complearn 0.6.2
Sign up to get free protection for your applications and to get access to all the features.
- data/AUTHORS +13 -0
- data/COPYING +340 -0
- data/ChangeLog +0 -0
- data/INSTALL +231 -0
- data/Makefile +352 -0
- data/Makefile.am +76 -0
- data/Makefile.in +352 -0
- data/NEWS +7 -0
- data/README +0 -0
- data/aclocal.m4 +104 -0
- data/bin/Makefile +209 -0
- data/bin/Makefile.am +8 -0
- data/bin/Makefile.in +209 -0
- data/bin/labeltree +68 -0
- data/bin/labeltree.in +68 -0
- data/bin/makesvm +70 -0
- data/bin/makesvm.in +70 -0
- data/bin/maketree +98 -0
- data/bin/maketree.in +98 -0
- data/bin/ncd +43 -0
- data/bin/ncd.in +43 -0
- data/bin/ncdmatrix +54 -0
- data/bin/ncdmatrix.in +54 -0
- data/bin/ncdvector +50 -0
- data/bin/ncdvector.in +50 -0
- data/complearn-0.6.2.gem +0 -0
- data/complearn.gemspec +57 -0
- data/config.log +597 -0
- data/config.status +1082 -0
- data/configure +4922 -0
- data/configure.ac +91 -0
- data/confstat5FpLBf/config.h +65 -0
- data/confstat5FpLBf/subs-1.sed +50 -0
- data/confstat5FpLBf/subs-2.sed +13 -0
- data/confstat5FpLBf/subs.frag +0 -0
- data/confstat5FpLBf/subs.sed +59 -0
- data/confstat5FpLBf/undefs.sed +24 -0
- data/doc/FAQ.txt +67 -0
- data/doc/Makefile +286 -0
- data/doc/Makefile.am +11 -0
- data/doc/Makefile.in +286 -0
- data/doc/devguide.txt +15 -0
- data/doc/example.complearnrc +14 -0
- data/doc/examples.txt +35 -0
- data/doc/man/Makefile +255 -0
- data/doc/man/Makefile.am +11 -0
- data/doc/man/Makefile.in +255 -0
- data/doc/man/complearn.5 +91 -0
- data/doc/man/labeltree.1 +35 -0
- data/doc/man/makesvm.1 +60 -0
- data/doc/man/maketree.1 +58 -0
- data/doc/man/ncd.1 +51 -0
- data/doc/man/ncdmatrix.1 +40 -0
- data/doc/man/ncdvector.1 +42 -0
- data/doc/readme.txt +101 -0
- data/doc/userguide.txt +46 -0
- data/examples/genes/blueWhale.txt +1 -0
- data/examples/genes/cat.txt +1 -0
- data/examples/genes/chimpanzee.txt +1 -0
- data/examples/genes/finWhale.txt +1 -0
- data/examples/genes/graySeal.txt +1 -0
- data/examples/genes/harborSeal.txt +1 -0
- data/examples/genes/horse.txt +1 -0
- data/examples/genes/human.txt +1 -0
- data/examples/genes/mouse.txt +1 -0
- data/examples/genes/rat.txt +1 -0
- data/ext/Makefile +167 -0
- data/ext/Quartet.c +399 -0
- data/ext/Quartet.h +62 -0
- data/ext/TreeScore.c +244 -0
- data/ext/TreeScore.h +3 -0
- data/ext/config.h +65 -0
- data/ext/config.h.in +64 -0
- data/ext/extconf.rb +3 -0
- data/ext/lib/CompLearnLib/CLConfig.rb +241 -0
- data/ext/lib/CompLearnLib/CompressionObject.rb +59 -0
- data/ext/lib/CompLearnLib/CompressionTask.rb +99 -0
- data/ext/lib/CompLearnLib/DistMatrix.rb +18 -0
- data/ext/lib/CompLearnLib/FoundComp.rb +10 -0
- data/ext/lib/CompLearnLib/FoundComp.rb.in +10 -0
- data/ext/lib/CompLearnLib/Ncd.rb +248 -0
- data/ext/lib/CompLearnLib/RunEnv.rb +150 -0
- data/ext/lib/CompLearnLib/Task.rb +39 -0
- data/ext/lib/CompLearnLib/TaskMaster.rb +13 -0
- data/ext/lib/CompLearnLib/TaskMasterMPI.rb +112 -0
- data/ext/lib/CompLearnLib/TaskMasterSingle.rb +39 -0
- data/ext/lib/CompLearnLib/Tree.rb +300 -0
- data/install-sh +294 -0
- data/missing +336 -0
- data/mkinstalldirs +111 -0
- data/o +24 -0
- data/scripts/CompLearn.iss +89 -0
- data/scripts/CompLearn.iss.in +89 -0
