From 13f45e61241e43d709df10228b946ed9870e8ebb Mon Sep 17 00:00:00 2001
From: Samo Penic <samo.penic@gmail.com>
Date: Tue, 23 Apr 2019 16:12:05 +0000
Subject: [PATCH] Fixing the vesicle 123 and neighbours just for a test
---
INSTALL | 379 ++++++++++++++++++++++++++++++++++++++++++++++++++++--
1 files changed, 364 insertions(+), 15 deletions(-)
diff --git a/INSTALL b/INSTALL
index bf93067..2099840 100644
--- a/INSTALL
+++ b/INSTALL
@@ -1,21 +1,370 @@
-This will be installation instructions
+Installation Instructions
+*************************
-To run automake:
+Copyright (C) 1994-1996, 1999-2002, 2004-2013 Free Software Foundation,
+Inc.
--- This should be performed by developers --
+ Copying and distribution of this file, with or without modification,
+are permitted in any medium without royalty provided the copyright
+notice and this notice are preserved. This file is offered as-is,
+without warranty of any kind.
-autoscan
-mv configure.scan configure.ac
-aclocal
-autoheader
-automake -ac
-autoconf
+Basic Installation
+==================
--- END --
+ Briefly, the shell command `./configure && make && make install'
+should configure, build, and install this package. The following
+more-detailed instructions are generic; see the `README' file for
+instructions specific to this package. Some packages provide this
+`INSTALL' file but do not implement all of the features documented
+below. The lack of an optional feature in a given package is not
+necessarily a bug. More recommendations for GNU packages can be found
+in *note Makefile Conventions: (standards)Makefile Conventions.
--- End user should do this --
-To build:
-./configure
-make
--- END --
+ The `configure' shell script attempts to guess correct values for
+various system-dependent variables used during compilation. It uses
+those values to create a `Makefile' in each directory of the package.
+It may also create one or more `.h' files containing system-dependent
+definitions. Finally, it creates a shell script `config.status' that
+you can run in the future to recreate the current configuration, and a
+file `config.log' containing compiler output (useful mainly for
+debugging `configure').
+ It can also use an optional file (typically called `config.cache'
+and enabled with `--cache-file=config.cache' or simply `-C') that saves
+the results of its tests to speed up reconfiguring. Caching is
+disabled by default to prevent problems with accidental use of stale
+cache files.
+
+ If you need to do unusual things to compile the package, please try
+to figure out how `configure' could check whether to do them, and mail
+diffs or instructions to the address given in the `README' so they can
+be considered for the next release. If you are using the cache, and at
+some point `config.cache' contains results you don't want to keep, you
+may remove or edit it.
+
+ The file `configure.ac' (or `configure.in') is used to create
+`configure' by a program called `autoconf'. You need `configure.ac' if
+you want to change it or regenerate `configure' using a newer version
+of `autoconf'.
+
+ The simplest way to compile this package is:
+
+ 1. `cd' to the directory containing the package's source code and type
+ `./configure' to configure the package for your system.
+
+ Running `configure' might take a while. While running, it prints
+ some messages telling which features it is checking for.
+
+ 2. Type `make' to compile the package.
+
+ 3. Optionally, type `make check' to run any self-tests that come with
+ the package, generally using the just-built uninstalled binaries.
+
+ 4. Type `make install' to install the programs and any data files and
+ documentation. When installing into a prefix owned by root, it is
+ recommended that the package be configured and built as a regular
+ user, and only the `make install' phase executed with root
+ privileges.
+
+ 5. Optionally, type `make installcheck' to repeat any self-tests, but
+ this time using the binaries in their final installed location.
+ This target does not install anything. Running this target as a
+ regular user, particularly if the prior `make install' required
+ root privileges, verifies that the installation completed
+ correctly.
+
+ 6. You can remove the program binaries and object files from the
+ source code directory by typing `make clean'. To also remove the
+ files that `configure' created (so you can compile the package for
+ a different kind of computer), type `make distclean'. There is
+ also a `make maintainer-clean' target, but that is intended mainly
+ for the package's developers. If you use it, you may have to get
+ all sorts of other programs in order to regenerate files that came
+ with the distribution.
+
+ 7. Often, you can also type `make uninstall' to remove the installed
+ files again. In practice, not all packages have tested that
+ uninstallation works correctly, even though it is required by the
+ GNU Coding Standards.
+
+ 8. Some packages, particularly those that use Automake, provide `make
+ distcheck', which can by used by developers to test that all other
+ targets like `make install' and `make uninstall' work correctly.
+ This target is generally not run by end users.
+
+Compilers and Options
+=====================
+
+ Some systems require unusual options for compilation or linking that
+the `configure' script does not know about. Run `./configure --help'
+for details on some of the pertinent environment variables.
+
+ You can give `configure' initial values for configuration parameters
+by setting variables in the command line or in the environment. Here
+is an example:
+
+ ./configure CC=c99 CFLAGS=-g LIBS=-lposix
+
+ *Note Defining Variables::, for more details.
