[med-svn] [Git][med-team/seqan-raptor][master] 9 commits: append CPPFLAGS, don't replace it
Michael R. Crusoe (@crusoe)
gitlab at salsa.debian.org
Tue Nov 1 12:01:50 GMT 2022
Michael R. Crusoe pushed to branch master at Debian Med / seqan-raptor
Commits:
679d43de by Michael R. Crusoe at 2022-11-01T11:21:42+01:00
append CPPFLAGS, don't replace it
- - - - -
c0de706a by Michael R. Crusoe at 2022-11-01T11:21:43+01:00
Don't compile with -march=native
- - - - -
0677e816 by Michael R. Crusoe at 2022-11-01T11:59:43+01:00
Revert "Upstream says doxygen docs aren't ready yet, so skip that for now."
This reverts commit 2317fd6531e382e38695f2af4f238eec2e9eaf9a.
- - - - -
e16804a0 by Michael R. Crusoe at 2022-11-01T12:25:05+01:00
Also include man page for raptor build
- - - - -
2d91db2c by Michael R. Crusoe at 2022-11-01T12:59:31+01:00
d/rules: build hardening
- - - - -
a5dd854e by Michael R. Crusoe at 2022-11-01T12:59:32+01:00
d/control: remove first-person language from the descriptions
- - - - -
faa7e6e9 by Michael R. Crusoe at 2022-11-01T12:59:32+01:00
d/control: -doc goes in the doc section
- - - - -
2a63e4c5 by Michael R. Crusoe at 2022-11-01T12:59:32+01:00
d/patches/spelling: fix a typo
- - - - -
d1d60e6f by Michael R. Crusoe at 2022-11-01T13:00:02+01:00
routine-update: Ready to upload to unstable
- - - - -
6 changed files:
- debian/changelog
- debian/control
- debian/patches/series
- + debian/patches/spelling
- debian/rules
- + debian/seqan-raptor.install
Changes:
=====================================
debian/changelog
=====================================
@@ -1,3 +1,16 @@
+seqan-raptor (2.0.0.0.git.fecfbca+ds-3) unstable; urgency=medium
+
+ * Append the CPPFLAGS, not overwrite it
+ * Don't compile with -march=native
+ * Revert: Upstream says doxygen docs aren't ready yet, so skip that for now.
+ * Also include man page for raptor build
+ * d/rules: build hardening
+ * d/control: remove first-person language from the descriptions
+ * d/control: -doc goes in the doc section
+ * d/patches/spelling: fix a typo
+
+ -- Michael R. Crusoe <crusoe at debian.org> Tue, 01 Nov 2022 13:00:02 +0100
+
seqan-raptor (2.0.0.0.git.fecfbca+ds-2) unstable; urgency=medium
* Generate and package the man pages.
=====================================
debian/control
=====================================
@@ -10,16 +10,15 @@ Build-Depends: debhelper-compat (= 13),
libxxhash-dev,
libcereal-dev,
libsimde-dev,
- pkg-config
-# # https://github.com/seqan/raptor/issues/170#issuecomment-1285818250
-# doxygen <!nodoc>,
-# texlive-font-utils <!nodoc>,
-# texlive-latex-base <!nodoc>,
-# texlive-latex-recommended <!nodoc>,
-# texlive-latex-extra <!nodoc>,
-# texlive-plain-generic <!nodoc>,
-# texlive-fonts-recommended <!nodoc>,
-# ghostscript <!nodoc>
+ pkg-config,
+ doxygen <!nodoc>,
+ texlive-font-utils <!nodoc>,
+ texlive-latex-base <!nodoc>,
+ texlive-latex-recommended <!nodoc>,
+ texlive-latex-extra <!nodoc>,
+ texlive-plain-generic <!nodoc>,
+ texlive-fonts-recommended <!nodoc>,
+ ghostscript <!nodoc>
Standards-Version: 4.6.1
Vcs-Browser: https://salsa.debian.org/med-team/seqan-raptor
Vcs-Git: https://salsa.debian.org/med-team/seqan-raptor.git
@@ -35,24 +34,20 @@ Description: pre-filter for querying very large collections of nucleotide sequen
nucleotide sequences. Raptor uses winnowing minimizers to define a set of
representative k-mers, an extension of the interleaved Bloom filters (IBFs) as
a set membership data structure and probabilistic thresholding for minimizers.
- Our approach allows compression and partitioning of the IBF to enable the
- effective use of secondary memory. We test and show the performance and
- limitations of the new features using simulated and real datasets. Our data
- structure can be used to accelerate various core bioinformatics applications.
+ This approach allows compression and partitioning of the IBF to enable the
+ effective use of secondary memory.
-# https://github.com/seqan/raptor/issues/170#issuecomment-1285818250
-# Package: seqan-raptor-doc
-# Architecture: all
-# Depends: ${misc:Depends}
-# Description: HTML & PDF documentation for seqan-raptor and its APIs
-# Raptor is a system for approximately searching many queries such as
-# next-generation sequencing reads or transcripts in large collections of
-# nucleotide sequences. Raptor uses winnowing minimizers to define a set of
-# representative k-mers, an extension of the interleaved Bloom filters (IBFs) as
-# a set membership data structure and probabilistic thresholding for minimizers.
-# Our approach allows compression and partitioning of the IBF to enable the
-# effective use of secondary memory. We test and show the performance and
-# limitations of the new features using simulated and real datasets. Our data
-# structure can be used to accelerate various core bioinformatics applications.
-# .
-# This package contains Raptor's docs (HTML & PDF).