- data/scripts/debian/changelog +6 -0
- data/scripts/debian/control +14 -0
- data/scripts/makeSetup.sh +23 -0
- data/scripts/makeSetup.sh.in +23 -0
- data/scripts/makedeb.zsh +46 -0
- data/scripts/makedeb.zsh.in +46 -0
- data/tests/alltests.rb +2 -0
- data/tests/bz2test.rb +516 -0
- data/tests/sshagent-test.rb +48 -0
- data/tests/tests.rb +275 -0
- metadata +164 -0
data/doc/Makefile.am
ADDED
data/doc/Makefile.in
ADDED
@@ -0,0 +1,286 @@
|
|
1
|
+
# Makefile.in generated automatically by automake 1.4-p4 from Makefile.am
|
2
|
+
|
3
|
+
# Copyright (C) 1994, 1995-8, 1999 Free Software Foundation, Inc.
|
4
|
+
# This Makefile.in is free software; the Free Software Foundation
|
5
|
+
# gives unlimited permission to copy and/or distribute it,
|
6
|
+
# with or without modifications, as long as this notice is preserved.
|
7
|
+
|
8
|
+
# This program is distributed in the hope that it will be useful,
|
9
|
+
# but WITHOUT ANY WARRANTY, to the extent permitted by law; without
|
10
|
+
# even the implied warranty of MERCHANTABILITY or FITNESS FOR A
|
11
|
+
# PARTICULAR PURPOSE.
|
12
|
+
|
13
|
+
|
14
|
+
SHELL = @SHELL@
|
15
|
+
|
16
|
+
srcdir = @srcdir@
|
17
|
+
top_srcdir = @top_srcdir@
|
18
|
+
VPATH = @srcdir@
|
19
|
+
prefix = @prefix@
|
20
|
+
exec_prefix = @exec_prefix@
|
21
|
+
|
22
|
+
bindir = @bindir@
|
23
|
+
sbindir = @sbindir@
|
24
|
+
libexecdir = @libexecdir@
|
25
|
+
datadir = @datadir@
|
26
|
+
sysconfdir = @sysconfdir@
|
27
|
+
sharedstatedir = @sharedstatedir@
|
28
|
+
localstatedir = @localstatedir@
|
29
|
+
libdir = @libdir@
|
30
|
+
infodir = @infodir@
|
31
|
+
mandir = @mandir@
|
32
|
+
includedir = @includedir@
|
33
|
+
oldincludedir = /usr/include
|
34
|
+
|
35
|
+
DESTDIR =
|
36
|
+
|
37
|
+
pkgdatadir = $(datadir)/@PACKAGE@
|
38
|
+
pkglibdir = $(libdir)/@PACKAGE@
|
39
|
+
pkgincludedir = $(includedir)/@PACKAGE@
|
40
|
+
|
41
|
+
top_builddir = ..
|
42
|
+
|
43
|
+
ACLOCAL = @ACLOCAL@
|
44
|
+
AUTOCONF = @AUTOCONF@
|
45
|
+
AUTOMAKE = @AUTOMAKE@
|
46
|
+
AUTOHEADER = @AUTOHEADER@
|
47
|
+
|
48
|
+
INSTALL = @INSTALL@
|
49
|
+
INSTALL_PROGRAM = @INSTALL_PROGRAM@ $(AM_INSTALL_PROGRAM_FLAGS)
|
50
|
+
INSTALL_DATA = @INSTALL_DATA@
|
51
|
+
INSTALL_SCRIPT = @INSTALL_SCRIPT@
|
52
|
+
transform = @program_transform_name@
|
53
|
+
|
54
|
+
NORMAL_INSTALL = :
|
55
|
+
PRE_INSTALL = :
|
56
|
+
POST_INSTALL = :
|
57
|
+
NORMAL_UNINSTALL = :
|
58
|
+
PRE_UNINSTALL = :
|
59
|
+
POST_UNINSTALL = :
|
60
|
+
CC = @CC@
|
61
|
+
FOUNDBZIP2 = @FOUNDBZIP2@
|
62
|
+
FOUNDGZIP = @FOUNDGZIP@
|
63
|
+
MAKEINFO = @MAKEINFO@
|
64
|
+
PACKAGE = @PACKAGE@
|
65
|
+
RANLIB = @RANLIB@
|
66
|
+
RUBYBIN = @RUBYBIN@
|
67
|
+
SET_MAKE = @SET_MAKE@
|
68
|
+
TOPDIR = @TOPDIR@
|
69
|
+
VERSION = @VERSION@
|
70
|
+
WINBUILDDIR = @WINBUILDDIR@
|
71
|
+
|
72
|
+
SUBDIRS = man
|
73
|
+
mkinstalldirs = $(SHELL) $(top_srcdir)/mkinstalldirs
|
74
|
+
CONFIG_CLEAN_FILES =
|
75
|
+
DIST_COMMON = Makefile.am Makefile.in
|
76
|
+
|
77
|
+
|
78
|
+
DISTFILES = $(DIST_COMMON) $(SOURCES) $(HEADERS) $(TEXINFOS) $(EXTRA_DIST)
|
79
|
+
|
80
|
+
TAR = tar
|
81
|
+
GZIP_ENV = --best
|
82
|
+
all: all-redirect
|
83
|
+
.SUFFIXES:
|
84
|
+
$(srcdir)/Makefile.in: Makefile.am $(top_srcdir)/configure.ac $(ACLOCAL_M4)