+
+Compiling For Multiple Architectures
+====================================
+
+ You can compile the package for more than one kind of computer at the
+same time, by placing the object files for each architecture in their
+own directory. To do this, you can use GNU `make'. `cd' to the
+directory where you want the object files and executables to go and run
+the `configure' script. `configure' automatically checks for the
+source code in the directory that `configure' is in and in `..'. This
+is known as a "VPATH" build.
+
+ With a non-GNU `make', it is safer to compile the package for one
+architecture at a time in the source code directory. After you have
+installed the package for one architecture, use `make distclean' before
+reconfiguring for another architecture.
+
+ On MacOS X 10.5 and later systems, you can create libraries and
+executables that work on multiple system types--known as "fat" or
+"universal" binaries--by specifying multiple `-arch' options to the
+compiler but only a single `-arch' option to the preprocessor. Like
+this:
+
+ ./configure CC="gcc -arch i386 -arch x86_64 -arch ppc -arch ppc64" \
+ CXX="g++ -arch i386 -arch x86_64 -arch ppc -arch ppc64" \
+ CPP="gcc -E" CXXCPP="g++ -E"
+
+ This is not guaranteed to produce working output in all cases, you
+may have to build one architecture at a time and combine the results
+using the `lipo' tool if you have problems.
+
+Installation Names
+==================
+
+ By default, `make install' installs the package's commands under
+`/usr/local/bin', include files under `/usr/local/include', etc. You
+can specify an installation prefix other than `/usr/local' by giving
+`configure' the option `--prefix=PREFIX', where PREFIX must be an
+absolute file name.
+
+ You can specify separate installation prefixes for
+architecture-specific files and architecture-independent files. If you
+pass the option `--exec-prefix=PREFIX' to `configure', the package uses
+PREFIX as the prefix for installing programs and libraries.
+Documentation and other data files still use the regular prefix.
+
+ In addition, if you use an unusual directory layout you can give
+options like `--bindir=DIR' to specify different values for particular
+kinds of files. Run `configure --help' for a list of the directories
+you can set and what kinds of files go in them. In general, the
+default for these options is expressed in terms of `${prefix}', so that
+specifying just `--prefix' will affect all of the other directory
+specifications that were not explicitly provided.
+
+ The most portable way to affect installation locations is to pass the
+correct locations to `configure'; however, many packages provide one or
+both of the following shortcuts of passing variable assignments to the
+`make install' command line to change installation locations without
+having to reconfigure or recompile.
+
+ The first method involves providing an override variable for each
+affected directory. For example, `make install
+prefix=/alternate/directory' will choose an alternate location for all
+directory configuration variables that were expressed in terms of
+`${prefix}'. Any directories that were specified during `configure',
+but not in terms of `${prefix}', must each be overridden at install
+time for the entire installation to be relocated. The approach of
+makefile variable overrides for each directory variable is required by
+the GNU Coding Standards, and ideally causes no recompilation.
+However, some platforms have known limitations with the semantics of
+shared libraries that end up requiring recompilation when using this
+method, particularly noticeable in packages that use GNU Libtool.
+
+ The second method involves providing the `DESTDIR' variable. For
+example, `make install DESTDIR=/alternate/directory' will prepend
+`/alternate/directory' before all installation names. The approach of
+`DESTDIR' overrides is not required by the GNU Coding Standards, and
+does not work on platforms that have drive letters. On the other hand,
+it does better at avoiding recompilation issues, and works well even
+when some directory options were not specified in terms of `${prefix}'
+at `configure' time.
+
+Optional Features
+=================
+
+ If the package supports it, you can cause programs to be installed
+with an extra prefix or suffix on their names by giving `configure' the
+option `--program-prefix=PREFIX' or `--program-suffix=SUFFIX'.
+
+ Some packages pay attention to `--enable-FEATURE' options to
+`configure', where FEATURE indicates an optional part of the package.
+They may also pay attention to `--with-PACKAGE' options, where PACKAGE
+is something like `gnu-as' or `x' (for the X Window System). The
+`README' should mention any `--enable-' and `--with-' options that the
+package recognizes.
+
+ For packages that use the X Window System, `configure' can usually
+find the X include and library files automatically, but if it doesn't,
+you can use the `configure' options `--x-includes=DIR' and
+`--x-libraries=DIR' to specify their locations.
+
+ Some packages offer the ability to configure how verbose the
+execution of `make' will be. For these packages, running `./configure
+--enable-silent-rules' sets the default to minimal output, which can be
+overridden with `make V=1'; while running `./configure
+--disable-silent-rules' sets the default to verbose, which can be
+overridden with `make V=0'.
+
+Particular systems
+==================
+
+ On HP-UX, the default C compiler is not ANSI C compatible. If GNU
+CC is not installed, it is recommended to use the following options in
+order to use an ANSI C compiler:
+
+ ./configure CC="cc -Ae -D_XOPEN_SOURCE=500"
+
+and if that doesn't work, install pre-built binaries of GCC for HP-UX.
