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authorDavid Seifert <soap@gentoo.org>2020-11-01 19:36:21 +0100
committerDavid Seifert <soap@gentoo.org>2020-11-01 19:36:21 +0100
commit053ec438e912e15f1a98959c59d4f08903d31138 (patch)
tree07465fcfb58dded0b04f2db8fe400cf9a4fcb489
parentsci-biology/seaview: Remove old 4.5.4 (diff)
downloadgentoo-053ec438e912e15f1a98959c59d4f08903d31138.tar.gz
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sci-biology/lagan: Port to EAPI 7
* Fix building against GCC 10 / -fno-common * Fix building against C99 / -O0 * Fix broken build system * Import patches from Debian Closes: https://bugs.gentoo.org/685736 Closes: https://bugs.gentoo.org/688700 Closes: https://bugs.gentoo.org/707404 Package-Manager: Portage-3.0.8, Repoman-3.0.2 Signed-off-by: David Seifert <soap@gentoo.org>
-rw-r--r--sci-biology/lagan/files/lagan-2.0-C99-static-inline.patch258
-rw-r--r--sci-biology/lagan/files/lagan-2.0-ambiguous-end.patch49
-rw-r--r--sci-biology/lagan/files/lagan-2.0-conflicting-getline.patch24
-rw-r--r--sci-biology/lagan/files/lagan-2.0-fix-c++14.patch473
-rw-r--r--sci-biology/lagan/files/lagan-2.0-gcc-10.patch27
-rw-r--r--sci-biology/lagan/files/lagan-2.0-gcc-4.8.patch25
-rw-r--r--sci-biology/lagan/files/lagan-2.0-gcc-9.patch25
-rw-r--r--sci-biology/lagan/files/lagan-2.0-gcc4.3.patch23
-rw-r--r--sci-biology/lagan/files/lagan-2.0-makefile.patch (renamed from sci-biology/lagan/files/lagan-2.0-flags.patch)109
-rw-r--r--sci-biology/lagan/files/lagan-2.0-qa-implicit-declarations.patch63
-rw-r--r--sci-biology/lagan/lagan-2.0-r3.ebuild71
-rw-r--r--sci-biology/lagan/lagan-2.0-r4.ebuild67
12 files changed, 550 insertions, 664 deletions
diff --git a/sci-biology/lagan/files/lagan-2.0-C99-static-inline.patch b/sci-biology/lagan/files/lagan-2.0-C99-static-inline.patch
new file mode 100644
index 00000000000..2c9d88111ae
--- /dev/null
+++ b/sci-biology/lagan/files/lagan-2.0-C99-static-inline.patch
@@ -0,0 +1,258 @@
+--- a/src/fchaos.c
++++ b/src/fchaos.c
+@@ -985,7 +985,7 @@
+ SLremove(mylist, tbf->mysles[i]);
+ }
+
+-inline int CHmatchscore(unsigned char a, unsigned char b) {
++static inline int CHmatchscore(unsigned char a, unsigned char b) {
+ return substmatrix[a][b];
+ /*
+ if (translated)
+--- a/src/multial.c
++++ b/src/multial.c
+@@ -59,16 +59,16 @@
+ int normf;
+ int normprev;
+
+-inline int ismatch(char a, char b) {
++static inline int ismatch(char a, char b) {
+ return (a == b);
+ }
+
+-inline int isGap(align* ali, int seqn, int loc) {
++static inline int isGap(align* ali, int seqn, int loc) {
+ int i = !((ali->algn[loc] >> seqn) & 1);
+ return i;
+ }
+
+-inline int scoreLocal(int which, align* ali, int loc) {
++static inline int scoreLocal(int which, align* ali, int loc) {
+ int i, lets = 0;
+ for (i=0; i < 4; i++)
+ lets += ali->cnts[i][loc];
+@@ -83,7 +83,7 @@
+ return lets+ali->cnts[CNTS_GS][loc] * gapcont;
+ }
+
+-inline hll* reverseHLL(hll* tbr) {
++static inline hll* reverseHLL(hll* tbr) {
+ hll *nn, *prev=0;
+ while (tbr) {
+ nn = tbr->next;
+@@ -171,7 +171,7 @@
+ return res;
+ }
+
+-inline void reverse (long long int* a, int length) {
++static inline void reverse (long long int* a, int length) {
+ long long int lft;
+ int i;
+ for (i=0; i < length/2; i++) {
+@@ -409,7 +409,7 @@
+ */
+ }
+
+-inline int scoreGap(int numgs, int numgc, int numge, int numseq) {
++static inline int scoreGap(int numgs, int numgc, int numge, int numseq) {
+ return (MIN2(numgc, numseq-numgc) * gapcont) +
+ (MIN2(numgs, numseq-numgs) * gapstart) +
+ (MIN2(numge, numseq-numge) * gapend);
+@@ -493,7 +493,7 @@
+ fclose (file);
+ }
+
+-inline int chmatchscore (unsigned char a, unsigned char b, int substmatrix[256][256]) {
++static inline int chmatchscore (unsigned char a, unsigned char b, int substmatrix[256][256]) {
+ return substmatrix[a][b];
+ }
+
+@@ -539,14 +539,14 @@
+ // printcache();
+ }
+
+-inline int v (int y){
++static inline int v (int y){
+ if (y >= 0 && y <= MAX_SEQ) return y;
+ fprintf(stderr, "Got %d in v\n", y);
+ assert (0);
+ return 0;
+ }
+
+-inline int matchscore (align*a, int ai, align *b, int bi){
++static inline int matchscore (align*a, int ai, align *b, int bi){
+
+ return
+ matchcache[v(a->cnts[0][ai] + b->cnts[0][bi]) |
+@@ -559,30 +559,30 @@
+ (v(a->numseq + b->numseq - (a->cnts[CNTS_CB][ai] + b->cnts[CNTS_CB][bi])) << 18)];
+ }
+
+-inline int scoreOpp (align *other, int ow, int oppnum){
++static inline int scoreOpp (align *other, int ow, int oppnum){
+ return matchcache[v(other->cnts[0][ow]) |
+ (v(other->cnts[1][ow]) << 6) |
+ (v(other->cnts[2][ow]) << 12) |
+ (v(other->cnts[3][ow]) << 18)];
+ }
+
+-inline int endGap0 (align* a, int ai, align* b, int bi){
++static inline int endGap0 (align* a, int ai, align* b, int bi){
+ return gapcache[(v(a->cnts[CNTS_GE][ai]+b->cnts[CNTS_GE][bi])<<12) |
+ (v(a->numseq + b->numseq-(b->cnts[CNTS_CB][bi]+a->cnts[CNTS_CB][ai])) << 18)];
+ }
+
+-inline int endGap1 (align* a, int ai, align* b, int bi){
++static inline int endGap1 (align* a, int ai, align* b, int bi){
+
+ return gapcache[(v((b->numseq - b->cnts[CNTS_GS][bi] - b->cnts[CNTS_GC][bi]) + a->cnts[CNTS_GE][ai]) << 12) |
+ (v(a->numseq + b->numseq - (b->cnts[CNTS_CB][bi]+a->cnts[CNTS_CB][ai])) << 18)];
+ }
+
+-inline int endGap2 (align* a, int ai, align* b, int bi){
++static inline int endGap2 (align* a, int ai, align* b, int bi){
+ return gapcache[(v((a->numseq - a->cnts[CNTS_GS][ai] - a->cnts[CNTS_GC][ai]) + b->cnts[CNTS_GE][bi])<<12) |
+ (v(a->numseq + b->numseq - (b->cnts[CNTS_CB][bi]+a->cnts[CNTS_CB][ai])) << 18)];
+ }
+
+-inline int contGap(align* ali, int myw, align* other, int ow, int *sopp) {
++static inline int contGap(align* ali, int myw, align* other, int ow, int *sopp) {
+ return gapcache[(v(other->cnts[CNTS_GS][ow])) |
+ (v(ali->numseq + other->cnts[CNTS_GC][ow]) << 6) |
+ (v(other->cnts[CNTS_GE][ow]) << 12) |
+@@ -590,7 +590,7 @@
+ sopp[ow];
+ }
+
+-inline int openGap(align* ali, int w, align* other, int ow, int *sopp, char *desc) {
++static inline int openGap(align* ali, int w, align* other, int ow, int *sopp, char *desc) {
+ int alopen, pen, sav, i;
+
+ alopen = ali->cnts[CNTS_GC][w] + ali->cnts[CNTS_GE][w];
+--- a/src/order.c
++++ b/src/order.c
+@@ -454,11 +454,11 @@
+ }
+
+
+-inline int ismatch(char a, char b) {
++static inline int ismatch(char a, char b) {
+ return a == b;
+ }
+
+-inline int matchscore (unsigned char a, unsigned char b) {
