diff options
Diffstat (limited to 'sci-chemistry/azara/files/2.8-prll.patch')
| -rw-r--r-- | sci-chemistry/azara/files/2.8-prll.patch | 387 |
1 files changed, 387 insertions, 0 deletions
diff --git a/sci-chemistry/azara/files/2.8-prll.patch b/sci-chemistry/azara/files/2.8-prll.patch new file mode 100644 index 000000000000..4720bb659445 --- /dev/null +++ b/sci-chemistry/azara/files/2.8-prll.patch @@ -0,0 +1,387 @@ +diff --git a/DataRows/makefile b/DataRows/makefile +index 587e710..4e0a312 100644 +--- a/DataRows/makefile ++++ b/DataRows/makefile +@@ -28,7 +28,7 @@ GLOBAL_OBJS = \ + $(GLOBAL_DIR)/ref.o \ + $(GLOBAL_DIR)/utility.o + +-DataRows.so: locals globals ++DataRows.so: $(LOCAL_OBJS) $(GLOBAL_OBJS) + $(CC) $(SHARED_FLAGS) -o $@ $(CFLAGS) $(LFLAGS) \ + $(LOCAL_OBJS) \ + $(GLOBAL_OBJS) +diff --git a/azara/makefile b/azara/makefile +index 3ba0cd9..f7b4ce5 100644 +--- a/azara/makefile ++++ b/azara/makefile +@@ -12,7 +12,7 @@ LOCAL_OBJS = \ + GLOBAL_OBJS = \ + $(GLOBAL_DIR)/help.o + +-azara: locals globals ++azara: $(LOCAL_OBJS) $(GLOBAL_OBJS) + $(CC) -o $@ $(LFLAGS) \ + $(LOCAL_OBJS) \ + $(GLOBAL_OBJS) \ +diff --git a/combine/makefile b/combine/makefile +index a855236..7a83d8f 100644 +--- a/combine/makefile ++++ b/combine/makefile +@@ -20,7 +20,7 @@ GLOBAL_OBJS = \ + $(GLOBAL_DIR)/ref.o \ + $(GLOBAL_DIR)/utility.o + +-combine: locals globals ++combine: $(LOCAL_OBJS) $(GLOBAL_OBJS) + $(CC) -o $@ $(LFLAGS) \ + $(LOCAL_OBJS) \ + $(GLOBAL_OBJS) \ +diff --git a/connect/makefile b/connect/makefile +index d75e7da..d238507 100644 +--- a/connect/makefile ++++ b/connect/makefile +@@ -23,7 +23,7 @@ GLOBAL_OBJS = \ + $(GLOBAL_DIR)/ref.o \ + $(GLOBAL_DIR)/utility.o + +-connect: locals globals ++connect: $(LOCAL_OBJS) $(GLOBAL_OBJS) + $(CC) -o $@ $(LFLAGS) \ + $(LOCAL_OBJS) \ + $(GLOBAL_OBJS) \ +diff --git a/contours/makefile b/contours/makefile +index 5b832b8..49175dd 100644 +--- a/contours/makefile ++++ b/contours/makefile +@@ -19,7 +19,7 @@ GLOBAL_OBJS = \ + $(GLOBAL_DIR)/ref.o \ + $(GLOBAL_DIR)/utility.o + +-contours: locals globals ++contours: $(LOCAL_OBJS) $(GLOBAL_OBJS) + $(CC) -o $@ $(LFLAGS) \ + $(LOCAL_OBJS) \ + $(GLOBAL_OBJS) \ +diff --git a/deflate/makefile b/deflate/makefile +index 4c4e02e..42d5c30 100644 +--- a/deflate/makefile ++++ b/deflate/makefile +@@ -18,7 +18,7 @@ GLOBAL_OBJS = \ + $(GLOBAL_DIR)/ref.o \ + $(GLOBAL_DIR)/utility.o + +-deflate: locals globals ++deflate: $(LOCAL_OBJS) $(GLOBAL_OBJS) + $(CC) -o $@ $(LFLAGS) \ + $(LOCAL_OBJS) \ + $(GLOBAL_OBJS) \ +diff --git a/extract/makefile b/extract/makefile +index 3212cb9..fed874b 100644 +--- a/extract/makefile ++++ b/extract/makefile +@@ -18,7 +18,7 @@ GLOBAL_OBJS = \ + $(GLOBAL_DIR)/ref.o \ + $(GLOBAL_DIR)/utility.o + +-extract: locals globals ++extract: $(LOCAL_OBJS) $(GLOBAL_OBJS) + $(CC) -o $@ $(LFLAGS) \ + $(LOCAL_OBJS) \ + $(GLOBAL_OBJS) \ +diff --git a/global/makefile b/global/makefile +index 364fa41..5272a31 100644 +--- a/global/makefile ++++ b/global/makefile +@@ -42,6 +42,31 @@ LINPACK_OBJS = \ + AZARA_OBJS = \ + help.o + ++all: \ ++ azara_objects \ ++ decay_objects \ ++ simulate_objects \ ++ viewer_objects \ ++ components_objects \ ++ shuffle_objects \ ++ connect_objects \ ++ slides_objects \ ++ peak_find_objects \ ++ peak_fit_objects \ ++ plot1_objects \ ++ reflate_objects \ ++ deflate_objects \ ++ combine_objects \ ++ unblock_objects \ ++ extract_objects \ ++ project_objects \ ++ contours_objects \ ++ plot2_nog_objects \ ++ plot2_objects \ ++ process_objects \ ++ python_objects \ ++ integrate_objects ++ + azara_objects: $(AZARA_OBJS) + + DECAY_OBJS = \ +diff --git a/help/makefile b/help/makefile +index 9e99a7c..59a86a3 100644 +--- a/help/makefile ++++ b/help/makefile +@@ -39,7 +39,7 @@ globals: + + .c.o:; $(CC) -c $(CFLAGS) $< + +-hlp: ++hlp: txt2hlp + $(TXT2HLP) azara + $(TXT2HLP) combine + $(TXT2HLP) connect +@@ -78,7 +78,7 @@ hlp: + $(TXT2HLP) plot1/text + $(TXT2HLP) DataRows + +-html: ++html: txt2html + $(TXT2HTML) azara + $(TXT2HTML) combine + $(TXT2HTML) connect +diff --git a/makefile b/makefile +index 9965b07..f4383af 100644 +--- a/makefile ++++ b/makefile +@@ -14,7 +14,7 @@ all: help nongui DataRows gui + help: \ + help_program + +-nongui: \ ++nongui: help \ + process_program \ + plot2_nog_program \ + peak_program \ +@@ -29,63 +29,66 @@ nongui: \ + connect_program \ + azara_program + +-gui: \ ++gui: help \ + plot2_program \ + plot1_program + +-DataRows: \ ++DataRows: help \ + DataRows + +-process_program: +- cd process; $(MAKE) ++global: ++ $(MAKE) -C global + +-plot2_program: +- cd plot2; $(MAKE) plot2 ++process_program: global ++ $(MAKE) -C process + +-plot2_nog_program: +- cd plot2; $(MAKE) plot2_nog ++plot2_program: global ++ $(MAKE) -C plot2 + +-plot1_program: +- cd plot1; $(MAKE) ++plot2_nog_program: global ++ $(MAKE) -C plot2 plot2_nog + +-peak_program: +- cd peak; $(MAKE) ++plot1_program: global ++ $(MAKE) -C plot1 + +-extract_program: +- cd extract; $(MAKE) ++peak_program: global process_program ++ $(MAKE) -C peak + +-project_program: +- cd project; $(MAKE) ++extract_program: global ++ $(MAKE) -C extract + +-unblock_program: +- cd unblock; $(MAKE) ++project_program: global ++ $(MAKE) -C project + +-contours_program: +- cd contours; $(MAKE) ++unblock_program: global ++ $(MAKE) -C unblock + +-combine_program: +- cd combine; $(MAKE) ++contours_program: global ++ $(MAKE) -C contours + +-deflate_program: +- cd deflate; $(MAKE) ++combine_program: global ++ $(MAKE) -C combine + +-reflate_program: +- cd reflate; $(MAKE) ++deflate_program: global ++ $(MAKE) -C deflate + +-utility_program: +- cd utility; $(MAKE) ++reflate_program: global ++ $(MAKE) -C reflate + +-connect_program: +- cd connect; $(MAKE) ++utility_program: global ++ $(MAKE) -C utility + +-help_program: +- cd help; $(MAKE) ++connect_program: global ++ $(MAKE) -C connect + +-azara_program: +- cd azara; $(MAKE) ++help_program: global ++ $(MAKE) -C help + +-DataRows: +- cd DataRows; $(MAKE) ++azara_program: global ++ $(MAKE) -C azara ++ ++DataRows: global ++ $(MAKE) -C DataRows + + clean: \ + global_clean \ +@@ -227,3 +230,5 @@ azara_realclean: + DataRows_realclean: + cd DataRows; $(MAKE) realclean + ++ ++.PHONY: global process_program +diff --git a/peak/makefile b/peak/makefile +index f3c13b7..4211221 