|
85
|
+
cd $(top_srcdir) && $(AUTOMAKE) --gnu --include-deps doc/Makefile
|
86
|
+
|
87
|
+
Makefile: $(srcdir)/Makefile.in $(top_builddir)/config.status
|
88
|
+
cd $(top_builddir) \
|
89
|
+
&& CONFIG_FILES=$(subdir)/$@ CONFIG_HEADERS= $(SHELL) ./config.status
|
90
|
+
|
91
|
+
|
92
|
+
# This directory's subdirectories are mostly independent; you can cd
|
93
|
+
# into them and run `make' without going through this Makefile.
|
94
|
+
# To change the values of `make' variables: instead of editing Makefiles,
|
95
|
+
# (1) if the variable is set in `config.status', edit `config.status'
|
96
|
+
# (which will cause the Makefiles to be regenerated when you run `make');
|
97
|
+
# (2) otherwise, pass the desired values on the `make' command line.
|
98
|
+
|
99
|
+
@SET_MAKE@
|
100
|
+
|
101
|
+
all-recursive install-data-recursive install-exec-recursive \
|
102
|
+
installdirs-recursive install-recursive uninstall-recursive \
|
103
|
+
check-recursive installcheck-recursive info-recursive dvi-recursive:
|
104
|
+
@set fnord $(MAKEFLAGS); amf=$$2; \
|
105
|
+
dot_seen=no; \
|
106
|
+
target=`echo $@ | sed s/-recursive//`; \
|
107
|
+
list='$(SUBDIRS)'; for subdir in $$list; do \
|
108
|
+
echo "Making $$target in $$subdir"; \
|
109
|
+
if test "$$subdir" = "."; then \
|
110
|
+
dot_seen=yes; \
|
111
|
+
local_target="$$target-am"; \
|
112
|
+
else \
|
113
|
+
local_target="$$target"; \
|
114
|
+
fi; \
|
115
|
+
(cd $$subdir && $(MAKE) $(AM_MAKEFLAGS) $$local_target) \
|
116
|
+
|| case "$$amf" in *=*) exit 1;; *k*) fail=yes;; *) exit 1;; esac; \
|
117
|
+
done; \
|
118
|
+
if test "$$dot_seen" = "no"; then \
|
119
|
+
$(MAKE) $(AM_MAKEFLAGS) "$$target-am" || exit 1; \
|
120
|
+
fi; test -z "$$fail"
|
121
|
+
|
122
|
+
mostlyclean-recursive clean-recursive distclean-recursive \
|
123
|
+
maintainer-clean-recursive:
|
124
|
+
@set fnord $(MAKEFLAGS); amf=$$2; \
|
125
|
+
dot_seen=no; \
|
126
|
+
rev=''; list='$(SUBDIRS)'; for subdir in $$list; do \
|
127
|
+
rev="$$subdir $$rev"; \
|
128
|
+
test "$$subdir" = "." && dot_seen=yes; \
|
129
|
+
done; \
|
130
|
+
test "$$dot_seen" = "no" && rev=". $$rev"; \
|
131
|
+
target=`echo $@ | sed s/-recursive//`; \
|
132
|
+
for subdir in $$rev; do \
|
133
|
+
echo "Making $$target in $$subdir"; \
|
134
|
+
if test "$$subdir" = "."; then \
|
135
|
+
local_target="$$target-am"; \
|
136
|
+
else \
|
137
|
+
local_target="$$target"; \
|
138
|
+
fi; \
|
139
|
+
(cd $$subdir && $(MAKE) $(AM_MAKEFLAGS) $$local_target) \
|
140
|
+
|| case "$$amf" in *=*) exit 1;; *k*) fail=yes;; *) exit 1;; esac; \
|
141
|
+
done && test -z "$$fail"
|
142
|
+
tags-recursive:
|
143
|
+
list='$(SUBDIRS)'; for subdir in $$list; do \
|
144
|
+
test "$$subdir" = . || (cd $$subdir && $(MAKE) $(AM_MAKEFLAGS) tags); \
|
145
|
+
done
|
146
|
+
|
147
|
+
tags: TAGS
|
148
|
+
|
149
|
+
ID: $(HEADERS) $(SOURCES) $(LISP)
|
150
|
+
list='$(SOURCES) $(HEADERS)'; \
|
151
|
+
unique=`for i in $$list; do echo $$i; done | \
|
152
|
+
awk ' { files[$$0] = 1; } \
|
153
|
+
END { for (i in files) print i; }'`; \
|
154
|
+
here=`pwd` && cd $(srcdir) \
|
155
|
+
&& mkid -f$$here/ID $$unique $(LISP)
|
156
|
+
|
157
|
+
TAGS: tags-recursive $(HEADERS) $(SOURCES) $(TAGS_DEPENDENCIES) $(LISP)
|
158
|
+
tags=; \
|
159
|
+
here=`pwd`; \
|
160
|
+
list='$(SUBDIRS)'; for subdir in $$list; do \
