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/mkinstalldirs
ADDED
|
@@ -0,0 +1,111 @@
|
|
|
1
|
+
#! /bin/sh
|
|
2
|
+
# mkinstalldirs --- make directory hierarchy
|
|
3
|
+
# Author: Noah Friedman <friedman@prep.ai.mit.edu>
|
|
4
|
+
# Created: 1993-05-16
|
|
5
|
+
# Public domain
|
|
6
|
+
|
|
7
|
+
errstatus=0
|
|
8
|
+
dirmode=""
|
|
9
|
+
|
|
10
|
+
usage="\
|
|
11
|
+
Usage: mkinstalldirs [-h] [--help] [-m mode] dir ..."
|
|
12
|
+
|
|
13
|
+
# process command line arguments
|
|
14
|
+
while test $# -gt 0 ; do
|
|
15
|
+
case $1 in
|
|
16
|
+
-h | --help | --h*) # -h for help
|
|
17
|
+
echo "$usage" 1>&2
|
|
18
|
+
exit 0
|
|
19
|
+
;;
|
|
20
|
+
-m) # -m PERM arg
|
|
21
|
+
shift
|
|
22
|
+
test $# -eq 0 && { echo "$usage" 1>&2; exit 1; }
|
|
23
|
+
dirmode=$1
|
|
24
|
+
shift
|
|
25
|
+
;;
|
|
26
|
+
--) # stop option processing
|
|
27
|
+
shift
|
|
28
|
+
break
|
|
29
|
+
;;
|
|
30
|
+
-*) # unknown option
|
|
31
|
+
echo "$usage" 1>&2
|
|
32
|
+
exit 1
|
|
33
|
+
;;
|
|
34
|
+
*) # first non-opt arg
|
|
35
|
+
break
|
|
36
|
+
;;
|
|
37
|
+
esac
|
|
38
|
+
done
|
|
39
|
+
|
|
40
|
+
for file
|
|
41
|
+
do
|
|
42
|
+
if test -d "$file"; then
|
|
43
|
+
shift
|
|
44
|
+
else
|
|
45
|
+
break
|
|
46
|
+
fi
|
|
47
|
+
done
|
|
48
|
+
|
|
49
|
+
case $# in
|
|
50
|
+
0) exit 0 ;;
|
|
51
|
+
esac
|
|
52
|
+
|
|
53
|
+
case $dirmode in
|
|
54
|
+
'')
|
|
55
|
+
if mkdir -p -- . 2>/dev/null; then
|
|
56
|
+
echo "mkdir -p -- $*"
|
|
57
|
+
exec mkdir -p -- "$@"
|
|
58
|
+
fi
|
|
59
|
+
;;
|
|
60
|
+
*)
|
|
61
|
+
if mkdir -m "$dirmode" -p -- . 2>/dev/null; then
|
|
62
|
+
echo "mkdir -m $dirmode -p -- $*"
|
|
63
|
+
exec mkdir -m "$dirmode" -p -- "$@"
|
|
64
|
+
fi
|
|
65
|
+
;;
|
|
66
|
+
esac
|
|
67
|
+
|
|
68
|
+
for file
|
|
69
|
+
do
|
|
70
|
+
set fnord `echo ":$file" | sed -ne 's/^:\//#/;s/^://;s/\// /g;s/^#/\//;p'`
|
|
71
|
+
shift
|
|
72
|
+
|
|
73
|
+
pathcomp=
|
|
74
|
+
for d
|
|
75
|
+
do
|
|
76
|
+
pathcomp="$pathcomp$d"
|
|
77
|
+
case $pathcomp in
|
|
78
|
+
-*) pathcomp=./$pathcomp ;;
|
|
79
|
+
esac
|
|
80
|
+
|
|
81
|
+
if test ! -d "$pathcomp"; then
|
|
82
|
+
echo "mkdir $pathcomp"
|
|
83
|
+
|
|
84
|
+
mkdir "$pathcomp" || lasterr=$?
|
|
85
|
+
|
|
86
|
+
if test ! -d "$pathcomp"; then
|
|
87
|
+
errstatus=$lasterr
|
|
88
|
+
else
|
|
89
|
+
if test ! -z "$dirmode"; then
|
|
90
|
+
echo "chmod $dirmode $pathcomp"
|
|
91
|
+
lasterr=""
|
|
92
|
+
chmod "$dirmode" "$pathcomp" || lasterr=$?
