Changeset: 4070ca6c31f0 for MonetDB
URL: https://dev.monetdb.org/hg/MonetDB?cmd=changeset;node=4070ca6c31f0
Added Files:
sql/backends/monet5/UDF/pyapi3/connection.h
sql/backends/monet5/UDF/pyapi3/conversion.h
sql/backends/monet5/UDF/pyapi3/convert_loops.h
sql/backends/monet5/UDF/pyapi3/emit.h
sql/backends/monet5/UDF/pyapi3/formatinput.h
sql/backends/monet5/UDF/pyapi3/pyapi.h
sql/backends/monet5/UDF/pyapi3/pyheader.h
sql/backends/monet5/UDF/pyapi3/pytypes.h
sql/backends/monet5/UDF/pyapi3/type_conversion.h
sql/backends/monet5/UDF/pyapi3/undef.h
sql/backends/monet5/UDF/pyapi3/unicode.h
sql/test/analytics/Tests/analytics14.sql
sql/test/analytics/Tests/analytics14.stable.err
sql/test/analytics/Tests/analytics14.stable.out
sql/test/analytics/Tests/analytics15.sql
sql/test/analytics/Tests/analytics15.stable.err
sql/test/analytics/Tests/analytics15.stable.out
sql/test/analytics/Tests/analytics16.sql
sql/test/analytics/Tests/analytics16.stable.err
sql/test/analytics/Tests/analytics16.stable.out
sql/test/analytics/Tests/analytics17.sql
sql/test/analytics/Tests/analytics17.stable.err
sql/test/analytics/Tests/analytics17.stable.out
Removed Files:
clients/examples/python/mclient-python2.py
debian/libmonetdb5-server-bam.install
debian/monetdb-python2.install
sql/backends/monet5/Tests/createorreplace.sql
sql/backends/monet5/Tests/createorreplace.stable.err
sql/backends/monet5/Tests/createorreplace.stable.out
sql/backends/monet5/Tests/pyapi00.sql
sql/backends/monet5/Tests/pyapi00.stable.err
sql/backends/monet5/Tests/pyapi00.stable.out
sql/backends/monet5/Tests/pyapi01.sql
sql/backends/monet5/Tests/pyapi01.stable.err
sql/backends/monet5/Tests/pyapi01.stable.out
sql/backends/monet5/Tests/pyapi02.sql
sql/backends/monet5/Tests/pyapi02.stable.err
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sql/backends/monet5/Tests/pyapi03.sql
sql/backends/monet5/Tests/pyapi03.stable.err
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sql/backends/monet5/Tests/pyapi04.sql
sql/backends/monet5/Tests/pyapi04.stable.err
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sql/backends/monet5/Tests/pyapi05.sql
sql/backends/monet5/Tests/pyapi05.stable.err
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sql/backends/monet5/Tests/pyapi06.sql
sql/backends/monet5/Tests/pyapi06.stable.err
sql/backends/monet5/Tests/pyapi06.stable.out
sql/backends/monet5/Tests/pyapi07.sql
sql/backends/monet5/Tests/pyapi07.stable.err
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sql/backends/monet5/Tests/pyapi08.sql
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sql/backends/monet5/Tests/pyapi09.sql
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sql/backends/monet5/Tests/pyapi10.sql
sql/backends/monet5/Tests/pyapi10.stable.err
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sql/backends/monet5/Tests/pyapi11.sql
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sql/backends/monet5/Tests/pyapi12.sql
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sql/backends/monet5/Tests/pyapi13.sql
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sql/backends/monet5/Tests/pyapi14.sql
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sql/backends/monet5/Tests/pyapi20.sql
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sql/backends/monet5/Tests/pyapi21.sql