+
+ HP-UX `make' updates targets which have the same time stamps as
+their prerequisites, which makes it generally unusable when shipped
+generated files such as `configure' are involved. Use GNU `make'
+instead.
+
+ On OSF/1 a.k.a. Tru64, some versions of the default C compiler cannot
+parse its `<wchar.h>' header file. The option `-nodtk' can be used as
+a workaround. If GNU CC is not installed, it is therefore recommended
+to try
+
+ ./configure CC="cc"
+
+and if that doesn't work, try
+
+ ./configure CC="cc -nodtk"
+
+ On Solaris, don't put `/usr/ucb' early in your `PATH'. This
+directory contains several dysfunctional programs; working variants of
+these programs are available in `/usr/bin'. So, if you need `/usr/ucb'
+in your `PATH', put it _after_ `/usr/bin'.
+
+ On Haiku, software installed for all users goes in `/boot/common',
+not `/usr/local'. It is recommended to use the following options:
+
+ ./configure --prefix=/boot/common
+
+Specifying the System Type
+==========================
+
+ There may be some features `configure' cannot figure out
+automatically, but needs to determine by the type of machine the package
+will run on. Usually, assuming the package is built to be run on the
+_same_ architectures, `configure' can figure that out, but if it prints
+a message saying it cannot guess the machine type, give it the
+`--build=TYPE' option. TYPE can either be a short name for the system
+type, such as `sun4', or a canonical name which has the form:
+
+ CPU-COMPANY-SYSTEM
+
+where SYSTEM can have one of these forms:
+
+ OS
+ KERNEL-OS
+
+ See the file `config.sub' for the possible values of each field. If
+`config.sub' isn't included in this package, then this package doesn't
+need to know the machine type.
+
+ If you are _building_ compiler tools for cross-compiling, you should
+use the option `--target=TYPE' to select the type of system they will
+produce code for.
+
+ If you want to _use_ a cross compiler, that generates code for a
+platform different from the build platform, you should specify the
+"host" platform (i.e., that on which the generated programs will
+eventually be run) with `--host=TYPE'.
+
+Sharing Defaults
+================
+
+ If you want to set default values for `configure' scripts to share,
+you can create a site shell script called `config.site' that gives
+default values for variables like `CC', `cache_file', and `prefix'.
+`configure' looks for `PREFIX/share/config.site' if it exists, then
+`PREFIX/etc/config.site' if it exists. Or, you can set the
+`CONFIG_SITE' environment variable to the location of the site script.
+A warning: not all `configure' scripts look for a site script.
+
+Defining Variables
+==================
+
+ Variables not defined in a site shell script can be set in the
+environment passed to `configure'. However, some packages may run
+configure again during the build, and the customized values of these
+variables may be lost. In order to avoid this problem, you should set
+them in the `configure' command line, using `VAR=value'. For example:
+
+ ./configure CC=/usr/local2/bin/gcc
+
+causes the specified `gcc' to be used as the C compiler (unless it is
+overridden in the site shell script).
+
+Unfortunately, this technique does not work for `CONFIG_SHELL' due to
+an Autoconf limitation. Until the limitation is lifted, you can use
+this workaround:
+
+ CONFIG_SHELL=/bin/bash ./configure CONFIG_SHELL=/bin/bash
+
+`configure' Invocation
+======================
+
+ `configure' recognizes the following options to control how it
+operates.
+
+`--help'
+`-h'
+ Print a summary of all of the options to `configure', and exit.
+
+`--help=short'
+`--help=recursive'
+ Print a summary of the options unique to this package's
+ `configure', and exit. The `short' variant lists options used
+ only in the top level, while the `recursive' variant lists options
+ also present in any nested packages.
+
+`--version'
+`-V'
+ Print the version of Autoconf used to generate the `configure'
+ script, and exit.
+
+`--cache-file=FILE'
+ Enable the cache: use and save the results of the tests in FILE,
+ traditionally `config.cache'. FILE defaults to `/dev/null' to
+ disable caching.
+
+`--config-cache'
+`-C'
+ Alias for `--cache-file=config.cache'.
+
+`--quiet'
+`--silent'
+`-q'
+ Do not print messages saying which checks are being made. To
+ suppress all normal output, redirect it to `/dev/null' (any error
+ messages will still be shown).
+
+`--srcdir=DIR'
+ Look for the package's source code in directory DIR. Usually
+ `configure' can determine that directory automatically.
+
+`--prefix=DIR'
+ Use DIR as the installation prefix. *note Installation Names::
+ for more details, including other options available for fine-tuning
+ the installation locations.
+
+`--no-create'
+`-n'
+ Run the configure checks, but stop before creating any output
+ files.
+
+`configure' also accepts some other, not widely useful, options. Run
+`configure --help' for more details.
--
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