laws that apply to other kinds
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``The Program'' refers to any copyrightable work licensed under this
License.  Each licensee is addressed as ``you''.  ``Licensees'' and
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To ``modify'' a work means to copy from or adapt all or part of the work
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A ``covered work'' means either the unmodified Program or a work based
on the Program.

To ``propagate'' a work means to do anything with it that, without
permission, would make you directly or secondarily liable for
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public, and in some countries other activities as well.

To ``convey'' a work means any kind of propagation that enables other
parties to make or receive copies.  Mere interaction with a user
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An interactive user interface displays ``Appropriate Legal Notices'' to
the extent that it includes a convenient and prominently visible
feature that (1) displays an appropriate copyright notice, and (2)
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work under this License, and how to view a copy of this License.  If
the interface presents a list of user commands or options, such as a
menu, a prominent item in the list meets this criterion.

@item Source Code.

The ``source code'' for a work means the preferred form of the work for
making modifications to it.  ``Object code'' means any non-source form
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A ``Standard Interface'' means an interface that either is an official
standard defined by a recognized standards body, or, in the case of
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The ``System Libraries'' of an executable work include anything, other
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The ``Corresponding Source'' for a work in object code form means all
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The Corresponding Source need not include anything that users can
regenerate automatically from other parts of the Corresponding Source.

The Corresponding Source for a work in source code form is that same
work.

@item Basic Permissions.

All rights granted under this License are granted for the term of
copyright on the Program, and are irrevocable provided the stated
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permission to run the unmodified Program.  The output from running a
covered work is covered by this License only if the output, given its
content, constitutes a covered work.  This License acknowledges your
rights of fair use or other equivalent, as provided by copyright law.

You may make, run and propagate covered works that you do not convey,
without conditions so long as your license otherwise remains in force.
You may convey covered works to others for the sole purpose of having
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terms of this License in conveying all material for which you do not
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you must do so exclusively on your behalf, under your direction and
control, on terms that prohibit them from making any copies of your
copyrighted material outside their relationship with you.

Conveying under any other circumstances is permitted solely under the
conditions stated below.  Sublicensing is not allowed; section 10
makes it unnecessary.

@item Protecting Users' Legal Rights From Anti-Circumvention Law.

No covered work shall be deemed part of an effective technological
measure under any applicable law fulfilling obligations under article
11 of the WIPO copyright treaty adopted on 20 December 1996, or
similar laws prohibiting or restricting circumvention of such
measures.

When you convey a covered work, you waive any legal power to forbid
circumvention of technological measures to the extent such
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respect to the covered work, and you disclaim any intention to limit
operation or modification of the work as a means of enforcing, against
the work's users, your or third parties' legal rights to forbid
circumvention of technological measures.

@item Conveying Verbatim Copies.

You may convey verbatim copies of the Program's source code as you
receive it, in any medium, provided that you conspicuously and
appropriately publish on each copy an appropriate copyright notice;
keep intact all notices stating that this License and any
non-permissive terms added in accord with section 7 apply to the code;
keep intact all notices of the absence of any warranty; and give all
recipients a copy of this License along with the Program.

You may charge any price or no price for each copy that you convey,
and you may offer support or warranty protection for a fee.

@item Conveying Modified Source Versions.

You may convey a work based on the Program, or the modifications to
produce it from the Program, in the form of source code under the
terms of section 4, provided that you also meet all of these
conditions:

@enumerate a
@item 
The work must carry prominent notices stating that you modified it,
and giving a relevant date.

@item
The work must carry prominent notices stating that it is released
under this License and any conditions added under section 7.  This
requirement modifies the requirement in section 4 to ``keep intact all
notices''.

@item
You must license the entire work, as a whole, under this License to
anyone who comes into possession of a copy.  This License will
therefore apply, along with any applicable section 7 additional terms,
to the whole of the work, and all its parts, regardless of how they
are packaged.  This License gives no permission to license the work in
any other way, but it does not invalidate such permission if you have
separately received it.