|
|
93
|
+
|
|
94
|
+
if test ! -z "$lasterr"; then
|
|
95
|
+
errstatus=$lasterr
|
|
96
|
+
fi
|
|
97
|
+
fi
|
|
98
|
+
fi
|
|
99
|
+
fi
|
|
100
|
+
|
|
101
|
+
pathcomp="$pathcomp/"
|
|
102
|
+
done
|
|
103
|
+
done
|
|
104
|
+
|
|
105
|
+
exit $errstatus
|
|
106
|
+
|
|
107
|
+
# Local Variables:
|
|
108
|
+
# mode: shell-script
|
|
109
|
+
# sh-indentation: 2
|
|
110
|
+
# End:
|
|
111
|
+
# mkinstalldirs ends here
|
data/o
ADDED
|
@@ -0,0 +1,24 @@
|
|
|
1
|
+
Making clean in .
|
|
2
|
+
make[1]: Entering directory `/mnt/goliath/home/cilibrar/src/complearngem/complearn-0.6.2'
|
|
3
|
+
make[1]: Nothing to be done for `clean-am'.
|
|
4
|
+
make[1]: Leaving directory `/mnt/goliath/home/cilibrar/src/complearngem/complearn-0.6.2'
|
|
5
|
+
Making clean in ext
|
|
6
|
+
make[1]: Entering directory `/mnt/goliath/home/cilibrar/src/complearngem/complearn-0.6.2/ext'
|
|
7
|
+
make[1]: Leaving directory `/mnt/goliath/home/cilibrar/src/complearngem/complearn-0.6.2/ext'
|
|
8
|
+
Making clean in bin
|
|
9
|
+
make[1]: Entering directory `/mnt/goliath/home/cilibrar/src/complearngem/complearn-0.6.2/bin'
|
|
10
|
+
make[1]: Nothing to be done for `clean'.
|
|
11
|
+
make[1]: Leaving directory `/mnt/goliath/home/cilibrar/src/complearngem/complearn-0.6.2/bin'
|
|
12
|
+
Making clean in doc
|
|
13
|
+
make[1]: Entering directory `/mnt/goliath/home/cilibrar/src/complearngem/complearn-0.6.2/doc'
|
|
14
|
+
Making clean in .
|
|
15
|
+
make[2]: Entering directory `/mnt/goliath/home/cilibrar/src/complearngem/complearn-0.6.2/doc'
|
|
16
|
+
make[2]: Nothing to be done for `clean-am'.
|
|
17
|
+
make[2]: Leaving directory `/mnt/goliath/home/cilibrar/src/complearngem/complearn-0.6.2/doc'
|
|
18
|
+
Making clean in man
|
|
19
|
+
make[2]: Entering directory `/mnt/goliath/home/cilibrar/src/complearngem/complearn-0.6.2/doc/man'
|
|
20
|
+
make[2]: Nothing to be done for `clean'.
|
|
21
|
+
make[2]: Leaving directory `/mnt/goliath/home/cilibrar/src/complearngem/complearn-0.6.2/doc/man'
|
|
22
|
+
rm -rf rdoc
|
|
23
|
+
make[1]: Leaving directory `/mnt/goliath/home/cilibrar/src/complearngem/complearn-0.6.2/doc'
|
|
24
|
+
rm -rf confstat*
|
|
@@ -0,0 +1,89 @@
|
|
|
1
|
+
[Setup]
|
|
2
|
+
AppName=complearn
|
|
3
|
+
AppVerName=complearn 0.6.2
|
|
4
|
+
CreateAppDir=true
|
|
5
|
+
DefaultGroupName=complearn
|
|
6
|
+
DefaultDirName={pf}\complearn
|
|
7
|
+
;DefaultDirName=C:
|
|
8
|
+
;Compression=lzma
|
|
9
|
+
;SolidCompression=yes
|
|
10
|
+
AllowRootDirectory=true
|
|
11
|
+
EnableDirDoesntExistWarning=false
|
|
12
|
+
UsePreviousAppDir=false
|
|
13
|
+
ShowLanguageDialog=no
|
|
14
|
+
OutputBaseFilename=complearn-0.6.2-win
|
|
15
|
+
VersionInfoVersion=0.6.2
|
|
16
|
+
VersionInfoCompany=Rudi Cilibrasi
|
|
17
|
+
SourceDir=c:\build
|
|
18
|
+
|
|
19
|
+
[Files]
|
|
20
|
+
Source: CompLearnLib/CompressionObject.rb; DestDir: {sd}\msys\1.0\local\lib\ruby\site_ruby\1.8; Check: MyCheck
|
|
21
|
+
Source: CompLearnLib/CompressionTask.rb; DestDir: {sd}\msys\1.0\local\lib\ruby\site_ruby\1.8; Check: MyCheck
|
|
22
|
+
Source: CompLearnLib/Config.rb; DestDir: {sd}\msys\1.0\local\lib\ruby\site_ruby\1.8; Check: MyCheck
