Fixes fo various problems, #346883

Package-Manager: portage-2.2.0_alpha5/cvs/Linux x86_64

4 files changed, 310 insertions, 0 deletions

diff --git a/sci-biology/readseq/files/19930201-buffer.patch b/sci-biology/readseq/files/19930201-buffer.patch
new file mode 100644
index 000000000000..8229074dbbc3
--- /dev/null
+++ b/sci-biology/readseq/files/19930201-buffer.patch
@@ -0,0 +1,13 @@
+diff --git a/ureadseq.c b/ureadseq.c
+index 337b16f..3f8e7f6 100644
+--- a/ureadseq.c
++++ b/ureadseq.c
+@@ -1578,7 +1578,7 @@ short writeSeq(FILE *outf, const char *seq, const long seqlen,
+ 
+   short linesout = 0, seqtype = kNucleic;
+   long  i, j, l, l1, ibase;
+-  char  idword[31], endstr[10];
++  char  idword[31], endstr[32];
+   char  seqnamestore[128], *seqname = seqnamestore;
+   char  s[kMaxseqwidth], *cp;
+   char  nameform[10], numform[10], nocountsymbols[10];
diff --git a/sci-biology/readseq/files/19930201-getline.patch b/sci-biology/readseq/files/19930201-getline.patch
new file mode 100644
index 000000000000..34f6339209de
--- /dev/null
+++ b/sci-biology/readseq/files/19930201-getline.patch
@@ -0,0 +1,260 @@
+diff --git a/ureadseq.c b/ureadseq.c
+index b11115d..337b16f 100644
+--- a/ureadseq.c
++++ b/ureadseq.c
+@@ -136,7 +136,7 @@ Local void readline(FILE *f, char *s, long *linestart)
+     }
+ }
+ 
+-Local void getline(struct ReadSeqVars *V)
++Local void ghettoline(struct ReadSeqVars *V)
+ {
+   readline(V->f, V->s, &V->linestart);
+ }
+@@ -215,7 +215,7 @@ Local void readLoop(short margin, boolean addfirst,
+ 
+   if (addfirst) addseq(V->s, V);
+   do {
+-    getline(V);
++    ghettoline(V);
+     V->done = feof(V->f);
+     V->done |= (*endTest)( &addend, &ungetend, V);
+     if (V->addit && (addend || !V->done) && (strlen(V->s) > margin)) {
+@@ -246,7 +246,7 @@ Local void readIG(struct ReadSeqVars *V)
+ 
+   while (!V->allDone) {
+     do {
+-      getline(V);
++      ghettoline(V);
+       for (si= V->s; *si != 0 && *si < ' '; si++) *si= ' '; /* drop controls */
+       if (*si == 0) *V->s= 0; /* chop line to empty */
+     } while (! (feof(V->f) || ((*V->s != 0) && (*V->s != ';') ) ));
+@@ -272,13 +272,13 @@ Local void readStrider(struct ReadSeqVars *V)
+ { /* ? only 1 seq/file ? */
+ 
+   while (!V->allDone) {
+-    getline(V);
++    ghettoline(V);
+     if (strstr(V->s,"; DNA sequence  ") == V->s)
+       strcpy(V->seqid, (V->s)+16);
+     else
+       strcpy(V->seqid, (V->s)+1);
+     while ((!feof(V->f)) && (*V->s == ';')) {
+-      getline(V);
++      ghettoline(V);
+       }
+     if (feof(V->f)) V->allDone = true;
+     else readLoop(0, true, endStrider, V);
+@@ -298,16 +298,16 @@ Local void readPIR(struct ReadSeqVars *V)
+ 
+   while (!V->allDone) {
+     while (! (feof(V->f) || strstr(V->s,"ENTRY")  || strstr(V->s,"SEQUENCE")) )
+-      getline(V);
++      ghettoline(V);
+     strcpy(V->seqid, (V->s)+16);
+     while (! (feof(V->f) || strstr(V->s,"SEQUENCE") == V->s))
+-      getline(V);
++      ghettoline(V);
+     readLoop(0, false, endPIR, V);
+ 
+     if (!V->allDone) {
+      while (! (feof(V->f) || ((*V->s != 0)
+        && (strstr( V->s,"ENTRY") == V->s))))
+-        getline(V);
++        ghettoline(V);
+       }
+     if (feof(V->f)) V->allDone = true;
+   }
+@@ -327,13 +327,13 @@ Local void readGenBank(struct ReadSeqVars *V)
+   while (!V->allDone) {
+     strcpy(V->seqid, (V->s)+12);
+     while (! (feof(V->f) || strstr(V->s,"ORIGIN") == V->s))
+-      getline(V);
++      ghettoline(V);
+     readLoop(0, false, endGB, V);
+ 
+     if (!V->allDone) {
