[med-svn] [Git][med-team/ngs-sdk][upstream] New upstream version 2.10.9

Andreas Tille gitlab at salsa.debian.org
Sun Jan 17 18:13:41 GMT 2021



Andreas Tille pushed to branch upstream at Debian Med / ngs-sdk


Commits:
297264b3 by Andreas Tille at 2021-01-17T18:52:44+01:00
New upstream version 2.10.9
- - - - -


25 changed files:

- CHANGES.md
- ngs-bam/Makefile.vers
- ngs-bam/configure
- ngs-bam/setup/konfigure.perl
- ngs-java/Makefile.vers
- ngs-java/build.xml
- ngs-java/configure
- ngs-java/examples/Makefile
- ngs-java/gov/nih/nlm/ncbi/ngs/LibDependencies.java
- ngs-java/gov/nih/nlm/ncbi/ngs/LibVersionChecker.java
- ngs-java/setup/konfigure.perl
- ngs-python/Makefile.python
- ngs-python/Makefile.vers
- ngs-python/configure
- ngs-python/examples/Makefile
- ngs-python/examples/NGS_FastQ.py
- ngs-python/setup.py
- ngs-python/setup/konfigure.perl
- ngs-sdk/Makefile.vers
- ngs-sdk/configure
- ngs-sdk/dispatch/version.h
- ngs-sdk/examples/Makefile
- ngs-sdk/ngs/itf/Refcount.hpp
- ngs-sdk/setup/konfigure.perl
- ngs-sdk/win/vs2017/ngs-test.vcxproj


Changes:

=====================================
CHANGES.md
=====================================
@@ -1,10 +1,23 @@
 # NCBI External Developer Release:
 
 
+## NGS SDK 2.10.9
+**December 16, 2020**
+
+  **build**: added configure option to produce build in output directory relative to sources  
+  **ngs**: created NGS release 2.10.8 Linux tarball from build of the libraries by gcc-7.3.0  
+
+
+## NGS SDK 2.10.8
+**June 29, 2020**
+
+  **ngs**: changed version to match that of _ncbi-vdb_
+
+
 ## NGS SDK 2.10.5
 **April 1, 2020**
 
-  **ncbi-vdb, ngs, ngs-tools, sra-tools**: all Linux builds now use g++ 7.3 (C++11 ABI)
+  **ngs, ncbi-vdb, sra-tools, ngs-tools**: all Linux builds now use g++ 7.3 (C++11 ABI)
 
 
 ## NGS SDK 2.10.4


=====================================
ngs-bam/Makefile.vers
=====================================
@@ -23,4 +23,4 @@
 # ===========================================================================
 
 # NGS-BAM and library version
-VERSION = 2.10.5
+VERSION = 2.10.9


=====================================
ngs-bam/configure
=====================================
@@ -41,5 +41,5 @@ else
         echo >&2 "configure: error: perl not found."; exit 1; }
 
     cd $CURDIR/setup
-    perl  konfigure.perl "$@"
+    perl konfigure.perl "$@"
 fi


=====================================
ngs-bam/setup/konfigure.perl
=====================================
@@ -86,6 +86,7 @@ my @options = ( 'build-prefix=s',
                 'help',
                 'prefix=s',
                 'reconfigure',
+                'relative-build-out-dir',
                 'status',
                 'with-debug',
                 'without-debug', );
@@ -136,11 +137,12 @@ EndText
 }
 
