jlec 15/03/02 14:09:51
Added: ncbi-tools-2.2.26-_DEFAULT_SOURCE.patch
ncbi-tools-2.2.26-format-security.patch
Log:
Fix format-security and SLOT operators
(Portage version: 2.2.17/cvs/Linux x86_64, signed Manifest commit with key
B9D4F231BD1558AB!)
Revision Changes Path
1.1
sci-biology/ncbi-tools/files/ncbi-tools-2.2.26-_DEFAULT_SOURCE.patch
file :
http://sources.gentoo.org/viewvc.cgi/gentoo-x86/sci-biology/ncbi-tools/files/ncbi-tools-2.2.26-_DEFAULT_SOURCE.patch?rev=1.1&view=markup
plain:
http://sources.gentoo.org/viewvc.cgi/gentoo-x86/sci-biology/ncbi-tools/files/ncbi-tools-2.2.26-_DEFAULT_SOURCE.patch?rev=1.1&content-type=text/plain
Index: ncbi-tools-2.2.26-_DEFAULT_SOURCE.patch
===================================================================
corelib/ncbilcl.beos | 2 +-
corelib/ncbilcl.hlx | 2 +-
corelib/ncbilcl.lnx | 4 ++--
corelib/ncbilcl.plx | 2 +-
corelib/ncbilcl.qnx | 2 +-
5 files changed, 6 insertions(+), 6 deletions(-)
diff --git a/corelib/ncbilcl.beos b/corelib/ncbilcl.beos
index f720567..fe6346f 100644
--- a/corelib/ncbilcl.beos
+++ b/corelib/ncbilcl.beos
@@ -77,7 +77,7 @@
#endif
/* good for the EGCS C/C++ compiler on Linux(e.g. putenv(), tempnam() proto) */
-#define _SVID_SOURCE 1
+#define _DEFAULT_SOURCE 1
/*----------------------------------------------------------------------*/
diff --git a/corelib/ncbilcl.hlx b/corelib/ncbilcl.hlx
index 1492f93..0e98fb6 100644
--- a/corelib/ncbilcl.hlx
+++ b/corelib/ncbilcl.hlx
@@ -67,7 +67,7 @@
#endif
/* good for the EGCS C/C++ compiler on Linux(e.g. putenv(), tempnam() proto) */
-/*#define _SVID_SOURCE 1 */
+/*#define _DEFAULT_SOURCE 1 */
/*----------------------------------------------------------------------*/
diff --git a/corelib/ncbilcl.lnx b/corelib/ncbilcl.lnx
index 46e2978..b3256b3 100644
--- a/corelib/ncbilcl.lnx
+++ b/corelib/ncbilcl.lnx
@@ -65,7 +65,7 @@
* fixes for new RedHat6.2
*
* Revision 6.3 2000/02/10 16:36:32 vakatov
-* Added _SVID_SOURCE
+* Added _DEFAULT_SOURCE
*
* Revision 6.2 1999/07/12 05:50:49 vakatov
* Avoid redefinition of #_REENTRANT
@@ -141,7 +141,7 @@
#endif
/* good for the EGCS C/C++ compiler on Linux(e.g. putenv(), tempnam() proto) */
-#define _SVID_SOURCE 1
+#define _DEFAULT_SOURCE 1
#define _GNU_SOURCE 1
/*----------------------------------------------------------------------*/
diff --git a/corelib/ncbilcl.plx b/corelib/ncbilcl.plx
index bf5824c..f2b53e1 100644
--- a/corelib/ncbilcl.plx
+++ b/corelib/ncbilcl.plx
@@ -68,7 +68,7 @@
#endif
/* good for the EGCS C/C++ compiler on Linux(e.g. putenv(), tempnam() proto) */
-/*#define _SVID_SOURCE 1 */
+/*#define _DEFAULT_SOURCE 1 */
/*----------------------------------------------------------------------*/
diff --git a/corelib/ncbilcl.qnx b/corelib/ncbilcl.qnx