+      while (! (feof(V->f) || ((*V->s != 0)
+        && (strstr( V->s,"LOCUS") == V->s))))
+-        getline(V);
++        ghettoline(V);
+       }
+     if (feof(V->f)) V->allDone = true;
+   }
+@@ -364,11 +364,11 @@ Local void readNBRF(struct ReadSeqVars *V)
+ {
+   while (!V->allDone) {
+     strcpy(V->seqid, (V->s)+4);
+-    getline(V);   /*skip title-junk line*/
++    ghettoline(V);   /*skip title-junk line*/
+     readLoop(0, false, endNBRF, V);
+     if (!V->allDone) {
+      while (!(feof(V->f) || (*V->s != 0 && *V->s == '>')))
+-        getline(V);
++        ghettoline(V);
+       }
+     if (feof(V->f)) V->allDone = true;
+   }
+@@ -390,7 +390,7 @@ Local void readPearson(struct ReadSeqVars *V)
+     readLoop(0, false, endPearson, V);
+     if (!V->allDone) {
+      while (!(feof(V->f) || ((*V->s != 0) && (*V->s == '>'))))
+-        getline(V);
++        ghettoline(V);
+       }
+     if (feof(V->f)) V->allDone = true;
+   }
+@@ -410,14 +410,14 @@ Local void readEMBL(struct ReadSeqVars *V)
+   while (!V->allDone) {
+     strcpy(V->seqid, (V->s)+5);
+     do {
+-      getline(V);
++      ghettoline(V);
+     } while (!(feof(V->f) | (strstr(V->s,"SQ   ") == V->s)));
+ 
+     readLoop(0, false, endEMBL, V);
+     if (!V->allDone) {
+       while (!(feof(V->f) |
+          ((*V->s != '\0') & (strstr(V->s,"ID   ") == V->s))))
+-      getline(V);
++      ghettoline(V);
+     }
+     if (feof(V->f)) V->allDone = true;
+   }
+@@ -437,13 +437,13 @@ Local void readZuker(struct ReadSeqVars *V)
+   /*! 1st string is Zuker's Fortran format */
+ 
+   while (!V->allDone) {
+-    getline(V);  /*s == "seqLen seqid string..."*/
++    ghettoline(V);  /*s == "seqLen seqid string..."*/
+     strcpy(V->seqid, (V->s)+6);
+     readLoop(0, false, endZuker, V);
+     if (!V->allDone) {
+       while (!(feof(V->f) |
+         ((*V->s != '\0') & (*V->s == '('))))
+-          getline(V);
++          ghettoline(V);
+       }
+     if (feof(V->f)) V->allDone = true;
+   }
+@@ -486,7 +486,7 @@ Local void readPlain(struct ReadSeqVars *V)
+   do {
+     addseq(V->s, V);
+     V->done = feof(V->f);
+-    getline(V);
++    ghettoline(V);
+   } while (!V->done);
+   if (V->choice == kListSequences) addinfo(V->seqid, V);
+   V->allDone = true;
+@@ -498,7 +498,7 @@ Local void readUWGCG(struct ReadSeqVars *V)
+ /*
+ 10nov91: Reading GCG files casued duplication of last line when
+          EOF followed that line !!!
+-    fix: getline now sets *V->s = 0
++    fix: ghettoline now sets *V->s = 0
+ */
+   char  *si;
+ 
+@@ -512,7 +512,7 @@ Local void readUWGCG(struct ReadSeqVars *V)
+   else if (si = strstr(V->seqid,"..")) *si = 0;
+   do {
+     V->done = feof(V->f);
+-    getline(V);
++    ghettoline(V);
+     if (!V->done) addseq((V->s), V);
+   } while (!V->done);
+   if (V->choice == kListSequences) addinfo(V->seqid, V);
+@@ -531,7 +531,7 @@ Local void readOlsen(struct ReadSeqVars *V)
+   if (V->addit) V->seqlen = 0;
+   rewind(V->f); V->nseq= 0;
+   do {
+-    getline(V);
++    ghettoline(V);
+     V->done = feof(V->f);
+ 
+     if (V->done && !(*V->s)) break;
+@@ -614,7 +614,7 @@ Local void readMSF(struct ReadSeqVars *V)
+   if (V->addit) V->seqlen = 0;
+   rewind(V->f); V->nseq= 0;
+   do {
+-    getline(V);
++    ghettoline(V);
+     V->done = feof(V->f);
+ 
+     if (V->done && !(*V->s)) break;
+@@ -685,7 +685,7 @@ Local void readPAUPinterleaved(struct ReadSeqVars *V)
+   domatch= (V->matchchar > 0);
+ 
+   do {
+-    getline(V);
++    ghettoline(V);
+     V->done = feof(V->f);
+ 
+     if (V->done && !(*V->s)) break;