 $OPT{'local-build-out'} = $LOCAL_BUILD_OUT;
+unless ($OPT{'local-build-out'})
+{   $OPT{'local-build-out'} = $OPT{'relative-build-out-dir'} }
 my $OUTDIR = File::Spec->catdir($HOME, $PKG{OUT});
-if ($OPT{'local-build-out'}) {
-    my $o = expand_path(File::Spec->catdir($Bin, $PKG{LOCOUT}));
-    $OUTDIR = $o if ($o);
-}
+my $REL_OUTDIR = expand_path(File::Spec->catdir($Bin, $PKG{LOCOUT}));
+if ($OPT{'local-build-out'})
+{   $OUTDIR = $REL_OUTDIR if ($REL_OUTDIR) }
 
 if ($OPT{'help'}) {
     help();
@@ -1022,9 +1024,9 @@ EndText
         T($F, '$(CC) -o $@ $< $(PIC) $(CFLAGS)');
     }
     L($F, '$(OBJDIR)/%.$(OBJX): %.cpp');
-    T($F, '$(CP) -o $@ $< $(CFLAGS)');
+    T($F, '$(CP) -std=c++11 -o $@ $< $(CFLAGS)');
     L($F, '$(OBJDIR)/%.$(LOBX): %.cpp');
-    T($F, '$(CP) -o $@ $< $(PIC) $(CFLAGS)');
+    T($F, '$(CP) -std=c++11 -o $@ $< $(PIC) $(CFLAGS)');
     L($F);
 
     # this is part of Makefile
@@ -1925,22 +1927,24 @@ EndText
         }
 
         print <<EndText;
-  --build-prefix=DIR      generate build output into DIR directory
-                          [$OUTDIR]
+  --relative-build-out-dir generate build output into directory
+                           relative to sources [$OUTDIR]
+  --build-prefix=DIR       generate build output into DIR directory
+                           [$OUTDIR]
 
 EndText
     }
 
     println 'Miscellaneous:';
-    println '  --reconfigure           rerun `configure\'';
-    println '                          using the same command-line arguments';
+    println '  --reconfigure            rerun `configure\'';
+    println '                           using the same command-line arguments';
     if ($^O ne 'MSWin32') {
         println
-            '  --status                print current configuration information'
+            '  --status                 print current configuration information'
     }
     print <<EndText;
-  --clean                 remove all configuration results
-  --debug                 print lots of debugging information
+  --clean                  remove all configuration results
+  --debug                  print lots of debugging information
 
 If `configure' was already run running `configure' without options
 will rerun `configure' using the same command-line arguments.


=====================================
ngs-java/Makefile.vers
=====================================
@@ -23,4 +23,4 @@
 # ===========================================================================
 
 # NGS-JAVA and library version
-VERSION = 2.10.5
+VERSION = 2.10.9


=====================================
ngs-java/build.xml
=====================================
@@ -37,6 +37,9 @@
     </target>
 
     <target name="jar" depends="ncbi">
+        <property environment="my_env" />
+        <echo message="PATH=${my_env.PATH}"/>
+        <echo message="APPDATA=${my_env.APPDATA}"/>
         <mkdir dir="${build.dir}\jar"/>
         <jar destfile="${build.dir}\jar\ngs-java.jar" >
             <fileset dir="${classes.dir}" includes="ngs\**" />


=====================================
ngs-java/configure
=====================================
@@ -41,5 +41,5 @@ else
         echo >&2 "configure: error: perl not found."; exit 1; }
 
     cd $CURDIR/setup
-    perl  konfigure.perl "$@"
+    perl konfigure.perl "$@"
 fi


=====================================
ngs-java/examples/Makefile
=====================================
@@ -67,7 +67,7 @@ JAVAFLAGS = -classpath $(CLASSPATH):$(NGS_CLASS_PATH):.
 JAVAFLAGS += -Djava.library.path=$(LD_LIBRARY_PATH) -Dvdb.System.loadLibrary=1
 
