gentoo resync : 25.11.2020

13 files changed, 559 insertions, 669 deletions

diff --git a/sci-biology/lagan/Manifest b/sci-biology/lagan/Manifest
index bb94011e3eae..6b6322158a4d 100644
--- a/sci-biology/lagan/Manifest
+++ b/sci-biology/lagan/Manifest
@@ -1,7 +1,11 @@
-AUX lagan-2.0-fix-c++14.patch 13525 BLAKE2B 79037fa65301393f3a007adb424f4a88f72f46ad0cf7c310a07f14b64437fb8fd3dc6da90df5c79e468b424a895797cf01e5b30413435a18ea933d912eb0428e SHA512 f62b523cf9692a1394276ac674ccf7ce9a0070c646c95d1f20b8e0ace61afffd04aae3a098511bb106ab62089e70bebfae6ba25aaffcccbbe7f8397a30c2900a
-AUX lagan-2.0-flags.patch 5848 BLAKE2B 41394e65d15be217dea753a9641ee72833ff87f5101fa19ba009f4ca4b97d8fe22594d041105ba03ddb53ad83f635fec79e9125f539eff3cd1cbcdc186d3023e SHA512 63917ed217c44cade1c87dd6498cb7f6180c30eaba3875fa77f7e73b894aadab1469aca87650d1017a44fcac548552c3bdfcaff29b24023d23c7424079ad91cf
-AUX lagan-2.0-gcc4.3.patch 821 BLAKE2B c25d5afef654a27a61fb658de4fc26afe713400133123b47202fab8861c95b6ed56a229b0f88a811b5dc36e94125d0c333c6b13a14e1f1ff944c68c2ee3acd1c SHA512 91b56b0cfc27f799fed164a8a32b4840ea2e7f7796d334b2bce8bd27bc2fb96b4cdb0912c737c874f767a16ffcdd4e4623a0f80a35082aa4289882d1502cc0df
-AUX lagan-2.0-qa-implicit-declarations.patch 2371 BLAKE2B e6ad9e67c322271fab92bf32094903d201f5cd81ce6cbf5f5f14708d53eac649024ca1c7e378a2a7ee26b0e4a7d99b275476f32ec32d1e20575d09dc9e2845c5 SHA512 eec54cec02a5c8c875a4d64238276f116baa8f3d780573ca5143621ca62a1e96ba4045ae37d45321fc040b78216607d787c2c6c909a8264f17f99a0e07295bf5
+AUX lagan-2.0-C99-static-inline.patch 7673 BLAKE2B 42b4ab27fa4a86786cdf02c8d7b16b1dc1439d2a6af15b6b9a7bfd46c97debf150140b5a9697d8d47d40d983388cd2f7f9167971b8166f385be83870ea095790 SHA512 db1798730a3dc093d56e6f778dd7380d8dab8f1919b74e3eb752cde353e85385755cdabf61c2692e666acf50b21f34d341c79a3c67ddefbc824d8c78d077345d
+AUX lagan-2.0-ambiguous-end.patch 1445 BLAKE2B 3d5e0467dfe60e2d5c25b8f90ba5d25e22bfcf63f8cf3b016cd02a837b51a1e653f8cb2ff5afb73ab7dbd38a22bc9d7fb7646080b6b02cde50fbe4beb55cce60 SHA512 85a9d3d1ce9efd00fdb98835e849fe4d22c059d5e4b8b3c11b7c227d5fd74ae522e3189c38c2ea62fb98c21228591dcaa8ea5a80c9d56c46420e716c30ce8a4d
+AUX lagan-2.0-conflicting-getline.patch 711 BLAKE2B 7ab19955c833e47dee06f214b52a79a55313ce7abf338cdeb4121a84b93027af601eb4379686bb2e4a5ebe215bf4321f8504ad4d91d8e7434575e0dead871d54 SHA512 867613347b50ab20e6640c7250609cd697d2217fe1c7731ee2688ccaff5e959fd1f0c96c80eabcb878d35bd679eb28931c75be808502fd4ad0fe184ddc2a6ea2
+AUX lagan-2.0-gcc-10.patch 506 BLAKE2B 0c35eb155a80e3c71f70d2013d47e77f38f1c6a6f7db8cace6f80a3839b9d6ea97429802a4c4081195c5fb3dd17680ee0d1f37a9ffd3cb2c47223812ef8245e3 SHA512 fe71d037d89a888e14c7c5d411ef2dd80f4cd3627fdc706c0d78d89a9befbec55cd06a5eb763d5d16d708156f067cad6f515c04235dbc5f9e842f663eb44b8e7
+AUX lagan-2.0-gcc-4.8.patch 649 BLAKE2B 4a4f76ce4709a3ae6210574604549aedc66ecbe27b6276d4470bb910765326028b94d2fdc1a28b5cfc63ff6b44005e2a33b42b42adb3f633af1649897e08b522 SHA512 504b9dbddbca07fd1bb3ebec8a8087af6548ac17c96acb8e76740ca2e63d40b695aed1e1e94cfbd24c6b2836c98e787dffddbb9884c338fd69a8b4e37046f7cb
+AUX lagan-2.0-gcc-9.patch 781 BLAKE2B 8280ebd4f445441d41a73e786568e4d1e17bbd2e73ac52f828651576bfb128986911efb8ce8b988bc540643f647d992bbf6793e0081adffe6aacace81174e0c7 SHA512 ecc007c8e266e5d859f9f5db99c9ea9d1048b7faba7dbad29ee9c04ee8cbd628e052615cec4123446d54f05f5c906a58e6e90cf6ac449e245c02d721750998ff
