Browse code

Switch to boost 1.58.0

From: Steffen Neumann <sneumann@ipb-halle.de>

git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/mzR@125186 bc3139a8-67e5-0310-9ffc-ced21a209358

l.gatto authored on 15/12/2016 10:53:18
Showing1 changed files
... ...
@@ -5,6 +5,9 @@
5 5
 
6 6
 cd src
7 7
 
8
+if /bin/false ; then
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+#------------------
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+    
8 11
 rm -rf pwiz
9 12
 mkdir pwiz
10 13
 cd pwiz
... ...
@@ -16,32 +19,19 @@ for DIR in data/msdata data/identdata data/proteome data/common utility/chemistr
16 19
     svn co $PWIZREPO/pwiz/$DIR $DIR
17 20
 done
18 21
 
22
+cd ..
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+
19 24
 #------------------
20 25
 
21
-cd ..
22 26
 rm -rf boost
23
-mkdir boost
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-cd boost
25 27
 
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-BOOSTVER=Boost_1_55_0
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-BOOSTREPO=http://svn.boost.org/svn/boost/tags/release/$BOOSTVER/boost
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+BOOSTVER=1_58_0
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+BOOSTVERDOT=1.58.0
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+BOOSTURL=https://freefr.dl.sourceforge.net/project/boost/boost/$BOOSTVERDOT/boost_$BOOSTVER.tar.gz
28 31
 
29
-svn co --non-recursive $BOOSTREPO .
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+wget -O- "$BOOSTURL" | tar xzvf -
30 33
 
31
-for DIR in smart_ptr  config config mpl detail iostreams exception function_types \
32
-    io type_traits preprocessor format algorithm logic optional range numeric math\
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-    iterator function utility concept bind regex filesystem system thread container\
34
-    date_time lambda proto typeof fusion spirit tuple multi_index serialization\
35
-    ratio chrono atomic move variant archive functional integer locale predef ; do 
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-    svn co $BOOSTREPO/$DIR $DIR
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-done
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-
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-BOOSTLIBSREPO=http://svn.boost.org/svn/boost/tags/release/$BOOSTVER/libs
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-for DIR in chrono/src iostreams/src thread/src/pthread/ filesystem/src/ regex/src system/src ; do 
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-    svn co $BOOSTLIBSREPO/$DIR $DIR
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-done
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-
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-cd ..
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+mv boost_$BOOSTVER boost
45 35
            
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 #------------------
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... ...
@@ -55,14 +45,19 @@ svn co $PWIZBOOSTREPO boost
55 45
 cd ..
56 46
 
57 47
 #------------------
48
+fi 
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+#------------------
58 50
 
59 51
 
60 52
 PWIZ_MAJOR=$(grep "constant PWIZ_MAJOR" pwiz/Jamroot.jam | sed -e 's/constant PWIZ_MAJOR : \([0-9+]\) ;/\1/')
61 53
 PWIZ_MINOR=$(grep "constant PWIZ_MINOR" pwiz/Jamroot.jam | sed -e 's/constant PWIZ_MINOR : \([0-9+]\) ;/\1/')
62 54
 
63
-lastchangedrev=$(svn info pwiz/data/msdata | grep "Last Changed Rev:" | cut -d: -f 2)
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-lastchangeddate=$(svn info pwiz/data/msdata | grep "Last Changed Date:" | cut -d" " -f 4 | tr "-" " ")
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-revisioninfo="($lastchangedrev $lastchangeddate)"
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+#lastchangedrev=$(svn info pwiz/data/msdata | grep "Last Changed Rev:" | cut -d: -f 2)
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+#lastchangeddate=$(svn info pwiz/data/msdata | grep "Last Changed Date:" | cut -d" " -f 4 | tr "-" " ")
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+lastchangedrev=666
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+lastchangeddate="1016-03-22"
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+revisioninfo=( $lastchangedrev $lastchangeddate 3 4 )
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+echo ${revisioninfo[*]}
66 61
 