 # uncomment to see detailed log"
-JAVAFLAGS += -Dvdb.log=FINEST
+#JAVAFLAGS += -Dvdb.log=FINEST
 
 run_frag: NGS-JavaTest.jar
 	java $(JAVAFLAGS) examples.FragTest ERR225922 10000 2  $(REDIRECT)
@@ -105,7 +105,7 @@ expected.txt update_expected:
 	rm -f expected.txt; LD_LIBRARY_PATH=$(LD_LIBRARY_PATH) $(MAKE) run_all REDIRECT=">>expected.txt"
 
 run_and_diff: expected.txt  
-	rm -f actual.txt; LD_LIBRARY_PATH=$(LD_LIBRARY_PATH) $(MAKE) run_all REDIRECT=">>actual.txt"
-	diff expected.txt actual.txt && rm actual.txt && echo NGS Java examples work as expected
+	@ rm -f actual.txt; LD_LIBRARY_PATH=$(LD_LIBRARY_PATH) $(MAKE) run_all REDIRECT=">>actual.txt"
+	@ diff expected.txt actual.txt && rm actual.txt && echo NGS Java examples work as expected
 
 .PHONY: update_expected run_and_diff


=====================================
ngs-java/gov/nih/nlm/ncbi/ngs/LibDependencies.java
=====================================
@@ -29,6 +29,6 @@ package gov.nih.nlm.ncbi.ngs;
 class LibDependencies {
     final static String NGS_SDK  = "ngs-sdk";
     final static String NCBI_VDB = "ncbi-vdb";
-    final static String NGS_SDK_VERSION = "2.10.5";
-    final static String NCBI_VDB_VERSION = "2.10.5";
+    final static String NGS_SDK_VERSION = "2.10.9";
+    final static String NCBI_VDB_VERSION = "2.10.9";
 }


=====================================
ngs-java/gov/nih/nlm/ncbi/ngs/LibVersionChecker.java
=====================================
@@ -186,7 +186,7 @@ class LibVersionChecker {
     private static boolean tryJava(Vector<String> cmdarray) {
         try {
             Process p
-                    = Runtime.getRuntime().exec(cmdarray.elementAt(0) + " -?");
+                    = Runtime.getRuntime().exec(cmdarray.elementAt(0) + " -version");
             if (p.waitFor() == 0) {
                 return true;
             }


=====================================
ngs-java/setup/konfigure.perl
=====================================
@@ -86,6 +86,7 @@ my @options = ( 'build-prefix=s',
                 'help',
                 'prefix=s',
                 'reconfigure',
+                'relative-build-out-dir',
                 'status',
                 'with-debug',
                 'without-debug', );
@@ -136,11 +137,12 @@ EndText
 }
 
 $OPT{'local-build-out'} = $LOCAL_BUILD_OUT;
+unless ($OPT{'local-build-out'})
+{   $OPT{'local-build-out'} = $OPT{'relative-build-out-dir'} }
 my $OUTDIR = File::Spec->catdir($HOME, $PKG{OUT});
-if ($OPT{'local-build-out'}) {
-    my $o = expand_path(File::Spec->catdir($Bin, $PKG{LOCOUT}));
-    $OUTDIR = $o if ($o);
-}
+my $REL_OUTDIR = expand_path(File::Spec->catdir($Bin, $PKG{LOCOUT}));
+if ($OPT{'local-build-out'})
+{   $OUTDIR = $REL_OUTDIR if ($REL_OUTDIR) }
 
 if ($OPT{'help'}) {
     help();
@@ -1022,9 +1024,9 @@ EndText
         T($F, '$(CC) -o $@ $< $(PIC) $(CFLAGS)');
     }
     L($F, '$(OBJDIR)/%.$(OBJX): %.cpp');
-    T($F, '$(CP) -o $@ $< $(CFLAGS)');
+    T($F, '$(CP) -std=c++11 -o $@ $< $(CFLAGS)');
     L($F, '$(OBJDIR)/%.$(LOBX): %.cpp');
-    T($F, '$(CP) -o $@ $< $(PIC) $(CFLAGS)');
+    T($F, '$(CP) -std=c++11 -o $@ $< $(PIC) $(CFLAGS)');
     L($F);
 
     # this is part of Makefile
@@ -1925,22 +1927,24 @@ EndText
         }
 
         print <<EndText;
-  --build-prefix=DIR      generate build output into DIR directory
-                          [$OUTDIR]
+  --relative-build-out-dir generate build output into directory
+                           relative to sources [$OUTDIR]
+  --build-prefix=DIR       generate build output into DIR directory
+                           [$OUTDIR]
 