@item
If the work has interactive user interfaces, each must display
Appropriate Legal Notices; however, if the Program has interactive
interfaces that do not display Appropriate Legal Notices, your work
need not make them do so.
@end enumerate

A compilation of a covered work with other separate and independent
works, which are not by their nature extensions of the covered work,
and which are not combined with it such as to form a larger program,
in or on a volume of a storage or distribution medium, is called an
``aggregate'' if the compilation and its resulting copyright are not
used to limit the access or legal rights of the compilation's users
beyond what the individual works permit.  Inclusion of a covered work
in an aggregate does not cause this License to apply to the other
parts of the aggregate.

@item  Conveying Non-Source Forms.

You may convey a covered work in object code form under the terms of
sections 4 and 5, provided that you also convey the machine-readable
Corresponding Source under the terms of this License, in one of these
ways:

@enumerate a
@item
Convey the object code in, or embodied in, a physical product
(including a physical distribution medium), accompanied by the
Corresponding Source fixed on a durable physical medium customarily
used for software interchange.

@item
Convey the object code in, or embodied in, a physical product
(including a physical distribution medium), accompanied by a written
offer, valid for at least three years and valid for as long as you
offer spare parts or customer support for that product model, to give
anyone who possesses the object code either (1) a copy of the
Corresponding Source for all the software in the product that is
covered by this License, on a durable physical medium customarily used
for software interchange, for a price no more than your reasonable
cost of physically performing this conveying of source, or (2) access
to copy the Corresponding Source from a network server at no charge.

@item
Convey individual copies of the object code with a copy of the written
offer to provide the Corresponding Source.  This alternative is
allowed only occasionally and noncommercially, and only if you
received the object code with such an offer, in accord with subsection
6b.

@item
Convey the object code by offering access from a designated place
(gratis or for a charge), and offer equivalent access to the
Corresponding Source in the same way through the same place at no
further charge.  You need not require recipients to copy the
Corresponding Source along with the object code.  If the place to copy
the object code is a network server, the Corresponding Source may be
on a different server (operated by you or a third party) that supports
equivalent copying facilities, provided you maintain clear directions
next to the object code saying where to find the Corresponding Source.
Regardless of what server hosts the Corresponding Source, you remain
obligated to ensure that it is available for as long as needed to
satisfy these requirements.

@item
Convey the object code using peer-to-peer transmission, provided you
inform other peers where the object code and Corresponding Source of
the work are being offered to the general public at no charge under
subsection 6d.

@end enumerate

A separable portion of the object code, whose source code is excluded
from the Corresponding Source as a System Library, need not be
included in conveying the object code work.

A ``User Product'' is either (1) a ``consumer product'', which means any
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Product from a modified version of its Corresponding Source.  The
information must suffice to ensure that the continued functioning of
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solely because modification has been made.

If you convey an object code work under this section in, or with, or
specifically for use in, a User Product, and the conveying occurs as
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Corresponding Source conveyed under this section must be accompanied
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if neither you nor any third party retains the ability to install
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The requirement to provide Installation Information does not include a
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@item Additional Terms.

``Additional permissions'' are terms that supplement the terms of this
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Additional permissions that are applicable to the entire Program shall
be treated as though they were included in this License, to the extent
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When you convey a copy of a covered work, you may at your option
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Notwithstanding any other provision of this License, for material you
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of that material) supplement the terms of this License with terms:

@enumerate a
@item
Disclaiming warranty or limiting liability differently from the terms
of sections 15 and 16 of this License; or

@item
Requiring preservation of specified reasonable legal notices or author
attributions in that material or in the Appropriate Legal Notices
displayed by works containing it; or

@item
Prohibiting misrepresentation of the origin of that material, or
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reasonable ways as different from the original version; or

@item
Limiting the use for publicity purposes of names of licensors or
authors of the material; or

@item
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names, trademarks, or service marks; or

@item
Requiring indemnification of licensors and authors of that material by
anyone who conveys the material (or modified versions of it) with
contractual assumptions of liability to the recipient, for any
liability that these contractual assumptions directly impose on those
licensors and authors.
@end enumerate

All other non-permissive additional terms are considered ``further
restrictions'' within the meaning of section 10.  If the Program as you
received it, or any part of it, contains a notice stating that it is
governed by this License along with a term that is a further
restriction, you may remove that term.  If a license document contains
a further restriction but permits relicensing or conveying under this
License, you may add to a covered work material governed by the terms
of that license document, provided that the further restriction does
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If you add terms to a covered work in accord with this section, you
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where to find the applicable terms.

