Miroirs/slackbuilds_ponce
1
0
Fork 0
mirror of https://github.com/Ponce/slackbuilds synced 2024-11-06 08:26:50 +01:00
Code Issues Projects Releases Packages Wiki Activity Actions

academic/tophat: Patched for gcc >= 6.x.

Browse source 
Signed-off-by: Matteo Bernardini <ponce@slackbuilds.org>
This commit is contained in:
Matteo Bernardini 2019-08-03 09:56:23 +02:00 committed by Robby Workman
parent 9cf0a89ff7
commit c920f65d43
2 changed files with 27 additions and 0 deletions
Show stats Download patch file Download diff file Expand all files Collapse all files

24
academic/tophat/make_pair.patch Normal file
View file

@ -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());

3
academic/tophat/tophat.SlackBuild
View file

@ -69,6 +69,9 @@ find -L . \
\( -perm 666 -o -perm 664 -o -perm 640 -o -perm 600 -o -perm 444 \ \( -perm 666 -o -perm 664 -o -perm 640 -o -perm 600 -o -perm 444 \
-o -perm 440 -o -perm 400 \) -exec chmod 644 {} \; -o -perm 440 -o -perm 400 \) -exec chmod 644 {} \;
# Thanks archlinux
patch -p1 < $CWD/make_pair.patch
./autogen.sh ./autogen.sh
CFLAGS="$SLKCFLAGS" \ CFLAGS="$SLKCFLAGS" \