67 62
 cat >pwiz/data/msdata/Version.cpp <<EOF
68 63
 // This file was generated by the \"svnrev\" utility
... ...
@@ -103,3 +98,52 @@ string Version::str()
103 98
 EOF
104 99
 
105 100
 #------------------
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+
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+
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+PWIZ_MAJOR=$(grep "constant PWIZ_MAJOR" pwiz/Jamroot.jam | sed -e 's/constant PWIZ_MAJOR : \([0-9+]\) ;/\1/')
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+PWIZ_MINOR=$(grep "constant PWIZ_MINOR" pwiz/Jamroot.jam | sed -e 's/constant PWIZ_MINOR : \([0-9+]\) ;/\1/')
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+
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+#lastchangedrev=$(svn info pwiz/data/msdata | grep "Last Changed Rev:" | cut -d: -f 2)
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+#lastchangeddate=$(svn info pwiz/data/msdata | grep "Last Changed Date:" | cut -d" " -f 4 | tr "-" " ")
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+lastchangedrev=666
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+lastchangeddate="1016-03-22"
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+revisioninfo=( $lastchangedrev $lastchangeddate 3 4 )
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+echo ${revisioninfo[*]}
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+
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+cat >pwiz/data/identdata/Version.cpp <<EOF
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+// This file was generated by the \"svnrev\" utility
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+// You should not modify it manually, as it may be re-generated.
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+//
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+// $Revision: ${revisioninfo[1]} $
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+// $Date: ${revisioninfo[2]}-${revisioninfo[3]}-${revisioninfo[4]} $
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+//
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+
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+#define PWIZ_SOURCE
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+#include "Version.hpp"
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+#include <sstream>
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+
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+#ifdef PWIZ_USER_VERSION_INFO_H // in case you need to add any info version of your own
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+#include PWIZ_USER_VERSION_INFO_H  // must define PWIZ_USER_VERSION_INFO_H_STR for use below
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+#endif
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+
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+namespace pwiz {
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+namespace identdata {
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+
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+using std::string;
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+
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+int Version::Major()                {return 0${PWIZ_MAJOR};}
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+int Version::Minor()                {return 0${PWIZ_MINOR};}
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+int Version::Revision()             {return 0${revisioninfo[1]};}
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+string Version::LastModified()      {return "${revisioninfo[2]}-${revisioninfo[3]}-${revisioninfo[4]}";}
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+string Version::str()               
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+{
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+	std::ostringstream v;
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+	v << Major() << '.' << Minor() << '.' << Revision();
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+#ifdef PWIZ_USER_VERSION_INFO_H
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+	v << " (" << PWIZ_USER_VERSION_INFO_H_STR << ")";
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+#endif
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+	return v.str();
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+}
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+}
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+}
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+EOF
Browse code

checkout latest pwiz, ammend Makevars

From: Laurent <lg390@cam.ac.uk>

git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/mzR@125180 bc3139a8-67e5-0310-9ffc-ced21a209358

l.gatto authored on 15/12/2016 10:21:41
Showing1 changed files
... ...
@@ -12,7 +12,7 @@ cd pwiz
12 12
 PWIZREPO=http://svn.code.sf.net/p/proteowizard/code/trunk/pwiz/
13 13
 svn co --non-recursive $PWIZREPO .
14 14
 
15
-for DIR in data/msdata data/common utility/chemistry/ utility/misc/ utility/math/ utility/minimxml/ ; do 
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+for DIR in data/msdata data/identdata data/proteome data/common utility/chemistry/ utility/misc/ utility/math/ utility/minimxml/ ; do 
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     svn co $PWIZREPO/pwiz/$DIR $DIR
17 17
 done
18 18
 
... ...
@@ -35,9 +35,9 @@ for DIR in smart_ptr  config config mpl detail iostreams exception function_type
35 35
     ratio chrono atomic move variant archive functional integer locale predef ; do 
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     svn co $BOOSTREPO/$DIR $DIR
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 done
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-       
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+
39 39
 BOOSTLIBSREPO=http://svn.boost.org/svn/boost/tags/release/$BOOSTVER/libs
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-for DIR in iostreams/src thread/src/pthread/ filesystem/src/ regex/src system/src ; do 
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+for DIR in chrono/src iostreams/src thread/src/pthread/ filesystem/src/ regex/src system/src ; do 
41 41
     svn co $BOOSTLIBSREPO/$DIR $DIR
42 42
 done
43 43
 
