This is an automated email from the git hooks/post-receive script. afif pushed a commit to branch master in repository pbbam.
commit 2e7d209029e0e3602fe191b05a93b0b5cdddbc0d Author: Afif Elghraoui <[email protected]> Date: Sun Dec 18 22:00:44 2016 -0800 Update patches --- debian/patches/dont-try-building-gtest.patch | 26 ----- debian/patches/remove-bam2sam.patch | 14 +-- debian/patches/series | 2 - debian/patches/use-PATH-for-test-programs.patch | 125 ------------------------ 4 files changed, 7 insertions(+), 160 deletions(-) diff --git a/debian/patches/dont-try-building-gtest.patch b/debian/patches/dont-try-building-gtest.patch deleted file mode 100644 index d264b33..0000000 --- a/debian/patches/dont-try-building-gtest.patch +++ /dev/null @@ -1,26 +0,0 @@ -Description: Do not look for gtest sources - The upstream build system expects to build gtest and specifies a location - for its sources. Since we're using the Debian package, this variable is - useless and gets in the way, so just get rid of it here. -Author: Afif Elghraoui <[email protected]> -Forwarded: not-needed -Last-Update: 2015-09-07 ---- pbbam.orig/CMakeLists.txt -+++ pbbam/CMakeLists.txt -@@ -174,16 +174,6 @@ - - if(PacBioBAM_build_tests) - -- if (NOT GTEST_SRC_DIR) -- set(PREBUILT_GTEST_SRC ${PacBioBAM_RootDir}/../../../../prebuilt.tmpout/gtest/gtest_1.7.0/) -- if(EXISTS ${PREBUILT_GTEST_SRC}) -- set(GTEST_SRC_DIR ${PREBUILT_GTEST_SRC}) -- else() -- set(GTEST_SRC_DIR ../gtest) # keep old fallback behavior for external builds, for now at least -- endif() -- endif() -- -- add_subdirectory(${GTEST_SRC_DIR} external/gtest/build) - add_subdirectory(tests) - - endif() diff --git a/debian/patches/remove-bam2sam.patch b/debian/patches/remove-bam2sam.patch index df2447d..a4dec35 100644 --- a/debian/patches/remove-bam2sam.patch +++ b/debian/patches/remove-bam2sam.patch @@ -8,11 +8,11 @@ Last-Update: 2016-07-04 --- pbbam.orig/tools/CMakeLists.txt +++ pbbam/tools/CMakeLists.txt -@@ -11,7 +11,6 @@ - set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} ${PacBioBAM_CXX_FLAGS}") +@@ -39,7 +39,6 @@ + set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} ${PacBioBAM_CXX_FLAGS}") - # tools --add_subdirectory(bam2sam) - add_subdirectory(pbindex) - add_subdirectory(pbindexdump) - add_subdirectory(pbmerge) + # tools +- add_subdirectory(bam2sam) + add_subdirectory(pbindex) + add_subdirectory(pbindexdump) + add_subdirectory(pbmerge) diff --git a/debian/patches/series b/debian/patches/series index 1989259..78015f5 100644 --- a/debian/patches/series +++ b/debian/patches/series @@ -1,4 +1,2 @@ -dont-try-building-gtest.patch ssl-md5.patch remove-bam2sam.patch -use-PATH-for-test-programs.patch diff --git a/debian/patches/use-PATH-for-test-programs.patch b/debian/patches/use-PATH-for-test-programs.patch deleted file mode 100644 index 0d852d5..0000000 --- a/debian/patches/use-PATH-for-test-programs.patch +++ /dev/null @@ -1,125 +0,0 @@ -From 2feac0af36e5d360e74b9e02d5b29901ebabb036 Mon Sep 17 00:00:00 2001 -From: Afif Elghraoui <[email protected]> -Date: Tue, 5 Jul 2016 00:47:08 -0700 -Subject: [PATCH] Rely on PATH to find test programs - -Add flexibility to the tests so that they can be used if the -executables are installed elsewhere rather than fresh out of -the build tree. ---- - tests/src/cram/bam2sam.t | 4 +++- - tests/src/cram/pbindexdump_cpp.t | 4 +++- - tests/src/cram/pbindexdump_json.t | 4 +++- - tests/src/cram/pbmerge_aligned_ordering.t | 6 +++--- - tests/src/cram/pbmerge_dataset.t | 6 +++--- - tests/src/cram/pbmerge_fofn.t | 6 +++--- - tests/src/cram/pbmerge_mixed_ordering.t | 6 +++--- - tests/src/cram/pbmerge_pacbio_ordering.t | 6 +++--- - 8 files changed, 24 insertions(+), 18 deletions(-) - ---- pbbam.orig/tests/src/cram/bam2sam.t -+++ pbbam/tests/src/cram/bam2sam.t -@@ -1,6 +1,8 @@ - Setup: - -- $ BAM2SAM="$TESTDIR/../../../bin/bam2sam" && export BAM2SAM -+ $ PATH="$TESTDIR/../../../bin:$PATH" && export PATH -+ -+ $ BAM2SAM="bam2sam" && export BAM2SAM - - $ DATADIR="$TESTDIR/../../data" && export DATADIR - ---- pbbam.orig/tests/src/cram/pbindexdump_cpp.t -+++ pbbam/tests/src/cram/pbindexdump_cpp.t -@@ -1,6 +1,8 @@ - Setup: - -- $ PBINDEXDUMP="$TESTDIR/../../../bin/pbindexdump" && export PBINDEXDUMP -+ $ PATH="$TESTDIR/../../../bin:$PATH" && export PATH -+ -+ $ PBINDEXDUMP="pbindexdump" && export PBINDEXDUMP - - $ DATADIR="$TESTDIR/../../data" && export DATADIR - ---- pbbam.orig/tests/src/cram/pbindexdump_json.t -+++ pbbam/tests/src/cram/pbindexdump_json.t -@@ -1,6 +1,8 @@ - Setup: - -- $ PBINDEXDUMP="$TESTDIR/../../../bin/pbindexdump" && export PBINDEXDUMP -+ $ PATH="$TESTDIR/../../../bin:$PATH" && export PATH -+ -+ $ PBINDEXDUMP="pbindexdump" && export PBINDEXDUMP - - $ DATADIR="$TESTDIR/../../data" && export DATADIR - ---- pbbam.orig/tests/src/cram/pbmerge_aligned_ordering.t -+++ pbbam/tests/src/cram/pbmerge_aligned_ordering.t -@@ -1,8 +1,8 @@ - Setup: - -- $ TOOLS_BIN="$TESTDIR/../../../bin" && export TOOLS_BIN -- $ PBMERGE="$TOOLS_BIN/pbmerge" && export PBMERGE -- $ BAM2SAM="$TOOLS_BIN/bam2sam" && export BAM2SAM -+ $ PATH="$TESTDIR/../../../bin:$PATH" && export PATH -+ $ PBMERGE="pbmerge" && export PBMERGE -+ $ BAM2SAM="bam2sam" && export BAM2SAM - - $ DATADIR="$TESTDIR/../../data" && export DATADIR - $ INPUT_1="$DATADIR/dataset/bam_mapping_1.bam" && export INPUT_1 ---- pbbam.orig/tests/src/cram/pbmerge_dataset.t -+++ pbbam/tests/src/cram/pbmerge_dataset.t -@@ -1,8 +1,8 @@ - Setup: - -- $ TOOLS_BIN="$TESTDIR/../../../bin" && export TOOLS_BIN -- $ PBMERGE="$TOOLS_BIN/pbmerge" && export PBMERGE -- $ BAM2SAM="$TOOLS_BIN/bam2sam" && export BAM2SAM -+ $ PATH="$TESTDIR/../../../bin:$PATH" && export PATH -+ $ PBMERGE="pbmerge" && export PBMERGE -+ $ BAM2SAM="bam2sam" && export BAM2SAM - - $ DATADIR="$TESTDIR/../../data" && export DATADIR - $ INPUT_XML="$DATADIR/polymerase/consolidate.subread.dataset.xml" && export INPUT_XML ---- pbbam.orig/tests/src/cram/pbmerge_fofn.t -+++ pbbam/tests/src/cram/pbmerge_fofn.t -@@ -1,8 +1,8 @@ - Setup: - -- $ TOOLS_BIN="$TESTDIR/../../../bin" && export TOOLS_BIN -- $ PBMERGE="$TOOLS_BIN/pbmerge" && export PBMERGE -- $ BAM2SAM="$TOOLS_BIN/bam2sam" && export BAM2SAM -+ $ PATH="$TESTDIR/../../../bin:$PATH" && export PATH -+ $ PBMERGE="pbmerge" && export PBMERGE -+ $ BAM2SAM="bam2sam" && export BAM2SAM - - $ DATADIR="$TESTDIR/../../data" && export DATADIR - $ INPUT_FOFN="$DATADIR/merge.fofn" && export INPUT_FOFN ---- pbbam.orig/tests/src/cram/pbmerge_mixed_ordering.t -+++ pbbam/tests/src/cram/pbmerge_mixed_ordering.t -@@ -1,8 +1,8 @@ - Setup: - -- $ TOOLS_BIN="$TESTDIR/../../../bin" && export TOOLS_BIN -- $ PBMERGE="$TOOLS_BIN/pbmerge" && export PBMERGE -- $ BAM2SAM="$TOOLS_BIN/bam2sam" && export BAM2SAM -+ $ PATH="$TESTDIR/../../../bin:$PATH" && export PATH -+ $ PBMERGE="pbmerge" && export PBMERGE -+ $ BAM2SAM="bam2sam" && export BAM2SAM - - $ DATADIR="$TESTDIR/../../data" && export DATADIR - $ UNALIGNED_BAM="$DATADIR/polymerase/internal.hqregions.bam" && export UNALIGNED_BAM ---- pbbam.orig/tests/src/cram/pbmerge_pacbio_ordering.t -+++ pbbam/tests/src/cram/pbmerge_pacbio_ordering.t -@@ -1,8 +1,8 @@ - Setup: - -- $ TOOLS_BIN="$TESTDIR/../../../bin" && export TOOLS_BIN -- $ PBMERGE="$TOOLS_BIN/pbmerge" && export PBMERGE -- $ BAM2SAM="$TOOLS_BIN/bam2sam" && export BAM2SAM -+ $ PATH="$TESTDIR/../../../bin:$PATH" && export PATH -+ $ PBMERGE="pbmerge" && export PBMERGE -+ $ BAM2SAM="bam2sam" && export BAM2SAM - - $ DATADIR="$TESTDIR/../../data" && export DATADIR - $ HQREGION_BAM="$DATADIR/polymerase/internal.hqregions.bam" && export HQREGION_BAM -- Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/debian-med/pbbam.git _______________________________________________ debian-med-commit mailing list [email protected] http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