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sql/backends/monet5/Tests/pyapi23.sql
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sql/backends/monet5/Tests/pyapi24.sql
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sql/backends/monet5/vaults/bam/bam_db_interface.h
sql/backends/monet5/vaults/bam/bam_export.c
sql/backends/monet5/vaults/bam/bam_export.h
sql/backends/monet5/vaults/bam/bam_globals.c
sql/backends/monet5/vaults/bam/bam_globals.h
sql/backends/monet5/vaults/bam/bam_lib.c
sql/backends/monet5/vaults/bam/bam_lib.h
sql/backends/monet5/vaults/bam/bam_loader.c
sql/backends/monet5/vaults/bam/bam_loader.h
sql/backends/monet5/vaults/bam/bam_wrapper.c
sql/backends/monet5/vaults/bam/bam_wrapper.h
sql/backends/monet5/vaults/bam/default_schema.dia
sql/backends/monet5/vaults/bam/default_schema.png
sql/backends/monet5/vaults/bam/metadata.dia
sql/backends/monet5/vaults/bam/metadata.png
sql/backends/monet5/vaults/bam/mykstring.h
sql/backends/monet5/vaults/bam/paired_schema.dia
sql/backends/monet5/vaults/bam/paired_schema.png
sql/test/BugTracker-2016/Tests/assert-on-project.Bug-6078.sql
sql/test/BugTracker-2016/Tests/assert-on-project.Bug-6078.stable.err
sql/test/BugTracker-2016/Tests/assert-on-project.Bug-6078.stable.out
sql/test/BugTracker-2016/Tests/assert-on-push-project-up.Bug-6077.sql
sql/test/BugTracker-2016/Tests/assert-on-push-project-up.Bug-6077.stable.err
sql/test/BugTracker-2016/Tests/assert-on-push-project-up.Bug-6077.stable.out
sql/test/BugTracker-2018/Tests/truncate_bam_tables.Bug-6543.reqtests
sql/test/BugTracker-2018/Tests/truncate_bam_tables.Bug-6543.sql
sql/test/BugTracker-2018/Tests/truncate_bam_tables.Bug-6543.stable.err
sql/test/BugTracker-2018/Tests/truncate_bam_tables.Bug-6543.stable.out
sql/test/mapi/Tests/python2_dbapi.SQL.bat
sql/test/mapi/Tests/python2_dbapi.SQL.sh
sql/test/mapi/Tests/python2_dbapi.stable.err
sql/test/mapi/Tests/python2_dbapi.stable.out
sql/test/mapi/Tests/python2_dec38.SQL.bat
sql/test/mapi/Tests/python2_dec38.SQL.sh
sql/test/mapi/Tests/python2_dec38.stable.err
sql/test/mapi/Tests/python2_dec38.stable.out.int128
sql/test/mapi/Tests/python2_int128.SQL.bat
sql/test/mapi/Tests/python2_int128.SQL.sh
sql/test/mapi/Tests/python2_int128.stable.err
sql/test/mapi/Tests/python2_int128.stable.out.int128
sql/test/mergetables/Tests/mergedb.Bug-6820.reqtests
sql/test/mergetables/Tests/mergedb.Bug-6820.sql
sql/test/mergetables/Tests/mergedb.Bug-6820.stable.err
sql/test/mergetables/Tests/mergedb.Bug-6820.stable.out
sql/test/mergetables/Tests/sqlsmith.Bug-6426.reqtests
sql/test/mergetables/Tests/sqlsmith.Bug-6426.sql
sql/test/mergetables/Tests/sqlsmith.Bug-6426.stable.err
sql/test/mergetables/Tests/sqlsmith.Bug-6426.stable.out
sql/test/mergetables/Tests/sqlsmith.Bug-6455.reqtests
sql/test/mergetables/Tests/sqlsmith.Bug-6455.sql
sql/test/mergetables/Tests/sqlsmith.Bug-6455.stable.err
sql/test/mergetables/Tests/sqlsmith.Bug-6455.stable.out
sql/test/sys-schema/Tests/bam_tables_checks.sql
sql/test/sys-schema/Tests/bam_tables_checks.stable.err
sql/test/sys-schema/Tests/bam_tables_checks.stable.out
Modified Files:
ChangeLog
MonetDB.spec
NT/mksqlwxs.py
NT/monetdb_config.h.in
NT/rules.msc
README-Debian
README-Fedora
buildtools/doc/windowsbuild.rst
clients/Tests/All
clients/Tests/MAL-signatures.stable.out