Additional terms, permissive or non-permissive, may be stated in the
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above requirements apply either way.

@item Termination.

You may not propagate or modify a covered work except as expressly
provided under this License.  Any attempt otherwise to propagate or
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this License (including any patent licenses granted under the third
paragraph of section 11).

However, if you cease all violation of this License, then your license
from a particular copyright holder is reinstated (a) provisionally,
unless and until the copyright holder explicitly and finally
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Moreover, your license from a particular copyright holder is
reinstated permanently if the copyright holder notifies you of the
violation by some reasonable means, this is the first time you have
received notice of violation of this License (for any work) from that
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your receipt of the notice.

Termination of your rights under this section does not terminate the
licenses of parties who have received copies or rights from you under
this License.  If your rights have been terminated and not permanently
reinstated, you do not qualify to receive new licenses for the same
material under section 10.

@item Acceptance Not Required for Having Copies.

You are not required to accept this License in order to receive or run
a copy of the Program.  Ancillary propagation of a covered work
occurring solely as a consequence of using peer-to-peer transmission
to receive a copy likewise does not require acceptance.  However,
nothing other than this License grants you permission to propagate or
modify any covered work.  These actions infringe copyright if you do
not accept this License.  Therefore, by modifying or propagating a
covered work, you indicate your acceptance of this License to do so.

@item Automatic Licensing of Downstream Recipients.

Each time you convey a covered work, the recipient automatically
receives a license from the original licensors, to run, modify and
propagate that work, subject to this License.  You are not responsible
for enforcing compliance by third parties with this License.

An ``entity transaction'' is a transaction transferring control of an
organization, or substantially all assets of one, or subdividing an
organization, or merging organizations.  If propagation of a covered
work results from an entity transaction, each party to that
transaction who receives a copy of the work also receives whatever
licenses to the work the party's predecessor in interest had or could
give under the previous paragraph, plus a right to possession of the
Corresponding Source of the work from the predecessor in interest, if
the predecessor has it or can get it with reasonable efforts.

You may not impose any further restrictions on the exercise of the
rights granted or affirmed under this License.  For example, you may
not impose a license fee, royalty, or other charge for exercise of
rights granted under this License, and you may not initiate litigation
(including a cross-claim or counterclaim in a lawsuit) alleging that
any patent claim is infringed by making, using, selling, offering for
sale, or importing the Program or any portion of it.

@item Patents.

A ``contributor'' is a copyright holder who authorizes use under this
License of the Program or a work on which the Program is based.  The
work thus licensed is called the contributor's ``contributor version''.

A contributor's ``essential patent claims'' are all patent claims owned
or controlled by the contributor, whether already acquired or
hereafter acquired, that would be infringed by some manner, permitted
by this License, of making, using, or selling its contributor version,
but do not include claims that would be infringed only as a
consequence of further modification of the contributor version.  For
purposes of this definition, ``control'' includes the right to grant
patent sublicenses in a manner consistent with the requirements of
this License.

Each contributor grants you a non-exclusive, worldwide, royalty-free
patent license under the contributor's essential patent claims, to
make, use, sell, offer for sale, import and otherwise run, modify and
propagate the contents of its contributor version.

In the following three paragraphs, a ``patent license'' is any express
agreement or commitment, however denominated, not to enforce a patent
(such as an express permission to practice a patent or covenant not to
sue for patent infringement).  To ``grant'' such a patent license to a
party means to make such an agreement or commitment not to enforce a
patent against the party.