++static inline int matchscore (unsigned char a, unsigned char b) {
+ return substmatrix[a][b];
+ /*
+
+--- a/src/utils/cstat.c
++++ b/src/utils/cstat.c
+@@ -121,7 +121,7 @@
+ return res;
+ }
+
+-inline int getScore (align* a, int i){
++static inline int getScore (align* a, int i){
+ return
+ ((a->cnts[0][i] * (a->cnts[0][i] - 1)) +
+ (a->cnts[1][i] * (a->cnts[1][i] - 1)) +
+--- a/src/utils/getbounds.c
++++ b/src/utils/getbounds.c
+@@ -6,8 +6,8 @@
+
+ #define EXPAND 2
+
+-inline int max (int a, int b){ if (a > b) return a; return b; }
+-inline int min (int a, int b){ if (a < b) return a; return b; }
++static inline int max (int a, int b){ if (a > b) return a; return b; }
++static inline int min (int a, int b){ if (a < b) return a; return b; }
+
+ int getLength (char *filename){
+ FILE *file;
+--- a/src/utils/scorealign.c
++++ b/src/utils/scorealign.c
+@@ -18,17 +18,17 @@
+ int matchscore[256][256];
+ int gapopen = -1500, gapcont = -50;
+
+-inline int min (int a, int b){
++static inline int min (int a, int b){
+ if (a < b) return a;
+ return b;
+ }
+
+-inline int max (int a, int b){
++static inline int max (int a, int b){
+ if (a > b) return a;
+ return b;
+ }
+
+-inline int scoreMatch (char c, char d){
++static inline int scoreMatch (char c, char d){
+ if (c == '-' && d == '-') return 0;
+ if (c == '-' || d == '-') return gapcont;
+ return matchscore[(unsigned char) c][(unsigned char) d];
+@@ -235,7 +235,7 @@
+ }
+ }
+
+-inline int issymbol (char ch){
++static inline int issymbol (char ch){
+ return ch == 'A' || ch == 'C' || ch == 'G' || ch == 'T' || ch == 'N' || ch == '.' || ch == '-';
+ }
+
+--- a/src/utils/scorecontigs.c
++++ b/src/utils/scorecontigs.c
+@@ -133,7 +133,7 @@
+ return res;
+ }
+
+-inline int getstate (char c, char d){
++static inline int getstate (char c, char d){
+ if (c == '-' || d == '-') return 2;
+ if (c == 'N' || d == 'N') return 3;
+ return c == d;
+@@ -235,7 +235,7 @@
+ return r;
+ }
+
+-inline int getdata (rangelist **ranges, int *offs, int j, int i){
++static inline int getdata (rangelist **ranges, int *offs, int j, int i){
+ i -= offs[j];
+ if (i >= 0 && i < ranges[j]->seqlen)
+ return ranges[j]->score[i];
+@@ -243,14 +243,14 @@
+ }
+
+
+-inline int match (rangelist **ranges, int numContigs, int i, int j, int *offs){
++static inline int match (rangelist **ranges, int numContigs, int i, int j, int *offs){
+ int k;
+ for (k = 0; k < numContigs; k++)
+ if ((getdata (ranges, offs, k, i) != 0) != (getdata (ranges, offs, k, j) != 0)) return 0;
+ return 1;
+ }
+
+-inline int allzeroes (rangelist **ranges, int numContigs, int pos, int *offs){
++static inline int allzeroes (rangelist **ranges, int numContigs, int pos, int *offs){
+ int i;
+
+ for (i = 0; i < numContigs; i++)
+@@ -258,7 +258,7 @@
+ return 1;
+ }
+
+-inline void print (int start, int end, int *score, int numContigs){
++static inline void print (int start, int end, int *score, int numContigs){
+ int j;
+
+ printf ("(%7d %7d)", start, end);
+@@ -303,7 +303,7 @@
+ free (pattern);
+ }
+
+-inline double scoregap (int gaplen){
++static inline double scoregap (int gaplen){
+ if (gaplen == 0) return 0;
+ //return (gaplen - 1) * -1 - 50;
+ return (log (gaplen) / log (10) + 1) * scoreGapOpen;
diff --git a/sci-biology/lagan/files/lagan-2.0-ambiguous-end.patch b/sci-biology/lagan/files/lagan-2.0-ambiguous-end.patch
new file mode 100644
index 00000000000..945120b1fc4
--- /dev/null
+++ b/sci-biology/lagan/files/lagan-2.0-ambiguous-end.patch
@@ -0,0 +1,49 @@
+Author: Steffen Moeller
+Last-Update: 2018-09-07 15:08:19 +0200
+Description: Fix build issue
+
+Index: lagan/src/glocal/rightinfluence.cpp
+===================================================================
+--- lagan.orig/src/glocal/rightinfluence.cpp
++++ lagan/src/glocal/rightinfluence.cpp
+@@ -1,6 +1,6 @@
+ #include <rightinfluence.h>
+
+-Fragment origin, end;
++static Fragment originFrag, endFrag;
+
+ // Sets the first default owner of the whole region
+ void initRI(RI *RightInfluence, long long int scoreIndex) {
+@@ -13,22 +13,22 @@ void initRI(RI *RightInfluence, long lon
+ }
+
+ // will lose to anyone
+- origin.seq1End = 0; origin.seq2End = 0;
+- origin.seq1Start = 0; origin.seq2Start = 0;
++ originFrag.seq1End = 0; originFrag.seq2End = 0;
++ originFrag.seq1Start = 0; originFrag.seq2Start = 0;
+
+ // hack to aid winner selection
+- origin.score = -1;
+- end.score = -2;
+- origin.totalScore = end.totalScore = 0;
++ originFrag.score = -1;
++ endFrag.score = -2;
++ originFrag.totalScore = endFrag.totalScore = 0;
+
+ // will win against anyone
+- end.seq1End = 0; end.seq2End = 0;
+- end.seq1Start = 0; end.seq2Start = 0;
++ endFrag.seq1End = 0; endFrag.seq2End = 0;
++ endFrag.seq1Start = 0; endFrag.seq2Start = 0;
+
+- origin.back = NULL;
++ originFrag.back = NULL;
+
+- RightInfluence->act[-INF] = &origin;
+- RightInfluence->act[+INF] = &end;
++ RightInfluence->act[-INF] = &originFrag;
++ RightInfluence->act[+INF] = &endFrag;
+ }
+
+
diff --git a/sci-biology/lagan/files/lagan-2.0-conflicting-getline.patch b/sci-biology/lagan/files/lagan-2.0-conflicting-getline.patch
new file mode 100644
index 00000000000..075753a924c
--- /dev/null
+++ b/sci-biology/lagan/files/lagan-2.0-conflicting-getline.patch
@@ -0,0 +1,24 @@
+Author: Andreas Tille <tille@debian.org>
+LastChanged: Fri, 15 Nov 2013 10:31:20 +0100
+Description: Prevent conflicting getline by simply renaming it
+
+--- a/src/anchors.c
++++ b/src/anchors.c
+@@ -225,7 +225,7 @@ char* rolltonum(char* str) {
+ return &str[i];
+ }
+
+-int getline(FILE* infile, hll* tt) {
++int anchors_getline(FILE* infile, hll* tt) {
+ char temp[1024];
+ char* help;
+ int z, h;
+@@ -248,7 +248,7 @@ hll* parseCHAOS(FILE* infile, int* totnu
+ *totnum = 0;
+ while(!feof(infile)) {
+ tt = (hll*) malloc(sizeof(hll));
+- while (!feof(infile) && !getline(infile, tt))
++ while (!feof(infile) && !anchors_getline(infile, tt))
+ ;
+ if (feof(infile)) break;
+ if (gapfreechunks) {
diff --git a/sci-biology/lagan/files/lagan-2.0-fix-c++14.patch b/sci-biology/lagan/files/lagan-2.0-fix-c++14.patch
deleted file mode 100644
index 9865f2756c5..00000000000
--- a/sci-biology/lagan/files/lagan-2.0-fix-c++14.patch
+++ /dev/null
@@ -1,473 +0,0 @@
-Fix building with C++14, which errors out due to namespace collisions with std::end
-in C++14 mode, due to crappy 'using namespace std' declared everywhere.