clients/Tests/MAL-signatures.stable.out.int128
clients/Tests/exports.stable.out
clients/mapiclient/mclient.c
clients/mapiclient/mhelp.c
clients/odbc/samples/testgetinfo.c
configure.ag
debian/control
debian/monetdb5-server.install
debian/rules
gdk/gdk_aggr.c
gdk/gdk_analytic.h
gdk/gdk_analytic_func.c
gdk/gdk_batop.c
gdk/gdk_calc.h
gdk/gdk_cand.h
gdk/gdk_project.c
gdk/gdk_select.c
gdk/gdk_string.c
gdk/gdk_unique.c
monetdb5/NT/M5server.bat
monetdb5/extras/mal_optimizer_template/Tests/opt_sql_append.stable.err.Windows
monetdb5/extras/mal_optimizer_template/Tests/opt_sql_append.stable.out
monetdb5/extras/mal_optimizer_template/Tests/opt_sql_append.stable.out.Windows
monetdb5/mal/mal_linker.c
monetdb5/modules/atoms/uuid.c
monetdb5/modules/kernel/00_aggr_hge.mal
monetdb5/modules/kernel/00_aggr_hge.mal.sh
monetdb5/modules/kernel/aggr.c
monetdb5/modules/kernel/aggr.mal
monetdb5/modules/kernel/aggr.mal.sh
monetdb5/modules/kernel/alarm.mal
monetdb5/modules/kernel/algebra.c
monetdb5/modules/kernel/algebra.h
monetdb5/modules/kernel/algebra.mal
monetdb5/modules/mal/01_batcalc.mal
monetdb5/modules/mal/01_batcalc.mal.sh
monetdb5/modules/mal/calc.c
monetdb5/modules/mal/mal_mapi.c
monetdb5/optimizer/opt_mitosis.c
monetdb5/optimizer/opt_prelude.c
monetdb5/optimizer/opt_prelude.h
monetdb5/optimizer/opt_support.c
sql/ChangeLog
sql/backends/monet5/Makefile.ag
sql/backends/monet5/Tests/All
sql/backends/monet5/UDF/Makefile.ag
sql/backends/monet5/UDF/pyapi3/Makefile.ag
sql/backends/monet5/UDF/pyapi3/connection3.c
sql/backends/monet5/UDF/pyapi3/conversion3.c
sql/backends/monet5/UDF/pyapi3/emit3.c
sql/backends/monet5/UDF/pyapi3/formatinput3.c
sql/backends/monet5/UDF/pyapi3/pyapi3.c
sql/backends/monet5/UDF/pyapi3/pyloader3.c
sql/backends/monet5/UDF/pyapi3/pytypes3.c
sql/backends/monet5/UDF/pyapi3/type_conversion3.c
sql/backends/monet5/UDF/pyapi3/unicode3.c
sql/backends/monet5/generator/generator.c
sql/backends/monet5/rel_bin.c
sql/backends/monet5/sql.mal
sql/backends/monet5/sql_cat.c
sql/backends/monet5/sql_gencode.c
sql/backends/monet5/sql_gencode.h
sql/backends/monet5/sql_hge.mal
sql/backends/monet5/sql_optimizer.c
sql/backends/monet5/sql_rank.c
sql/backends/monet5/sql_rank.h
sql/backends/monet5/sql_rank.mal
sql/backends/monet5/sql_rank.mal.sh
sql/backends/monet5/sql_rank_hge.mal
sql/backends/monet5/sql_rank_hge.mal.sh
sql/backends/monet5/sql_scenario.c
sql/backends/monet5/sql_statement.c
sql/backends/monet5/sql_statement.h
sql/backends/monet5/sql_upgrades.c
sql/backends/monet5/vaults/Makefile.ag
sql/benchmarks/ssbm/Tests/check1.sql
sql/benchmarks/tpcds/Tests/47.stable.out
sql/benchmarks/tpcds/Tests/47.stable.out.int128
sql/benchmarks/tpcds/Tests/53.stable.out
sql/benchmarks/tpcds/Tests/53.stable.out.int128
sql/benchmarks/tpcds/Tests/57.stable.out
sql/benchmarks/tpcds/Tests/57.stable.out.int128
sql/benchmarks/tpcds/Tests/63.stable.out
sql/benchmarks/tpcds/Tests/63.stable.out.int128
sql/benchmarks/tpcds/Tests/79.sql
sql/benchmarks/tpcds/Tests/79.stable.out
sql/benchmarks/tpcds/Tests/79.stable.out.int128
sql/benchmarks/tpcds/Tests/89.stable.out
sql/benchmarks/tpcds/Tests/89.stable.out.int128
sql/benchmarks/tpch/Tests/check1.sql
sql/benchmarks/tpch/Tests/lowcardinality.sql
sql/benchmarks/tpch/Tests/lowcardinality.stable.out