|
161
|
+
if test "$$subdir" = .; then :; else \
|
162
|
+
test -f $$subdir/TAGS && tags="$$tags -i $$here/$$subdir/TAGS"; \
|
163
|
+
fi; \
|
164
|
+
done; \
|
165
|
+
list='$(SOURCES) $(HEADERS)'; \
|
166
|
+
unique=`for i in $$list; do echo $$i; done | \
|
167
|
+
awk ' { files[$$0] = 1; } \
|
168
|
+
END { for (i in files) print i; }'`; \
|
169
|
+
test -z "$(ETAGS_ARGS)$$unique$(LISP)$$tags" \
|
170
|
+
|| (cd $(srcdir) && etags $(ETAGS_ARGS) $$tags $$unique $(LISP) -o $$here/TAGS)
|
171
|
+
|
172
|
+
mostlyclean-tags:
|
173
|
+
|
174
|
+
clean-tags:
|
175
|
+
|
176
|
+
distclean-tags:
|
177
|
+
-rm -f TAGS ID
|
178
|
+
|
179
|
+
maintainer-clean-tags:
|
180
|
+
|
181
|
+
distdir = $(top_builddir)/$(PACKAGE)-$(VERSION)/$(subdir)
|
182
|
+
|
183
|
+
subdir = doc
|
184
|
+
|
185
|
+
distdir: $(DISTFILES)
|
186
|
+
@for file in $(DISTFILES); do \
|
187
|
+
d=$(srcdir); \
|
188
|
+
if test -d $$d/$$file; then \
|
189
|
+
cp -pr $$d/$$file $(distdir)/$$file; \
|
190
|
+
else \
|
191
|
+
test -f $(distdir)/$$file \
|
192
|
+
|| ln $$d/$$file $(distdir)/$$file 2> /dev/null \
|
193
|
+
|| cp -p $$d/$$file $(distdir)/$$file || :; \
|
194
|
+
fi; \
|
195
|
+
done
|
196
|
+
for subdir in $(SUBDIRS); do \
|
197
|
+
if test "$$subdir" = .; then :; else \
|
198
|
+
test -d $(distdir)/$$subdir \
|
199
|
+
|| mkdir $(distdir)/$$subdir \
|
200
|
+
|| exit 1; \
|
201
|
+
chmod 777 $(distdir)/$$subdir; \
|
202
|
+
(cd $$subdir && $(MAKE) $(AM_MAKEFLAGS) top_distdir=../$(top_distdir) distdir=../$(distdir)/$$subdir distdir) \
|
203
|
+
|| exit 1; \
|
204
|
+
fi; \
|
205
|
+
done
|
206
|
+
info-am:
|
207
|
+
info: info-recursive
|
208
|
+
dvi-am:
|
209
|
+
dvi: dvi-recursive
|
210
|
+
check-am: all-am
|
211
|
+
check: check-recursive
|
212
|
+
installcheck-am:
|
213
|
+
installcheck: installcheck-recursive
|
214
|
+
install-exec-am:
|
215
|
+
install-exec: install-exec-recursive
|
216
|
+
|
217
|
+
install-data-am:
|
218
|
+
install-data: install-data-recursive
|
219
|
+
|
220
|
+
install-am: all-am
|
221
|
+
@$(MAKE) $(AM_MAKEFLAGS) install-exec-am install-data-am
|
222
|
+
install: install-recursive
|
223
|
+
uninstall-am:
|
224
|
+
uninstall: uninstall-recursive
|
225
|
+
all-am: Makefile
|
226
|
+
all-redirect: all-recursive
|
227
|
+
install-strip:
|
228
|
+
$(MAKE) $(AM_MAKEFLAGS) AM_INSTALL_PROGRAM_FLAGS=-s install
|
229
|
+
installdirs: installdirs-recursive
|
230
|
+
installdirs-am:
|
231
|
+
|
232
|
+
|
233
|
+
mostlyclean-generic:
|
234
|
+
|
235
|
+
clean-generic:
|
236
|
+
|
237
|
+
distclean-generic:
|
238
|
+
-rm -f Makefile $(CONFIG_CLEAN_FILES)
|
239
|
+
-rm -f config.cache config.log stamp-h stamp-h[0-9]*
|
240
|
+
|
241
|
+
maintainer-clean-generic:
|
242
|
+
mostlyclean-am: mostlyclean-tags mostlyclean-generic
|
243
|
+
|
244
|
+
mostlyclean: mostlyclean-recursive
|
245
|
+
|
246
|
+
clean-am: clean-tags clean-generic mostlyclean-am
|
247
|
+
|
248
|
+
clean: clean-recursive
|
249
|
+
|
250
|
+
distclean-am: distclean-tags distclean-generic clean-am
|
251
|
+
|
252
|
+
distclean: distclean-recursive
|
253
|
+
|
254
|
+
maintainer-clean-am: maintainer-clean-tags maintainer-clean-generic \
|
255
|
+
distclean-am
|
256
|
+
@echo "This command is intended for maintainers to use;"
|
257
|
+
@echo "it deletes files that may require special tools to rebuild."