-See also: https://bugs.gentoo.org/show_bug.cgi?id=594148
-
---- a/src/ancseq.cpp
-+++ b/src/ancseq.cpp
-@@ -30,7 +30,6 @@
- #include <stdlib.h>
- #include <stdio.h>
-
--using namespace std;
-
- #include "util.cpp"
- #include "faindex.cpp"
---- a/src/ancseqrest.cpp
-+++ b/src/ancseqrest.cpp
-@@ -31,7 +31,6 @@
- #include <stdlib.h>
- #include <stdio.h>
-
--using namespace std;
-
- #define fastaRowLength 50
- typedef char* pchar;
---- a/src/cutmfa.cpp
-+++ b/src/cutmfa.cpp
-@@ -45,7 +45,6 @@
- #include <stdlib.h>
- #include <stdio.h>
-
--using namespace std;
-
- // TODO refactor in classes and normal make project
-
---- a/src/glocal/glocal.cpp
-+++ b/src/glocal/glocal.cpp
-@@ -7,9 +7,9 @@
- }
-
- //vectors that would be needed globally
--vector<Fragment> fragments;
--vector<Point>startPoints;
--vector<Point>endPoints;
-+std::vector<Fragment> fragments;
-+std::vector<Point>startPoints;
-+std::vector<Point>endPoints;
- long long int numFragments;
- InterPoint inter;
-
-@@ -19,7 +19,7 @@
- RI RI_regions[1<<(UPSTRANDBITS+DOWNSTRANDBITS+RELPOSBITS)];
- LI LI_regions[1<<(UPSTRANDBITS+DOWNSTRANDBITS+RELPOSBITS)];
-
--vector<class Score*> scoreFunctions[1<<(UPSTRANDBITS+DOWNSTRANDBITS+RELPOSBITS)];
-+std::vector<class Score*> scoreFunctions[1<<(UPSTRANDBITS+DOWNSTRANDBITS+RELPOSBITS)];
-
- Name allNames;
-
---- a/src/glocal/io.cpp
-+++ b/src/glocal/io.cpp
-@@ -3,9 +3,9 @@
- #include<io.h>
- #include<algorithm>
-
--extern vector <Fragment> fragments;
--extern vector <Point> startPoints;
--extern vector <Point> endPoints;
-+extern std::vector <Fragment> fragments;
-+extern std::vector <Point> startPoints;
-+extern std::vector <Point> endPoints;
- extern Name allNames;
-
- bool PointCompare(const Point &f1, const Point &f2) {
-@@ -223,8 +223,8 @@
- startPoints.push_back(startPoint);
- endPoints.push_back(endPoint);
- }
-- sort(startPoints.begin(), startPoints.end(), PointCompare);
-- sort(endPoints.begin(), endPoints.end(), PointCompare);
-+ std::sort(startPoints.begin(), startPoints.end(), PointCompare);
-+ std::sort(endPoints.begin(), endPoints.end(), PointCompare);
- }
-
-
---- a/src/glocal/leftinfluence.cpp
-+++ b/src/glocal/leftinfluence.cpp
-@@ -154,8 +154,8 @@
-
- if (second->score == -1) { return TRUE; }
-
-- dummy.seq1Start = max(first->seq1End, second->seq1End) + 2;
-- dummy.seq2Start = max(first->getSeq2End(LeftInfluence->reflectFlag), second->getSeq2End(LeftInfluence->reflectFlag)) + 1;
-+ dummy.seq1Start = std::max(first->seq1End, second->seq1End) + 2;
-+ dummy.seq2Start = std::max(first->getSeq2End(LeftInfluence->reflectFlag), second->getSeq2End(LeftInfluence->reflectFlag)) + 1;
-
- if (first->getSeq2End(LeftInfluence->reflectFlag) > second->getSeq2End(LeftInfluence->reflectFlag)) {
- dummy.nameIter = first->nameIter;
-@@ -444,7 +444,7 @@
- temp.seq1 = col - diag;
- temp.seq2 = col;
-
-- pair<Point,LI*> pairp(temp, LeftInfluence);
-+ std::pair<Point,LI*> pairp(temp, LeftInfluence);
- tempinter = inter.insert(pairp);
-
- colInter->second = tempinter;
---- a/src/glocal/leftinfluence.h
-+++ b/src/glocal/leftinfluence.h
-@@ -39,15 +39,15 @@
-
-
-
--typedef list<Fragment*> Owner;
--typedef map <long long int ,Owner::iterator,longlongCompare2> CBound;
-+typedef std::list<Fragment*> Owner;
-+typedef std::map <long long int ,Owner::iterator,longlongCompare2> CBound;
-
--typedef multimap <Point ,struct LI *,paircomp> InterPoint;
-+typedef std::multimap <Point ,struct LI *,paircomp> InterPoint;
-
--typedef map <long long int ,InterPoint::iterator,longlongCompare2> CInter;
--typedef map <long long int,Owner::iterator,longlongCompare2> DBound;
-+typedef std::map <long long int ,InterPoint::iterator,longlongCompare2> CInter;
-+typedef std::map <long long int,Owner::iterator,longlongCompare2> DBound;
-
--typedef map <long long int,InterPoint::iterator,longlongCompare2> DInter;
-+typedef std::map <long long int,InterPoint::iterator,longlongCompare2> DInter;
-
-
-
---- a/src/glocal/rightinfluence.h
-+++ b/src/glocal/rightinfluence.h
-@@ -17,7 +17,7 @@
- };
-
-
--typedef map<const long long int , Fragment*,longlongCompare> Active;
-+typedef std::map<const long long int , Fragment*,longlongCompare> Active;
-
- typedef struct RI {
- //List of active regions
---- a/src/glocal/score.cpp
-+++ b/src/glocal/score.cpp
-@@ -4,7 +4,7 @@
- #include<rightinfluence.h>
- #include<fstream>
-
--extern vector<class Score*> scoreFunctions[1<<(UPSTRANDBITS+DOWNSTRANDBITS+RELPOSBITS)];
-+extern std::vector<class Score*> scoreFunctions[1<<(UPSTRANDBITS+DOWNSTRANDBITS+RELPOSBITS)];
-
-
- float Score::getScore(Fragment *up, Fragment * down) {
-@@ -36,7 +36,7 @@
-
-
- void initScoreFunctionPointers(char * scoreFileName) {
-- ifstream SFP;
-+ std::ifstream SFP;
- char line[255];
-
- SFP.open(scoreFileName);
---- a/src/glocal/structs.h
-+++ b/src/glocal/structs.h
-@@ -12,7 +12,6 @@
- #include <list>
- #include <string.h>
-
--using namespace std;
-
- #define RIGHT 0
- #define LEFT 1
-@@ -49,7 +48,7 @@
- };
-
-
--typedef map<const char*,long long int ,ltstr> Name;
-+typedef std::map<const char*,long long int ,ltstr> Name;
-
-
- typedef struct Fragment {
---- a/src/lagan2mfa.cpp
-+++ b/src/lagan2mfa.cpp
-@@ -6,7 +6,6 @@
- #include <stdlib.h>
- #include <stdio.h>
-
--using namespace std;
-
- // TODO refactor in classes and normal make project
-
---- a/src/makecons.cpp
-+++ b/src/makecons.cpp
-@@ -18,7 +18,6 @@
- #include <ctype.h>
- #include <time.h>
-
--using namespace std;
-
- #define fastaRowLength 50
- #define bufSize 2000
---- a/src/utils/Glue.cpp
-+++ b/src/utils/Glue.cpp
-@@ -170,7 +170,7 @@
- }
-
- void printCoordinates (int seq, int begin, int end){
-- cout << seqs[seq].getID() << ":" << getSeqCoord(seq, begin) << "-" << getSeqCoord(seq, end) << " ";
