[med-svn] [Git][med-team/ngs-sdk][master] 7 commits: New upstream version 2.10.9
Andreas Tille
gitlab at salsa.debian.org
Sun Jan 17 18:13:36 GMT 2021
Andreas Tille pushed to branch master at Debian Med / ngs-sdk
Commits:
297264b3 by Andreas Tille at 2021-01-17T18:52:44+01:00
New upstream version 2.10.9
- - - - -
0b8a3cd1 by Andreas Tille at 2021-01-17T18:52:44+01:00
routine-update: New upstream version
- - - - -
5106ef94 by Andreas Tille at 2021-01-17T18:52:52+01:00
Update upstream source from tag 'upstream/2.10.9'
Update to upstream version '2.10.9'
with Debian dir bccd036147d00e232fee60e97c6f6bf2b2d8cf4f
- - - - -
08fbe0fe by Andreas Tille at 2021-01-17T18:52:52+01:00
routine-update: Standards-Version: 4.5.1
- - - - -
efdac1fa by Andreas Tille at 2021-01-17T18:52:52+01:00
routine-update: debhelper-compat 13
- - - - -
8edec1dd by Andreas Tille at 2021-01-17T18:52:55+01:00
routine-update: watch file standard 4
- - - - -
be70e856 by Andreas Tille at 2021-01-17T18:54:30+01:00
routine-update: Ready to upload to unstable
- - - - -
28 changed files:
- CHANGES.md
- debian/changelog
- debian/control
- debian/watch
- 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
=====================================
debian/changelog
=====================================
@@ -1,3 +1,12 @@
+ngs-sdk (2.10.9-1) unstable; urgency=medium
+
+ * New upstream version
+ * Standards-Version: 4.5.1 (routine-update)
+ * debhelper-compat 13 (routine-update)
+ * watch file standard 4 (routine-update)
+
+ -- Andreas Tille <tille at debian.org> Sun, 17 Jan 2021 18:52:56 +0100
+
ngs-sdk (2.10.5-1) unstable; urgency=medium
* New upstream version
=====================================
debian/control
=====================================
@@ -5,7 +5,7 @@ Uploaders: Andreas Tille <tille at debian.org>,
Vincent Danjean <vdanjean at debian.org>
Section: science
Priority: optional
-Build-Depends: debhelper-compat (= 12),
+Build-Depends: debhelper-compat (= 13),
d-shlibs,
markdown <!nodoc>,
python3-all,
@@ -14,7 +14,7 @@ Build-Depends: debhelper-compat (= 12),
javahelper,
maven-repo-helper,
default-jdk
-Standards-Version: 4.5.0
+Standards-Version: 4.5.1
Vcs-Browser: https://salsa.debian.org/med-team/ngs-sdk
Vcs-Git: https://salsa.debian.org/med-team/ngs-sdk.git
Homepage: https://github.com/ncbi/ngs
=====================================
debian/watch
=====================================
@@ -1,3 +1,3 @@
-version=3
+version=4
https://github.com/ncbi/ngs/releases .*/archive/(\d[\d.-]+)\.(?:tar(?:\.gz|\.bz2)?|tgz)
=====================================
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/-/compare/9982eb134844a8e988bdd0fe1da3fbd6425217d9...be70e856219ca55a73e1c83414166c71381d3a12
--
View it on GitLab: https://salsa.debian.org/med-team/ngs-sdk/-/compare/9982eb134844a8e988bdd0fe1da3fbd6425217d9...be70e856219ca55a73e1c83414166c71381d3a12
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