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author Matteo Bernardini2019-08-03 09:56:23 +0200
committer Matteo Bernardini2021-03-06 10:55:07 +0100
commit13ab35fa213ac5540e3c6a07b4522b06245ea0fb (patch)
tree686d00b388340c7674760f522074dacf6f59ff94
parent3c59cb22425adf5d8a0d1a79baf00e6d9334c620 (diff)
downloadslackbuilds-tophat.tar.gz
academic/tophat: Patched for gcc >= 6.x.tophat
Signed-off-by: Matteo Bernardini <ponce@slackbuilds.org>
-rw-r--r--academic/tophat/make_pair.patch24
-rw-r--r--academic/tophat/tophat.SlackBuild3
2 files changed, 27 insertions, 0 deletions
diff --git a/academic/tophat/make_pair.patch b/academic/tophat/make_pair.patch
new file mode 100644
index 0000000000..44b71d1059
--- /dev/null
+++ b/academic/tophat/make_pair.patch
@@ -0,0 +1,24 @@
+diff -uBw -aur tophat-2.1.1/src/juncs_db.cpp tophat-2.1.1-patched/src/juncs_db.cpp
+--- tophat-2.1.1/src/juncs_db.cpp 2016-02-14 19:21:17.354079000 +0100
++++ tophat-2.1.1-patched/src/juncs_db.cpp 2016-06-02 11:26:34.097425159 +0200
+@@ -338,7 +338,7 @@
+ uint32_t left_coord = atoi(scan_left_coord);
+ uint32_t right_coord = atoi(scan_right_coord);
+ bool antisense = *orientation == '-';
+- junctions.insert(make_pair<Junction, JunctionStats>(Junction(ref_id, left_coord, right_coord, antisense), JunctionStats()));
++ junctions.insert(make_pair(Junction(ref_id, left_coord, right_coord, antisense), JunctionStats()));
+ }
+ }
+
+diff -uBw -aur tophat-2.1.1/src/tophat_reports.cpp tophat-2.1.1-patched/src/tophat_reports.cpp
+--- tophat-2.1.1/src/tophat_reports.cpp 2016-02-23 22:20:44.320710000 +0100
++++ tophat-2.1.1-patched/src/tophat_reports.cpp 2016-06-02 11:26:22.057239478 +0200
+@@ -2705,7 +2705,7 @@
+ junction_stat.gtf_match = true;
+ junction_stat.accepted = true;
+
+- gtf_junctions.insert(make_pair<Junction, JunctionStats>(Junction(ref_id, left_coord, right_coord, antisense), junction_stat));
++ gtf_junctions.insert(make_pair(Junction(ref_id, left_coord, right_coord, antisense), junction_stat));
+ }
+ }
+ fprintf(stderr, "Loaded %d GFF junctions from %s.\n", (int)(gtf_junctions.size()), gtf_juncs.c_str());
diff --git a/academic/tophat/tophat.SlackBuild b/academic/tophat/tophat.SlackBuild
index f32fb590f5..e3e97fcc85 100644
--- a/academic/tophat/tophat.SlackBuild
+++ b/academic/tophat/tophat.SlackBuild
@@ -69,6 +69,9 @@ find -L . \
\( -perm 666 -o -perm 664 -o -perm 640 -o -perm 600 -o -perm 444 \
-o -perm 440 -o -perm 400 \) -exec chmod 644 {} \;
+# Thanks archlinux
+patch -p1 < $CWD/make_pair.patch
+
./autogen.sh
CFLAGS="$SLKCFLAGS" \