index c3d1f0a..4b27bd1 100644
--- a/corelib/ncbilcl.qnx
+++ b/corelib/ncbilcl.qnx
@@ -72,7 +72,7 @@
#endif
/* good for the EGCS C/C++ compiler on Linux(e.g. putenv(), tempnam() proto) */
-#define _SVID_SOURCE 1
+#define _DEFAULT_SOURCE 1
1.1
sci-biology/ncbi-tools/files/ncbi-tools-2.2.26-format-security.patch
file :
http://sources.gentoo.org/viewvc.cgi/gentoo-x86/sci-biology/ncbi-tools/files/ncbi-tools-2.2.26-format-security.patch?rev=1.1&view=markup
plain:
http://sources.gentoo.org/viewvc.cgi/gentoo-x86/sci-biology/ncbi-tools/files/ncbi-tools-2.2.26-format-security.patch?rev=1.1&content-type=text/plain
Index: ncbi-tools-2.2.26-format-security.patch
===================================================================
api/alignmgr2.c | 2 +-
api/pgppop.c | 2 +-
api/txalign.c | 10 +++++-----
desktop/seqpanel.c | 4 ++--
tools/spidey.c | 4 ++--
5 files changed, 11 insertions(+), 11 deletions(-)
diff --git a/api/alignmgr2.c b/api/alignmgr2.c
index 5b43ef3..4b9007e 100644
--- a/api/alignmgr2.c
+++ b/api/alignmgr2.c
@@ -5616,7 +5616,7 @@ NLM_EXTERN void AlnMgr2PrintSeqAlign(SeqAlignPtr sap,
Int4 linesize, Boolean isn
spp = SeqPortNew(bsp, amp->from_row, amp->to_row, amp->strand,
seqcode);
ctr = SeqPortRead(spp, (Uint1Ptr)buf,
amp->to_row-amp->from_row+1);
buf[ctr] = '\0';
- fprintf(ofp, buf);
+ fprintf(ofp, "%s", buf);
SeqPortFree(spp);
}
}
diff --git a/api/pgppop.c b/api/pgppop.c
index d16d79d..b359378 100644
--- a/api/pgppop.c
+++ b/api/pgppop.c
@@ -2994,7 +2994,7 @@ Char DefLine[255];
if (szSeq){
if
(!DDV_GetSequenceFromParaG(pgp,&szSeq,bspLength,IsAA,NULL,
NULL,NULL)) continue;
- fprintf(fp,szSeq);
+ fprintf(fp, "%s", szSeq);
fprintf(fp,"\n");
MemFree(szSeq);
}
diff --git a/api/txalign.c b/api/txalign.c
index 5877f9c..cb35fbc 100644
--- a/api/txalign.c
+++ b/api/txalign.c
@@ -1767,13 +1767,13 @@ static CharPtr DrawTextToBuffer(ValNodePtr tdp_list,
CharPtr PNTR m_buf, Boolean
if(options&TXALIGN_HTML&&options&TXALIGN_MASTER&&DbHasGi&&(options&TXALIGN_GET_SEQUENCE)){
Char checkboxBuf[200];
sprintf(checkboxBuf, "<input
type=\"checkbox\" name=\"getSeqGi\" value=\"%ld\"
onClick=\"synchronizeCheck(this.value, 'getSeqAlignment%ld', 'getSeqGi',
this.checked)\">", sip->data.intvalue, query_number_glb);
- sprintf(docbuf+pos,checkboxBuf);
+ sprintf(docbuf+pos,"%s", checkboxBuf);
pos += StringLen(checkboxBuf);
}
html_len = StringLen(HTML_buffer);
- sprintf(docbuf+pos, HTML_buffer);
+ sprintf(docbuf+pos, "%s", HTML_buffer);
pos += html_len;
pos +=
print_label_to_buffer_all_ex(docbuf+pos, tdp->label, tdp->pos,
@@ -1790,7 +1790,7 @@ static CharPtr DrawTextToBuffer(ValNodePtr tdp_list,
CharPtr PNTR m_buf, Boolean
sprintf(HTML_buffer, "<a name =
THC%ld></a><a
