diff options
author | David Seifert <soap@gentoo.org> | 2016-10-03 00:20:26 +0200 |
---|---|---|
committer | David Seifert <soap@gentoo.org> | 2016-10-03 22:21:00 +0200 |
commit | 6e813f13ba23ea1b7adc4b635b4d9508d0a9954c (patch) | |
tree | ef4b117bf0f526d48f43f0b15e7b12a1b1443fc9 /sci-biology/phred/files | |
parent | net-misc/remmina: warn about encrypted VNC deps. (diff) | |
download | gentoo-6e813f13ba23ea1b7adc4b635b4d9508d0a9954c.tar.gz gentoo-6e813f13ba23ea1b7adc4b635b4d9508d0a9954c.tar.bz2 gentoo-6e813f13ba23ea1b7adc4b635b4d9508d0a9954c.zip |
sci-biology/phred: Revbump to EAPI=6
Package-Manager: portage-2.3.1
Diffstat (limited to 'sci-biology/phred/files')
-rw-r--r-- | sci-biology/phred/files/phred-071220-fix-build-system.patch | 82 | ||||
-rw-r--r-- | sci-biology/phred/files/phred-071220-fix-qa.patch | 36 |
2 files changed, 118 insertions, 0 deletions
diff --git a/sci-biology/phred/files/phred-071220-fix-build-system.patch b/sci-biology/phred/files/phred-071220-fix-build-system.patch new file mode 100644 index 000000000000..997f39941a07 --- /dev/null +++ b/sci-biology/phred/files/phred-071220-fix-build-system.patch @@ -0,0 +1,82 @@ +* Fix build system to honour CC, CFLAGS, CPPFLAGS and LDFLAGS +* Specify a default target, in order to keep the ebuild slim + +--- a/Makefile ++++ b/Makefile +@@ -12,9 +12,9 @@ + + # UNIX specific definitions (default) + # +-CC= cc +-CFLAGS= -O -DANSI_C $(LXFLAGS) +-CLIB= -lm ++CC ?= cc ++CPPFLAGS += -DANSI_C $(LXFLAGS) ++LIBS += -lm + + # Windows 'nmake' specific definitions + # +@@ -133,9 +133,6 @@ + $(objdir)writeSDF.o \ + $(objdir)writeSeq.o + +-SRCS = $(OBJS:.o=.c) +-WOBJ = $(OBJS:.o=.obj) +- + INCS = \ + $(incdir)chromatData.h \ + $(incdir)freeChromatData.h \ +@@ -179,48 +176,18 @@ + # UNIX make specific phred target + # note: a horizontal tab character must precede `$(CC)' + # +-phred: $(OBJS) +- $(CC) $(CFLAGS) -o phred $(OBJS) $(CLIB) + + +-# Windows nmake specific phred target +-# +-forwindows: $(WOBJ) +- $(CC) $(CFLAGS) /Fephred $(WOBJ) +-# $(CC) $(CFLAGS) /Fedaev daev.c ++.PHONY: all ++all: phred daev + + +-# test CC: refuse to compile if +-# +-# o SunOS +-# +-# AND +-# +-# o using /usr/ucb/cc compiler +-# +-# NOTE: this compiler causes problems: see PHRED.DOC +-# +-test_cc: +- @if [ `uname` = SunOS ] ; \ +- then \ +- if [ `which $(CC)` = "/usr/ucb/cc" ] ; \ +- then \ +- echo ""; \ +- echo "============================================================"; \ +- echo "| |"; \ +- echo "| This SUN C compiler produces a bad phred executable. |"; \ +- echo "| |"; \ +- echo "| Please see the PHRED.DOC file for more information. |"; \ +- echo "| |"; \ +- echo "============================================================"; \ +- echo ""; \ +- exit 1; \ +- fi \ +- fi ++phred: $(OBJS) ++ $(CC) $(LDFLAGS) $(CFLAGS) -o phred $^ $(LIBS) + + + daev: daev.o +- $(CC) $(CFLAGS) -o daev daev.o -lm ++ $(CC) $(LDFLAGS) $(CFLAGS) -o daev $^ $(LIBS) + + + clean: diff --git a/sci-biology/phred/files/phred-071220-fix-qa.patch b/sci-biology/phred/files/phred-071220-fix-qa.patch new file mode 100644 index 000000000000..ab4d2ea023f6 --- /dev/null +++ b/sci-biology/phred/files/phred-071220-fix-qa.patch @@ -0,0 +1,36 @@ +Fix implicit declarations: +* daev.c: In function ‘processParameters’: +* daev.c:849:14: warning: implicit declaration of function ‘isdigit’ [-Wimplicit-function-declaration] +* if( !isdigit( argv[iarg][0] ) ) + +--- a/autoPhred.c ++++ b/autoPhred.c +@@ -57,6 +57,7 @@ + static int xstrcmp(); + #endif + ++int freeMBRData( MBRData *mbrData ); + #ifdef ANSI_C + int autoPhred( Option *option ) + #else +--- a/daev.c ++++ b/daev.c +@@ -58,6 +58,7 @@ + #include <sys/stat.h> + #include <time.h> + #include <math.h> ++#include <ctype.h> + + #ifndef _WIN32 + #include <dirent.h> +--- a/mergedBaseRead.c ++++ b/mergedBaseRead.c +@@ -63,7 +63,7 @@ + Peak *peak; + Observed_peak *obs_peak; + +- static initFlag = 0; ++ static int initFlag = 0; + static char mchar[256][256]; + + if( initFlag == 0 ) |