+AUX lagan-2.0-makefile.patch 6257 BLAKE2B 284dc6f21dd303f4b10f6e8cb30054c4ddd8df62c7c43c42a20351f4d81db4360c75feea8f55d32323c3349dc896c94213da7ab9074ee78f78e8ed82b0a0e211 SHA512 fc255585fc53c66b0a2f4e46788a59f8fdfae67b5f9ca4f4b0ac9224a7a915a387d991cb20315aa18a42df82ffa2b832270f0919f9939faf3b979d026e562c81
+AUX lagan-2.0-qa-implicit-declarations.patch 1396 BLAKE2B 556a43acf76e20a8484fd6ab5d0682b4b29206568b657b8daf09f79577890afd8a594b3897fc2322fffb5e2810a018638af0488c872e9d0794cb685a55b91e79 SHA512 4275aacf1dfa7d712a14ea5d8eafe11045c3b47a02c92915703d095af7b00f2206687eec568d14bfd00718f6b2430bd38cf70ac86cc5d550870d19f5fe6c6d97
 DIST lagan20.tar.gz 589115 BLAKE2B 8aaee40b767d7c1828760449e3bf2718210ad345447524ec2c391eb9f2856023f9258618d3d2625b15c42af814615870082bff6320ba0372dff79221798d2618 SHA512 f77217ab534df33834a725eb6e1b716f7bbffa98768a42c2294a6ab62404192e560bb05ffd41e4cdccb5b96ef9efceb8ecdc06472bbc6a301e1d11572ba29b98
-EBUILD lagan-2.0-r3.ebuild 1659 BLAKE2B 0ee31ba110a6238ac9218fc3d59347c9ee97fa11ce097c0a1f5e53c45fefa74ed83e35a1314e2f7fd57fbb3bdb64863109400af32f39f6dba13c273d722ded99 SHA512 b5efe429851ae0a3676a6e63017ebabdcae169667d091b2e69c0c2daa401f34e0ff3b789f8bacd78376befc466bb20de8f0d80bae63c332a6c412f01794f457b
+EBUILD lagan-2.0-r4.ebuild 1493 BLAKE2B 81a03c4ab005e5190a2275fa160b86fb16bfb3d8ef1dc794363df692cce7eb8389974af99acbaa5677903db2d75e02e63920cae712abcd7aa421fe7326b8afda SHA512 b9b8e5e12a9ea1276f38806f933cbe7e73b63782510f4e66336ab0a5e1ceeb634d46b81eecf953421d5eaf7e1ce42e130df40b66e6137f0aa8af68155e36363f
 MISC metadata.xml 267 BLAKE2B 7cf386952842945148119de3263231db4d1046d5f54811f7e303ed8ec4d27cbc1960b99c92daf6f32e5b981c2fb9f50ec666be6193865d6e18541b7427a152a9 SHA512 91ab266d9ab24401bc0fec759c5b6cfcf44a3c5669fc31c7301d79770839bb5dfa0e155d949392ef06176b4a0b2c32b91b1b54b0027f972db61f0a5e54644403
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 000000000000..2c9d88111aee
--- /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 000000000000..945120b1fc47
--- /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 000000000000..075753a924c9
--- /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 9865f2756c5a..000000000000
--- 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 000000000000..bd9824cf2ed0
--- /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 000000000000..3d7ed780445f
--- /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 000000000000..6ea30e57a854
--- /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 a4b1d6808e2f..000000000000
--- 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 e324ef64c4c6..1bef6721ab9b 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 4ba4ce49d770..29db043d5f34 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 e326331e09fb..000000000000
--- 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${PN}
-
-	dodoc Readmes/README.*
-}
diff --git a/sci-biology/lagan/lagan-2.0-r4.ebuild b/sci-biology/lagan/lagan-2.0-r4.ebuild
new file mode 100644
index 000000000000..4582d8f1078e
--- /dev/null
+++ b/sci-biology/lagan/lagan-2.0-r4.ebuild
@@ -0,0 +1,67 @@
+# Copyright 1999-2020 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=7
+
+inherit toolchain-funcs
+
+MY_P="lagan20"
+
+DESCRIPTION="The LAGAN suite of tools for whole-genome multiple alignment of genomic DNA"
+HOMEPAGE="http://lagan.stanford.edu/lagan_web/index.shtml"
+SRC_URI="http://lagan.stanford.edu/lagan_web/${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.*
+}