-+ std::cout << seqs[seq].getID() << ":" << getSeqCoord(seq, begin) << "-" << getSeqCoord(seq, end) << " ";
- }
-
- int printRegion (int begin, int end){
-@@ -183,7 +183,7 @@
- score += rescoreRegion (seqs[i], seqs[j], begin, end);
- }
- }
-- cout << score << endl;
-+ std::cout << score << std::endl;
- return score;
- }
-
-@@ -223,7 +223,7 @@
- }
- }
-
-- cout << "= score=" << score << endl;
-+ std::cout << "= score=" << score << std::endl;
- }
-
- int countLets (SafeVector<char> &data){
-@@ -355,7 +355,7 @@
- FILE* outfile;
-
- if (argc < 2 || argc > 3){
-- cerr << "Usage: Glue align.mfa \n" << endl;
-+ std::cerr << "Usage: Glue align.mfa \n" << std::endl;
- exit (1);
- }
-
-@@ -375,7 +375,7 @@
- SafeVector<int> merged1label, merged2label;
- int begin1 = 1, end1 = 1;
-
-- ifstream data (argv[1]);
-+ std::ifstream data (argv[1]);
- int alignNum = 0;
- strand.push_back ('?'); // nothing for alignNum 0
-
-@@ -452,7 +452,7 @@
- SafeVector<char> temp1 (begin1 - 1, 'N');
- SafeVector<char> temp2 (begin1 - 1, '-');
-
-- for (int i = 0; i < min ((int) temp2.size(), CNTG_BRK_N); i++)
-+ for (int i = 0; i < std::min ((int) temp2.size(), CNTG_BRK_N); i++)
- temp2[i] = 'N';
-
- merged1 = merge (temp1, merged1);
-@@ -471,12 +471,12 @@
- if (isalpha(merged2[j])) pos2++;
-
- if (merged1label[j] == i){
-- min1 = min (min1, pos1);
-- max1 = max (max1, pos1);
-+ min1 = std::min (min1, pos1);
-+ max1 = std::max (max1, pos1);
- }
- if (merged2label[j] == i){
-- min2 = min (min2, pos2);
-- max2 = max (max2, pos2);
-+ min2 = std::min (min2, pos2);
-+ max2 = std::max (max2, pos2);
- }
- }
-
-@@ -489,6 +489,6 @@
- fprintf (outfile, "%d %d %d 0 0 0 0 %c 0 %d %d\n", i, min1, max1, strand[i], min2, max2);
- }
-
-- printMFA (cout, merged1, string ("first"), 60);
-- printMFA (cout, merged2, string ("second"), 60);
-+ printMFA (std::cout, merged1, std::string ("first"), 60);
-+ printMFA (std::cout, merged2, std::string ("second"), 60);
- }
---- a/src/utils/MultiSequence.h
-+++ b/src/utils/MultiSequence.h
-@@ -12,7 +12,6 @@
- #include "Sequence.h"
- #include "SafeVector.h"
-
--using namespace std;
-
- class MultiSequence {
- private:
-@@ -54,10 +53,10 @@
-
- // Read in all of the Sequences in an MFA file and append them to the
- // existing MultiSequence object.
-- void addRawFromMFA (const string& filename){
-+ void addRawFromMFA (const std::string& filename){
-
- // open up file for reading
-- ifstream infile (filename.c_str());
-+ std::ifstream infile (filename.c_str());
-
- // check for error
- assert (!infile.fail());
-@@ -75,7 +74,7 @@
-
- // Read in all of the Sequences in an MFA file and append them to the
- // existing MultiSequence object.
-- void addRawFromMFA (ifstream &infile){
-+ void addRawFromMFA (std::ifstream &infile){
-
- // check for error
- assert (!infile.fail());
-@@ -89,7 +88,7 @@
- }
-
- // Writes sequences to outfile in XMFA format.
-- void writeToXMFA (ostream &outfile, int numColumns) const {
-+ void writeToXMFA (std::ostream &outfile, int numColumns) const {
- for (int i = 0; i < (int) sequences.size(); ++i){
- sequences[i].writeToXMFA (outfile, numColumns);
- }
---- a/src/utils/Output.h
-+++ b/src/utils/Output.h
-@@ -2,18 +2,18 @@
- #define OUTPUT_H
-
- // print reversed string in MFA format
--void printMFA (ostream &outfile, SafeVector<char> &data, string comment, int numColumns){
-+void printMFA (std::ostream &outfile, SafeVector<char> &data, std::string comment, int numColumns){
-
- int charsWritten = 0;
-
-- outfile << ">" << comment << endl;
-+ outfile << ">" << comment << std::endl;
- for (int i = 0; i < (int) data.size(); i++){
- outfile << data[i];
- charsWritten++;
-- if (charsWritten % numColumns == 0) outfile << endl;
-+ if (charsWritten % numColumns == 0) outfile << std::endl;
- }
-
-- if (charsWritten % numColumns != 0) outfile << endl;
-+ if (charsWritten % numColumns != 0) outfile << std::endl;
- }
-
-
---- a/src/utils/SafeVector.h
-+++ b/src/utils/SafeVector.h
-@@ -10,7 +10,6 @@
- #include <assert.h>
- #include <vector>
-
--using namespace std;
-
- // class derived from the STL std::vector
- template<class TYPE>
-@@ -19,9 +18,9 @@
-
- // miscellaneous constructors
- SafeVector () {}
-- SafeVector (size_t size) : vector<TYPE>(size) {}
-- SafeVector (size_t size, const TYPE &value) : vector<TYPE>(size, value) {}
-- SafeVector (const SafeVector &source) : vector<TYPE>(source) {}
-+ SafeVector (size_t size) : std::vector<TYPE>(size) {}
-+ SafeVector (size_t size, const TYPE &value) : std::vector<TYPE>(size, value) {}
-+ SafeVector (const SafeVector &source) : std::vector<TYPE>(source) {}
-
- #ifdef ENABLE_CHECKS
-
---- a/src/utils/Sequence.h
-+++ b/src/utils/Sequence.h
-@@ -8,15 +8,14 @@
- #include <string>
- #include "SafeVector.h"
-
--using namespace std;
-
- class Sequence {
-
- private:
-
- // Read header of MFA/XMFA file.
-- bool readHeader (ifstream &infile, bool &isXMFA){
-- string header;
-+ bool readHeader (std::ifstream &infile, bool &isXMFA){
-+ std::string header;
-
- while (true){
-
-@@ -24,7 +23,7 @@
- if (infile.fail() || infile.eof()) return false;
-
- // get new header line
-- getline (infile, header);
-+ std::getline (infile, header);
-
- // check that header line is not empty
- if (header.length() != 0) break;
-@@ -64,7 +63,7 @@
- int startCoord; // sequence position of first character
- int endCoord; // sequence position of last character
- char direction; // + or -
-- string comment; // comments
-+ std::string comment; // comments
-
- public:
-
-@@ -77,7 +76,7 @@
- }
-
- // Constructor. Reads in a sequence from the input file.
-- Sequence (ifstream &infile){
-+ Sequence (std::ifstream &infile){
-
- bool isXMFA = true;
-
-@@ -147,7 +146,7 @@
- }
-
- // Constructor. Gets sequence from array data.