|
|
23
|
+
Source: CompLearnLib/DistMatrix.rb; DestDir: {sd}\msys\1.0\local\lib\ruby\site_ruby\1.8; Check: MyCheck
|
|
24
|
+
Source: CompLearnLib/Tree.rb; DestDir: {sd}\msys\1.0\local\lib\ruby\site_ruby\1.8; Check: MyCheck
|
|
25
|
+
Source: CompLearnLib/Ncd.rb; DestDir: {sd}\msys\1.0\local\lib\ruby\site_ruby\1.8; Check: MyCheck
|
|
26
|
+
Source: CompLearnLib/RunEnv.rb; DestDir: {sd}\msys\1.0\local\lib\ruby\site_ruby\1.8; Check: MyCheck
|
|
27
|
+
Source: CompLearnLib/Task.rb; DestDir: {sd}\msys\1.0\local\lib\ruby\site_ruby\1.8; Check: MyCheck
|
|
28
|
+
Source: CompLearnLib/TaskMaster.rb; DestDir: {sd}\msys\1.0\local\lib\ruby\site_ruby\1.8; Check: MyCheck
|
|
29
|
+
Source: CompLearnLib/TaskMasterMPI.rb; DestDir: {sd}\msys\1.0\local\lib\ruby\site_ruby\1.8; Check: MyCheck
|
|
30
|
+
Source: CompLearnLib/TaskMasterSingle.rb; DestDir: {sd}\msys\1.0\local\lib\ruby\site_ruby\1.8; Check: MyCheck
|
|
31
|
+
Source: CompLearnLib/FoundComp.rb; DestDir: {sd}\msys\1.0\local\lib\ruby\site_ruby\1.8; Check: MyCheck
|
|
32
|
+
Source: CompLearn.so; DestDir: {sd}\msys\1.0\local\lib\ruby\site_ruby\1.8\i386-msvcrt; Check: MyCheck
|
|
33
|
+
Source: bz2.so; DestDir: {sd}\msys\1.0\local\lib\ruby\site_ruby\1.8\i386-msvcrt; Check: MyCheck
|
|
34
|
+
Source: bin/labeltree; DestDir: {sd}\msys\1.0\local; Check: MyCheck
|
|
35
|
+
Source: bin/ncdvector; DestDir: {sd}\msys\1.0\local; Check: MyCheck
|
|
36
|
+
Source: bin/maketree; DestDir: {sd}\msys\1.0\local; Check: MyCheck
|
|
37
|
+
Source: bin/ncd; DestDir: {sd}\msys\1.0\local; Check: MyCheck
|
|
38
|
+
Source: bin/ncdmatrix; DestDir: {sd}\msys\1.0\local; Check: MyCheck
|
|
39
|
+
Source: bin/makesvm; DestDir: {sd}\msys\1.0\local; Check: MyCheck
|
|
40
|
+
Source: man/man1/labeltree.1; DestDir: {sd}\msys\1.0\local; Check: MyCheck
|
|
41
|
+
Source: man/man1/ncdvector.1; DestDir: {sd}\msys\1.0\local; Check: MyCheck
|
|
42
|
+
Source: man/man1/maketree.1; DestDir: {sd}\msys\1.0\local; Check: MyCheck
|
|
43
|
+
Source: man/man1/ncd.1; DestDir: {sd}\msys\1.0\local; Check: MyCheck
|
|
44
|
+
Source: man/man1/ncdmatrix.1; DestDir: {sd}\msys\1.0\local; Check: MyCheck
|
|
45
|
+
Source: man/man1/makesvm.1; DestDir: {sd}\msys\1.0\local; Check: MyCheck
|
|
46
|
+
Source: man/man5/complearn.5; DestDir: {sd}\msys\1.0\local; Check: MyCheck
|
|
47
|
+
[Code]
|
|
48
|
+
var
|
|
49
|
+
myProgChecked: Boolean;
|
|
50
|
+
myProgResult: Boolean;
|
|
51
|
+
function MyCheck(): Boolean;
|
|
52
|
+
var
|
|
53
|
+
msysFileName: String;
|
|
54
|
+
begin
|
|
55
|
+
if not myProgChecked then begin
|
|
56
|
+
myProgChecked := True;
|
|
57
|
+
msysFileName := ExpandConstant('{sd}\msys\1.0\bin\cat.exe');
|
|
58
|
+
if FileExists(msysFileName) then
|
|
59
|
+
begin
|
|
60
|
+
msysFileName := ExpandConstant('{sd}\msys\1.0\local\lib\ruby\1.8\yaml.rb');
|
|
61
|
+
if FileExists(msysFileName) then
|
|
62
|
+
begin
|
|
63
|
+
myProgResult := True;
|
|
64
|
+
end
|
|
65
|
+
else
|
|
66
|
+
begin
|
|
67
|
+
MsgBox('You must install Ruby for MinGW/MSYS first' , mbInformation, MB_OK);
|
|
68
|
+
myProgResult := False;
|
|
69
|
+
exit
|
|
70
|
+
end
|
|
71