sql/common/sql_backend.c
sql/common/sql_backend.h
sql/common/sql_types.c
sql/common/sql_types.h
sql/include/sql_catalog.h
sql/scripts/39_analytics.sql
sql/scripts/39_analytics_hge.sql
sql/scripts/51_sys_schema_extension.sql
sql/server/rel_dump.c
sql/server/rel_exp.c
sql/server/rel_exp.h
sql/server/rel_optimizer.c
sql/server/rel_propagate.c
sql/server/rel_psm.c
sql/server/rel_rel.c
sql/server/rel_schema.c
sql/server/rel_select.c
sql/server/rel_select.h
sql/server/rel_sequence.c
sql/server/rel_unnest.c
sql/server/rel_updates.c
sql/server/sql_parser.y
sql/server/sql_scan.c
sql/server/sql_semantic.c
sql/storage/store.c
sql/test/BugTracker-2008/Tests/too_many_nested_operators.SF-2102167.sql
sql/test/BugTracker-2008/Tests/too_many_nested_operators.SF-2102167.stable.err
sql/test/BugTracker-2008/Tests/too_many_nested_operators.SF-2102167.stable.out
sql/test/BugTracker-2009/Tests/union_where_combined.SF-2887282.stable.out
sql/test/BugTracker-2009/Tests/use_order_column_first.SF-2686008.stable.out
sql/test/BugTracker-2010/Tests/sum_on_date_crash.Bug-2643.stable.err
sql/test/BugTracker-2012/Tests/All
sql/test/BugTracker-2012/Tests/create_function.Bug-3172.stable.err
sql/test/BugTracker-2012/Tests/table_function_with_column_subselects.Bug-3172.stable.err
sql/test/BugTracker-2012/Tests/table_functions_fail_after_restart-0.Bug-3063.stable.out
sql/test/BugTracker-2012/Tests/table_functions_fail_after_restart-1.Bug-3063.stable.out
sql/test/BugTracker-2014/Tests/aggregates-intervals.Bug-3533.sql
sql/test/BugTracker-2014/Tests/aggregates-intervals.Bug-3533.stable.err
sql/test/BugTracker-2014/Tests/aggregates-intervals.Bug-3533.stable.out
sql/test/BugTracker-2015/Tests/nil_cast.Bug-3787.stable.out
sql/test/BugTracker-2016/Tests/All
sql/test/BugTracker-2016/Tests/isaUUID_function.Bug-3997.stable.err
sql/test/BugTracker-2017/Tests/All
sql/test/BugTracker-2017/Tests/corr_coersion.Bug-6287.stable.out
sql/test/BugTracker-2018/Tests/All
sql/test/BugTracker-2019/Tests/rank-nan.Bug-6780.sql
sql/test/BugTracker-2019/Tests/rank-nan.Bug-6780.stable.out
sql/test/BugTracker-2019/Tests/subselect.Bug-6688.sql
sql/test/BugTracker-2019/Tests/subselect.Bug-6688.stable.out
sql/test/BugTracker-2019/Tests/subselect.Bug-6700.sql
sql/test/BugTracker-2019/Tests/subselect.Bug-6700.stable.out
sql/test/Dependencies/Tests/All
sql/test/Dependencies/Tests/Dependencies.stable.out
sql/test/Dependencies/Tests/Dependencies.stable.out.int128
sql/test/Tests/All
sql/test/Tests/comment-on.stable.err
sql/test/Tests/keys.stable.out
sql/test/analytics/Tests/All
sql/test/analytics/Tests/analytics00.stable.out
sql/test/analytics/Tests/analytics01.sql
sql/test/analytics/Tests/analytics01.stable.err
sql/test/analytics/Tests/analytics01.stable.out
sql/test/analytics/Tests/analytics13.stable.out
sql/test/bugs/Tests/All
sql/test/bugs/Tests/groupby_having_charlength-bug-sf-943566.stable.out
sql/test/emptydb-upgrade-chain-hge/Tests/All
sql/test/emptydb-upgrade-chain-hge/Tests/upgrade.stable.out.int128
sql/test/emptydb-upgrade-chain-hge/Tests/upgrade.stable.out.powerpc64.int128
sql/test/emptydb-upgrade-chain/Tests/All
sql/test/emptydb-upgrade-chain/Tests/upgrade.stable.out
sql/test/emptydb-upgrade-chain/Tests/upgrade.stable.out.32bit
sql/test/emptydb-upgrade-chain/Tests/upgrade.stable.out.int128
