| 1 |
commit: 59b2be273d92b67c4c7f581657151a5e7cbb63ae |
| 2 |
Author: Jakov Smolić <jsmolic <AT> gentoo <DOT> org> |
| 3 |
AuthorDate: Mon Aug 30 17:17:23 2021 +0000 |
| 4 |
Commit: Jakov Smolić <jsmolic <AT> gentoo <DOT> org> |
| 5 |
CommitDate: Mon Aug 30 17:38:50 2021 +0000 |
| 6 |
URL: https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=59b2be27 |
| 7 |
|
| 8 |
sci-biology/ncbi-tools: Remove last-rited package |
| 9 |
|
| 10 |
Closes: https://bugs.gentoo.org/649930 |
| 11 |
Closes: https://bugs.gentoo.org/782790 |
| 12 |
Closes: https://bugs.gentoo.org/741188 |
| 13 |
Closes: https://bugs.gentoo.org/715636 |
| 14 |
Closes: https://bugs.gentoo.org/710338 |
| 15 |
Closes: https://bugs.gentoo.org/701340 |
| 16 |
Closes: https://bugs.gentoo.org/586982 |
| 17 |
Closes: https://bugs.gentoo.org/295584 |
| 18 |
Signed-off-by: Jakov Smolić <jsmolic <AT> gentoo.org> |
| 19 |
|
| 20 |
profiles/package.mask | 6 - |
| 21 |
sci-biology/ncbi-tools/Manifest | 1 - |
| 22 |
sci-biology/ncbi-tools/files/21ncbi-r1 | 6 - |
| 23 |
.../files/ncbi-tools-2.2.26-_DEFAULT_SOURCE.patch | 81 ---------- |
| 24 |
.../files/ncbi-tools-2.2.26-bfr-overflow.patch | 103 ------------- |
| 25 |
.../files/ncbi-tools-2.2.26-format-security.patch | 124 --------------- |
| 26 |
.../ncbi-tools/files/ncbi-tools-extra_vib.patch | 37 ----- |
| 27 |
sci-biology/ncbi-tools/files/ncbi-tools-lop.patch | 15 -- |
| 28 |
sci-biology/ncbi-tools/files/ncbirc | 2 - |
| 29 |
sci-biology/ncbi-tools/metadata.xml | 8 - |
| 30 |
sci-biology/ncbi-tools/ncbi-tools-2.2.26-r3.ebuild | 169 --------------------- |
| 31 |
11 files changed, 552 deletions(-) |
| 32 |
|
| 33 |
diff --git a/profiles/package.mask b/profiles/package.mask |
| 34 |
index a91a2a5b53e..05bca5f6c4a 100644 |
| 35 |
--- a/profiles/package.mask |
| 36 |
+++ b/profiles/package.mask |
| 37 |
@@ -280,12 +280,6 @@ sys-apps/habitat |
| 38 |
# revdeps. Bug #790137, #792870, removal in 30 days. |
| 39 |
sci-libs/sktime |
| 40 |
|
| 41 |
-# David Seifert <soap@g.o> (2021-08-01) |
| 42 |
-# Last release 10 years ago, EOL upstream, no other distro packages this |
| 43 |
-# anymore, tons of bugs. Revdeps are unmaintained too and out of date. |
| 44 |
-# Bug #798015, removal in 30 days. |
| 45 |
-sci-biology/ncbi-tools |
| 46 |
- |
| 47 |
# Andreas K. Hüttel <dilfridge@g.o> (2021-07-31) |
| 48 |
# Obsolete; all versions in current Perl core distributions |
| 49 |
# are newer, and no virtuals currently pull these packages. |
| 50 |
|
| 51 |
diff --git a/sci-biology/ncbi-tools/Manifest b/sci-biology/ncbi-tools/Manifest |
| 52 |
deleted file mode 100644 |
| 53 |
index 3513d8ffc44..00000000000 |
| 54 |
--- a/sci-biology/ncbi-tools/Manifest |
| 55 |
+++ /dev/null |
| 56 |
@@ -1 +0,0 @@ |
| 57 |
-DIST ncbi-tools-2.2.26.tar.gz 68691452 BLAKE2B 21444227c6896c387f46a5490db1e4cf3ac437f94029c68f11ee3c5438bf2c34584d4b1b0ab18d3996f9c4e423a7e17fece510a96a1aa8be5dea6c5a2688f24c SHA512 da167216b56386b8c91a660e8ea0f3ac39b991d4519af9e02fc26aa16ed602eb3d9d874446f69a8f6840ae31a4d5a29da170e04e8a72b56f8c3ca038d1437014 |
| 58 |
|
| 59 |
diff --git a/sci-biology/ncbi-tools/files/21ncbi-r1 b/sci-biology/ncbi-tools/files/21ncbi-r1 |
| 60 |
deleted file mode 100644 |
| 61 |
index d4de68e6081..00000000000 |
| 62 |
--- a/sci-biology/ncbi-tools/files/21ncbi-r1 |
| 63 |
+++ /dev/null |
| 64 |
@@ -1,6 +0,0 @@ |
| 65 |
-# Location of the formatdb data sets |
| 66 |
-BLASTDB="/usr/share/ncbi/formatdb" |
| 67 |
-# Location of the BLAST matrixes. |
| 68 |
-BLASTMAT="/usr/share/ncbi/data" |
| 69 |
-# Location of the ".ncbi.rc" file which sets the default path for shared data. |
| 70 |
-NCBI=/etc/ncbi |