|
258
|
+
|
259
|
+
maintainer-clean: maintainer-clean-recursive
|
260
|
+
|
261
|
+
.PHONY: install-data-recursive uninstall-data-recursive \
|
262
|
+
install-exec-recursive uninstall-exec-recursive installdirs-recursive \
|
263
|
+
uninstalldirs-recursive all-recursive check-recursive \
|
264
|
+
installcheck-recursive info-recursive dvi-recursive \
|
265
|
+
mostlyclean-recursive distclean-recursive clean-recursive \
|
266
|
+
maintainer-clean-recursive tags tags-recursive mostlyclean-tags \
|
267
|
+
distclean-tags clean-tags maintainer-clean-tags distdir info-am info \
|
268
|
+
dvi-am dvi check check-am installcheck-am installcheck install-exec-am \
|
269
|
+
install-exec install-data-am install-data install-am install \
|
270
|
+
uninstall-am uninstall all-redirect all-am all installdirs-am \
|
271
|
+
installdirs mostlyclean-generic distclean-generic clean-generic \
|
272
|
+
maintainer-clean-generic clean mostlyclean distclean maintainer-clean
|
273
|
+
|
274
|
+
|
275
|
+
rdoc:
|
276
|
+
(cd .. ; rdoc --op doc/rdoc)
|
277
|
+
|
278
|
+
www:
|
279
|
+
(cd .. ; rdoc --op www/rdoc)
|
280
|
+
|
281
|
+
clean:
|
282
|
+
rm -rf rdoc
|
283
|
+
|
284
|
+
# Tell versions [3.59,3.63) of GNU make to not export all variables.
|
285
|
+
# Otherwise a system limit (for SysV at least) may be exceeded.
|
286
|
+
.NOEXPORT:
|
data/doc/devguide.txt
ADDED
@@ -0,0 +1,15 @@
|
|
1
|
+
For developers:
|
2
|
+
|
3
|
+
This project requires automake at least version 1.7
|
4
|
+
|
5
|
+
When adjusting Makefile.am's or configure.ac,
|
6
|
+
make sure to use the following commands:
|
7
|
+
aclocal
|
8
|
+
autoconf
|
9
|
+
automake
|
10
|
+
./configure
|
11
|
+
|
12
|
+
To make a new release package:
|
13
|
+
|
14
|
+
make dist-gzip
|
15
|
+
|
@@ -0,0 +1,14 @@
|
|
1
|
+
---
|
2
|
+
SingleProcess: true
|
3
|
+
Symmetric: true
|
4
|
+
UnpairedPenalty: 0.0
|
5
|
+
MaxFailedTries: 10
|
6
|
+
InputDir: in
|
7
|
+
Hosts:
|
8
|
+
- localhost
|
9
|
+
OutputDir: out
|
10
|
+
WorkDir: work
|
11
|
+
InternalNodePrefix: n
|
12
|
+
UseBestThirdOnly: false
|
13
|
+
TreesPerTry: 1000
|
14
|
+
Compressor: bzip2
|
data/doc/examples.txt
ADDED
@@ -0,0 +1,35 @@
|
|
1
|
+
In the examples/ directory, you will see a subdirectory called "genes".
|
2
|
+
This contains the genetic sequences from the mitochondria of several well
|
3
|
+
known animals. To run these examples, first follow the instructions in
|
4
|
+
readme.txt to compile and install this package.
|
5
|
+
|
6
|
+
Now, from the top-level directory execute the following command:
|
7
|
+
|
8
|
+
ncdmatrix examples/genes > test.dm
|
9
|
+
|
10
|
+
This command should create a distance matrix file called "test.dm"
|
11
|
+
It contains a list of computed distances for each pair of animals
|
12
|
+
represented. Next, we must calculate a tree:
|
13
|
+
|
14
|
+
maketree test.dm tree.dot
|
15
|
+
|
16
|
+
This should take a moment to compute a best-fitting tree according to
|
17
|
+
the distance matrix. The tree is stored in a file called test.dot.
|
18
|
+
(this is a graphviz-format file)
|
19
|
+
|
20
|
+
Now, it's time to relabel the numbered external nodes according to the
|
21
|
+
original species they represent. This is most easily done using
|
22
|
+
|
23
|
+
labeltree tree.dot examples/genes
|
24
|
+
|
25
|
+
Finally, it's time to create a PostScript or PDF file to look at your
|
26
|
+
tree results:
|
27
|
+
|
28
|
+
neato tree.dot -Tps >tree.ps
|
29
|
+
|
30
|
+
(this last step is optional)
|
31
|
+
ps2pdf tree.ps tree.pdf
|
32
|
+
|
33
|
+
Now, you should be able to view or print out these files, for example
|
34
|
+
by using gv or xpdf.