sql/test/emptydb-upgrade-chain/Tests/upgrade.stable.out.powerpc64
sql/test/emptydb-upgrade-chain/Tests/upgrade.stable.out.powerpc64.int128
sql/test/emptydb-upgrade-hge/Tests/All
sql/test/emptydb-upgrade-hge/Tests/upgrade.stable.out.int128
sql/test/emptydb-upgrade/Tests/All
sql/test/emptydb-upgrade/Tests/upgrade.stable.out
sql/test/emptydb-upgrade/Tests/upgrade.stable.out.32bit
sql/test/emptydb-upgrade/Tests/upgrade.stable.out.int128
sql/test/emptydb/Tests/All
sql/test/emptydb/Tests/check.stable.out
sql/test/emptydb/Tests/check.stable.out.32bit
sql/test/emptydb/Tests/check.stable.out.int128
sql/test/group-concat/Tests/groupconcat05.sql
sql/test/group-concat/Tests/groupconcat05.stable.out
sql/test/mapi/Tests/All
sql/test/mapi/Tests/python3_dbapi.SQL.bat
sql/test/mapi/Tests/python3_dbapi.SQL.sh
sql/test/merge-partitions/Tests/All
sql/test/mergetables/Tests/All
sql/test/pg_regress/Tests/interval.stable.out
sql/test/pg_regress/Tests/interval.stable.out.int128
sql/test/subquery/Tests/correlated.stable.err
sql/test/subquery/Tests/correlated.stable.out
sql/test/subquery/Tests/subquery3.sql
sql/test/subquery/Tests/subquery3.stable.err
sql/test/subquery/Tests/subquery3.stable.out
sql/test/sys-schema/Tests/All
sql/test/sys-schema/Tests/systemfunctions.stable.out
sql/test/sys-schema/Tests/systemfunctions.stable.out.int128
sql/test/testdb-upgrade-chain-hge/Tests/upgrade.stable.out.int128
sql/test/testdb-upgrade-chain/Tests/upgrade.stable.out
sql/test/testdb-upgrade-chain/Tests/upgrade.stable.out.32bit
sql/test/testdb-upgrade-chain/Tests/upgrade.stable.out.int128
sql/test/testdb-upgrade-hge/Tests/upgrade.stable.out.int128
sql/test/testdb-upgrade/Tests/upgrade.stable.out
sql/test/testdb-upgrade/Tests/upgrade.stable.out.32bit
sql/test/testdb-upgrade/Tests/upgrade.stable.out.int128
testing/Mfilter.py
testing/Mtest.py.in
tools/merovingian/daemon/forkmserver.c
tools/mserver/mserver5.1.in
tools/mserver/mserver5.c
Branch: mosaic
Log Message:
Merge with default.
diffs (truncated from 265975 to 300 lines):
diff --git a/ChangeLog b/ChangeLog
--- a/ChangeLog
+++ b/ChangeLog
@@ -1,6 +1,9 @@
# ChangeLog file for devel
# This file is updated with Maddlog
+* Thu Jan 30 2020 Sjoerd Mullender <sjo...@acm.org>
+- Removed support for bam and sam files.
+
* Fri Dec 6 2019 Panagiotis Koutsourakis <kutsu...@monetdbsolutions.com>
- Added mserver5 option (--set raw_strings=true|false) and monetdb
database property (raw_strings=yes|no) to control interpretation
diff --git a/MonetDB.spec b/MonetDB.spec
--- a/MonetDB.spec
+++ b/MonetDB.spec
@@ -66,16 +66,6 @@
%endif
%endif
-%if %{?rhel:0}%{!?rhel:1}
-# By default create the MonetDB-bam-MonetDB5 package.
-# Note that the samtools-devel RPM is not available on RedHat
-# Enterprise Linux and derivatives, even with EPEL availabe.
-# (Actually, at the moment of writing, samtools-devel is available in
-# EPEL for RHEL 6, but not for RHEL 7. We don't make the distinction
-# here and just not build the MonetDB-bam-MonetDB5 RPM.)
-%bcond_without samtools
-%endif
-
# By default use PCRE for the implementation of the SQL LIKE and ILIKE
# operators. Otherwise the POSIX regex functions are used.
%bcond_without pcre
@@ -85,11 +75,6 @@
%bcond_without rintegration
%endif
-# On Fedora <= 30 and RHEL 7, create the MonetDB-python2 package.