 EndText
     }
 
     println 'Miscellaneous:';
-    println '  --reconfigure           rerun `configure\'';
-    println '                          using the same command-line arguments';
+    println '  --reconfigure            rerun `configure\'';
+    println '                           using the same command-line arguments';
     if ($^O ne 'MSWin32') {
         println
-            '  --status                print current configuration information'
+            '  --status                 print current configuration information'
     }
     print <<EndText;
-  --clean                 remove all configuration results
-  --debug                 print lots of debugging information
+  --clean                  remove all configuration results
+  --debug                  print lots of debugging information
 
 If `configure' was already run running `configure' without options
 will rerun `configure' using the same command-line arguments.


=====================================
ngs-python/Makefile.python
=====================================
@@ -80,12 +80,17 @@ $(INST_PYTHONDIR):
 
 install: $(TARGETS) $(INST_PYTHONDIR) copyexamples
 ifeq (0, $(shell id -u))
-	@ echo "Installing ngs package..."
+	@ echo "Installing ngs-python package..."
 	@ python setup.py -q install
    
 else
-	@ echo "Installing ngs package..."
-	@ python setup.py -q install --user
+	@ echo "Installing ngs-python package to the current user..."
+	  echo '$$ python -m site --user-base'
+	  python -m site --user-base
+	  echo '$$ python -m site --user-site'
+	  python -m site --user-site
+	  python setup.py  -q install --user
+	@ echo "... installed"
 endif
 
 ifneq (, $(NGS_LIBDIR))


=====================================
ngs-python/Makefile.vers
=====================================
@@ -23,4 +23,4 @@
 # ===========================================================================
 
 # NGS-PYTHON and library version
-VERSION = 2.10.5
+VERSION = 2.10.9


=====================================
ngs-python/configure
=====================================
@@ -41,5 +41,5 @@ else
         echo >&2 "configure: error: perl not found."; exit 1; }
 
     cd $CURDIR/setup
-    perl  konfigure.perl "$@"
+    perl konfigure.perl "$@"
 fi


=====================================
ngs-python/examples/Makefile
=====================================
@@ -83,14 +83,14 @@ run_all: $(ALL_TESTS)
 # expected results for auto-testing
 #
 expected.txt update_expected:
-	if [ "$(PYTHON_VERS)" = "26" ] ; then \
+	@if [ "$(PYTHON_VERS)" = "26" ] ; then \
 		echo Python 2.6 is not supported ; \
 	else \
 		rm -f expected.txt; LD_LIBRARY_PATH=$(LD_LIBRARY_PATH) $(MAKE) run_all REDIRECT=">>expected.txt" ; \
 	fi
 
 run_and_diff: expected.txt
-	if [ "$(PYTHON_VERS)" = "26" ] ; then \
+	@if [ "$(PYTHON_VERS)" = "26" ] ; then \
 		echo Python 2.6 is not supported ; \
 	else \
 		rm -f actual.txt; LD_LIBRARY_PATH=$(LD_LIBRARY_PATH) $(MAKE) run_all REDIRECT=">>actual.txt" ; \


=====================================
ngs-python/examples/NGS_FastQ.py
=====================================


=====================================
ngs-python/setup.py
=====================================
@@ -18,6 +18,6 @@ setup(name='ngs',
       author_email='sra-tools at ncbi.nlm.nih.gov',
       packages=['ngs'],
       include_package_data=True,
-      scripts=[],
+      #scripts=[],
       #test_suite="tests",
       )


=====================================
ngs-python/setup/konfigure.perl
=====================================
@@ -86,6 +86,7 @@ my @options = ( 'build-prefix=s',
                 'help',
                 'prefix=s',
                 'reconfigure',
+                'relative-build-out-dir',
                 'status',
                 'with-debug',
                 'without-debug', );
@@ -136,11 +137,12 @@ EndText
 }
 