If you convey a covered work, knowingly relying on a patent license,
and the Corresponding Source of the work is not available for anyone
to copy, free of charge and under the terms of this License, through a
publicly available network server or other readily accessible means,
then you must either (1) cause the Corresponding Source to be so
available, or (2) arrange to deprive yourself of the benefit of the
patent license for this particular work, or (3) arrange, in a manner
consistent with the requirements of this License, to extend the patent
license to downstream recipients.  ``Knowingly relying'' means you have
actual knowledge that, but for the patent license, your conveying the
covered work in a country, or your recipient's use of the covered work
in a country, would infringe one or more identifiable patents in that
country that you have reason to believe are valid.

If, pursuant to or in connection with a single transaction or
arrangement, you convey, or propagate by procuring conveyance of, a
covered work, and grant a patent license to some of the parties
receiving the covered work authorizing them to use, propagate, modify
or convey a specific copy of the covered work, then the patent license
you grant is automatically extended to all recipients of the covered
work and works based on it.

A patent license is ``discriminatory'' if it does not include within the
scope of its coverage, prohibits the exercise of, or is conditioned on
the non-exercise of one or more of the rights that are specifically
granted under this License.  You may not convey a covered work if you
are a party to an arrangement with a third party that is in the
business of distributing software, under which you make payment to the
third party based on the extent of your activity of conveying the
work, and under which the third party grants, to any of the parties
who would receive the covered work from you, a discriminatory patent
license (a) in connection with copies of the covered work conveyed by
you (or copies made from those copies), or (b) primarily for and in
connection with specific products or compilations that contain the
covered work, unless you entered into that arrangement, or that patent
license was granted, prior to 28 March 2007.

Nothing in this License shall be construed as excluding or limiting
any implied license or other defenses to infringement that may
otherwise be available to you under applicable patent law.

@item No Surrender of Others' Freedom.

If conditions are imposed on you (whether by court order, agreement or
otherwise) that contradict the conditions of this License, they do not
excuse you from the conditions of this License.  If you cannot convey
a covered work so as to satisfy simultaneously your obligations under
this License and any other pertinent obligations, then as a
consequence you may not convey it at all.  For example, if you agree
to terms that obligate you to collect a royalty for further conveying
from those to whom you convey the Program, the only way you could
satisfy both those terms and this License would be to refrain entirely
from conveying the Program.

@item Use with the GNU Affero General Public License.

Notwithstanding any other provision of this License, you have
permission to link or combine any covered work with a work licensed
under version 3 of the GNU Affero General Public License into a single
combined work, and to convey the resulting work.  The terms of this
License will continue to apply to the part which is the covered work,
but the special requirements of the GNU Affero General Public License,
section 13, concerning interaction through a network will apply to the
combination as such.

@item Revised Versions of this License.

The Free Software Foundation may publish revised and/or new versions
of the GNU General Public License from time to time.  Such new
versions will be similar in spirit to the present version, but may
differ in detail to address new problems or concerns.

Each version is given a distinguishing version number.  If the Program
specifies that a certain numbered version of the GNU General Public
License ``or any later version'' applies to it, you have the option of
following the terms and conditions either of that numbered version or
of any later version published by the Free Software Foundation.  If
the Program does not specify a version number of the GNU General
Public License, you may choose any version ever published by the Free
Software Foundation.

If the Program specifies that a proxy can decide which future versions
of the GNU General Public License can be used, that proxy's public
statement of acceptance of a version permanently authorizes you to
choose that version for the Program.

Later license versions may give you additional or different
permissions.  However, no additional obligations are imposed on any
author or copyright holder as a result of your choosing to follow a
later version.

@item Disclaimer of Warranty.

THERE IS NO WARRANTY FOR THE PROGRAM, TO THE EXTENT PERMITTED BY
APPLICABLE LAW.  EXCEPT WHEN OTHERWISE STATED IN WRITING THE COPYRIGHT
HOLDERS AND/OR OTHER PARTIES PROVIDE THE PROGRAM ``AS IS'' WITHOUT
WARRANTY OF ANY KIND, EITHER EXPRESSED OR IMPLIED, INCLUDING, BUT NOT
LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR
A PARTICULAR PURPOSE.  THE ENTIRE RISK AS TO THE QUALITY AND
PERFORMANCE OF THE PROGRAM IS WITH YOU.  SHOULD THE PROGRAM PROVE
DEFECTIVE, YOU ASSUME THE COST OF ALL NECESSARY SERVICING, REPAIR OR
CORRECTION.