-# On RHEL 6, numpy is too old.
-%if 0%{?rhel} == 7 || %{!?fedora:1000}%{?fedora} <= 30
-%bcond_without py2integration
-%endif
%if %{?rhel:0}%{!?rhel:1}
# On RHEL 6, Python 3 is too old, and on RHEL 7, the default Python 3
# is too old (in both cases 3.4).
@@ -156,18 +141,6 @@ BuildRequires: readline-devel
BuildRequires: unixODBC-devel
# BuildRequires: uriparser-devel
BuildRequires: pkgconfig(zlib)
-%if %{with samtools}
-BuildRequires: samtools-devel
-%endif
-%if %{with py2integration}
-BuildRequires: python-devel
-%if %{?rhel:1}%{!?rhel:0}
-# RedHat Enterprise Linux calls it simply numpy
-BuildRequires: numpy
-%else
-BuildRequires: python2-numpy
-%endif
-%endif
%if %{with py3integration}
BuildRequires: python3-devel >= 3.5
BuildRequires: python3-numpy
@@ -467,29 +440,6 @@ This package contains support for readin
%{_libdir}/monetdb5/lib_lidar.so
%endif
-%if %{with samtools}
-%package bam-MonetDB5
-Summary: MonetDB5 SQL interface to the bam library
-Group: Applications/Databases
-Requires: MonetDB5-server%{?_isa} = %{version}-%{release}
-
-%description bam-MonetDB5
-MonetDB is a database management system that is developed from a
-main-memory perspective with use of a fully decomposed storage model,
-automatic index management, extensibility of data types and search
-accelerators. It also has an SQL front end.
-
-This package contains the interface to load and query BAM (binary
-version of Sequence Alignment/Map) data.
-
-%files bam-MonetDB5
-%defattr(-,root,root)
-%{_libdir}/monetdb5/autoload/*_bam.mal
-%{_libdir}/monetdb5/createdb/*_bam.sql
-%{_libdir}/monetdb5/bam.mal
-%{_libdir}/monetdb5/lib_bam.so
-%endif
-
%if %{with rintegration}
%package R
Summary: Integration of MonetDB and R, allowing use of R from within SQL
@@ -516,32 +466,6 @@ install it.
%{_libdir}/monetdb5/lib_rapi.so
%endif
-%if %{with py2integration}
-%package python2
-Summary: Integration of MonetDB and Python, allowing use of Python from within
SQL
-Group: Applications/Databases
-Requires: MonetDB-SQL-server5%{?_isa} = %{version}-%{release}
-
-%description python2
-MonetDB is a database management system that is developed from a
-main-memory perspective with use of a fully decomposed storage model,
-automatic index management, extensibility of data types and search
-accelerators. It also has an SQL front end.
-
-This package contains the interface to use the Python language from
-within SQL queries. This package is for Python 2.
-
-NOTE: INSTALLING THIS PACKAGE OPENS UP SECURITY ISSUES. If you don't
-know how this package affects the security of your system, do not
-install it.