100644 +--- a/peak/makefile ++++ b/peak/makefile +@@ -97,13 +97,13 @@ COMMAND_OBJS = \ + + all: peak_find peak_fit + +-peak_find: local_find global_find ++peak_find: $(LOCAL_FIND_OBJS) $(GLOBAL_FIND_OBJS) + $(CC) -o $@ $(LFLAGS) \ + $(LOCAL_FIND_OBJS) \ + $(GLOBAL_FIND_OBJS) \ + $(LIB) $(MATH_LIB) + +-peak_fit: local_fit global_fit commands ++peak_fit: $(LOCAL_FIT_OBJS) $(GLOBAL_FIT_OBJS) $(COMMAND_OBJS) + $(CC) -o $@ $(LFLAGS) \ + $(LOCAL_FIT_OBJS) \ + $(GLOBAL_FIT_OBJS) \ +diff --git a/plot1/makefile b/plot1/makefile +index d1dce2d..e729443 100644 +--- a/plot1/makefile ++++ b/plot1/makefile +@@ -95,7 +95,7 @@ GLOBAL_OBJS = \ + $(GLOBAL_DIR)/utility.o \ + $(GLOBAL_DIR)/window.o + +-plot1: locals globals ++plot1: $(LOCAL_OBJS) $(GLOBAL_OBJS) + $(CC) -o $@ $(LFLAGS) \ + $(LOCAL_OBJS) \ + $(GLOBAL_OBJS) \ +@@ -110,7 +110,7 @@ locals: + globals: + cd $(GLOBAL_DIR); $(MAKE) plot1_objects + +-.c.o:; $(CC) $(X11_INCLUDE_DIR) $(MOTIF_INCLUDE_DIR) -c $(CFLAGS) $< ++.c.o:; $(CC) $(X11_INCLUDE_DIR) $(MOTIF_INCLUDE_DIR) -c $(CFLAGS) -I../plot2 $< + + clean: + rm -f *.o +diff --git a/plot2/makefile b/plot2/makefile +index a6b7b4a..98e286e 100644 +--- a/plot2/makefile ++++ b/plot2/makefile +@@ -129,7 +129,7 @@ GLOBAL_PLOT2_NOG_OBJS = \ + + all: plot2 plot2_nog + +-plot2: local_plot2 global_plot2 ++plot2: $(LOCAL_PLOT2_OBJS) $(GLOBAL_PLOT2_OBJS) + $(CC) -o $@ $(CFLAGS) $(LFLAGS) \ + $(LOCAL_PLOT2_OBJS) \ + $(GLOBAL_PLOT2_OBJS) \ +@@ -137,7 +137,7 @@ plot2: local_plot2 global_plot2 + $(LIB) $(MATH_LIB) \ + $(MOTIF_LIB) $(X11_LIB) $(XPM_LIB) + +-plot2_nog: local_plot2_nog global_plot2_nog ++plot2_nog: $(LOCAL_PLOT2_NOG_OBJS) $(GLOBAL_PLOT2_NOG_OBJS) + $(CC) -o $@ $(CFLAGS) $(LFLAGS) \ + $(LOCAL_PLOT2_NOG_OBJS) \ + $(GLOBAL_PLOT2_NOG_OBJS) \ +diff --git a/process/makefile b/process/makefile +index 22ceeed..72d587b 100644 +--- a/process/makefile ++++ b/process/makefile +@@ -72,7 +72,7 @@ GLOBAL_OBJS = \ + $(GLOBAL_DIR)/utility.o \ + $(LINPACK_OBJS) + +-process: locals globals ++process: $(LOCAL_OBJS) $(GLOBAL_OBJS) + $(CC) -o $@ $(LFLAGS) \ + $(LOCAL_OBJS) \ + $(GLOBAL_OBJS) \ +diff --git a/project/makefile b/project/makefile +index 78143fc..ed0f296 100644 +--- a/project/makefile ++++ b/project/makefile +@@ -18,7 +18,7 @@ GLOBAL_OBJS = \ + $(GLOBAL_DIR)/ref.o \ + $(GLOBAL_DIR)/utility.o + +-project: locals globals ++project: $(LOCAL_OBJS) $(GLOBAL_OBJS) + $(CC) -o $@ $(LFLAGS) \ + $(LOCAL_OBJS) \ + $(GLOBAL_OBJS) \ +diff --git a/reflate/makefile b/reflate/makefile +index 079a3fc..01ec311 100644 +--- a/reflate/makefile ++++ b/reflate/makefile +@@ -18,7 +18,7 @@ GLOBAL_OBJS = \ + $(GLOBAL_DIR)/ref.o \ + $(GLOBAL_DIR)/utility.o + +-reflate: locals globals ++reflate: $(LOCAL_OBJS) $(GLOBAL_OBJS) + $(CC) -o $@ $(LFLAGS) \ + $(LOCAL_OBJS) \ + $(GLOBAL_OBJS) \ +diff --git a/unblock/makefile b/unblock/makefile +index 510dc9e..d9a0f2b 100644 +--- a/unblock/makefile ++++ b/unblock/makefile +@@ -18,7 +18,7 @@ GLOBAL_OBJS = \ + $(GLOBAL_DIR)/ref.o \ + $(GLOBAL_DIR)/utility.o + +-unblock: locals globals ++unblock: $(LOCAL_OBJS) $(GLOBAL_OBJS) + $(CC) -o $@ $(LFLAGS) \ + $(LOCAL_OBJS) \ + $(GLOBAL_OBJS) \ |