1. mzR
  2. checkoutpwiz.sh
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
Showing 1 changed files
checkoutpwiz.sh
History View file @ a02f5ad5b3
... ... 
@@ -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 $DIR
17 20 
 done
18 21
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+cd ..
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+
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 #------------------
20 25
21 
-cd ..
22 26 
 rm -rf boost
23 
-mkdir boost
24 
-cd boost
25 27
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-BOOSTVER=Boost_1_55_0
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-BOOSTREPO=http://svn.boost.org/svn/boost/tags/release/$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
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-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\
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
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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
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 #------------------
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... ... 
@@ -55,14 +45,19 @@ svn co $PWIZBOOSTREPO boost
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 cd ..
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57 47 
 #------------------
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+fi
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+#------------------
58 50
59 51
60 52 
 PWIZ_MAJOR=$(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
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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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-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 ${revisioninfo[*]}
66 61
67 62 
 cat >pwiz/data/msdata/Version.cpp <<EOF
68 63 
 // This file was generated by the \"svnrev\" utility
... ... 
@@ -103,3 +98,52 @@ string Version::str()
103 98 
 EOF
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105 100 
 #------------------
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+
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+
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+PWIZ_MAJOR=$(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
Showing 1 changed files
checkoutpwiz.sh
History View file @ 94d4ecf589
... ... 
@@ -12,7 +12,7 @@ cd pwiz
12 12 
 PWIZREPO=http://svn.code.sf.net/p/proteowizard/code/trunk/pwiz/
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 svn co --non-recursive $PWIZREPO .
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-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
16 16 
     svn co $PWIZREPO/pwiz/$DIR $DIR
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 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
36 36 
     svn co $BOOSTREPO/$DIR $DIR
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 done
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-
38 
+
39 39 
 BOOSTLIBSREPO=http://svn.boost.org/svn/boost/tags/release/$BOOSTVER/libs
40 
-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
Showing 1 changed files
checkoutpwiz.sh
History View file @ 53fd2127eb
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
Showing 1 changed files
checkoutpwiz.sh
History View file @ 5b27a21e30
... ... 
@@ -9,7 +9,7 @@ rm -rf pwiz
9 9 
 mkdir pwiz
10 10 
 cd pwiz
11 11
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-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/
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 svn co --non-recursive $PWIZREPO .
14 14
15 15 
 for DIR in data/msdata data/common utility/chemistry/ utility/misc/ utility/math/ utility/minimxml/ ; do
... ... 
@@ -23,15 +23,16 @@ rm -rf boost
23 23 
 mkdir boost
24 24 
 cd boost
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-BOOSTVER=Boost_1_43_0
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+BOOSTVER=Boost_1_55_0
27 27 
 BOOSTREPO=http://svn.boost.org/svn/boost/tags/release/$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
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 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/
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 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
Showing 1 changed files
checkoutpwiz.sh
History View file @ bcff5d52a8
1 1 
new file mode 100755
... ... 
@@ -0,0 +1,104 @@
1 
+#!/bin/bash
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+#------------------
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+
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+# 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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+
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+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 $DIR
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+done
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+
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+#------------------
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+
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+cd ..
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+rm -rf boost
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+mkdir boost
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+cd boost
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+
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+BOOSTVER=Boost_1_43_0
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+BOOSTREPO=http://svn.boost.org/svn/boost/tags/release/$BOOSTVER/boost
28 
+
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+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
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+    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 $PWIZBOOSTREPO boost
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+
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+cd ..
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+
56 
+#------------------
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+
58 
+
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+PWIZ_MAJOR=$(grep "constant PWIZ_MAJOR" pwiz/Jamroot.jam | sed -e 's/constant PWIZ_MAJOR : \([0-9+]\) ;/\1/')
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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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+
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 
+//
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+
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+#define PWIZ_SOURCE
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+#include "Version.hpp"
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+#include <sstream>
77 
+
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+#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${revisioninfo[1]};}
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+string Version::LastModified()      {return "${revisioninfo[2]}-${revisioninfo[3]}-${revisioninfo[4]}";}
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+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 
+#------------------