-
-%files python2
-%defattr(-,root,root)
-%{_libdir}/monetdb5/pyapi.*
-%{_libdir}/monetdb5/autoload/*_pyapi.mal
-%{_libdir}/monetdb5/lib_pyapi.so
-%endif
-
%if %{with py3integration}
%package python3
Summary: Integration of MonetDB and Python, allowing use of Python from within
SQL
@@ -642,9 +566,6 @@ exit 0
%if %{with lidar}
%exclude %{_libdir}/monetdb5/lidar.mal
%endif
-%if %{with py2integration}
-%exclude %{_libdir}/monetdb5/pyapi.mal
-%endif
%if %{with py3integration}
%exclude %{_libdir}/monetdb5/pyapi3.mal
%endif
@@ -663,9 +584,6 @@ exit 0
%if %{with lidar}
%exclude %{_libdir}/monetdb5/autoload/*_lidar.mal
%endif
-%if %{with py2integration}
-%exclude %{_libdir}/monetdb5/autoload/*_pyapi.mal
-%endif
%if %{with py3integration}
%exclude %{_libdir}/monetdb5/autoload/*_pyapi3.mal
%endif
@@ -674,10 +592,6 @@ exit 0
%endif
%exclude %{_libdir}/monetdb5/autoload/??_sql*.mal
%{_libdir}/monetdb5/autoload/*.mal
-%if %{with samtools}
-%exclude %{_libdir}/monetdb5/bam.mal
-%exclude %{_libdir}/monetdb5/autoload/*_bam.mal
-%endif
%{_libdir}/monetdb5/lib_capi.so
%{_libdir}/monetdb5/lib_generator.so
%{_libdir}/monetdb5/lib_udf.so
@@ -781,9 +695,6 @@ use SQL with MonetDB, you will need to i
%if %{with lidar}
%exclude %{_libdir}/monetdb5/createdb/*_lidar.sql
%endif
-%if %{with samtools}
-%exclude %{_libdir}/monetdb5/createdb/*_bam.sql
-%endif
%{_libdir}/monetdb5/createdb/*.sql
%{_libdir}/monetdb5/sql*.mal
%if %{with hugeint}
@@ -967,7 +878,6 @@ export CFLAGS
--enable-netcdf=no \
--enable-odbc=yes \
--enable-profiler=no \
-
--enable-py2integration=%{?with_py2integration:yes}%{!?with_py2integration:no} \
--enable-py3integration=%{?with_py3integration:yes}%{!?with_py3integration:no} \
--enable-rintegration=%{?with_rintegration:yes}%{!?with_rintegration:no} \
--enable-sanitizer=no \
@@ -986,11 +896,9 @@ export CFLAGS
--with-openssl=yes \
--with-proj=no \
--with-pthread=yes \
- --with-python2=%{?with_py2integration:yes}%{!?with_py2integration:no} \
--with-python3=yes \
--with-readline=yes \
--with-regex=%{?with_pcre:PCRE}%{!?with_pcre:POSIX} \
- --with-samtools=%{?with_samtools:yes}%{!?with_samtools:no} \
--with-snappy=no \
--with-unixodbc=yes \
--with-uuid=yes \
diff --git a/NT/mksqlwxs.py b/NT/mksqlwxs.py
--- a/NT/mksqlwxs.py
+++ b/NT/mksqlwxs.py
@@ -51,7 +51,6 @@ def main():
extend = []
debug = []
geom = []
- pyapi2 = []
pyapi3 = []
print(r'<?xml version="1.0"?>')
print(r'<Wix xmlns="http://schemas.microsoft.com/wix/2006/wi";>')
@@ -85,14 +84,6 @@ def main():
print(r' <FileSearch Id="CheckFile3" Name="geom.mal"/>')
print(r' </DirectorySearch>')
print(r' </Property>')
- print(r' <Property Id="PYAPI2EXISTS">')
- print(r' <DirectorySearch Id="CheckFileDir4" Path="[INSTALLDIR]"
Depth="0">')
- print(r' <FileSearch Id="CheckFile4"
Name="pyapi_locatepython.bat"/>')
- print(r' </DirectorySearch>')
- print(r' <DirectorySearch Id="CheckFileDir42" Path="[INSTALLDIR]"
Depth="0">')
- print(r' <FileSearch Id="CheckFile42"
Name="pyapi_locatepython2.bat"/>')
- print(r' </DirectorySearch>')
- print(r' </Property>')
print(r' <Property Id="PYAPI3EXISTS">')
print(r' <DirectorySearch Id="CheckFileDir5" Path="[INSTALLDIR]"
Depth="0">')
print(r' <FileSearch Id="CheckFile5"
Name="pyapi_locatepython3.bat"/>')
@@ -181,8 +172,6 @@ def main():
[r'lib\monetdb5\autoload\{}'.format(x) for x in
sorted(filter(lambda x: x.endswith('.mal') and ('geom' not in x) and ('pyapi'
not in x) and ('opt_sql_append' not in x), os.listdir(os.path.join(sys.argv[3],
'lib', 'monetdb5', 'autoload'))))])
id = comp(geom, id, 18,