-- Sequence (SafeVector<char> data, string comment) : data(data), comment(comment) {
-+ Sequence (SafeVector<char> data, std::string comment) : data(data), comment(comment) {
- length = data.size() - 1;
- id = 0;
- startCoord = 1;
-@@ -165,7 +164,7 @@
- return temp;
- }
-
-- const string getComment () const {
-+ const std::string getComment () const {
- return comment;
- }
-
-@@ -197,9 +196,9 @@
- const int getEndCoord () const { assert (isValid); return endCoord; }
-
- // Print XMFA header only.
-- void writeXMFAHeader (ostream &outfile) const {
-+ void writeXMFAHeader (std::ostream &outfile) const {
- assert (isValid);
-- outfile << '>' << id << ':' << startCoord << '-' << endCoord << ' ' << direction << ' ' << comment << endl;
-+ outfile << '>' << id << ':' << startCoord << '-' << endCoord << ' ' << direction << ' ' << comment << std::endl;
- }
-
- // Return sequence ID.
-@@ -209,20 +208,20 @@
- void setID (int id) { assert (isValid); this->id = id; }
-
- // Writes sequence to XMFA format.
-- void writeToXMFA (ostream &outfile, int numColumns) const {
-+ void writeToXMFA (std::ostream &outfile, int numColumns) const {
-
- assert (isValid);
-
- // print XMFA header
-- outfile << ">" << comment << endl;
-+ outfile << ">" << comment << std::endl;
- // outfile << '>' << id << ':' << startCoord << '-' << endCoord << ' ' << direction << ' ' << comment << endl;
-
- // print character data
- for (int i = 1; i <= length; ++i){
- outfile << data[i];
-- if (i % numColumns == 0) outfile << endl;
-+ if (i % numColumns == 0) outfile << std::endl;
- }
-- if (length % numColumns != 0) outfile << endl;
-+ if (length % numColumns != 0) outfile << std::endl;
- }
- };
-
diff --git a/sci-biology/lagan/files/lagan-2.0-gcc-10.patch b/sci-biology/lagan/files/lagan-2.0-gcc-10.patch
new file mode 100644
index 00000000000..bd9824cf2ed
--- /dev/null
+++ b/sci-biology/lagan/files/lagan-2.0-gcc-10.patch
@@ -0,0 +1,27 @@
+Description: Add patch to build with GCC-10
+Bug-Debian: https://bugs.debian.org/957415
+Author: Nilesh Patra <npatra974@gmail.com>
+Date: Fri Apr 17 21:13:21 2020 +0530
+
+--- a/src/fchaos.c
++++ b/src/fchaos.c
+@@ -29,7 +29,7 @@
+ int offset;
+ } match;
+
+-extern int indeces[256];
++int indeces[256];
+
+
+ void remElem(LList* tbf, int i);
+--- a/src/thrtrie.h
++++ b/src/thrtrie.h
+@@ -2,7 +2,7 @@
+ #define MAX_DEGEN 2
+
+
+-int indeces[256];
++extern int indeces[256];
+
+ typedef struct PrevHits {
+ int* inds1;
diff --git a/sci-biology/lagan/files/lagan-2.0-gcc-4.8.patch b/sci-biology/lagan/files/lagan-2.0-gcc-4.8.patch
new file mode 100644
index 00000000000..3d7ed780445
--- /dev/null
+++ b/sci-biology/lagan/files/lagan-2.0-gcc-4.8.patch
@@ -0,0 +1,25 @@
+Author: Andreas Tille <tille@debian.org>
+LastChanged: Fri, 15 Nov 2013 10:31:20 +0100
+Description: Fix some includes to build using gcc-4.8
+
+--- a/src/utils/Glue.cpp
++++ b/src/utils/Glue.cpp
+@@ -6,6 +6,7 @@
+ #include <fstream>
+ #include <iostream>
+ #include <algorithm>
++#include <string.h>
+
+ #define NUCLEOTIDE_MATRIX_FILE "nucmatrix.txt"
+ #define MAX_LINE_LENGTH 1024
+--- a/src/glocal/score.cpp
++++ b/src/glocal/score.cpp
+@@ -2,7 +2,7 @@
+ #include<score.h>
+ #include<leftinfluence.h>
+ #include<rightinfluence.h>
+-#include<fstream.h>
++#include<fstream>
+
+ extern vector<class Score*> scoreFunctions[1<<(UPSTRANDBITS+DOWNSTRANDBITS+RELPOSBITS)];
+
diff --git a/sci-biology/lagan/files/lagan-2.0-gcc-9.patch b/sci-biology/lagan/files/lagan-2.0-gcc-9.patch
new file mode 100644
index 00000000000..6ea30e57a85
--- /dev/null
+++ b/sci-biology/lagan/files/lagan-2.0-gcc-9.patch
@@ -0,0 +1,25 @@
+# Two patches to bring lagan up to speed with gcc-9
+Index: lagan/src/fchaos.c
+===================================================================
+--- lagan.orig/src/fchaos.c
++++ lagan/src/fchaos.c
+@@ -430,7 +430,7 @@ int chain(LList* second, int off2, LList
+ int tc =0;
+ int wc = 0;
+
+-inline void findPrev(LList* curr, int position, int offset, float baseval) {
++void findPrev(LList* curr, int position, int offset, float baseval) {
+ int j,k;
+ LList* temp;
+ sle* iterator;
+Index: lagan/src/filebuffer.c
+===================================================================
+--- lagan.orig/src/filebuffer.c
++++ lagan/src/filebuffer.c
+@@ -1,5 +1,6 @@
+ #include "filebuffer.h"
+ #include <stdlib.h>
++#include <ctype.h>
+ #include <string.h>
+ #include <stdio.h>
+ #include <assert.h>
diff --git a/sci-biology/lagan/files/lagan-2.0-gcc4.3.patch b/sci-biology/lagan/files/lagan-2.0-gcc4.3.patch
deleted file mode 100644
index a4b1d6808e2..00000000000
--- a/sci-biology/lagan/files/lagan-2.0-gcc4.3.patch
+++ /dev/null
@@ -1,23 +0,0 @@
-diff -durr lagan20-orig/src/glocal/score.cpp lagan20/src/glocal/score.cpp
---- lagan20-orig/src/glocal/score.cpp 2009-02-04 15:25:57.698333297 +0000
-+++ lagan20/src/glocal/score.cpp 2009-02-04 15:27:23.894092890 +0000
-@@ -2,7 +2,7 @@
- #include<score.h>
- #include<leftinfluence.h>
- #include<rightinfluence.h>
--#include<fstream.h>
-+#include<fstream>
-
- extern vector<class Score*> scoreFunctions[1<<(UPSTRANDBITS+DOWNSTRANDBITS+RELPOSBITS)];
-
-diff -durr lagan20-orig/src/utils/Glue.cpp lagan20/src/utils/Glue.cpp
---- lagan20-orig/src/utils/Glue.cpp 2009-02-04 15:25:57.702333182 +0000
-+++ lagan20/src/utils/Glue.cpp 2009-02-04 15:27:04.190822654 +0000
-@@ -1,6 +1,7 @@
- #include "MultiSequence.h"
- #include "SafeVector.h"
- #include "Output.h"
-+#include <string.h>
- #include <math.h>
- #include <assert.h>
- #include <fstream>
diff --git a/sci-biology/lagan/files/lagan-2.0-flags.patch b/sci-biology/lagan/files/lagan-2.0-makefile.patch
index e324ef64c4c..1bef6721ab9 100644
--- a/sci-biology/lagan/files/lagan-2.0-flags.patch
+++ b/sci-biology/lagan/files/lagan-2.0-makefile.patch
@@ -1,107 +1,120 @@
-diff --git a/Makefile b/Makefile
-index fbbbe79..a1d449b 100644
--- a/Makefile
+++ b/Makefile
-@@ -1,5 +1,5 @@
+@@ -1,5 +1,8 @@
all:
- (cd src; $(MAKE))
+ $(MAKE) -C src
clean:
rm -f chaos anchors order glocal utils/bin2bl mlagan utils/cstat utils/bin2mf utils/rc *~ utils/contigorder utils/getbounds utils/cextract utils/seqmerge utils/getlength utils/getoverlap utils/*~ utils/scorealign utils/scorecontigs mlagan.purify utils/getcontigpos utils/fa2xfa utils/Glue utils/dotplot utils/overlay
- (cd src; $(MAKE) clean)
-diff --git a/src/Makefile b/src/Makefile
-index 7f6b6fd..dd6309b 100644
+- (cd src; $(MAKE) clean)
++ $(MAKE) -C src clean
++
++check: all
++ (LAGAN_DIR="." ./mlagan -h || true) | grep -q version && echo "[ok]" || echo "[fail]"
+--- a/src/glocal/Makefile
++++ b/src/glocal/Makefile
+@@ -1,19 +1,13 @@
+-CC = g++
+-OPTFLAGS =
+-CFLAGS = $(OPTFLAGS) -O3
+-CLINKER = g++
+-# LIBDIR = -L/usr/local/lib
++CXXFLAGS += -Wno-deprecated
++CPPFLAGS += -I./
++
+ MLIB = -lm
+-INCDIR = -I./
+ TRGT_DIR = ../..