|
+
end
|
|
72
|
+
else
|
|
73
|
+
begin
|
|
74
|
+
MsgBox(ExpandConstant('You must install MinGW/MSYS in the default directory on {sd}') , mbInformation, MB_OK);
|
|
75
|
+
myProgResult := False;
|
|
76
|
+
exit
|
|
77
|
+
end;
|
|
78
|
+
end;
|
|
79
|
+
Result := myProgResult;
|
|
80
|
+
end;
|
|
81
|
+
[Icons]
|
|
82
|
+
;Name: {group}\NSD; Filename: {app}\nsd.exe
|
|
83
|
+
;Name: {group}\MODEEGDRIVER; Filename: {app}\modeegdriver.exe
|
|
84
|
+
Name: {group}\{cm:UninstallProgram, complearn}; Filename: {uninstallexe}
|
|
85
|
+
[UninstallDelete]
|
|
86
|
+
;Name: {app}\modeegdriver.exe; Type: files
|
|
87
|
+
;Name: {app}\nsd.exe; Type: files
|
|
88
|
+
;Name: {app}\readedf.exe; Type: files
|
|
89
|
+
;Name: {app}\writeedf.exe; Type: files
|
|
@@ -0,0 +1,89 @@
|
|
|
1
|
+
[Setup]
|
|
2
|
+
AppName=@PACKAGE@
|
|
3
|
+
AppVerName=@PACKAGE@ @VERSION@
|
|
4
|
+
CreateAppDir=true
|
|
5
|
+
DefaultGroupName=@PACKAGE@
|
|
6
|
+
DefaultDirName={pf}\@PACKAGE@
|
|
7
|
+
;DefaultDirName=C:
|
|
8
|
+
;Compression=lzma
|
|
9
|
+
;SolidCompression=yes
|
|
10
|
+
AllowRootDirectory=true
|
|
11
|
+
EnableDirDoesntExistWarning=false
|
|
12
|
+
UsePreviousAppDir=false
|
|
13
|
+
ShowLanguageDialog=no
|
|
14
|
+
OutputBaseFilename=@PACKAGE@-@VERSION@-win
|
|
15
|
+
VersionInfoVersion=@VERSION@
|
|
16
|
+
VersionInfoCompany=Rudi Cilibrasi
|
|
17
|
+
SourceDir=@WINBUILDDIR@
|
|
18
|
+
|
|
19
|
+
[Files]
|
|
20
|
+
Source: CompLearnLib/CompressionObject.rb; DestDir: {sd}\msys\1.0\local\lib\ruby\site_ruby\1.8; Check: MyCheck
|
|
21
|
+
Source: CompLearnLib/CompressionTask.rb; DestDir: {sd}\msys\1.0\local\lib\ruby\site_ruby\1.8; Check: MyCheck
|
|
22
|
+
Source: CompLearnLib/Config.rb; DestDir: {sd}\msys\1.0\local\lib\ruby\site_ruby\1.8; Check: MyCheck
|
|
23
|
+
Source: CompLearnLib/DistMatrix.rb; DestDir: {sd}\msys\1.0\local\lib\ruby\site_ruby\1.8; Check: MyCheck
|
|
24
|
+
Source: CompLearnLib/Tree.rb; DestDir: {sd}\msys\1.0\local\lib\ruby\site_ruby\1.8; Check: MyCheck
|
|
25
|
+
Source: CompLearnLib/Ncd.rb; DestDir: {sd}\msys\1.0\local\lib\ruby\site_ruby\1.8; Check: MyCheck
|
|
26
|
+
Source: CompLearnLib/RunEnv.rb; DestDir: {sd}\msys\1.0\local\lib\ruby\site_ruby\1.8; Check: MyCheck
|
|
27
|
+
Source: CompLearnLib/Task.rb; DestDir: {sd}\msys\1.0\local\lib\ruby\site_ruby\1.8; Check: MyCheck
|
|
28
|
+
Source: CompLearnLib/TaskMaster.rb; DestDir: {sd}\msys\1.0\local\lib\ruby\site_ruby\1.8; Check: MyCheck
|
|
29
|
+
Source: CompLearnLib/TaskMasterMPI.rb; DestDir: {sd}\msys\1.0\local\lib\ruby\site_ruby\1.8; Check: MyCheck
|
|
30
|
+
Source: CompLearnLib/TaskMasterSingle.rb; DestDir: {sd}\msys\1.0\local\lib\ruby\site_ruby\1.8; Check: MyCheck
|
|
31
|
+
Source: CompLearnLib/FoundComp.rb; DestDir: {sd}\msys\1.0\local\lib\ruby\site_ruby\1.8; Check: MyCheck
|
|
32
|
+
Source: CompLearn.so; DestDir: {sd}\msys\1.0\local\lib\ruby\site_ruby\1.8\i386-msvcrt; Check: MyCheck
|
|
33
|
+
Source: bz2.so; DestDir: {sd}\msys\1.0\local\lib\ruby\site_ruby\1.8\i386-msvcrt; Check: MyCheck
|
|
34
|
+
Source: bin/labeltree; DestDir: {sd}\msys\1.0\local; Check: MyCheck
|
|
35
|
+