+@@ -766,7 +766,7 @@ Local void readPAUPsequential(struct ReadSeqVars *V)
+   /* rewind(V->f); V->nseq= 0;  << do in caller !*/
+   indata= true; /* call here after we find "matrix" */
+   do {
+-    getline(V);
++    ghettoline(V);
+     V->done = feof(V->f);
+ 
+     if (V->done && !(*V->s)) break;
+@@ -851,7 +851,7 @@ Local void readPhylipInterleaved(struct ReadSeqVars *V)
+   /* fprintf(stderr,"Phylip-ileaf: topnseq=%d  topseqlen=%d\n",V->topnseq, V->topseqlen); */
+ 
+   do {
+-    getline(V);
++    ghettoline(V);
+     V->done = feof(V->f);
+ 
+     if (V->done && !(*V->s)) break;
+@@ -904,7 +904,7 @@ Local void readPhylipSequential(struct ReadSeqVars *V)
+   while (isdigit(*si)) si++;
+   skipwhitespace(si);
+   V->topseqlen= atol(si);
+-  getline(V);
++  ghettoline(V);
+   while (!V->allDone) {
+     V->seqlencount= 0;
+     strncpy(V->seqid, (V->s), 10);
+@@ -935,10 +935,10 @@ Local void readSeqMain(
+     V->err = eFileNotFound;
+   else {
+ 
+-    for (l = skiplines_; l > 0; l--) getline( V);
++    for (l = skiplines_; l > 0; l--) ghettoline( V);
+ 
+     do {
+-      getline( V);
++      ghettoline( V);
+       for (l= strlen(V->s); (l > 0) && (V->s[l] == ' '); l--) ;
+     } while ((l == 0) && !feof(V->f));
+ 
+@@ -963,7 +963,7 @@ Local void readSeqMain(
+         char  *cp;
+         /* rewind(V->f); V->nseq= 0; ?? assume it is at top ?? skiplines ... */
+         while (!done) {
+-          getline( V);
++          ghettoline( V);
+           tolowerstr( V->s);
+           if (strstr( V->s, "matrix")) done= true;
+           if (strstr( V->s, "interleav")) interleaved= true;
+@@ -995,7 +995,7 @@ Local void readSeqMain(
+         break;
+ 
+       case kFitch :
+-        strcpy(V->seqid, V->s); getline(V);
++        strcpy(V->seqid, V->s); ghettoline(V);
+         readFitch(V);
+         break;
+ 
+@@ -1003,7 +1003,7 @@ Local void readSeqMain(
+         do {
+           gotuw = (strstr(V->s,"..") != NULL);
+           if (gotuw) readUWGCG(V);
+-          getline(V);
++          ghettoline(V);
+         } while (!(feof(V->f) || V->allDone));
+         break;
+       }
diff --git a/sci-biology/readseq/files/19930201-impl-dec.patch b/sci-biology/readseq/files/19930201-impl-dec.patch
new file mode 100644
index 000000000000..8e9448224e2c
--- /dev/null
+++ b/sci-biology/readseq/files/19930201-impl-dec.patch
@@ -0,0 +1,24 @@
+diff --git a/readseq.c b/readseq.c
+index 305d23a..9b02a17 100644
+--- a/readseq.c
++++ b/readseq.c
+@@ -171,6 +171,7 @@ link -w -o readseq -t MPST -c 'MPS ' 
+ #include <stdio.h>
+ #include <string.h>
+ #include <ctype.h>
++#include <stdlib.h>
+ 
+ #include "ureadseq.h"
+ 
+diff --git a/ureadseq.c b/ureadseq.c
+index 3f8e7f6..799b315 100644
+--- a/ureadseq.c
++++ b/ureadseq.c
+@@ -20,6 +20,7 @@
+ #include <stdio.h>
+ #include <ctype.h>
+ #include <string.h>
++#include <stdlib.h>
+ 
+ #define UREADSEQ_G
+ #include "ureadseq.h"
diff --git a/sci-biology/readseq/files/19930201-ldflags.patch b/sci-biology/readseq/files/19930201-ldflags.patch
new file mode 100644
index 000000000000..e1929c634479
--- /dev/null
+++ b/sci-biology/readseq/files/19930201-ldflags.patch
@@ -0,0 +1,13 @@
+diff --git a/Makefile b/Makefile
+index 40a5a92..f073aaa 100644
+--- a/Makefile
++++ b/Makefile
+@@ -40,7 +40,7 @@ all: build test
+ 
+ build: $(SOURCES)
+ 	@echo "Compiling readseq..."
+-	$(CC) $(CFLAGS) -o readseq readseq.c ureadseq.c
++	$(CC) $(LDFLAGS) $(CFLAGS) -o readseq readseq.c ureadseq.c
+ 
+ # if using NCBI, uncomment these lines in place of build: above
+ #build: $(SOURCES)