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From: "Justin Lecher (jlec)" <jlec@g.o>
To: gentoo-commits@l.g.o
Subject: [gentoo-commits] gentoo-x86 commit in sci-biology/ncbi-tools/files: ncbi-tools-2.2.26-_DEFAULT_SOURCE.patch ncbi-tools-2.2.26-format-security.patch
Date: Mon, 02 Mar 2015 14:09:57
Message-Id: 20150302140951.BD83F12E1A@oystercatcher.gentoo.org
1 jlec 15/03/02 14:09:51
2
3 Added: ncbi-tools-2.2.26-_DEFAULT_SOURCE.patch
4 ncbi-tools-2.2.26-format-security.patch
5 Log:
6 Fix format-security and SLOT operators
7
8 (Portage version: 2.2.17/cvs/Linux x86_64, signed Manifest commit with key B9D4F231BD1558AB!)
9
10 Revision Changes Path
11 1.1 sci-biology/ncbi-tools/files/ncbi-tools-2.2.26-_DEFAULT_SOURCE.patch
12
13 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
14 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
15
16 Index: ncbi-tools-2.2.26-_DEFAULT_SOURCE.patch
17 ===================================================================
18 corelib/ncbilcl.beos | 2 +-
19 corelib/ncbilcl.hlx | 2 +-
20 corelib/ncbilcl.lnx | 4 ++--
21 corelib/ncbilcl.plx | 2 +-
22 corelib/ncbilcl.qnx | 2 +-
23 5 files changed, 6 insertions(+), 6 deletions(-)
24
25 diff --git a/corelib/ncbilcl.beos b/corelib/ncbilcl.beos
26 index f720567..fe6346f 100644
27 --- a/corelib/ncbilcl.beos
28 +++ b/corelib/ncbilcl.beos
29 @@ -77,7 +77,7 @@
30 #endif
31
32 /* good for the EGCS C/C++ compiler on Linux(e.g. putenv(), tempnam() proto) */
33 -#define _SVID_SOURCE 1
34 +#define _DEFAULT_SOURCE 1
35
36
37 /*----------------------------------------------------------------------*/
38 diff --git a/corelib/ncbilcl.hlx b/corelib/ncbilcl.hlx
39 index 1492f93..0e98fb6 100644
40 --- a/corelib/ncbilcl.hlx
41 +++ b/corelib/ncbilcl.hlx
42 @@ -67,7 +67,7 @@
43 #endif
44
45 /* good for the EGCS C/C++ compiler on Linux(e.g. putenv(), tempnam() proto) */
46 -/*#define _SVID_SOURCE 1 */
47 +/*#define _DEFAULT_SOURCE 1 */
48
49
50 /*----------------------------------------------------------------------*/
51 diff --git a/corelib/ncbilcl.lnx b/corelib/ncbilcl.lnx
52 index 46e2978..b3256b3 100644
53 --- a/corelib/ncbilcl.lnx
54 +++ b/corelib/ncbilcl.lnx
55 @@ -65,7 +65,7 @@
56 * fixes for new RedHat6.2
57 *
58 * Revision 6.3 2000/02/10 16:36:32 vakatov
59 -* Added _SVID_SOURCE
60 +* Added _DEFAULT_SOURCE
61 *
62 * Revision 6.2 1999/07/12 05:50:49 vakatov
63 * Avoid redefinition of #_REENTRANT
64 @@ -141,7 +141,7 @@
65 #endif
66
67 /* good for the EGCS C/C++ compiler on Linux(e.g. putenv(), tempnam() proto) */
68 -#define _SVID_SOURCE 1
69 +#define _DEFAULT_SOURCE 1
70 #define _GNU_SOURCE 1
71
72 /*----------------------------------------------------------------------*/
73 diff --git a/corelib/ncbilcl.plx b/corelib/ncbilcl.plx
74 index bf5824c..f2b53e1 100644
75 --- a/corelib/ncbilcl.plx
76 +++ b/corelib/ncbilcl.plx
77 @@ -68,7 +68,7 @@
78 #endif
79
80 /* good for the EGCS C/C++ compiler on Linux(e.g. putenv(), tempnam() proto) */