Source: bin/ncdvector; DestDir: {sd}\msys\1.0\local; Check: MyCheck
|
|
36
|
+
Source: bin/maketree; DestDir: {sd}\msys\1.0\local; Check: MyCheck
|
|
37
|
+
Source: bin/ncd; DestDir: {sd}\msys\1.0\local; Check: MyCheck
|
|
38
|
+
Source: bin/ncdmatrix; DestDir: {sd}\msys\1.0\local; Check: MyCheck
|
|
39
|
+
Source: bin/makesvm; DestDir: {sd}\msys\1.0\local; Check: MyCheck
|
|
40
|
+
Source: man/man1/labeltree.1; DestDir: {sd}\msys\1.0\local; Check: MyCheck
|
|
41
|
+
Source: man/man1/ncdvector.1; DestDir: {sd}\msys\1.0\local; Check: MyCheck
|
|
42
|
+
Source: man/man1/maketree.1; DestDir: {sd}\msys\1.0\local; Check: MyCheck
|
|
43
|
+
Source: man/man1/ncd.1; DestDir: {sd}\msys\1.0\local; Check: MyCheck
|
|
44
|
+
Source: man/man1/ncdmatrix.1; DestDir: {sd}\msys\1.0\local; Check: MyCheck
|
|
45
|
+
Source: man/man1/makesvm.1; DestDir: {sd}\msys\1.0\local; Check: MyCheck
|
|
46
|
+
Source: man/man5/complearn.5; DestDir: {sd}\msys\1.0\local; Check: MyCheck
|
|
47
|
+
[Code]
|
|
48
|
+
var
|
|
49
|
+
myProgChecked: Boolean;
|
|
50
|
+
myProgResult: Boolean;
|
|
51
|
+
function MyCheck(): Boolean;
|
|
52
|
+
var
|
|
53
|
+
msysFileName: String;
|
|
54
|
+
begin
|
|
55
|
+
if not myProgChecked then begin
|
|
56
|
+
myProgChecked := True;
|
|
57
|
+
msysFileName := ExpandConstant('{sd}\msys\1.0\bin\cat.exe');
|
|
58
|
+
if FileExists(msysFileName) then
|
|
59
|
+
begin
|
|
60
|
+
msysFileName := ExpandConstant('{sd}\msys\1.0\local\lib\ruby\1.8\yaml.rb');
|
|
61
|
+
if FileExists(msysFileName) then
|
|
62
|
+
begin
|
|
63
|
+
myProgResult := True;
|
|
64
|
+
end
|
|
65
|
+
else
|
|
66
|
+
begin
|
|
67
|
+
MsgBox('You must install Ruby for MinGW/MSYS first' , mbInformation, MB_OK);
|
|
68
|
+
myProgResult := False;
|
|
69
|
+
exit
|
|
70
|
+
end
|
|
71
|
+
end
|
|
72
|
+
else
|
|
73
|
+
begin
|
|
74
|
+
MsgBox(ExpandConstant('You must install MinGW/MSYS in the default directory on {sd}') , mbInformation, MB_OK);
|
|
75
|
+
myProgResult := False;
|
|
76
|
+
exit
|
|
77
|
+
end;
|
|
78
|
+
end;
|
|
79
|
+
Result := myProgResult;
|
|
80
|
+
end;
|
|
81
|
+
[Icons]
|
|
82
|
+
;Name: {group}\NSD; Filename: {app}\nsd.exe
|
|
83
|
+
;Name: {group}\MODEEGDRIVER; Filename: {app}\modeegdriver.exe
|
|
84
|
+
Name: {group}\{cm:UninstallProgram, @PACKAGE@}; Filename: {uninstallexe}
|
|
85
|
+
[UninstallDelete]
|
|
86
|
+
;Name: {app}\modeegdriver.exe; Type: files
|
|
87
|
+
;Name: {app}\nsd.exe; Type: files
|
|
88
|
+
;Name: {app}\readedf.exe; Type: files
|
|
89
|
+
;Name: {app}\writeedf.exe; Type: files
|
|
@@ -0,0 +1,14 @@
|
|
|
1
|
+
Package: complearn
|
|
2
|
+
Version: 0.6.0-1
|
|
3
|
+
Section: science
|
|
4
|
+
Priority: optional
|
|
5
|
+
Architecture: i386
|
|
6
|
+
Depends: ruby1.8 (>= 1.8.0-1), zlib1g (>= 1.2.1-3), libbz2-1.0 (>= 1.0.2-1), libiconv-ruby1.8 (>= 1.8.1-7), libyaml-ruby1.8 (>= 1.8.1-7), libbz2-dev (>= 1.0.2-1), libtest-unit-ruby1.8 (>= 1.8.1-7), libbz2lib-ruby1.8 (>= 0.2.0-1)
|
|
7
|
+
Maintainer: Rudi Cilibrasi <cilibrar@ofb.net>
|
|
8
|
+
Description: data-compression based machine learning and data mining system
|
|
9
|
+
This package provides an implementation of compression-based learning.