Browse code

merge master

From: Laurent <lg390@cam.ac.uk>

git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/mzR@113918 bc3139a8-67e5-0310-9ffc-ced21a209358

l.gatto authored on 23/02/2016 00:45:13
Showing1 changed files
1 1
old mode 100755
2 2
new mode 100644
Browse code

Mavericks support

git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/mzR@90716 bc3139a8-67e5-0310-9ffc-ced21a209358

l.gatto authored on 26/05/2014 19:55:15
Showing1 changed files
... ...
@@ -9,7 +9,7 @@ rm -rf pwiz
9 9
 mkdir pwiz
10 10
 cd pwiz
11 11
 
12
-PWIZREPO=http://proteowizard.svn.sourceforge.net/svnroot/proteowizard/trunk/pwiz/
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+PWIZREPO=http://svn.code.sf.net/p/proteowizard/code/trunk/pwiz/
13 13
 svn co --non-recursive $PWIZREPO .
14 14
 
15 15
 for DIR in data/msdata data/common utility/chemistry/ utility/misc/ utility/math/ utility/minimxml/ ; do 
... ...
@@ -23,15 +23,16 @@ rm -rf boost
23 23
 mkdir boost
24 24
 cd boost
25 25
 
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-BOOSTVER=Boost_1_43_0
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+BOOSTVER=Boost_1_55_0
27 27
 BOOSTREPO=http://svn.boost.org/svn/boost/tags/release/$BOOSTVER/boost
28 28
 
29 29
 svn co --non-recursive $BOOSTREPO .
30 30
 
31 31
 for DIR in smart_ptr  config config mpl detail iostreams exception function_types \
32
-    io type_traits preprocessor format algorithm logic optional range \
33
-    iterator function utility concept bind regex filesystem system thread \
34
-    date_time lambda  tuple multi_index serialization archive functional integer ; do 
32
+    io type_traits preprocessor format algorithm logic optional range numeric math\
33
+    iterator function utility concept bind regex filesystem system thread container\
34
+    date_time lambda proto typeof fusion spirit tuple multi_index serialization\
35
+    ratio chrono atomic move variant archive functional integer locale predef ; do 
35 36
     svn co $BOOSTREPO/$DIR $DIR
36 37
 done
37 38
        
... ...
@@ -48,7 +49,7 @@ rm -rf boost_aux
48 49
 mkdir boost_aux
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 cd boost_aux
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-PWIZBOOSTREPO=http://proteowizard.svn.sourceforge.net/svnroot/proteowizard/trunk/pwiz/libraries/boost_aux/boost/
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+PWIZBOOSTREPO=http://svn.code.sf.net/p/proteowizard/code/trunk/pwiz/libraries/boost_aux/boost/
52 53
 svn co $PWIZBOOSTREPO boost
53 54
 
54 55
 cd ..
Browse code

Added the mzR package to the repository.

git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/mzR@57456 bc3139a8-67e5-0310-9ffc-ced21a209358

