Package: ncbi-tools6
Severity: normal
Tags: patch
When building 'ncbi-tools6' on amd64 with gcc-4.0,
I get the following error:
cc -c -g -Wall -O2 -I/usr/X11R6/include -D_PNG -fPIC -I../include
-I/usr/X11R6/include -DWIN_MOTIF edutil.c
edutil.c: In function 'SeqDeleteByLoc':
edutil.c:1035: warning: unused variable 'the_id'
edutil.c: In function 'IndexedSeqFeatsCopy':
edutil.c:2148: warning: unused variable 'head'
edutil.c: In function 'SeqFeatsCopy':
edutil.c:2252: warning: unused variable 'head'
edutil.c: In function 'SeqLocCopyRegion':
edutil.c:2369: warning: unused variable 'ptr'
edutil.c:2362: warning: unused variable 'last'
edutil.c: In function 'AffectedFeatFree':
edutil.c:3889: warning: 'return' with no value, in function returning non-void
edutil.c: At top level:
edutil.c:4029: error: static declaration of 'SeqEdSeqLocInsert' follows
non-static declaration
../include/edutil.h:612: error: previous declaration of 'SeqEdSeqLocInsert' was
here
make[1]: *** [edutil.o] Error 1
make[1]: Leaving directory `/ncbi-tools6-6.1.20041020/build'
make: *** [debian/stamp-shlibs] Error 2
With the attached patch 'ncbi-tools6' can be compiled
on amd64 using gcc-4.0.
Regards
Andreas Jochens
diff -urN ../tmp-orig/ncbi-tools6-6.1.20041020/api/asn2gnb3.c ./api/asn2gnb3.c
--- ../tmp-orig/ncbi-tools6-6.1.20041020/api/asn2gnb3.c 2004-08-17
23:24:14.000000000 +0200
+++ ./api/asn2gnb3.c 2005-02-13 16:01:30.000000000 +0100
@@ -952,7 +952,7 @@
return FALSE;
}
-static Boolean GetAccnVerFromServer (Int4 gi, CharPtr buf)
+static Boolean GetAccnVerFromServer3 (Int4 gi, CharPtr buf)
{
AccnVerLookupFunc func;
@@ -1012,7 +1012,7 @@
accn = FALSE;
if (sip->choice == SEQID_GI) {
gi = (Int4) sip->data.intvalue;
- if (GetAccnVerFromServer (gi, buf)) {
+ if (GetAccnVerFromServer3 (gi, buf)) {
accn = TRUE;
} else {
id = GetSeqIdForGI (gi);
@@ -3963,7 +3963,7 @@
} else if (sip->choice == SEQID_GI && sip->data.intvalue > 0) {
/* RELEASE_MODE requires that /protein_id is an accession */
gi = sip->data.intvalue;
- if (GetAccnVerFromServer (gi, buf)) {
+ if (GetAccnVerFromServer3 (gi, buf)) {
okay = TRUE;
} else {
sip = GetSeqIdForGI (gi);
diff -urN ../tmp-orig/ncbi-tools6-6.1.20041020/api/edutil.c ./api/edutil.c
--- ../tmp-orig/ncbi-tools6-6.1.20041020/api/edutil.c 2004-10-08
18:04:16.000000000 +0200
+++ ./api/edutil.c 2005-02-13 15:58:43.000000000 +0100
@@ -4024,7 +4024,7 @@
*
*
*****************************************************************************/
-static SeqLocPtr LIBCALL SeqEdSeqLocInsert (SeqLocPtr head, BioseqPtr target,
Int4 pos, Int4 len,
+SeqLocPtr LIBCALL SeqEdSeqLocInsert (SeqLocPtr head, BioseqPtr target, Int4
pos, Int4 len,
Boolean split, SeqIdPtr newid)
{
SeqIntPtr sip, sip2;
diff -urN ../tmp-orig/ncbi-tools6-6.1.20041020/desktop/salfiles.c
./desktop/salfiles.c
--- ../tmp-orig/ncbi-tools6-6.1.20041020/desktop/salfiles.c 2004-09-27
15:07:36.000000000 +0200
+++ ./desktop/salfiles.c 2005-02-13 16:12:09.000000000 +0100
@@ -151,7 +151,7 @@
}
/**********************************************************/
-static SeqEntryPtr make_seqentry_for_seqentry (SeqEntryPtr sep)
+SeqEntryPtr make_seqentry_for_seqentry (SeqEntryPtr sep)
{
SeqEntryPtr sep1 = NULL,
tmp;
diff -urN ../tmp-orig/ncbi-tools6-6.1.20041020/network/id1arch/idfetch.c
./network/id1arch/idfetch.c
--- ../tmp-orig/ncbi-tools6-6.1.20041020/network/id1arch/idfetch.c
2004-10-12 23:39:28.000000000 +0200
+++ ./network/id1arch/idfetch.c 2005-02-13 18:49:56.000000000 +0100
@@ -195,6 +195,8 @@
static Boolean IdFetch_func1(CharPtr data, Int2 maxplex);
static Boolean IdFetch_func(Int4 gi,CharPtr db, Int4 ent,Int2 maxplex);
+static int TryGetGi(int choice, char *accession, char *name, int version);
+
Args myargs[] = {
{"Filename for output ","stdout", NULL,NULL,FALSE,'o',ARG_FILE_OUT,
0.0,0,NULL},
{"Output type:\t\
diff -urN ../tmp-orig/ncbi-tools6-6.1.20041020/tools/salptool.c
./tools/salptool.c
--- ../tmp-orig/ncbi-tools6-6.1.20041020/tools/salptool.c 2004-08-26
20:16:29.000000000 +0200
+++ ./tools/salptool.c 2005-02-13 16:24:16.000000000 +0100
@@ -1942,7 +1942,7 @@
return vnp;
}
-static SeqIdPtr SeqIdReplaceID (SeqIdPtr head, SeqIdPtr pre, SeqIdPtr sip,
SeqIdPtr next)
+SeqIdPtr SeqIdReplaceID (SeqIdPtr head, SeqIdPtr pre, SeqIdPtr sip, SeqIdPtr
next)
{
SeqIdPtr tmp;
@@ -3269,7 +3269,7 @@
should be highlighted for this validation to work
******************************************************************/
-static SeqAlignPtr LIBCALL is_salp_in_sap (SeqAnnotPtr sap, Uint1 choice)
+SeqAlignPtr LIBCALL is_salp_in_sap (SeqAnnotPtr sap, Uint1 choice)
{
SeqAlignPtr salp = NULL;
--
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