|
|
10
|
+
It uses standard data compression programs like gzip, bzip2, and optionally
|
|
11
|
+
others to cluster and classify data. It has been used in bioinformatic
|
|
12
|
+
gene sequence analysis, handwritten digit recognition, language tree
|
|
13
|
+
construction, and many more. It is used in several scientific papers
|
|
14
|
+
including "Clustering by Compression" by Rudi Cilibrasi and Paul Vitanyi.
|
|
@@ -0,0 +1,23 @@
|
|
|
1
|
+
#!/bin/sh
|
|
2
|
+
WINECBUILDDIR=$HOME/.wine/c/build
|
|
3
|
+
(
|
|
4
|
+
cd /home/cilibrar/src/complearngem/complearn-0.6.2
|
|
5
|
+
#./configure --host=i586-mingw32msvc-gcc --build=i586-mingw32mwvc-gcc --program-suffix=.exe --prefix=/home/cilibrar/src/complearngem/complearn-0.6.2/scripts/buildtmp
|
|
6
|
+
./configure --enable-winbuild --prefix=/home/cilibrar/src/complearngem/complearn-0.6.2/scripts/buildtmp
|
|
7
|
+
make clean
|
|
8
|
+
make
|
|
9
|
+
make install
|
|
10
|
+
mkdir $WINECBUILDDIR/bin
|
|
11
|
+
cp /home/cilibrar/src/complearngem/complearn-0.6.2/scripts/buildtmp/bin/* $WINECBUILDDIR/bin
|
|
12
|
+
rm -rf /home/cilibrar/src/complearngem/complearn-0.6.2/scripts/buildtmp
|
|
13
|
+
cp /home/cilibrar/src/complearngem/complearn-0.6.2/scripts/CompLearn.iss $WINECBUILDDIR
|
|
14
|
+
)
|
|
15
|
+
mkdir $WINECBUILDDIR/CompLearnLib
|
|
16
|
+
cp /home/cilibrar/src/complearngem/complearn-0.6.2/ext/lib/CompLearnLib/*.rb $WINECBUILDDIR/CompLearnLib
|
|
17
|
+
cp /home/cilibrar/src/complearngem/complearn-0.6.2/ext/*.so $WINECBUILDDIR
|
|
18
|
+
cp /home/cilibrar/src/complearngem/complearn-0.6.2/ext/winbuild/*.so $WINECBUILDDIR
|
|
19
|
+
#mkdir $WINECBUILDER/ext/lib/CompLearnLib/CompressionObject.rb; DestDir: {app}\msys\1.0\local\lib\ruby\site_ruby\1.8\CompLearnLib
|
|
20
|
+
i586-mingw32msvc-strip $WINECBUILDDIR/bin/*.exe
|
|
21
|
+
i586-mingw32msvc-strip $WINECBUILDDIR/*.so
|
|
22
|
+
wineconsole ISCC.EXE c:\\build\\CompLearn.iss
|
|
23
|
+
cp $WINECBUILDDIR/Output/complearn-0.6.2-*.exe /home/cilibrar/src/complearngem/complearn-0.6.2/scripts
|
|
@@ -0,0 +1,23 @@
|
|
|
1
|
+
#!/bin/sh
|
|
2
|
+
WINECBUILDDIR=$HOME/.wine/c/build
|
|
3
|
+
(
|
|
4
|
+
cd @TOPDIR@
|
|
5
|
+
#./configure --host=i586-mingw32msvc-gcc --build=i586-mingw32mwvc-gcc --program-suffix=.exe --prefix=@TOPDIR@/scripts/buildtmp
|
|
6
|
+
./configure --enable-winbuild --prefix=@TOPDIR@/scripts/buildtmp
|
|
7
|
+
make clean
|
|
8
|
+
make
|
|
9
|
+
make install
|
|
10
|
+
mkdir $WINECBUILDDIR/bin
|
|
11
|
+
cp @TOPDIR@/scripts/buildtmp/bin/* $WINECBUILDDIR/bin
|
|
12
|
+
rm -rf @TOPDIR@/scripts/buildtmp
|
|
13
|
+
cp @TOPDIR@/scripts/CompLearn.iss $WINECBUILDDIR
|
|
14
|
+
)
|
|
15
|
+