+ TRGT = glocal
+ OBJECTS = glocal.o io.o rightinfluence.o leftinfluence.o score.o
+
+-.cpp.o:
+- $(CC) -Wno-deprecated $(CFLAGS) $(INCDIR) -c $*.cpp
+-
+ $(TRGT): $(OBJECTS)
+- $(CLINKER) $(OPTFLAGS) $(OBJECTS) -o $(TRGT_DIR)/$(TRGT) $(MLIB)
++ $(CXX) $(CXXFLAGS) $(LDFLAGS) $(OBJECTS) -o $(TRGT_DIR)/$(TRGT) $(MLIB)
+
+ clean :
+ rm -f *.o ./*~ *~ core
--- a/src/Makefile
+++ b/src/Makefile
-@@ -4,51 +4,51 @@ CFLAGS = -O3 # -Wall -W
+@@ -1,54 +1,51 @@
+-CC = gcc $(CFLAGS)
+-CPP = g++ $(CFLAGS)
+-CFLAGS = -O3 # -Wall -W
TRGT_DIR = ..
all: ../anchors ../chaos ../order ../mlagan ../prolagan ../utils/bin2mf ../utils/bin2bl ../utils/cextract ../utils/cstat ../utils/contigorder ../utils/getbounds ../utils/getlength ../utils/getoverlap ../utils/rc ../utils/seqmerge ../utils/scorealign ../utils/scorecontigs ../utils/getcontigpos ../utils/fa2xfa ../utils/Glue ../utils/dotplot ../utils/overlay
- (cd glocal; $(MAKE))
-+ $(MAKE) -C glocal
++ (cd glocal && $(MAKE))
clean:
rm -f *.o *~ utils/*~ mlagan.purify core
- (cd glocal; $(MAKE) clean)
+- (cd glocal; $(MAKE) clean)
++ (cd glocal && $(MAKE) clean)
../anchors: anchors.c skiplist.c
- $(CC) -o $(TRGT_DIR)/anchors anchors.c skiplist.c
-+ $(CC) $(CFLAGS) $(LDFLAGS) -o $(TRGT_DIR)/anchors anchors.c skiplist.c
++ $(CC) $(CFLAGS) $(CPPFLAGS) $(LDFLAGS) -o $(TRGT_DIR)/anchors anchors.c skiplist.c
../chaos: fchaos.c thrtrie.c skiplist.c global.c translate.c mempage.c filebuffer.c
- $(CC) -o $(TRGT_DIR)/chaos fchaos.c thrtrie.c skiplist.c global.c translate.c filebuffer.c -lm -DCHAOS__FLAG
-+ $(CC) $(CFLAGS) $(LDFLAGS) -o $(TRGT_DIR)/chaos fchaos.c thrtrie.c skiplist.c global.c translate.c filebuffer.c -lm -DCHAOS__FLAG
++ $(CC) $(CFLAGS) $(CPPFLAGS) $(LDFLAGS) -o $(TRGT_DIR)/chaos fchaos.c thrtrie.c skiplist.c global.c translate.c filebuffer.c -lm -DCHAOS__FLAG
../order: order.c diagmatrix.c filebuffer.c
- $(CC) -o $(TRGT_DIR)/order order.c diagmatrix.c filebuffer.c
-+ $(CC) $(CFLAGS) $(LDFLAGS) -o $(TRGT_DIR)/order order.c diagmatrix.c filebuffer.c
++ $(CC) $(CFLAGS) $(CPPFLAGS) $(LDFLAGS) -o $(TRGT_DIR)/order order.c diagmatrix.c filebuffer.c
../mlagan: mlagan.c diagmatrix.c multial.c skiplist.c filebuffer.c
- $(CC) -o $(TRGT_DIR)/mlagan mlagan.c multial.c diagmatrix.c skiplist.c filebuffer.c -lm -DMULTIAL__FLAG
-+ $(CC) $(CFLAGS) $(LDFLAGS) -o $(TRGT_DIR)/mlagan mlagan.c multial.c diagmatrix.c skiplist.c filebuffer.c -lm -DMULTIAL__FLAG
++ $(CC) $(CFLAGS) $(CPPFLAGS) $(LDFLAGS) -o $(TRGT_DIR)/mlagan mlagan.c multial.c diagmatrix.c skiplist.c filebuffer.c -lm -DMULTIAL__FLAG
../prolagan: prolagan.c diagmatrix.c multial.c skiplist.c filebuffer.c
- $(CC) -o $(TRGT_DIR)/prolagan prolagan.c multial.c diagmatrix.c skiplist.c filebuffer.c -lm -DMULTIAL__FLAG
-+ $(CC) $(CFLAGS) $(LDFLAGS) -o $(TRGT_DIR)/prolagan prolagan.c multial.c diagmatrix.c skiplist.c filebuffer.c -lm -DMULTIAL__FLAG
++ $(CC) $(CFLAGS) $(CPPFLAGS) $(LDFLAGS) -o $(TRGT_DIR)/prolagan prolagan.c multial.c diagmatrix.c skiplist.c filebuffer.c -lm -DMULTIAL__FLAG
../utils/bin2mf: utils/bin2mf.c
- $(CC) -o $(TRGT_DIR)/utils/bin2mf utils/bin2mf.c
-+ $(CC) $(CFLAGS) $(LDFLAGS) -o $(TRGT_DIR)/utils/bin2mf utils/bin2mf.c
++ $(CC) $(CFLAGS) $(CPPFLAGS) $(LDFLAGS) -o $(TRGT_DIR)/utils/bin2mf utils/bin2mf.c
../utils/bin2bl: utils/bin2bl.c
- $(CC) -o $(TRGT_DIR)/utils/bin2bl utils/bin2bl.c
-+ $(CC) $(CFLAGS) $(LDFLAGS) -o $(TRGT_DIR)/utils/bin2bl utils/bin2bl.c
++ $(CC) $(CFLAGS) $(CPPFLAGS) $(LDFLAGS) -o $(TRGT_DIR)/utils/bin2bl utils/bin2bl.c
../utils/cextract: utils/cextract.c
- $(CC) -o $(TRGT_DIR)/utils/cextract utils/cextract.c
-+ $(CC) $(CFLAGS) $(LDFLAGS) -o $(TRGT_DIR)/utils/cextract utils/cextract.c
++ $(CC) $(CFLAGS) $(CPPFLAGS) $(LDFLAGS) -o $(TRGT_DIR)/utils/cextract utils/cextract.c
../utils/cstat: utils/cstat.c
- $(CC) -o $(TRGT_DIR)/utils/cstat utils/cstat.c
-+ $(CC) $(CFLAGS) $(LDFLAGS) -o $(TRGT_DIR)/utils/cstat utils/cstat.c
++ $(CC) $(CFLAGS) $(CPPFLAGS) $(LDFLAGS) -o $(TRGT_DIR)/utils/cstat utils/cstat.c
../utils/contigorder: utils/contigorder.c
- $(CC) -o $(TRGT_DIR)/utils/contigorder utils/contigorder.c
-+ $(CC) $(CFLAGS) $(LDFLAGS) -o $(TRGT_DIR)/utils/contigorder utils/contigorder.c
++ $(CC) $(CFLAGS) $(CPPFLAGS) $(LDFLAGS) -o $(TRGT_DIR)/utils/contigorder utils/contigorder.c
