[med-svn] [Git][med-team/strelka][master] 2 commits: Prevent build error

[Andreas Tille]

Andreas Tille pushed to branch master at Debian Med / strelka


Commits:
be91af1e by Andreas Tille at 2020-05-14T15:59:40+02:00
Prevent build error

- - - - -
749d3dd0 by Andreas Tille at 2020-05-14T16:37:41+02:00
Fix htslib linking

- - - - -


4 changed files:

- debian/control
- + debian/patches/gcc.patch
- debian/patches/series
- debian/patches/use_debian_packaged_redist.patch


Changes:

=====================================
debian/control
=====================================
@@ -18,6 +18,7 @@ Build-Depends: debhelper-compat (= 12),
                zlib1g-dev,
                libhts-dev,
                rapidjson-dev,
+               samtools
 Standards-Version: 4.5.0
 Vcs-Browser: https://salsa.debian.org/med-team/strelka
 Vcs-Git: https://salsa.debian.org/med-team/strelka.git


=====================================
debian/patches/gcc.patch
=====================================
@@ -0,0 +1,15 @@
+Author: Andreas Tille <tille at debian.org>
+Last-Update: Wed, 13 May 2020 16:55:22 +0200
+Description: Prevent build error
+   error: moving a local object in a return statement prevents copy elision [-Werror=pessimizing-move]
+   note: remove ‘std::move’ call
+
+--- a/src/c++/lib/blt_util/algo_util_impl.hh
++++ b/src/c++/lib/blt_util/algo_util_impl.hh
+@@ -46,5 +46,5 @@ getDuplicatesInSortedInput(
+             begin2++;
+         }
+     }
+-    return std::move(dups);
++    return dups;
+ }


=====================================
debian/patches/series
=====================================
@@ -1,2 +1,3 @@
 2to3.patch
 use_debian_packaged_redist.patch
+gcc.patch


=====================================
debian/patches/use_debian_packaged_redist.patch
=====================================
@@ -14,7 +14,41 @@ Description: Use Debian packaged libs
  #
  # htslib
  #
-@@ -194,7 +194,7 @@ set (RAPIDJSON_FINAL_TASK ${RAPIDJSON_IN
+@@ -108,13 +108,18 @@ endif ()
+ set(THIS_HTSLIB "${THIS_PROJECT_NAME}_htslib")
+ add_custom_target(${THIS_HTSLIB} DEPENDS "${HTSLIB_FINAL_TASK}")
+ 
+-
+ if (NOT WIN32)
+     install(PROGRAMS "${HTSLIB_DIR}/bgzip" DESTINATION "${THIS_LIBEXECDIR}")
+     install(PROGRAMS "${HTSLIB_DIR}/htsfile" DESTINATION "${THIS_LIBEXECDIR}")
+     install(PROGRAMS "${HTSLIB_DIR}/tabix" DESTINATION "${THIS_LIBEXECDIR}")
+ endif ()
++else()
++message("Use Debian packaged htslib")
++message("================================")
++superset(HTSLIB_LIBRARY "-lhts")
++endif()
+ 
++if(!DEBIAN_BUILD)
+ #
+ # samtools
+ #
+@@ -175,7 +180,13 @@ if (NOT WIN32)
+     install(PROGRAMS "${BGCAT_PROG}" DESTINATION "${THIS_LIBEXECDIR}")
+     install(PROGRAMS "${BGZIP9_PROG}" DESTINATION "${THIS_LIBEXECDIR}")
+ endif ()
++else()
++message("Use Debian packaged samtools")
++message("================================")
++superset(SAMTOOLS_PROG "/usr/bin/samtools")
++endif()
+ 
++if(!DEBIAN_BUILD)
+ #
+ # rapidjson
+ #
+@@ -194,7 +205,7 @@ set (RAPIDJSON_FINAL_TASK ${RAPIDJSON_IN
  
  set(THIS_RAPIDJSON "${THIS_PROJECT_NAME}_rapidjson")
  add_custom_target(${THIS_RAPIDJSON} DEPENDS "${RAPIDJSON_FINAL_TASK}")
@@ -23,7 +57,7 @@ Description: Use Debian packaged libs
  
  
  #
-@@ -213,6 +213,7 @@ add_custom_command(
+@@ -213,6 +224,7 @@ add_custom_command(
  set(THIS_CODEMIN "${THIS_PROJECT_NAME}_codemin")
  add_custom_target(${THIS_CODEMIN} DEPENDS "${CODEMIN_MARK}")
  
@@ -31,7 +65,7 @@ Description: Use Debian packaged libs
  #
  # pyflow
  #
-@@ -242,13 +243,15 @@ install_python_lib_dir("${PYFLOW_DIR}/sr
+@@ -242,13 +254,15 @@ install_python_lib_dir("${PYFLOW_DIR}/sr
  
  set (THIS_PYFLOW "${THIS_PROJECT_NAME}_pyflow")
  add_custom_target(${THIS_PYFLOW} DEPENDS "${PYFLOW_DEPENDS}")



View it on GitLab: https://salsa.debian.org/med-team/strelka/-/compare/d26f9031df084d6110ef1d9746cd31a3793ebcc2...749d3dd02c287e5030a4c868f841015ffdba73d0

-- 
View it on GitLab: https://salsa.debian.org/med-team/strelka/-/compare/d26f9031df084d6110ef1d9746cd31a3793ebcc2...749d3dd02c287e5030a4c868f841015ffdba73d0
You're receiving this email because of your account on salsa.debian.org.


-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://alioth-lists.debian.net/pipermail/debian-med-commit/attachments/20200514/08bdd760/attachment-0001.html>