This is an automated email from the git hooks/post-receive script. afif-guest pushed a commit to branch master in repository pbbam.
commit 129b08efe6069266d0bcba5341e2ea2fe9225893 Author: Afif Elghraoui <[email protected]> Date: Mon Sep 7 21:06:52 2015 -0700 Add libssl dependency and missing linker flags to allow package build --- debian/control | 1 + debian/patches/series | 1 + debian/patches/ssl-md5 | 24 ++++++++++++++++++++++++ debian/rules | 3 ++- 4 files changed, 28 insertions(+), 1 deletion(-) diff --git a/debian/control b/debian/control index c5d8ede..e750bd8 100644 --- a/debian/control +++ b/debian/control @@ -9,6 +9,7 @@ Build-Depends: debhelper (>= 9), doxygen, libboost-dev (>= 1.54), zlib1g-dev, + libssl-dev, libhts-dev, samtools Standards-Version: 3.9.6 diff --git a/debian/patches/series b/debian/patches/series index 1a37804..f3a7560 100644 --- a/debian/patches/series +++ b/debian/patches/series @@ -1 +1,2 @@ set-samtools-path +ssl-md5 diff --git a/debian/patches/ssl-md5 b/debian/patches/ssl-md5 new file mode 100644 index 0000000..af927ec --- /dev/null +++ b/debian/patches/ssl-md5 @@ -0,0 +1,24 @@ +Description: Use libssl for md5.h rather than cram + cram/md5.h was part of HTSlib [1] (seems to have been removed in the current + development tree), but those headers are not installed by that + package's build system. md5.h in particular has a very generic function, + served apparently by libssl. Furthermore, the cram/* headers are not intended + to be used directly [2]. This patch uses libssl to provide md5.h for this + package. + . + 1. https://anonscm.debian.org/cgit/debian-med/htslib.git/tree/cram/md5.h?id=12251926b9d0265738d701bb0add6fe9d070ccb3 + 2. http://sourceforge.net/p/samtools/mailman/message/33488076/ +Author: Afif Elghraoui <[email protected]> +Forwarded: no +Last-Update: 2015-09-07 +--- pbbam.orig/src/ReadGroupInfo.cpp ++++ pbbam/src/ReadGroupInfo.cpp +@@ -37,7 +37,7 @@ + + #include "pbbam/ReadGroupInfo.h" + #include "SequenceUtils.h" +-#include <cram/md5.h> ++#include <openssl/md5.h> + #include <cstdio> + #include <set> + #include <sstream> diff --git a/debian/rules b/debian/rules index 1a9b4a7..c12d579 100755 --- a/debian/rules +++ b/debian/rules @@ -14,6 +14,7 @@ override_dh_auto_configure: -DPacBioBAM_build_tests=OFF \ -DCMAKE_LIBRARY_PATH=$(DEB_HOST_MULTIARCH) \ -DHTSLIB_INCLUDE_DIRS=/usr/include \ - -DHTSLIB_LIBRARIES=/usr/lib + -DHTSLIB_LIBRARIES=/usr/lib \ + -DCMAKE_SHARED_LINKER_FLAGS="-lssl -lhts" # -DPacBioBAM_wrap_python=ON \ # -DPacBioBAM_wrap_r=ON -- 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