+Package: seqan-raptor-doc
+Architecture: all
+Depends: ${misc:Depends}
+Section: doc
+Description: HTML & PDF documentation for seqan-raptor and its APIs
+ Raptor is a system for approximately searching many queries such as
+ next-generation sequencing reads or transcripts in large collections of
+ nucleotide sequences. Raptor uses winnowing minimizers to define a set of
+ representative k-mers, an extension of the interleaved Bloom filters (IBFs) as
+ a set membership data structure and probabilistic thresholding for minimizers.
+ This approach allows compression and partitioning of the IBF to enable the
+ effective use of secondary memory.
+ .
+ This package contains Raptor's docs (HTML & PDF).
=====================================
debian/patches/series
=====================================
@@ -1,3 +1,4 @@
+spelling
privacy
chopper_no_test
chopper_no_ccache
=====================================
debian/patches/spelling
=====================================
@@ -0,0 +1,14 @@
+Author: Michael R. Crusoe <crusoe at debian.org>
+Description: fix typo
+Forwarded: https://github.com/seqan/chopper/pull/111
+--- seqan-raptor.orig/lib/chopper/include/chopper/layout/ibf_query_cost.hpp
++++ seqan-raptor/lib/chopper/include/chopper/layout/ibf_query_cost.hpp
+@@ -41,7 +41,7 @@
+ }
+ else if (t_max > maximum_t_max)
+ {
+- throw std::invalid_argument("No data availabe for a t_max this large.");
++ throw std::invalid_argument("No data available for a t_max this large.");
+ }
+ else if (contains(t_max))
+ {
=====================================
debian/rules
=====================================
@@ -2,40 +2,31 @@
# DH_VERBOSE := 1
export LC_ALL=C.UTF-8
-
-include /usr/share/dpkg/default.mk
-export CPPFLAGS=-I/usr/include/seqan3/submodules/sdsl-lite/include/ -I/usr/include/simde -I${CURDIR}/lib/submodules/sharg-parser/include/ -I${CURDIR}/lib/submodules/lemon/include/
-# this provides:
-# DEB_SOURCE: the source package name
-# DEB_VERSION: the full version of the package (epoch + upstream vers. + revision)
-# DEB_VERSION_EPOCH_UPSTREAM: the package's version without the Debian revision
-# DEB_VERSION_UPSTREAM_REVISION: the package's version without the Debian epoch
-# DEB_VERSION_UPSTREAM: the package's upstream version
-# DEB_DISTRIBUTION: the distribution(s) listed in the current entry of debian/changelog
-# SOURCE_DATE_EPOCH: the source release date as seconds since the epoch, as
-# specified by <https://reproducible-builds.org/specs/source-date-epoch/>
-
-# for hardening you might like to uncomment this:
-# export DEB_BUILD_MAINT_OPTIONS=hardening=+all
+export DEB_BUILD_MAINT_OPTIONS=hardening=+all
+export DEB_CPPFLAGS_MAINT_APPEND=-I/usr/include/seqan3/submodules/sdsl-lite/include/ -I/usr/include/simde -I${CURDIR}/lib/submodules/sharg-parser/include/ -I${CURDIR}/lib/submodules/lemon/include/
+DPKG_EXPORT_BUILDFLAGS = 1
+include /usr/share/dpkg/buildflags.mk
%:
dh $@
-override_dh_auto_build:
- dh_auto_build
+override_dh_auto_configure:
+ dh_auto_configure -- -DRAPTOR_NATIVE_BUILD=OFF
+
+override_dh_auto_build-arch:
+ dh_auto_build --arch
obj-*/bin/raptor --export-help man > debian/raptor.1
+ obj-*/bin/raptor build --export-help man > debian/raptor-build.1
obj-*/bin/raptor search --export-help man > debian/raptor-search.1
obj-*/bin/raptor socks --export-help man > debian/raptor-socks.1
obj-*/bin/raptor socks build --export-help man > debian/raptor-socks-build.1
obj-*/bin/raptor socks lookup-kmer --export-help man > debian/raptor-socks-lookup-kmer.1
obj-*/bin/raptor upgrade --export-help man > debian/raptor-upgrade.1
-# # https://github.com/seqan/raptor/issues/170#issuecomment-1285818250
-# # see also d/control
-# override_dh_auto_build-indep:
-# ifeq (,$(filter nodoc,$(DEB_BUILD_OPTIONS) $(DEB_BUILD_PROFILES)))
-# cd obj-* && $(MAKE) doc && cd doc/latex && $(MAKE)
-# endif
+override_dh_auto_build-indep:
+ifeq (,$(filter nodoc,$(DEB_BUILD_OPTIONS) $(DEB_BUILD_PROFILES)))
+ cd obj-* && $(MAKE) doc && cd doc/latex && $(MAKE)
+endif
### When overriding auto_test make sure DEB_BUILD_OPTIONS will be respected
#override_dh_auto_test:
=====================================
debian/seqan-raptor.install
=====================================
@@ -0,0 +1 @@
+usr/bin/*
View it on GitLab: https://salsa.debian.org/med-team/seqan-raptor/-/compare/b56fd9e0cb6b0ab863e618bbc2b3b465083349a4...d1d60e6f23eee98801b99a7edbd0e386be5930c3
--
View it on GitLab: https://salsa.debian.org/med-team/seqan-raptor/-/compare/b56fd9e0cb6b0ab863e618bbc2b3b465083349a4...d1d60e6f23eee98801b99a7edbd0e386be5930c3
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