[med-svn] [Git][med-team/beast2-mcmc][master] 3 commits: Removing jsign from the build as it is needed for Microsoft Windows
Pierre Gruet
gitlab at salsa.debian.org
Tue Sep 15 09:52:12 BST 2020
Pierre Gruet pushed to branch master at Debian Med / beast2-mcmc
Commits:
fa097dde by Pierre Gruet at 2020-09-15T10:50:02+02:00
Removing jsign from the build as it is needed for Microsoft Windows
- - - - -
d59e3317 by Pierre Gruet at 2020-09-15T10:50:51+02:00
Deleting accents in MCMC.java as they caused build failures
- - - - -
5563694f by Pierre Gruet at 2020-09-15T10:51:51+02:00
Removing the import of useless and unpackaged org.fest.swing.security
- - - - -
4 changed files:
- + debian/patches/accents_in_source.patch
- + debian/patches/remove_import_swing_security.patch
- + debian/patches/remove_jsign_from_build.patch
- debian/patches/series
Changes:
=====================================
debian/patches/accents_in_source.patch
=====================================
@@ -0,0 +1,22 @@
+Description: Removing accents on names in a Java annotation
+ Those accents caused build failures as javac tried to encode US-ASCII but
+ could not.
+Author: Pierre Gruet <pgtdebian at free.fr>
+Forwarded: not-needed
+Last-Update: 2020-09-15
+
+--- a/src/beast/core/MCMC.java
++++ b/src/beast/core/MCMC.java
+@@ -49,9 +49,9 @@
+ // " evolutionary analysis. PLoS Computational Biology 10(4): e1003537"
+ // , year = 2014, firstAuthorSurname = "bouckaert",
+ // DOI="10.1371/journal.pcbi.1003537")
+- at Citation(value="Bouckaert, Remco, Timothy G. Vaughan, Joëlle Barido-Sottani, Sebastián Duchêne, Mathieu Fourment, \n"
+- + "Alexandra Gavryushkina, Joseph Heled, Graham Jones, Denise Kühnert, Nicola De Maio, Michael Matschiner, \n"
+- + "Fábio K. Mendes, Nicola F. Müller, Huw A. Ogilvie, Louis du Plessis, Alex Popinga, Andrew Rambaut, \n"
++ at Citation(value="Bouckaert, Remco, Timothy G. Vaughan, Joelle Barido-Sottani, Sebastian Duchene, Mathieu Fourment, \n"
++ + "Alexandra Gavryushkina, Joseph Heled, Graham Jones, Denise Kuhnert, Nicola De Maio, Michael Matschiner, \n"
++ + "Fabio K. Mendes, Nicola F. Muller, Huw A. Ogilvie, Louis du Plessis, Alex Popinga, Andrew Rambaut, \n"
+ + "David Rasmussen, Igor Siveroni, Marc A. Suchard, Chieh-Hsi Wu, Dong Xie, Chi Zhang, Tanja Stadler, \n"
+ + "Alexei J. Drummond \n"
+ + " BEAST 2.5: An advanced software platform for Bayesian evolutionary analysis. \n"
=====================================
debian/patches/remove_import_swing_security.patch
=====================================
@@ -0,0 +1,17 @@
+Description: Remove import of unused org.fest.swing.security package
+ The ExitException class form this package is not used, instead ExitException
+ if defined in the file as an override of java.lang.SecurityException.