mkdir $WINECBUILDDIR/CompLearnLib
|
|
16
|
+
cp @TOPDIR@/ext/lib/CompLearnLib/*.rb $WINECBUILDDIR/CompLearnLib
|
|
17
|
+
cp @TOPDIR@/ext/*.so $WINECBUILDDIR
|
|
18
|
+
cp @TOPDIR@/ext/winbuild/*.so $WINECBUILDDIR
|
|
19
|
+
#mkdir $WINECBUILDER/ext/lib/CompLearnLib/CompressionObject.rb; DestDir: {app}\msys\1.0\local\lib\ruby\site_ruby\1.8\CompLearnLib
|
|
20
|
+
i586-mingw32msvc-strip $WINECBUILDDIR/bin/*.exe
|
|
21
|
+
i586-mingw32msvc-strip $WINECBUILDDIR/*.so
|
|
22
|
+
wineconsole ISCC.EXE c:\\build\\CompLearn.iss
|
|
23
|
+
cp $WINECBUILDDIR/Output/@PACKAGE@-@VERSION@-*.exe @TOPDIR@/scripts
|
data/scripts/makedeb.zsh
ADDED
|
@@ -0,0 +1,46 @@
|
|
|
1
|
+
#!/bin/zsh
|
|
2
|
+
CURDIR=/home/cilibrar/src/complearngem/complearn-0.6.2/scripts
|
|
3
|
+
cd $CURDIR
|
|
4
|
+
TOPDIR=$CURDIR/..
|
|
5
|
+
INDEBCONTROLDIR=$CURDIR/debian
|
|
6
|
+
TMPDEBCONTROLDIR=$CURDIR/tmpDEBIAN
|
|
7
|
+
WORKDIR=$CURDIR/complearn-0.6.2
|
|
8
|
+
EXTDIR=$TOPDIR/ext
|
|
9
|
+
|
|
10
|
+
rm -rf $WORKDIR $WORKDIR.orig
|
|
11
|
+
|
|
12
|
+
cd $TOPDIR
|
|
13
|
+
make clean
|
|
14
|
+
echo ./configure --prefix=$WORKDIR
|
|
15
|
+
./configure --prefix=$WORKDIR
|
|
16
|
+
make
|
|
17
|
+
cd $TOPDIR/doc
|
|
18
|
+
make install
|
|
19
|
+
gzip --best $WORKDIR/man/**/*[0-9]
|
|
20
|
+
cd $TOPDIR/bin
|
|
21
|
+
make install
|
|
22
|
+
cd $TOPDIR/ext
|
|
23
|
+
mkdir $WORKDIR/usr
|
|
24
|
+
mkdir $WORKDIR/usr/lib
|
|
25
|
+
mkdir $WORKDIR/usr/lib/ruby
|
|
26
|
+
mkdir $WORKDIR/usr/lib/ruby/1.8
|
|
27
|
+
mkdir $WORKDIR/usr/lib/ruby/1.8/i386-linux
|
|
28
|
+
cp $EXTDIR/*.so $WORKDIR/usr/lib/ruby/1.8/i386-linux
|
|
29
|
+
strip -R .note -R .comment $WORKDIR/usr/lib/ruby/1.8/i386-linux/*.so
|
|
30
|
+
cp -r $EXTDIR/lib/CompLearnLib $WORKDIR/usr/lib/ruby/1.8
|
|
31
|
+
mv $WORKDIR/bin $WORKDIR/usr/bin
|
|
32
|
+
mkdir $WORKDIR/usr/share
|
|
33
|
+
mv $WORKDIR/man $WORKDIR/usr/share/man
|
|
34
|
+
cd $CURDIR
|
|
35
|
+
cp -r $INDEBCONTROLDIR $TMPDEBCONTROLDIR
|
|
36
|
+
mv $TMPDEBCONTROLDIR $WORKDIR/DEBIAN
|
|
37
|
+
mkdir $WORKDIR/usr/share/doc
|
|
38
|
+
mkdir $WORKDIR/usr/share/doc/complearn
|
|
39
|
+
cp -r $TOPDIR/doc/* $WORKDIR/usr/share/doc/complearn
|
|
40
|
+
cp -r $TOPDIR/tests $WORKDIR/usr/share/doc/complearn
|
|
41
|
+
rm -rf $WORKDIR/**/CVS
|
|
42
|
+
mv $WORKDIR/DEBIAN/changelog $WORKDIR/usr/share/doc/complearn/changelog.Debian
|
|
43
|
+
gzip --best $WORKDIR/usr/share/doc/complearn/changelog*
|
|
44
|
+
#chown -R root:root $WORKDIR/usr/share/doc
|
|
45
|
+
fakeroot dpkg -b $WORKDIR
|
|
46
|
+
rm -rf $WORKDIR
|
|
@@ -0,0 +1,46 @@
|
|
|
1
|
+
#!/bin/zsh
|
|
2
|
+
CURDIR=@TOPDIR@/scripts
|
|
3
|
+
cd $CURDIR
|
|
4
|
+
TOPDIR=$CURDIR/..