81 -/*#define _SVID_SOURCE 1 */
82 +/*#define _DEFAULT_SOURCE 1 */
83
84
85 /*----------------------------------------------------------------------*/
86 diff --git a/corelib/ncbilcl.qnx b/corelib/ncbilcl.qnx
87 index c3d1f0a..4b27bd1 100644
88 --- a/corelib/ncbilcl.qnx
89 +++ b/corelib/ncbilcl.qnx
90 @@ -72,7 +72,7 @@
91 #endif
92
93 /* good for the EGCS C/C++ compiler on Linux(e.g. putenv(), tempnam() proto) */
94 -#define _SVID_SOURCE 1
95 +#define _DEFAULT_SOURCE 1
96
97
98
99
100
101
102 1.1 sci-biology/ncbi-tools/files/ncbi-tools-2.2.26-format-security.patch
103
104 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
105 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
106
107 Index: ncbi-tools-2.2.26-format-security.patch
108 ===================================================================
109 api/alignmgr2.c | 2 +-
110 api/pgppop.c | 2 +-
111 api/txalign.c | 10 +++++-----
112 desktop/seqpanel.c | 4 ++--
113 tools/spidey.c | 4 ++--
114 5 files changed, 11 insertions(+), 11 deletions(-)
115
116 diff --git a/api/alignmgr2.c b/api/alignmgr2.c
117 index 5b43ef3..4b9007e 100644
118 --- a/api/alignmgr2.c
119 +++ b/api/alignmgr2.c
120 @@ -5616,7 +5616,7 @@ NLM_EXTERN void AlnMgr2PrintSeqAlign(SeqAlignPtr sap, Int4 linesize, Boolean isn
121 spp = SeqPortNew(bsp, amp->from_row, amp->to_row, amp->strand, seqcode);
122 ctr = SeqPortRead(spp, (Uint1Ptr)buf, amp->to_row-amp->from_row+1);
123 buf[ctr] = '\0';
124 - fprintf(ofp, buf);
125 + fprintf(ofp, "%s", buf);
126 SeqPortFree(spp);
127 }
128 }
129 diff --git a/api/pgppop.c b/api/pgppop.c
130 index d16d79d..b359378 100644
131 --- a/api/pgppop.c
132 +++ b/api/pgppop.c
133 @@ -2994,7 +2994,7 @@ Char DefLine[255];
134 if (szSeq){
135 if (!DDV_GetSequenceFromParaG(pgp,&szSeq,bspLength,IsAA,NULL,
136 NULL,NULL)) continue;
137 - fprintf(fp,szSeq);
138 + fprintf(fp, "%s", szSeq);
139 fprintf(fp,"\n");
140 MemFree(szSeq);
141 }
142 diff --git a/api/txalign.c b/api/txalign.c
143 index 5877f9c..cb35fbc 100644
144 --- a/api/txalign.c
145 +++ b/api/txalign.c
146 @@ -1767,13 +1767,13 @@ static CharPtr DrawTextToBuffer(ValNodePtr tdp_list, CharPtr PNTR m_buf, Boolean
147 if(options&TXALIGN_HTML&&options&TXALIGN_MASTER&&DbHasGi&&(options&TXALIGN_GET_SEQUENCE)){
148 Char checkboxBuf[200];
149 sprintf(checkboxBuf, "<input type=\"checkbox\" name=\"getSeqGi\" value=\"%ld\" onClick=\"synchronizeCheck(this.value, 'getSeqAlignment%ld', 'getSeqGi', this.checked)\">", sip->data.intvalue, query_number_glb);
150 - sprintf(docbuf+pos,checkboxBuf);
151 + sprintf(docbuf+pos,"%s", checkboxBuf);
152
153 pos += StringLen(checkboxBuf);
154 }
155
156 html_len = StringLen(HTML_buffer);
157 - sprintf(docbuf+pos, HTML_buffer);
158 + sprintf(docbuf+pos, "%s", HTML_buffer);
159 pos += html_len;
160
161 pos += print_label_to_buffer_all_ex(docbuf+pos, tdp->label, tdp->pos,