@item Limitation of Liability.

IN NO EVENT UNLESS REQUIRED BY APPLICABLE LAW OR AGREED TO IN WRITING
WILL ANY COPYRIGHT HOLDER, OR ANY OTHER PARTY WHO MODIFIES AND/OR
CONVEYS THE PROGRAM AS PERMITTED ABOVE, BE LIABLE TO YOU FOR DAMAGES,
INCLUDING ANY GENERAL, SPECIAL, INCIDENTAL OR CONSEQUENTIAL DAMAGES
ARISING OUT OF THE USE OR INABILITY TO USE THE PROGRAM (INCLUDING BUT
NOT LIMITED TO LOSS OF DATA OR DATA BEING RENDERED INACCURATE OR
LOSSES SUSTAINED BY YOU OR THIRD PARTIES OR A FAILURE OF THE PROGRAM
TO OPERATE WITH ANY OTHER PROGRAMS), EVEN IF SUCH HOLDER OR OTHER
PARTY HAS BEEN ADVISED OF THE POSSIBILITY OF SUCH DAMAGES.

@item Interpretation of Sections 15 and 16.

If the disclaimer of warranty and limitation of liability provided
above cannot be given local legal effect according to their terms,
reviewing courts shall apply local law that most closely approximates
an absolute waiver of all civil liability in connection with the
Program, unless a warranty or assumption of liability accompanies a
copy of the Program in return for a fee.

@end enumerate

@heading END OF TERMS AND CONDITIONS

@heading How to Apply These Terms to Your New Programs

If you develop a new program, and you want it to be of the greatest
possible use to the public, the best way to achieve this is to make it
free software which everyone can redistribute and change under these
terms.

To do so, attach the following notices to the program.  It is safest
to attach them to the start of each source file to most effectively
state the exclusion of warranty; and each file should have at least
the ``copyright'' line and a pointer to where the full notice is found.

@smallexample
@var{one line to give the program's name and a brief idea @*of what it does.}  
Copyright (C) @var{year} @var{name of author}

This program is free software: you can redistribute it and/or modify
it under the terms of the GNU General Public License as published by
the Free Software Foundation, either version 3 of the License, or (at
your option) any later version.

This program is distributed in the hope that it will be useful, but
WITHOUT ANY WARRANTY; without even the implied warranty of
MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU
General Public License for more details.

You should have received a copy of the GNU General Public License
along with this program.  If not, see @url{http://www.gnu.org/licenses/}.
@end smallexample

Also add information on how to contact you by electronic and paper mail.

If the program does terminal interaction, make it output a short
notice like this when it starts in an interactive mode:

@smallexample
@var{program} Copyright (C) @var{year} @var{name of author} 
This program comes with ABSOLUTELY NO WARRANTY; for details type @samp{show w}.
This is free software, and you are welcome to redistribute it
under certain conditions; type @samp{show c} for details.
@end smallexample

The hypothetical commands @samp{show w} and @samp{show c} should show
the appropriate parts of the General Public License.  Of course, your
program's commands might be different; for a GUI interface, you would
use an ``about box''.

You should also get your employer (if you work as a programmer) or school,
if any, to sign a ``copyright disclaimer'' for the program, if necessary.
For more information on this, and how to apply and follow the GNU GPL, see
@url{http://www.gnu.org/licenses/}.

The GNU General Public License does not permit incorporating your
program into proprietary programs.  If your program is a subroutine
library, you may consider it more useful to permit linking proprietary
applications with the library.  If this is what you want to do, use
the GNU Lesser General Public License instead of this License.  But
first, please read @url{http://www.gnu.org/philosophy/why-not-lgpl.html}.

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