../utils/getbounds: utils/getbounds.c
- $(CC) -o $(TRGT_DIR)/utils/getbounds utils/getbounds.c
-+ $(CC) $(CFLAGS) $(LDFLAGS) -o $(TRGT_DIR)/utils/getbounds utils/getbounds.c
++ $(CC) $(CFLAGS) $(CPPFLAGS) $(LDFLAGS) -o $(TRGT_DIR)/utils/getbounds utils/getbounds.c
../utils/getcontigpos: utils/getcontigpos.c
- $(CC) -o $(TRGT_DIR)/utils/getcontigpos utils/getcontigpos.c
-+ $(CC) $(CFLAGS) $(LDFLAGS) -o $(TRGT_DIR)/utils/getcontigpos utils/getcontigpos.c
++ $(CC) $(CFLAGS) $(CPPFLAGS) $(LDFLAGS) -o $(TRGT_DIR)/utils/getcontigpos utils/getcontigpos.c
../utils/getlength: utils/getlength.c
- $(CC) -o $(TRGT_DIR)/utils/getlength utils/getlength.c
-+ $(CC) $(CFLAGS) $(LDFLAGS) -o $(TRGT_DIR)/utils/getlength utils/getlength.c
++ $(CC) $(CFLAGS) $(CPPFLAGS) $(LDFLAGS) -o $(TRGT_DIR)/utils/getlength utils/getlength.c
../utils/getoverlap: utils/getoverlap.c
- $(CC) -o $(TRGT_DIR)/utils/getoverlap utils/getoverlap.c
-+ $(CC) $(CFLAGS) $(LDFLAGS) -o $(TRGT_DIR)/utils/getoverlap utils/getoverlap.c
++ $(CC) $(CFLAGS) $(CPPFLAGS) $(LDFLAGS) -o $(TRGT_DIR)/utils/getoverlap utils/getoverlap.c
../utils/rc: utils/rc.c
- $(CC) -o $(TRGT_DIR)/utils/rc utils/rc.c
-+ $(CC) $(CFLAGS) $(LDFLAGS) -o $(TRGT_DIR)/utils/rc utils/rc.c
++ $(CC) $(CFLAGS) $(CPPFLAGS) $(LDFLAGS) -o $(TRGT_DIR)/utils/rc utils/rc.c
../utils/seqmerge: utils/seqmerge.c
- $(CC) -o $(TRGT_DIR)/utils/seqmerge utils/seqmerge.c
-+ $(CC) $(CFLAGS) $(LDFLAGS) -o $(TRGT_DIR)/utils/seqmerge utils/seqmerge.c
++ $(CC) $(CFLAGS) $(CPPFLAGS) $(LDFLAGS) -o $(TRGT_DIR)/utils/seqmerge utils/seqmerge.c
../utils/scorealign: utils/scorealign.c
- $(CC) -o $(TRGT_DIR)/utils/scorealign utils/scorealign.c -lm
-+ $(CC) $(CFLAGS) $(LDFLAGS) -o $(TRGT_DIR)/utils/scorealign utils/scorealign.c -lm
++ $(CC) $(CFLAGS) $(CPPFLAGS) $(LDFLAGS) -o $(TRGT_DIR)/utils/scorealign utils/scorealign.c -lm
../utils/scorecontigs: utils/scorecontigs.c
- $(CC) -o $(TRGT_DIR)/utils/scorecontigs utils/scorecontigs.c -lm
-+ $(CC) $(CFLAGS) $(LDFLAGS) -o $(TRGT_DIR)/utils/scorecontigs utils/scorecontigs.c -lm
++ $(CC) $(CFLAGS) $(CPPFLAGS) $(LDFLAGS) -o $(TRGT_DIR)/utils/scorecontigs utils/scorecontigs.c -lm
../utils/fa2xfa: utils/fa2xfa.c
- $(CC) -o $(TRGT_DIR)/utils/fa2xfa utils/fa2xfa.c
-+ $(CC) $(CFLAGS) $(LDFLAGS) -o $(TRGT_DIR)/utils/fa2xfa utils/fa2xfa.c
++ $(CC) $(CFLAGS) $(CPPFLAGS) $(LDFLAGS) -o $(TRGT_DIR)/utils/fa2xfa utils/fa2xfa.c
../utils/overlay: utils/overlay.c
- $(CC) -o $(TRGT_DIR)/utils/overlay utils/overlay.c
-+ $(CC) $(CFLAGS) $(LDFLAGS) -o $(TRGT_DIR)/utils/overlay utils/overlay.c
++ $(CC) $(CFLAGS) $(CPPFLAGS) $(LDFLAGS) -o $(TRGT_DIR)/utils/overlay utils/overlay.c
../utils/Glue: utils/Glue.cpp
- $(CPP) -o $(TRGT_DIR)/utils/Glue utils/Glue.cpp
-+ $(CXX) $(CXXFLAGS) $(LDFLAGS) -o $(TRGT_DIR)/utils/Glue utils/Glue.cpp
++ $(CXX) $(CXXFLAGS) $(CPPFLAGS) $(LDFLAGS) -o $(TRGT_DIR)/utils/Glue utils/Glue.cpp
../utils/dotplot: utils/dotplot.cpp
- $(CPP) -o $(TRGT_DIR)/utils/dotplot utils/dotplot.cpp
-+ $(CXX) $(CXXFLAGS) $(LDFLAGS) -o $(TRGT_DIR)/utils/dotplot utils/dotplot.cpp
-diff --git a/src/glocal/Makefile b/src/glocal/Makefile
-index ce1421a..b82507f 100755
---- a/src/glocal/Makefile
-+++ b/src/glocal/Makefile
-@@ -10,10 +10,10 @@ TRGT = glocal
- OBJECTS = glocal.o io.o rightinfluence.o leftinfluence.o score.o
-
- .cpp.o:
-- $(CC) -Wno-deprecated $(CFLAGS) $(INCDIR) -c $*.cpp
-+ $(CXX) $(CXXFLAGS) $(INCDIR) -c $*.cpp
-
- $(TRGT): $(OBJECTS)
-- $(CLINKER) $(OPTFLAGS) $(OBJECTS) -o $(TRGT_DIR)/$(TRGT) $(MLIB)
-+ $(CXX) $(LDFLAGS) $(OBJECTS) -o $(TRGT_DIR)/$(TRGT) $(MLIB)
-
- clean :
- rm -f *.o ./*~ *~ core
++ $(CXX) $(CXXFLAGS) $(CPPFLAGS) $(LDFLAGS) -o $(TRGT_DIR)/utils/dotplot utils/dotplot.cpp
diff --git a/sci-biology/lagan/files/lagan-2.0-qa-implicit-declarations.patch b/sci-biology/lagan/files/lagan-2.0-qa-implicit-declarations.patch
index 4ba4ce49d77..29db043d5f3 100644
--- a/sci-biology/lagan/files/lagan-2.0-qa-implicit-declarations.patch
+++ b/sci-biology/lagan/files/lagan-2.0-qa-implicit-declarations.patch
@@ -1,69 +1,34 @@
-Fix QA warnings due to implicit declarations:
-* filebuffer.c:123:34: warning: implicit declaration of function ‘toupper’ [-Wimplicit-function-declaration]
-* temp[i] = (strchr (alphabet, toupper ((char) i)) != 0) ?