162 @@ -1790,7 +1790,7 @@ static CharPtr DrawTextToBuffer(ValNodePtr tdp_list, CharPtr PNTR m_buf, Boolean
163 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);
164
165 html_len = StringLen(HTML_buffer);
166 - sprintf(docbuf+pos, HTML_buffer);
167 + sprintf(docbuf+pos, "%s", HTML_buffer);
168 pos += html_len;
169 pos += print_label_to_buffer_all_ex(docbuf+pos, tdp->label, tdp->pos,
170 tdp->strand, FALSE, TRUE, label_size, num_size, show_strand, strip_semicolon);
171 @@ -1799,7 +1799,7 @@ static CharPtr DrawTextToBuffer(ValNodePtr tdp_list, CharPtr PNTR m_buf, Boolean
172 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);
173
174 html_len = StringLen(HTML_buffer);
175 - sprintf(docbuf+pos, HTML_buffer);
176 + sprintf(docbuf+pos, "%s", HTML_buffer);
177 pos += html_len;
178 pos += print_label_to_buffer_all_ex(docbuf+pos, tdp->label, tdp->pos,
179 tdp->strand, FALSE, TRUE, label_size, num_size, show_strand, strip_semicolon);
180 @@ -1816,7 +1816,7 @@ static CharPtr DrawTextToBuffer(ValNodePtr tdp_list, CharPtr PNTR m_buf, Boolean
181 if(options&TXALIGN_HTML&&options&TXALIGN_MASTER&&DbHasGi&&(options&TXALIGN_GET_SEQUENCE)){
182 Char checkboxBuf[200];
183 sprintf(checkboxBuf, "<input type=\"checkbox\" name=\"getSeqMaster\" value=\"\" onClick=\"uncheckable('getSeqAlignment%ld', 'getSeqMaster')\">", query_number_glb);
184 - sprintf(docbuf+pos,checkboxBuf);
185 + sprintf(docbuf+pos,"%s",checkboxBuf);
186
187 pos += StringLen(checkboxBuf);
188 }
189 diff --git a/desktop/seqpanel.c b/desktop/seqpanel.c
190 index 2e78e13..c7538aa 100644
191 --- a/desktop/seqpanel.c
192 +++ b/desktop/seqpanel.c
193 @@ -8661,7 +8661,7 @@ WriteAlignmentInterleaveToFileEx
194 seqbuf, alnbuf, &alnbuf_len,
195 show_substitutions);
196 MemCpy (printed_line + label_len + 1 + coord_len, alnbuf, alnbuf_len);
197 - fprintf (fp, printed_line);
198 + fprintf (fp, "%s", printed_line);
199 }
200 fprintf (fp, "\n");
201 start = stop + 1;
202 @@ -8757,7 +8757,7 @@ extern void WriteAlignmentContiguousToFile
203 seqbuf, alnbuf, &alnbuf_len,
204 show_substitutions);
205 MemCpy (printed_line, alnbuf, alnbuf_len);
206 - fprintf (fp, printed_line);
207 + fprintf (fp, "%s", printed_line);
208 start = stop + 1;
209 stop += seq_chars_per_row;
210 }
211 diff --git a/tools/spidey.c b/tools/spidey.c
212 index d6ce62d..ac9f59a 100644
213 --- a/tools/spidey.c
214 +++ b/tools/spidey.c
215 @@ -2088,7 +2088,7 @@ static void SPI_PrintResult(FILE *ofp, FILE *ofp2, SPI_RegionInfoPtr srip, Biose
216 fprintf(ofp2, " ");
217 ctr++;
218 }
219 - fprintf(ofp2, buf);
220 + fprintf(ofp2, "%s", buf);
221 if (spp){
222 SeqPortFree(spp);
223 }
224 @@ -2417,7 +2417,7 @@ static void SPI_PrintHerdResult(FILE *ofp, FILE *ofp2, SPI_mRNAToHerdPtr herd, S
225 ctr = SeqPortRead(spp, (Uint1Ptr)buf, 10);
226 if (ctr > 0)
227 buf[ctr] = '\0';
228 - fprintf(ofp2, buf);
229 + fprintf(ofp2, "%s", buf);
230 SeqPortFree(spp);
231 }
232 done = TRUE;
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