href=\"http://www.tigr.org/docs/tigr-scripts/hgi_scripts/thc_report.spl?est=THC%ld&report_type=n\";>",
(long) oip->id, (long) oip->id);
html_len = StringLen(HTML_buffer);
- sprintf(docbuf+pos, HTML_buffer);
+ sprintf(docbuf+pos, "%s",
HTML_buffer);
pos += html_len;
pos +=
print_label_to_buffer_all_ex(docbuf+pos, tdp->label, tdp->pos,
tdp->strand, FALSE,
TRUE, label_size, num_size, show_strand, strip_semicolon);
@@ -1799,7 +1799,7 @@ static CharPtr DrawTextToBuffer(ValNodePtr tdp_list,
CharPtr PNTR m_buf, Boolean
sprintf(HTML_buffer, "<a name =
TI%ld></a><a
href=\"http://www.ncbi.nlm.nih.gov/Traces/trace.cgi?cmd=retrieve&dopt=fasta&val=%ld\";>",
(long) oip->id, (long) oip->id);
html_len = StringLen(HTML_buffer);
- sprintf(docbuf+pos, HTML_buffer);
+ sprintf(docbuf+pos, "%s",
HTML_buffer);
pos += html_len;
pos +=
print_label_to_buffer_all_ex(docbuf+pos, tdp->label, tdp->pos,
tdp->strand, FALSE,
TRUE, label_size, num_size, show_strand, strip_semicolon);
@@ -1816,7 +1816,7 @@ static CharPtr DrawTextToBuffer(ValNodePtr tdp_list,
CharPtr PNTR m_buf, Boolean
if(options&TXALIGN_HTML&&options&TXALIGN_MASTER&&DbHasGi&&(options&TXALIGN_GET_SEQUENCE)){
Char checkboxBuf[200];
sprintf(checkboxBuf, "<input type=\"checkbox\"
name=\"getSeqMaster\" value=\"\" onClick=\"uncheckable('getSeqAlignment%ld',
'getSeqMaster')\">", query_number_glb);
- sprintf(docbuf+pos,checkboxBuf);
+ sprintf(docbuf+pos,"%s",checkboxBuf);
pos += StringLen(checkboxBuf);
}
diff --git a/desktop/seqpanel.c b/desktop/seqpanel.c
index 2e78e13..c7538aa 100644
--- a/desktop/seqpanel.c
+++ b/desktop/seqpanel.c
@@ -8661,7 +8661,7 @@ WriteAlignmentInterleaveToFileEx
seqbuf, alnbuf, &alnbuf_len,
show_substitutions);
MemCpy (printed_line + label_len + 1 + coord_len, alnbuf,
alnbuf_len);
- fprintf (fp, printed_line);
+ fprintf (fp, "%s", printed_line);
}
fprintf (fp, "\n");
start = stop + 1;
@@ -8757,7 +8757,7 @@ extern void WriteAlignmentContiguousToFile
seqbuf, alnbuf, &alnbuf_len,
show_substitutions);
MemCpy (printed_line, alnbuf, alnbuf_len);
- fprintf (fp, printed_line);
+ fprintf (fp, "%s", printed_line);
start = stop + 1;
stop += seq_chars_per_row;
}
diff --git a/tools/spidey.c b/tools/spidey.c
index d6ce62d..ac9f59a 100644
--- a/tools/spidey.c
+++ b/tools/spidey.c
@@ -2088,7 +2088,7 @@ static void SPI_PrintResult(FILE *ofp, FILE *ofp2,
SPI_RegionInfoPtr srip, Biose
fprintf(ofp2, " ");
ctr++;
}
- fprintf(ofp2, buf);
+ fprintf(ofp2, "%s", buf);
if (spp){
SeqPortFree(spp);
}
@@ -2417,7 +2417,7 @@ static void SPI_PrintHerdResult(FILE *ofp, FILE *ofp2,
SPI_mRNAToHerdPtr herd, S
ctr = SeqPortRead(spp, (Uint1Ptr)buf, 10);
if (ctr > 0)
buf[ctr] = '\0';
- fprintf(ofp2, buf);
+ fprintf(ofp2, "%s", buf);
SeqPortFree(spp);
}
done = TRUE;