c.wong authored on 15/08/2011 19:53:29
Showing1 changed files
1 1
new file mode 100755
... ...
@@ -0,0 +1,104 @@
1
+#!/bin/bash 
2
+#------------------
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+
4
+# http://proteowizard.svn.sourceforge.net/viewvc/proteowizard/trunk/pwiz/libraries/boost_aux/boost/utility/
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+
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+cd src
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+
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+rm -rf pwiz
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+mkdir pwiz
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+cd pwiz
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+
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+PWIZREPO=http://proteowizard.svn.sourceforge.net/svnroot/proteowizard/trunk/pwiz/
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+svn co --non-recursive $PWIZREPO .
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+
15
+for DIR in data/msdata data/common utility/chemistry/ utility/misc/ utility/math/ utility/minimxml/ ; do 
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+    svn co $PWIZREPO/pwiz/$DIR $DIR
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+done
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+
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+#------------------
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+
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+cd ..
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+rm -rf boost
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+mkdir boost
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+cd boost
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+
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+BOOSTVER=Boost_1_43_0
27
+BOOSTREPO=http://svn.boost.org/svn/boost/tags/release/$BOOSTVER/boost
28
+
29
+svn co --non-recursive $BOOSTREPO .
30
+
31
+for DIR in smart_ptr  config config mpl detail iostreams exception function_types \
32
+    io type_traits preprocessor format algorithm logic optional range \
33
+    iterator function utility concept bind regex filesystem system thread \
34
+    date_time lambda  tuple multi_index serialization archive functional integer ; do 
35
+    svn co $BOOSTREPO/$DIR $DIR
36
+done
37
+       
38
+BOOSTLIBSREPO=http://svn.boost.org/svn/boost/tags/release/$BOOSTVER/libs
39
+for DIR in iostreams/src thread/src/pthread/ filesystem/src/ regex/src system/src ; do 
40
+    svn co $BOOSTLIBSREPO/$DIR $DIR
41
+done
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+
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+cd ..
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+           
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+#------------------
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+
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+rm -rf boost_aux
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+mkdir boost_aux
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+cd boost_aux
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+
51
+PWIZBOOSTREPO=http://proteowizard.svn.sourceforge.net/svnroot/proteowizard/trunk/pwiz/libraries/boost_aux/boost/
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+svn co $PWIZBOOSTREPO boost
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+
54
+cd ..
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+
56
+#------------------
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+
58
+
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+PWIZ_MAJOR=$(grep "constant PWIZ_MAJOR" pwiz/Jamroot.jam | sed -e 's/constant PWIZ_MAJOR : \([0-9+]\) ;/\1/')
60
+PWIZ_MINOR=$(grep "constant PWIZ_MINOR" pwiz/Jamroot.jam | sed -e 's/constant PWIZ_MINOR : \([0-9+]\) ;/\1/')
61
+
62
+lastchangedrev=$(svn info pwiz/data/msdata | grep "Last Changed Rev:" | cut -d: -f 2)
63
+lastchangeddate=$(svn info pwiz/data/msdata | grep "Last Changed Date:" | cut -d" " -f 4 | tr "-" " ")
64
+revisioninfo="($lastchangedrev $lastchangeddate)"
65
+
66
+cat >pwiz/data/msdata/Version.cpp <<EOF
67
+// This file was generated by the \"svnrev\" utility
68
+// You should not modify it manually, as it may be re-generated.
69
+//
70
+// $Revision: ${revisioninfo[1]} $
71
+// $Date: ${revisioninfo[2]}-${revisioninfo[3]}-${revisioninfo[4]} $
72
+//
73
+
74
+#define PWIZ_SOURCE
75
+#include "Version.hpp"
76
+#include <sstream>
77
+
78
+#ifdef PWIZ_USER_VERSION_INFO_H // in case you need to add any info version of your own
79
+#include PWIZ_USER_VERSION_INFO_H  // must define PWIZ_USER_VERSION_INFO_H_STR for use below
80
+#endif
81
+
82
+namespace pwiz {
83
+namespace msdata {
84
+
85
+using std::string;
86
+
87
+int Version::Major()                {return 0${PWIZ_MAJOR};}
88
+int Version::Minor()                {return 0${PWIZ_MINOR};}
89
+int Version::Revision()             {return 0${revisioninfo[1]};}
90
+string Version::LastModified()      {return "${revisioninfo[2]}-${revisioninfo[3]}-${revisioninfo[4]}";}
91
+string Version::str()               
92
+{
93
+	std::ostringstream v;
94
+	v << Major() << '.' << Minor() << '.' << Revision();
95
+#ifdef PWIZ_USER_VERSION_INFO_H
96
+	v << " (" << PWIZ_USER_VERSION_INFO_H_STR << ")";
97
+#endif
98
+	return v.str();
99
+}
100
+}
101
+}
102
+EOF
103
+
104
+#------------------