-
---- a/src/filebuffer.c
-+++ b/src/filebuffer.c
-@@ -3,6 +3,7 @@
- #include <string.h>
- #include <stdio.h>
- #include <assert.h>
-+#include <ctype.h>
-
- #ifdef CHAOS__FLAG
- char* alphabet = "ATCGNPCMHDEKRQSILVFYWX*";
--- a/src/mlagan.c
+++ b/src/mlagan.c
-@@ -934,6 +934,7 @@
- return k;
+@@ -46,6 +46,7 @@
+ return 1;
}
+int printXMFAAlign(FILE* outfile, align* myalign);
- int main(int argc, char** argv) {
- FileBuffer seqfile;
+ void usage(void) {
+ printf("mlagan seqfile_1 seqfile_2 [... seqfile_%d] [-parameters]\n\n",
--- a/src/order.c
+++ b/src/order.c
-@@ -398,6 +398,9 @@
- free(ends);
- }
+@@ -28,6 +28,8 @@
+
+ align* makeAlign(dmat* mydm, char* seq1, char* seq2);
+int printMFAAlign(char* seq1, char* seq2, align* myalign, char* n1, char* n2);
+int printXMFAAlign(char* seq1, char* seq2, align* myalign, char* n1, char* n2);
-+
- void doAlign(dmat* mydm, seq* seq1, seq* seq2) {
- align *a = (align*) makeAlign(mydm, seq1->lets, seq2->lets);
- // printf("into printing\n");
+
+ char* alpha = "ATCGN.";
+
--- a/src/prolagan.c
+++ b/src/prolagan.c
-@@ -949,6 +949,7 @@
- return k;
+@@ -49,6 +49,7 @@
+ return 1;
}
+int printXMFAAlign(FILE* outfile, align* myalign);
- int main(int argc, char** argv) {
- FileBuffer seqfile;
---- a/src/utils/contigorder.c
-+++ b/src/utils/contigorder.c
-@@ -12,7 +12,7 @@
- int dummy, i;
-
- if (!(file = fopen (filename, "r"))){
-- fprintf (stderr, "contigorder: Error opening file: %s\n");
-+ fprintf (stderr, "contigorder: Error opening file: %s\n", filename);
- exit (1);
- }
-
-@@ -49,7 +49,7 @@
- }
-
- if (!(file = fopen (filename, "r"))){
-- fprintf (stderr, "contigorder: Error opening file: %s\n");
-+ fprintf (stderr, "contigorder: Error opening file: %s\n", filename);
- exit (1);
- }
-
+ void usage(void) {
+ printf("mlagan seqfile_1 seqfile_2 [... seqfile_%d] [-parameters]\n\n",
--- a/src/utils/cstat.c
+++ b/src/utils/cstat.c
@@ -3,6 +3,7 @@
diff --git a/sci-biology/lagan/lagan-2.0-r3.ebuild b/sci-biology/lagan/lagan-2.0-r3.ebuild
deleted file mode 100644
index e326331e09f..00000000000
--- a/sci-biology/lagan/lagan-2.0-r3.ebuild
+++ /dev/null
@@ -1,71 +0,0 @@
-# Copyright 1999-2016 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=6
-
-inherit toolchain-funcs
-
-MY_P="lagan20"
-
-DESCRIPTION="The LAGAN suite of tools for whole-genome multiple alignment of genomic DNA"
-HOMEPAGE="http://lagan.stanford.edu/lagan_web/index.shtml"
-SRC_URI="http://lagan.stanford.edu/lagan_web/${MY_P}.tar.gz"
-
-LICENSE="GPL-2"
-SLOT="0"
-IUSE=""
-KEYWORDS="~amd64 ~x86"
-
-RDEPEND="dev-lang/perl"
-
-S="${WORKDIR}/${MY_P}"
-
-PATCHES=(
- "${FILESDIR}/${PN}-2.0-flags.patch"
- "${FILESDIR}/${PN}-2.0-gcc4.3.patch"
- "${FILESDIR}/${PN}-2.0-fix-c++14.patch"
- "${FILESDIR}/${PN}-2.0-qa-implicit-declarations.patch"
-)
-
-src_prepare() {
- sed -i "/use Getopt::Long;/ i use lib \"/usr/$(get_libdir)/${PN}/lib\";" "${S}/supermap.pl" || die
- # NB: Testing with glibc-2.10 has uncovered a bug in src/utils/Sequence.h
- # where libc getline is erroneously used instead of own getline
- sed -i 's/getline/my_getline/' "${S}"/src/{anchors.c,glocal/io.cpp} || die
-
- default
-}
-
-src_compile() {
- emake \
- CC=$(tc-getCC) \
- CXX=$(tc-getCXX) \
- CXXFLAGS="${CXXFLAGS}" \
- CFLAGS="${CFLAGS}"
-}
-
-src_install() {
- newbin lagan.pl lagan
- newbin slagan.pl slagan
- dobin mlagan
- rm -f lagan.pl slagan.pl utils/Utils.pm || die
-
- insinto /usr/$(get_libdir)/${PN}/lib
- doins Utils.pm
-
- exeinto /usr/$(get_libdir)/${PN}/utils
- doexe utils/*
-
- exeinto /usr/$(get_libdir)/${PN}
- doexe *.pl anchors chaos glocal order prolagan
-
- insinto /usr/$(get_libdir)/${PN}
- doins *.txt
-
- dosym /usr/$(get_libdir)/${PN}/supermap.pl /usr/bin/supermap
-
- echo "LAGAN_DIR=\"/usr/$(get_libdir)/${PN}\"" > 99${PN} || die
- doenvd 99${PN}
-
- dodoc Readmes/README.*
-}
diff --git a/sci-biology/lagan/lagan-2.0-r4.ebuild b/sci-biology/lagan/lagan-2.0-r4.ebuild
new file mode 100644
index 00000000000..4582d8f1078
--- /dev/null
+++ b/sci-biology/lagan/lagan-2.0-r4.ebuild
@@ -0,0 +1,67 @@
+# Copyright 1999-2020 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=7
+
+inherit toolchain-funcs
+
+MY_P="lagan20"
+
+DESCRIPTION="The LAGAN suite of tools for whole-genome multiple alignment of genomic DNA"
+HOMEPAGE="http://lagan.stanford.edu/lagan_web/index.shtml"
+SRC_URI="http://lagan.stanford.edu/lagan_web/${MY_P}.tar.gz"
+
+LICENSE="GPL-2"
+SLOT="0"
+KEYWORDS="~amd64 ~x86"
+
+RDEPEND="dev-lang/perl"
+
+S="${WORKDIR}/${MY_P}"
+PATCHES=(
+ "${FILESDIR}"/${P}-makefile.patch
+ "${FILESDIR}"/${P}-conflicting-getline.patch
+ "${FILESDIR}"/${P}-gcc-4.8.patch
+ "${FILESDIR}"/${P}-ambiguous-end.patch
+ "${FILESDIR}"/${P}-gcc-9.patch
+ "${FILESDIR}"/${P}-gcc-10.patch
+ "${FILESDIR}"/${P}-C99-static-inline.patch
+ "${FILESDIR}"/${P}-qa-implicit-declarations.patch
+)
+
+src_prepare() {
+ default
+ sed -i "/use Getopt::Long;/ i use lib \"/usr/$(get_libdir)/lagan/lib\";" \
+ supermap.pl || die
+}
+
+src_configure() {
+ tc-export CC CXX
+}
+
+src_install() {
+ newbin lagan.pl lagan
+ newbin slagan.pl slagan
+ dobin mlagan
+ rm lagan.pl slagan.pl utils/Utils.pm || die
+
+ insinto /usr/$(get_libdir)/lagan/lib
+ doins Utils.pm
+
+ exeinto /usr/$(get_libdir)/lagan/utils
+ doexe utils/*
+
+ exeinto /usr/$(get_libdir)/lagan
+ doexe *.pl anchors chaos glocal order prolagan
+
+ insinto /usr/$(get_libdir)/lagan
+ doins *.txt
+
+ dosym ../$(get_libdir)/lagan/supermap.pl /usr/bin/supermap
+
+ newenvd - 99lagan <<- _EOF_
+ LAGAN_DIR="${EPREFIX}/usr/$(get_libdir)/lagan"
+ _EOF_
+
+ dodoc Readmes/README.*
+}