[r'lib\monetdb5\autoload\{}'.format(x) for x in
sorted(filter(lambda x: x.endswith('.mal') and ('geom' in x),
os.listdir(os.path.join(sys.argv[3], 'lib', 'monetdb5', 'autoload'))))])
- id = comp(pyapi2, id, 18,
- [r'lib\monetdb5\autoload\{}'.format(x) for x in
sorted(filter(lambda x: x.endswith('_pyapi.mal'),
os.listdir(os.path.join(sys.argv[3], 'lib', 'monetdb5', 'autoload'))))])
id = comp(pyapi3, id, 18,
[r'lib\monetdb5\autoload\{}'.format(x) for x in
sorted(filter(lambda x: x.endswith('_pyapi3.mal'),
os.listdir(os.path.join(sys.argv[3], 'lib', 'monetdb5', 'autoload'))))])
print(r' </Directory>')
@@ -202,9 +191,6 @@ def main():
[r'lib\monetdb5\{}'.format(x) for x in sorted(filter(lambda x:
x.endswith('.mal') and ('geom' in x), os.listdir(os.path.join(sys.argv[3],
'lib', 'monetdb5'))))])
id = comp(geom, id, 16,
[r'lib\monetdb5\{}'.format(x) for x in sorted(filter(lambda x:
x.startswith('lib_') and (x.endswith('.dll') or x.endswith('.pdb')) and ('geom'
in x), os.listdir(os.path.join(sys.argv[3], 'lib', 'monetdb5'))))])
- id = comp(pyapi2, id, 16,
- [r'lib\monetdb5\pyapi.mal',
- r'lib\monetdb5\lib_pyapi.dll'])
id = comp(pyapi3, id, 16,
[r'lib\monetdb5\pyapi3.mal',
r'lib\monetdb5\lib_pyapi3.dll'])
@@ -240,8 +226,6 @@ def main():
r'M5server.bat',
r'msqldump.bat',
r'stethoscope.bat'])
- id = comp(pyapi2, id, 12,
- [r'pyapi_locatepython2.bat'])
id = comp(pyapi3, id, 12,
[r'pyapi_locatepython3.bat'])
id = comp(features, id, 12,
@@ -272,11 +256,6 @@ def main():
print(r' <ComponentRef Id="{}"/>'.format(f))
print(r' <MergeRef Id="VCRedist"/>')
print(r' </Feature>')
- print(r' <Feature Id="PyAPI2" Level="1000" AllowAdvertise="no"
Absent="allow" Title="Include embedded Python 2" Description="Files required
for using embedded Python 2.">')
- for f in pyapi2:
- print(r' <ComponentRef Id="{}"/>'.format(f))
- print(r' <Condition Level="1">PYAPI2EXISTS</Condition>')
- print(r' </Feature>')
print(r' <Feature Id="PyAPI3" Level="1000" AllowAdvertise="no"
Absent="allow" Title="Include embedded Python 3" Description="Files required
for using embedded Python 3.">')
for f in pyapi3:
print(r' <ComponentRef Id="{}"/>'.format(f))
diff --git a/NT/monetdb_config.h.in b/NT/monetdb_config.h.in
--- a/NT/monetdb_config.h.in
+++ b/NT/monetdb_config.h.in
@@ -112,18 +112,6 @@
/* there is something very similar to asctime_r on Windows: */
#define asctime_r(t,b,s) asctime_s(b,s,t)
-/* Define to 1 if you have the <bam/bam.h> header file. */
-/* #undef HAVE_BAM_BAM_H */
-
-/* Define to 1 if you have the <bam/bgzf.h> header file. */
-/* #undef HAVE_BAM_BGZF_H */
-
-/* Define to 1 if you have the <bam/kstring.h> header file. */
-/* #undef HAVE_BAM_KSTRING_H */
-
-/* Define to 1 if you have the <bam/sam.h> header file. */
-/* #undef HAVE_BAM_SAM_H */
-
/* Define to 1 if you have the `cbrt' function. */
#define HAVE_CBRT 1
@@ -258,9 +246,6 @@
/* #undef HAVE_LIBPTHREAD */
/* Define if we can link to python */
-/* #undef HAVE_LIBPY2 */
-
-/* Define if we can link to python */
/* #undef HAVE_LIBPY3 */
/* Define if you have libR installed */
@@ -364,22 +349,6 @@
/* Define to 1 if you have the <pwd.h> header file. */
/* #undef HAVE_PWD_H */
-/* Define if you have the samtools version 0.1.x (providing the bam library)
- */
-/* #undef HAVE_SAMTOOLS */
-
-/* Define to 1 if you have the <samtools/bam.h> header file. */
-/* #undef HAVE_SAMTOOLS_BAM_H */
-
-/* Define to 1 if you have the <samtools/bgzf.h> header file. */
-/* #undef HAVE_SAMTOOLS_BGZF_H */
-
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