|
|
5
|
+
INDEBCONTROLDIR=$CURDIR/debian
|
|
6
|
+
TMPDEBCONTROLDIR=$CURDIR/tmpDEBIAN
|
|
7
|
+
WORKDIR=$CURDIR/@PACKAGE@-@VERSION@
|
|
8
|
+
EXTDIR=$TOPDIR/ext
|
|
9
|
+
|
|
10
|
+
rm -rf $WORKDIR $WORKDIR.orig
|
|
11
|
+
|
|
12
|
+
cd $TOPDIR
|
|
13
|
+
make clean
|
|
14
|
+
echo ./configure --prefix=$WORKDIR
|
|
15
|
+
./configure --prefix=$WORKDIR
|
|
16
|
+
make
|
|
17
|
+
cd $TOPDIR/doc
|
|
18
|
+
make install
|
|
19
|
+
gzip --best $WORKDIR/man/**/*[0-9]
|
|
20
|
+
cd $TOPDIR/bin
|
|
21
|
+
make install
|
|
22
|
+
cd $TOPDIR/ext
|
|
23
|
+
mkdir $WORKDIR/usr
|
|
24
|
+
mkdir $WORKDIR/usr/lib
|
|
25
|
+
mkdir $WORKDIR/usr/lib/ruby
|
|
26
|
+
mkdir $WORKDIR/usr/lib/ruby/1.8
|
|
27
|
+
mkdir $WORKDIR/usr/lib/ruby/1.8/i386-linux
|
|
28
|
+
cp $EXTDIR/*.so $WORKDIR/usr/lib/ruby/1.8/i386-linux
|
|
29
|
+
strip -R .note -R .comment $WORKDIR/usr/lib/ruby/1.8/i386-linux/*.so
|
|
30
|
+
cp -r $EXTDIR/lib/CompLearnLib $WORKDIR/usr/lib/ruby/1.8
|
|
31
|
+
mv $WORKDIR/bin $WORKDIR/usr/bin
|
|
32
|
+
mkdir $WORKDIR/usr/share
|
|
33
|
+
mv $WORKDIR/man $WORKDIR/usr/share/man
|
|
34
|
+
cd $CURDIR
|
|
35
|
+
cp -r $INDEBCONTROLDIR $TMPDEBCONTROLDIR
|
|
36
|
+
mv $TMPDEBCONTROLDIR $WORKDIR/DEBIAN
|
|
37
|
+
mkdir $WORKDIR/usr/share/doc
|
|
38
|
+
mkdir $WORKDIR/usr/share/doc/@PACKAGE@
|
|
39
|
+
cp -r $TOPDIR/doc/* $WORKDIR/usr/share/doc/@PACKAGE@
|
|
40
|
+
cp -r $TOPDIR/tests $WORKDIR/usr/share/doc/@PACKAGE@
|
|
41
|
+
rm -rf $WORKDIR/**/CVS
|
|
42
|
+
mv $WORKDIR/DEBIAN/changelog $WORKDIR/usr/share/doc/@PACKAGE@/changelog.Debian
|
|
43
|
+
gzip --best $WORKDIR/usr/share/doc/@PACKAGE@/changelog*
|
|
44
|
+
#chown -R root:root $WORKDIR/usr/share/doc
|
|
45
|
+
fakeroot dpkg -b $WORKDIR
|
|
46
|
+
rm -rf $WORKDIR
|