 $OPT{'local-build-out'} = $LOCAL_BUILD_OUT;
+unless ($OPT{'local-build-out'})
+{   $OPT{'local-build-out'} = $OPT{'relative-build-out-dir'} }
 my $OUTDIR = File::Spec->catdir($HOME, $PKG{OUT});
-if ($OPT{'local-build-out'}) {
-    my $o = expand_path(File::Spec->catdir($Bin, $PKG{LOCOUT}));
-    $OUTDIR = $o if ($o);
-}
+my $REL_OUTDIR = expand_path(File::Spec->catdir($Bin, $PKG{LOCOUT}));
+if ($OPT{'local-build-out'})
+{   $OUTDIR = $REL_OUTDIR if ($REL_OUTDIR) }
 
 if ($OPT{'help'}) {
     help();
@@ -1022,9 +1024,9 @@ EndText
         T($F, '$(CC) -o $@ $< $(PIC) $(CFLAGS)');
     }
     L($F, '$(OBJDIR)/%.$(OBJX): %.cpp');
-    T($F, '$(CP) -o $@ $< $(CFLAGS)');
+    T($F, '$(CP) -std=c++11 -o $@ $< $(CFLAGS)');
     L($F, '$(OBJDIR)/%.$(LOBX): %.cpp');
-    T($F, '$(CP) -o $@ $< $(PIC) $(CFLAGS)');
+    T($F, '$(CP) -std=c++11 -o $@ $< $(PIC) $(CFLAGS)');
     L($F);
 
     # this is part of Makefile
@@ -1925,22 +1927,24 @@ EndText
         }
 
         print <<EndText;
-  --build-prefix=DIR      generate build output into DIR directory
-                          [$OUTDIR]
+  --relative-build-out-dir generate build output into directory
+                           relative to sources [$OUTDIR]
+  --build-prefix=DIR       generate build output into DIR directory
+                           [$OUTDIR]
 
 EndText
     }
 
     println 'Miscellaneous:';
-    println '  --reconfigure           rerun `configure\'';
-    println '                          using the same command-line arguments';
+    println '  --reconfigure            rerun `configure\'';
+    println '                           using the same command-line arguments';
     if ($^O ne 'MSWin32') {
         println
-            '  --status                print current configuration information'
+            '  --status                 print current configuration information'
     }
     print <<EndText;
-  --clean                 remove all configuration results
-  --debug                 print lots of debugging information
+  --clean                  remove all configuration results
+  --debug                  print lots of debugging information
 
 If `configure' was already run running `configure' without options
 will rerun `configure' using the same command-line arguments.


=====================================
ngs-sdk/Makefile.vers
=====================================
@@ -23,4 +23,4 @@
 # ===========================================================================
 
 # NGS-SDK and library version
-VERSION = 2.10.5
+VERSION = 2.10.9


=====================================
ngs-sdk/configure
=====================================
@@ -41,5 +41,5 @@ else
         echo >&2 "configure: error: perl not found."; exit 1; }
 
     cd $CURDIR/setup
-    perl  konfigure.perl "$@"
+    perl konfigure.perl "$@"
 fi


=====================================
ngs-sdk/dispatch/version.h
=====================================
@@ -1 +1 @@
-#define NGS_SDK_VERSION "2.10.5"
+#define NGS_SDK_VERSION "2.10.9"


=====================================
ngs-sdk/examples/Makefile
=====================================
@@ -179,9 +179,9 @@ expected.txt update_expected:
 	export LD_LIBRARY_PATH=$(LD_LIBRARY_PATH) ; $(MAKE) run_all REDIRECT=">>expected.txt"
 
 run_and_diff: expected.txt
-	rm -f actual.txt
-	echo $(http_proxy)
-	export LD_LIBRARY_PATH=$(LD_LIBRARY_PATH) ; $(MAKE) run_all REDIRECT=">>actual.txt"
+	@ rm -f actual.txt
+	@ echo http_proxy=$(http_proxy)
+	@ export LD_LIBRARY_PATH=$(LD_LIBRARY_PATH) ; $(MAKE) run_all REDIRECT=">>actual.txt"
 	@ diff expected.txt actual.txt && rm actual.txt && echo "NGS C++ examples work as expected"
 