|
35
|
+
|
data/doc/man/Makefile
ADDED
@@ -0,0 +1,255 @@
|
|
1
|
+
# Makefile.in generated automatically by automake 1.4-p4 from Makefile.am
|
2
|
+
|
3
|
+
# Copyright (C) 1994, 1995-8, 1999 Free Software Foundation, Inc.
|
4
|
+
# This Makefile.in is free software; the Free Software Foundation
|
5
|
+
# gives unlimited permission to copy and/or distribute it,
|
6
|
+
# with or without modifications, as long as this notice is preserved.
|
7
|
+
|
8
|
+
# This program is distributed in the hope that it will be useful,
|
9
|
+
# but WITHOUT ANY WARRANTY, to the extent permitted by law; without
|
10
|
+
# even the implied warranty of MERCHANTABILITY or FITNESS FOR A
|
11
|
+
# PARTICULAR PURPOSE.
|
12
|
+
|
13
|
+
|
14
|
+
SHELL = /bin/sh
|
15
|
+
|
16
|
+
srcdir = .
|
17
|
+
top_srcdir = ../..
|
18
|
+
|
19
|
+
prefix = /usr/local
|
20
|
+
exec_prefix = ${prefix}
|
21
|
+
|
22
|
+
bindir = ${exec_prefix}/bin
|
23
|
+
sbindir = ${exec_prefix}/sbin
|
24
|
+
libexecdir = ${exec_prefix}/libexec
|
25
|
+
datadir = ${prefix}/share
|
26
|
+
sysconfdir = ${prefix}/etc
|
27
|
+
sharedstatedir = ${prefix}/com
|
28
|
+
localstatedir = ${prefix}/var
|
29
|
+
libdir = ${exec_prefix}/lib
|
30
|
+
infodir = ${prefix}/info
|
31
|
+
mandir = ${prefix}/man
|
32
|
+
includedir = ${prefix}/include
|
33
|
+
oldincludedir = /usr/include
|
34
|
+
|
35
|
+
DESTDIR =
|
36
|
+
|
37
|
+
pkgdatadir = $(datadir)/complearn
|
38
|
+
pkglibdir = $(libdir)/complearn
|
39
|
+
pkgincludedir = $(includedir)/complearn
|
40
|
+
|
41
|
+
top_builddir = ../..
|
42
|
+
|
43
|
+
ACLOCAL = aclocal
|
44
|
+
AUTOCONF = autoconf
|
45
|
+
AUTOMAKE = automake
|
46
|
+
AUTOHEADER = autoheader
|
47
|
+
|
48
|
+
INSTALL = /usr/bin/install -c
|
49
|
+
INSTALL_PROGRAM = ${INSTALL} $(AM_INSTALL_PROGRAM_FLAGS)
|
50
|
+
INSTALL_DATA = ${INSTALL} -m 644
|
51
|
+
INSTALL_SCRIPT = ${INSTALL}
|
52
|
+
transform = s,x,x,
|
53
|
+
|
54
|
+
NORMAL_INSTALL = :
|
55
|
+
PRE_INSTALL = :
|
56
|
+
POST_INSTALL = :
|
57
|
+
NORMAL_UNINSTALL = :
|
58
|
+
PRE_UNINSTALL = :
|
59
|
+
POST_UNINSTALL = :
|
60
|
+
CC = gcc
|
61
|
+
FOUNDBZIP2 = true
|
62
|
+
FOUNDGZIP = true
|
63
|
+
MAKEINFO = makeinfo
|
64
|
+
PACKAGE = complearn
|
65
|
+
RANLIB = ranlib
|
66
|
+
RUBYBIN = /usr/bin/ruby1.8
|
67
|
+
SET_MAKE =
|
68
|
+
TOPDIR = /home/cilibrar/src/complearngem/complearn-0.6.2
|
69
|
+
VERSION = 0.6.2
|
70
|
+
WINBUILDDIR = c:\build
|
71
|
+
|
72
|
+
man_MANS = complearn.5 labeltree.1 makesvm.1 maketree.1 ncd.1 ncdmatrix.1 ncdvector.1
|
73
|
+
|
74
|
+
|
75
|
+
EXTRA_DIST = $(man_MANS)
|
76
|
+
mkinstalldirs = $(SHELL) $(top_srcdir)/mkinstalldirs
|
77
|
+
CONFIG_CLEAN_FILES =
|
78
|
+
man1dir = $(mandir)/man1
|
79
|
+
man5dir = $(mandir)/man5
|
80
|
+
MANS = $(man_MANS)
|
81
|
+
|
82
|
+
NROFF = nroff
|
83
|
+
DIST_COMMON = Makefile.am Makefile.in
|
84
|
+
|
85
|
+
|
86
|
+
DISTFILES = $(DIST_COMMON) $(SOURCES) $(HEADERS) $(TEXINFOS) $(EXTRA_DIST)
|
87
|
+
|
88
|
+
TAR = tar
|
89
|
+
GZIP_ENV = --best
|
90
|
+
all: all-redirect
|
91
|
+
.SUFFIXES:
|