+Author: Pierre Gruet <pgtdebian at free.fr>
+Forwarded: https://github.com/CompEvol/beast2/issues/921
+Last-Update: 2020-09-15
+
+--- a/src/test/beast/integration/ExampleXmlParsingTest.java
++++ b/src/test/beast/integration/ExampleXmlParsingTest.java
+@@ -9,7 +9,6 @@
+ import java.util.ArrayList;
+ import java.util.List;
+
+-import org.fest.swing.security.ExitException;
+ import org.junit.Test;
+
+ import beast.app.beastapp.BeastMain;
=====================================
debian/patches/remove_jsign_from_build.patch
=====================================
@@ -0,0 +1,199 @@
+Description: net.jsign is used for WIndows releases, removing it from build.xml
+Author: Pierre Gruet <pgtdebian at free.fr>
+Forwarded: not-needed
+Last-Update: 2020-09-15
+
+--- a/build.xml
++++ b/build.xml
+@@ -293,8 +293,6 @@
+ <property name="Windows_package_dir" value="${Windows_dir}/${BEAST_name}" />
+
+
+- <taskdef name="jsign" classname="net.jsign.JsignTask" classpath="${lib}/jsign-3.1.jar"/>
+-
+ <!-- Need to either install Launch4j under {BEAST workspace}/${release}
+ or install it in the default directory and change the location of launch4j.dir -->
+ <!--depends="build_jar_all_BEAST_NoJUnitTest"-->
+@@ -365,31 +363,6 @@
+ -->
+ </launch4j>
+
+-<jsign file="${Windows_package_dir}/${BEAUti_name}.exe"
+- name="BEAUti"
+- url="http://beast2.org"
+- keystore="keystore.pfx"
+- alias="http://beast2.org"
+- storepass="${storepass}"
+- tsaurl="http://timestamp.comodoca.com/authenticode"/>
+-
+- <!-- BEAST v?.?.?.exe -->
+- <launch4j configFile="${Windows_dir}/BEAST_launch4j.xml"
+- jar="${dist}/launcher.jar"
+- outfile="${Windows_package_dir}/${BEAST_name}.exe"
+- fileVersion="${version_number}.0"
+- txtFileVersion="${version}"
+- productVersion="${version_number}.0"
+- txtProductVersion="${version}" />
+-
+-<jsign file="${Windows_package_dir}/${BEAST_name}.exe"
+- name="BEAST"
+- url="http://beast2.org"
+- keystore="keystore.pfx"
+- alias="http://beast2.org"
+- storepass="${storepass}"
+- tsaurl="http://timestamp.comodoca.com/authenticode"/>
+-
+ <!--<launch4j configFile="${Windows_dir}/TreeStat_launch4j.xml"
+ jar="${dist}/beast.jar"
+ outfile="${Windows_package_dir}/${TreeStat_name}.exe"
+@@ -415,14 +388,6 @@
+ productVersion="${version_number}.0"
+ txtProductVersion="${version}"/>
+
+-<jsign file="${Windows_package_dir}/${LogCombiner_name}.exe"
+- name="LogCombiner"
+- url="http://beast2.org"
+- keystore="keystore.pfx"
+- alias="http://beast2.org"
+- storepass="${storepass}"
+- tsaurl="http://timestamp.comodoca.com/authenticode"/>
+-
+ <launch4j configFile="${Windows_dir}/TreeAnnotator_launch4j.xml"
+ jar="${dist}/launcher.jar"
+ outfile="${Windows_package_dir}/TreeAnnotator.exe"
+@@ -431,14 +396,6 @@
+ productVersion="${version_number}.0"
+ txtProductVersion="${version}"/>
+
+-<jsign file="${Windows_package_dir}/TreeAnnotator.exe"
+- name="TreeAnnotator"
+- url="http://beast2.org"
+- keystore="keystore.pfx"
+- alias="http://beast2.org"
+- storepass="${storepass}"
+- tsaurl="http://timestamp.comodoca.com/authenticode"/>
+-
+ <launch4j configFile="${tools_dir}/DensiTree_launch4j.xml"
+ jar="${tools_dir}/DensiTree.jar"
+ outfile="${Windows_package_dir}/DensiTree.exe"
+@@ -447,15 +404,6 @@
+ productVersion="2.0.0.0"
+ txtProductVersion="2.0.0.0" />
+
+-<jsign file="${Windows_package_dir}/DensiTree.exe"
+- name="DensiTree"
+- url="http://beast2.org"
+- keystore="keystore.pfx"
+- alias="http://beast2.org"
+- storepass="${storepass}"
+- tsaurl="http://timestamp.comodoca.com/authenticode"/>
+-
+-
+ <launch4j configFile="${Windows_dir}/AppLauncher_launch4j.xml"
+ jar="${dist}/launcher.jar"
+ outfile="${Windows_package_dir}/AppLauncher.exe"
+@@ -464,14 +412,6 @@
+ productVersion="${version_number}.0"
+ txtProductVersion="${version}"/>
+
+-<jsign file="${Windows_package_dir}/AppLauncher.exe"
