[med-svn] [Git][med-team/diann][master] 3 commits: Fix syntax properly

[Nilesh Patra (@nilesh)]

Nilesh Patra pushed to branch master at Debian Med / diann


Commits:
079d9125 by Nilesh Patra at 2022-01-18T09:55:55-08:00
Fix syntax properly

- - - - -
2a2eed21 by Nilesh Patra at 2022-01-18T10:38:30-08:00
Add patch to initialise Makefile for easier maintainence

- - - - -
200f412d by Nilesh Patra at 2022-01-18T10:39:14-08:00
Remove home grown commands from d/rules, declare buildsystem as makefile

- - - - -


4 changed files:

- + debian/patches/Makefile.patch
- debian/patches/fix_syntax.patch
- debian/patches/series
- debian/rules


Changes:

=====================================
debian/patches/Makefile.patch
=====================================
@@ -0,0 +1,29 @@
+Description: Initialise makefile for building the package
+Author: Nilesh Patra <nilesh at debian.org>
+Last-Update: 2022-01-18
+--- /dev/null
++++ b/Makefile
+@@ -0,0 +1,22 @@
++CXX ?= g++
++LD = g++
++PROG = bin/diann
++OBJS = src/diann.o
++CXXFLAGS = -Wformat -Werror=format-security -std=c++17 -fpermissive -O3 -mfpmath=sse \
++           -I/usr/include/libmstoolkit \
++           -I/usr/include/eigen3 \
++           -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DGCC -DHAVE_EXPAT_CONFIG_H
++
++all: $(PROG)
++
++src/diann.cpp.o: src/diann.cpp
++	$(CXX) $(CXXFLAGS) -c $@ $<
++
++$(PROG): $(OBJS)
++	mkdir -p bin/
++	$(LD) -o $@ $< -lpthread -lmstoolkitlite -lstdc++fs $(LDFLAGS)
++
++clean:
++	rm -f src/diann.o bin/diann
++
++.PHONY: clean
+\ No newline at end of file


=====================================
debian/patches/fix_syntax.patch
=====================================
@@ -4,7 +4,7 @@ Description: Fix C++ syntax
 
 --- a/src/diann.cpp
 +++ b/src/diann.cpp
-@@ -606,6 +606,7 @@ bool load_unimod() {
+@@ -606,6 +606,7 @@
  		}
  	}
  	in.close();
@@ -12,3 +12,62 @@ Description: Fix C++ syntax
  }
  
  void init_unimod() {
+@@ -2549,12 +2550,22 @@
+ 			auto pos = std::lower_bound(frm.begin(), frm.end(), query);
+ 			if (pos == frm.end()) continue;
+ 			while (pos->mz < high) {
+-				if (open && iter == 1 && pos->charge != 1) goto finish;
++				if (open && iter == 1 && pos->charge != 1) {
++					pos++;
++					if (pos == frm.end())
++						break;
++					continue;
++				}
+ 				auto &pr = precursors[pos->pr];
+ 				if ((open || (pr.first > min && pr.first < max)) && pr.second == charge) {
+ 					if (size <= pos->pr) size = ((pos->pr * 5) / 4) + 1, temp.resize(size);
+ 					auto &match = temp[pos->pr].hit;
+-					if (p.score <= match[SCSFr - 1].score) goto finish;
++					if (p.score <= match[SCSFr - 1].score) {
++						pos++;
++						if (pos == frm.end())
++							break;
++						continue;
++					}
+ 					int fr, j; if (open) fr = pos->index;
+ 
+ 					for (i = 0; i < SCSFr - 1; i++) {
+@@ -2580,9 +2591,6 @@
+ 						if (open) match[j].fr = fr;
+ 					}
+ 				}
+-			finish:
+-				pos++;
+-				if (pos == frm.end()) break;
+ 			}
+ 		}
+ 
+@@ -5391,12 +5399,13 @@
+ 			}
+ 
+ 			int tot_pr = 0; for (i = 0; i < prs_n; i++) if (prn[i]) tot_pr++;
++			int ni = indices.size();
+ 			if (tot_pr < 2) {
+ 				for (i = 0; i < n_s; i++) quantities[i] = reference[i];
+ 				goto save;
+ 			}
+ 
+-			int ni = indices.size();
++			
+ 			B.resize(ni); A.resize(ni, ni);
+ 			for (i = 0; i < ni; i++) {
+ 				B(i) = 0.0;
+@@ -10869,7 +10878,7 @@
+ 	lib.close();
+ 
+ 	Run run(0);
+-	run.load("D:/Raw/USP/20181113_normalswath_4.wiff.dia");
++	run.load((char*)"D:/Raw/USP/20181113_normalswath_4.wiff.dia");
+ 	run.init();
+ 
+ 	ms1_rt.resize(run.ms1h.size()), ms1_peak_n.resize(run.ms1h.size());


=====================================
debian/patches/series
=====================================
@@ -1,2 +1,3 @@
 use_debian_packaged_eigen3.patch
 fix_syntax.patch
+Makefile.patch


=====================================
debian/rules
=====================================
@@ -9,17 +9,4 @@ include /usr/share/dpkg/default.mk
 export DEB_BUILD_MAINT_OPTIONS=hardening=+all
 
 %:
-	dh $@
-
-# Options removed from ../linux-build-gcc-7: -static -msse2 -march=core2
-override_dh_auto_build:
-	mkdir -p bin
-	# Does not build with option `-fstack-protector-strong` (--> needs -fpermissive for some goto statements)
-	g++ -Wformat -Werror=format-security -o bin/diann.o \
-		src/diann.cpp \
-		-std=c++17 -fpermissive -O3 -mfpmath=sse\
-		-I/usr/include/libmstoolkit \
-		-I/usr/include/eigen3 \
-		-D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DGCC -DHAVE_EXPAT_CONFIG_H
-	$(LD) -o bin/diann \
-		-lpthread -lstdc++fs -lmstoolkitlite # $(LDFLAGS)
+	dh $@ --buildsystem=makefile



View it on GitLab: https://salsa.debian.org/med-team/diann/-/compare/217fee6950d68b44f0d01ab291e830ecb04ddf3b...200f412dbfd639c94069408afa06cb043ce4825a

-- 
View it on GitLab: https://salsa.debian.org/med-team/diann/-/compare/217fee6950d68b44f0d01ab291e830ecb04ddf3b...200f412dbfd639c94069408afa06cb043ce4825a
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