92
|
+
$(srcdir)/Makefile.in: Makefile.am $(top_srcdir)/configure.ac $(ACLOCAL_M4)
|
93
|
+
cd $(top_srcdir) && $(AUTOMAKE) --gnu --include-deps doc/man/Makefile
|
94
|
+
|
95
|
+
Makefile: $(srcdir)/Makefile.in $(top_builddir)/config.status
|
96
|
+
cd $(top_builddir) \
|
97
|
+
&& CONFIG_FILES=$(subdir)/$@ CONFIG_HEADERS= $(SHELL) ./config.status
|
98
|
+
|
99
|
+
|
100
|
+
install-man1:
|
101
|
+
$(mkinstalldirs) $(DESTDIR)$(man1dir)
|
102
|
+
@list='$(man1_MANS)'; \
|
103
|
+
l2='$(man_MANS)'; for i in $$l2; do \
|
104
|
+
case "$$i" in \
|
105
|
+
*.1*) list="$$list $$i" ;; \
|
106
|
+
esac; \
|
107
|
+
done; \
|
108
|
+
for i in $$list; do \
|
109
|
+
if test -f $(srcdir)/$$i; then file=$(srcdir)/$$i; \
|
110
|
+
else file=$$i; fi; \
|
111
|
+
ext=`echo $$i | sed -e 's/^.*\\.//'`; \
|
112
|
+
inst=`echo $$i | sed -e 's/\\.[0-9a-z]*$$//'`; \
|
113
|
+
inst=`echo $$inst | sed '$(transform)'`.$$ext; \
|
114
|
+
echo " $(INSTALL_DATA) $$file $(DESTDIR)$(man1dir)/$$inst"; \
|
115
|
+
$(INSTALL_DATA) $$file $(DESTDIR)$(man1dir)/$$inst; \
|
116
|
+
done
|
117
|
+
|
118
|
+
uninstall-man1:
|
119
|
+
@list='$(man1_MANS)'; \
|
120
|
+
l2='$(man_MANS)'; for i in $$l2; do \
|
121
|
+
case "$$i" in \
|
122
|
+
*.1*) list="$$list $$i" ;; \
|
123
|
+
esac; \
|
124
|
+
done; \
|
125
|
+
for i in $$list; do \
|
126
|
+
ext=`echo $$i | sed -e 's/^.*\\.//'`; \
|
127
|
+
inst=`echo $$i | sed -e 's/\\.[0-9a-z]*$$//'`; \
|
128
|
+
inst=`echo $$inst | sed '$(transform)'`.$$ext; \
|
129
|
+
echo " rm -f $(DESTDIR)$(man1dir)/$$inst"; \
|
130
|
+
rm -f $(DESTDIR)$(man1dir)/$$inst; \
|
131
|
+
done
|
132
|
+
|
133
|
+
install-man5:
|
134
|
+
$(mkinstalldirs) $(DESTDIR)$(man5dir)
|
135
|
+
@list='$(man5_MANS)'; \
|
136
|
+
l2='$(man_MANS)'; for i in $$l2; do \
|
137
|
+
case "$$i" in \
|
138
|
+
*.5*) list="$$list $$i" ;; \
|
139
|
+
esac; \
|
140
|
+
done; \
|
141
|
+
for i in $$list; do \
|
142
|
+
if test -f $(srcdir)/$$i; then file=$(srcdir)/$$i; \
|
143
|
+
else file=$$i; fi; \
|
144
|
+
ext=`echo $$i | sed -e 's/^.*\\.//'`; \
|
145
|
+
inst=`echo $$i | sed -e 's/\\.[0-9a-z]*$$//'`; \
|
146
|
+
inst=`echo $$inst | sed '$(transform)'`.$$ext; \
|
147
|
+
echo " $(INSTALL_DATA) $$file $(DESTDIR)$(man5dir)/$$inst"; \
|
148
|
+
$(INSTALL_DATA) $$file $(DESTDIR)$(man5dir)/$$inst; \
|
149
|
+
done
|
150
|
+
|
151
|
+
uninstall-man5:
|
152
|
+
@list='$(man5_MANS)'; \
|
153
|
+
l2='$(man_MANS)'; for i in $$l2; do \
|
154
|
+
case "$$i" in \
|
155
|
+
*.5*) list="$$list $$i" ;; \
|
156
|
+
esac; \
|
157
|
+
done; \
|
158
|
+
for i in $$list; do \
|
159
|
+
ext=`echo $$i | sed -e 's/^.*\\.//'`; \
|
160
|
+
inst=`echo $$i | sed -e 's/\\.[0-9a-z]*$$//'`; \
|
161
|
+
inst=`echo $$inst | sed '$(transform)'`.$$ext; \
|
162
|
+
echo " rm -f $(DESTDIR)$(man5dir)/$$inst"; \
|
163
|
+
rm -f $(DESTDIR)$(man5dir)/$$inst; \
|
164
|
+
done
|
165
|
+
install-man: $(MANS)
|
166
|
+
@$(NORMAL_INSTALL)
|
167
|
+
$(MAKE) $(AM_MAKEFLAGS) install-man1 install-man5
|
168
|
+
uninstall-man:
|
169
|
+
@$(NORMAL_UNINSTALL)