 .PHONY: update_expected run_and_diff install


=====================================
ngs-sdk/ngs/itf/Refcount.hpp
=====================================
@@ -27,6 +27,8 @@
 #ifndef _hpp_ngs_itf_refcount_
 #define _hpp_ngs_itf_refcount_
 
+#pragma clang diagnostic ignored "-Wtautological-undefined-compare"
+
 #ifndef _hpp_ngs_itf_error_msg_
 #include <ngs/itf/ErrorMsg.hpp>
 #endif


=====================================
ngs-sdk/setup/konfigure.perl
=====================================
@@ -86,6 +86,7 @@ my @options = ( 'build-prefix=s',
                 'help',
                 'prefix=s',
                 'reconfigure',
+                'relative-build-out-dir',
                 'status',
                 'with-debug',
                 'without-debug', );
@@ -136,11 +137,12 @@ EndText
 }
 
 $OPT{'local-build-out'} = $LOCAL_BUILD_OUT;
+unless ($OPT{'local-build-out'})
+{   $OPT{'local-build-out'} = $OPT{'relative-build-out-dir'} }
 my $OUTDIR = File::Spec->catdir($HOME, $PKG{OUT});
-if ($OPT{'local-build-out'}) {
-    my $o = expand_path(File::Spec->catdir($Bin, $PKG{LOCOUT}));
-    $OUTDIR = $o if ($o);
-}
+my $REL_OUTDIR = expand_path(File::Spec->catdir($Bin, $PKG{LOCOUT}));
+if ($OPT{'local-build-out'})
+{   $OUTDIR = $REL_OUTDIR if ($REL_OUTDIR) }
 
 if ($OPT{'help'}) {
     help();
@@ -1925,22 +1927,24 @@ EndText
         }
 
         print <<EndText;
-  --build-prefix=DIR      generate build output into DIR directory
-                          [$OUTDIR]
+  --relative-build-out-dir generate build output into directory
+                           relative to sources [$OUTDIR]
+  --build-prefix=DIR       generate build output into DIR directory
+                           [$OUTDIR]
 
 EndText
     }
 
     println 'Miscellaneous:';
-    println '  --reconfigure           rerun `configure\'';
-    println '                          using the same command-line arguments';
+    println '  --reconfigure            rerun `configure\'';
+    println '                           using the same command-line arguments';
     if ($^O ne 'MSWin32') {
         println
-            '  --status                print current configuration information'
+            '  --status                 print current configuration information'
     }
     print <<EndText;
-  --clean                 remove all configuration results
-  --debug                 print lots of debugging information
+  --clean                  remove all configuration results
+  --debug                  print lots of debugging information
 
 If `configure' was already run running `configure' without options
 will rerun `configure' using the same command-line arguments.


=====================================
ngs-sdk/win/vs2017/ngs-test.vcxproj
=====================================
@@ -33,6 +33,6 @@
   </ItemDefinitionGroup>
   <Import Project="..\ngs-test.files" />
   <Target Name="AfterBuild" Condition="'$(Autorun)'=='true'">
-    <Exec Command="$(OutDir)$(TargetName)$(TargetExt)" WorkingDirectory="$(ProjectDir)\" />
+    <Exec Command=""$(OutDir)$(TargetName)$(TargetExt)"" WorkingDirectory="$(ProjectDir)\" />
   </Target>
 </Project>
\ No newline at end of file



View it on GitLab: https://salsa.debian.org/med-team/ngs-sdk/-/commit/297264b34380b1ab40a285e589df15d06fbb32df

-- 
View it on GitLab: https://salsa.debian.org/med-team/ngs-sdk/-/commit/297264b34380b1ab40a285e589df15d06fbb32df
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