+- name="AppLauncher"
+- url="http://beast2.org"
+- keystore="keystore.pfx"
+- alias="http://beast2.org"
+- storepass="${storepass}"
+- tsaurl="http://timestamp.comodoca.com/authenticode"/>
+-
+ <copy todir="${Windows_package_dir}/templates/">
+ <fileset dir="templates/" />
+ </copy>
+@@ -559,14 +499,6 @@
+ -->
+ </launch4j>
+
+- <jsign file="${Windows_package_dir}/${BEAUti_name}.exe"
+- name="BEAUti"
+- url="http://beast2.org"
+- keystore="keystore.pfx"
+- alias="http://beast2.org"
+- storepass="${storepass}"
+- tsaurl="http://timestamp.comodoca.com/authenticode"/>
+-
+ <!-- BEAST v?.?.?.exe -->
+ <launch4j configFile="${Windows_dir}/BEAST_launch4j_jre.xml"
+ jar="${dist}/launcher.jar"
+@@ -576,14 +508,6 @@
+ productVersion="${version_number}.0"
+ txtProductVersion="${version}" />
+
+- <jsign file="${Windows_package_dir}/${BEAST_name}.exe"
+- name="BEAST"
+- url="http://beast2.org"
+- keystore="keystore.pfx"
+- alias="http://beast2.org"
+- storepass="${storepass}"
+- tsaurl="http://timestamp.comodoca.com/authenticode"/>
+-
+ <!--<launch4j configFile="${Windows_dir}/TreeStat_launch4j.xml"
+ jar="${dist}/beast.jar"
+ outfile="${Windows_package_dir}/${TreeStat_name}.exe"
+@@ -609,14 +533,6 @@
+ productVersion="${version_number}.0"
+ txtProductVersion="${version}"/>
+
+- <jsign file="${Windows_package_dir}/${LogCombiner_name}.exe"
+- name="LogCombiner"
+- url="http://beast2.org"
+- keystore="keystore.pfx"
+- alias="http://beast2.org"
+- storepass="${storepass}"
+- tsaurl="http://timestamp.comodoca.com/authenticode"/>
+-
+ <launch4j configFile="${Windows_dir}/TreeAnnotator_launch4j_jre.xml"
+ jar="${dist}/launcher.jar"
+ outfile="${Windows_package_dir}/TreeAnnotator.exe"
+@@ -625,14 +541,6 @@
+ productVersion="${version_number}.0"
+ txtProductVersion="${version}"/>
+
+- <jsign file="${Windows_package_dir}/TreeAnnotator.exe"
+- name="TreeAnnotator"
+- url="http://beast2.org"
+- keystore="keystore.pfx"
+- alias="http://beast2.org"
+- storepass="${storepass}"
+- tsaurl="http://timestamp.comodoca.com/authenticode"/>
+-
+ <launch4j configFile="${tools_dir}/DensiTree_launch4j_jre.xml"
+ jar="${tools_dir}/DensiTree.jar"
+ outfile="${Windows_package_dir}/DensiTree.exe"
+@@ -641,14 +549,6 @@
+ productVersion="2.0.0.0"
+ txtProductVersion="2.0.0.0" />
+
+- <jsign file="${Windows_package_dir}/DensiTree.exe"
+- name="DensiTree"
+- url="http://beast2.org"
+- keystore="keystore.pfx"
+- alias="http://beast2.org"
+- storepass="${storepass}"
+- tsaurl="http://timestamp.comodoca.com/authenticode"/>
+-
+ <launch4j configFile="${Windows_dir}/AppLauncher_launch4j_jre.xml"
+ jar="${dist}/launcher.jar"
+ outfile="${Windows_package_dir}/AppLauncher.exe"
+@@ -657,14 +557,6 @@
+ productVersion="${version_number}.0"
+ txtProductVersion="${version}"/>
+
+- <jsign file="${Windows_package_dir}/AppLauncher.exe"
+- name="AppLauncher"
+- url="http://beast2.org"
+- keystore="keystore.pfx"
+- alias="http://beast2.org"
+- storepass="${storepass}"
+- tsaurl="http://timestamp.comodoca.com/authenticode"/>
+-
+
+ <copy todir="${Windows_package_dir}/templates/">
+ <fileset dir="templates/" />
=====================================
debian/patches/series
=====================================
@@ -4,3 +4,6 @@ remove_appbundler.patch
# revert_NewickLexer.java_to_antlr_4.5.patch
antlr-compatibility.patch
remove_mac_only_code.patch
+remove_jsign_from_build.patch
+accents_in_source.patch
+remove_import_swing_security.patch
View it on GitLab: https://salsa.debian.org/med-team/beast2-mcmc/-/compare/98151f7c6e58952310a65305316015b227ca4962...5563694f37e510a88cd1af59e7f74c548b4983eb
--
View it on GitLab: https://salsa.debian.org/med-team/beast2-mcmc/-/compare/98151f7c6e58952310a65305316015b227ca4962...5563694f37e510a88cd1af59e7f74c548b4983eb
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