|
170
|
+
$(MAKE) $(AM_MAKEFLAGS) uninstall-man1 uninstall-man5
|
171
|
+
tags: TAGS
|
172
|
+
TAGS:
|
173
|
+
|
174
|
+
|
175
|
+
distdir = $(top_builddir)/$(PACKAGE)-$(VERSION)/$(subdir)
|
176
|
+
|
177
|
+
subdir = doc/man
|
178
|
+
|
179
|
+
distdir: $(DISTFILES)
|
180
|
+
@for file in $(DISTFILES); do \
|
181
|
+
d=$(srcdir); \
|
182
|
+
if test -d $$d/$$file; then \
|
183
|
+
cp -pr $$d/$$file $(distdir)/$$file; \
|
184
|
+
else \
|
185
|
+
test -f $(distdir)/$$file \
|
186
|
+
|| ln $$d/$$file $(distdir)/$$file 2> /dev/null \
|
187
|
+
|| cp -p $$d/$$file $(distdir)/$$file || :; \
|
188
|
+
fi; \
|
189
|
+
done
|
190
|
+
info-am:
|
191
|
+
info: info-am
|
192
|
+
dvi-am:
|
193
|
+
dvi: dvi-am
|
194
|
+
check-am: all-am
|
195
|
+
check: check-am
|
196
|
+
installcheck-am:
|
197
|
+
installcheck: installcheck-am
|
198
|
+
install-exec-am:
|
199
|
+
install-exec: install-exec-am
|
200
|
+
|
201
|
+
install-data-am: install-man
|
202
|
+
install-data: install-data-am
|
203
|
+
|
204
|
+
install-am: all-am
|
205
|
+
@$(MAKE) $(AM_MAKEFLAGS) install-exec-am install-data-am
|
206
|
+
install: install-am
|
207
|
+
uninstall-am: uninstall-man
|
208
|
+
uninstall: uninstall-am
|
209
|
+
all-am: Makefile $(MANS)
|
210
|
+
all-redirect: all-am
|
211
|
+
install-strip:
|
212
|
+
$(MAKE) $(AM_MAKEFLAGS) AM_INSTALL_PROGRAM_FLAGS=-s install
|
213
|
+
installdirs:
|
214
|
+
$(mkinstalldirs) $(DESTDIR)$(mandir)/man1 $(DESTDIR)$(mandir)/man5
|
215
|
+
|
216
|
+
|
217
|
+
mostlyclean-generic:
|
218
|
+
|
219
|
+
clean-generic:
|
220
|
+
|
221
|
+
distclean-generic:
|
222
|
+
-rm -f Makefile $(CONFIG_CLEAN_FILES)
|
223
|
+
-rm -f config.cache config.log stamp-h stamp-h[0-9]*
|
224
|
+
|
225
|
+
maintainer-clean-generic:
|
226
|
+
mostlyclean-am: mostlyclean-generic
|
227
|
+
|
228
|
+
mostlyclean: mostlyclean-am
|
229
|
+
|
230
|
+
clean-am: clean-generic mostlyclean-am
|
231
|
+
|
232
|
+
clean: clean-am
|
233
|
+
|
234
|
+
distclean-am: distclean-generic clean-am
|
235
|
+
|
236
|
+
distclean: distclean-am
|
237
|
+
|
238
|
+
maintainer-clean-am: maintainer-clean-generic distclean-am
|
239
|
+
@echo "This command is intended for maintainers to use;"
|
240
|
+
@echo "it deletes files that may require special tools to rebuild."
|
241
|
+
|
242
|
+
maintainer-clean: maintainer-clean-am
|
243
|
+
|
244
|
+
.PHONY: install-man1 uninstall-man1 install-man5 uninstall-man5 \
|
245
|
+
install-man uninstall-man tags distdir info-am info dvi-am dvi check \
|
246
|
+
check-am installcheck-am installcheck install-exec-am install-exec \
|
247
|
+
install-data-am install-data install-am install uninstall-am uninstall \
|
248
|
+
all-redirect all-am all installdirs mostlyclean-generic \
|
249
|
+
distclean-generic clean-generic maintainer-clean-generic clean \
|
250
|
+
mostlyclean distclean maintainer-clean
|
251
|
+
|
252
|
+
|
253
|
+
# Tell versions [3.59,3.63) of GNU make to not export all variables.
|
254
|
+
# Otherwise a system limit (for SysV at least) may be exceeded.
|
255
|
+
.NOEXPORT:
|