| 71 |
|
| 72 |
diff --git a/sci-biology/ncbi-tools/files/ncbi-tools-2.2.26-_DEFAULT_SOURCE.patch b/sci-biology/ncbi-tools/files/ncbi-tools-2.2.26-_DEFAULT_SOURCE.patch |
| 73 |
deleted file mode 100644 |
| 74 |
index bbc4623609c..00000000000 |
| 75 |
--- a/sci-biology/ncbi-tools/files/ncbi-tools-2.2.26-_DEFAULT_SOURCE.patch |
| 76 |
+++ /dev/null |
| 77 |
@@ -1,81 +0,0 @@ |
| 78 |
- corelib/ncbilcl.beos | 2 +- |
| 79 |
- corelib/ncbilcl.hlx | 2 +- |
| 80 |
- corelib/ncbilcl.lnx | 4 ++-- |
| 81 |
- corelib/ncbilcl.plx | 2 +- |
| 82 |
- corelib/ncbilcl.qnx | 2 +- |
| 83 |
- 5 files changed, 6 insertions(+), 6 deletions(-) |
| 84 |
- |
| 85 |
-diff --git a/corelib/ncbilcl.beos b/corelib/ncbilcl.beos |
| 86 |
-index f720567..fe6346f 100644 |
| 87 |
---- a/corelib/ncbilcl.beos |
| 88 |
-+++ b/corelib/ncbilcl.beos |
| 89 |
-@@ -77,7 +77,7 @@ |
| 90 |
- #endif |
| 91 |
- |
| 92 |
- /* good for the EGCS C/C++ compiler on Linux(e.g. putenv(), tempnam() proto) */ |
| 93 |
--#define _SVID_SOURCE 1 |
| 94 |
-+#define _DEFAULT_SOURCE 1 |
| 95 |
- |
| 96 |
- |
| 97 |
- /*----------------------------------------------------------------------*/ |
| 98 |
-diff --git a/corelib/ncbilcl.hlx b/corelib/ncbilcl.hlx |
| 99 |
-index 1492f93..0e98fb6 100644 |
| 100 |
---- a/corelib/ncbilcl.hlx |
| 101 |
-+++ b/corelib/ncbilcl.hlx |
| 102 |
-@@ -67,7 +67,7 @@ |
| 103 |
- #endif |
| 104 |
- |
| 105 |
- /* good for the EGCS C/C++ compiler on Linux(e.g. putenv(), tempnam() proto) */ |
| 106 |
--/*#define _SVID_SOURCE 1 */ |
| 107 |
-+/*#define _DEFAULT_SOURCE 1 */ |
| 108 |
- |
| 109 |
- |
| 110 |
- /*----------------------------------------------------------------------*/ |
| 111 |
-diff --git a/corelib/ncbilcl.lnx b/corelib/ncbilcl.lnx |
| 112 |
-index 46e2978..b3256b3 100644 |
| 113 |
---- a/corelib/ncbilcl.lnx |
| 114 |
-+++ b/corelib/ncbilcl.lnx |
| 115 |
-@@ -65,7 +65,7 @@ |
| 116 |
- * fixes for new RedHat6.2 |
| 117 |
- * |
| 118 |
- * Revision 6.3 2000/02/10 16:36:32 vakatov |
| 119 |
--* Added _SVID_SOURCE |
| 120 |
-+* Added _DEFAULT_SOURCE |
| 121 |
- * |
| 122 |
- * Revision 6.2 1999/07/12 05:50:49 vakatov |
| 123 |
- * Avoid redefinition of #_REENTRANT |
| 124 |
-@@ -141,7 +141,7 @@ |
| 125 |
- #endif |
| 126 |
- |
| 127 |
- /* good for the EGCS C/C++ compiler on Linux(e.g. putenv(), tempnam() proto) */ |
| 128 |
--#define _SVID_SOURCE 1 |
| 129 |
-+#define _DEFAULT_SOURCE 1 |
| 130 |
- #define _GNU_SOURCE 1 |
| 131 |
- |
| 132 |
- /*----------------------------------------------------------------------*/ |
| 133 |
-diff --git a/corelib/ncbilcl.plx b/corelib/ncbilcl.plx |
| 134 |
-index bf5824c..f2b53e1 100644 |
| 135 |
---- a/corelib/ncbilcl.plx |
| 136 |
-+++ b/corelib/ncbilcl.plx |
| 137 |
-@@ -68,7 +68,7 @@ |
| 138 |
- #endif |
| 139 |
- |
| 140 |
- /* good for the EGCS C/C++ compiler on Linux(e.g. putenv(), tempnam() proto) */ |
| 141 |
--/*#define _SVID_SOURCE 1 */ |
| 142 |
-+/*#define _DEFAULT_SOURCE 1 */ |
| 143 |
- |
| 144 |
- |
| 145 |
- /*----------------------------------------------------------------------*/ |
| 146 |
-diff --git a/corelib/ncbilcl.qnx b/corelib/ncbilcl.qnx |
| 147 |
-index c3d1f0a..4b27bd1 100644 |
| 148 |
---- a/corelib/ncbilcl.qnx |
| 149 |
-+++ b/corelib/ncbilcl.qnx |
| 150 |
-@@ -72,7 +72,7 @@ |
| 151 |
- #endif |
| 152 |
- |
| 153 |
- /* good for the EGCS C/C++ compiler on Linux(e.g. putenv(), tempnam() proto) */ |
| 154 |
--#define _SVID_SOURCE 1 |
| 155 |
-+#define _DEFAULT_SOURCE 1 |
| 156 |
- |
| 157 |
- |
| 158 |
- |
| 159 |
|
| 160 |
diff --git a/sci-biology/ncbi-tools/files/ncbi-tools-2.2.26-bfr-overflow.patch b/sci-biology/ncbi-tools/files/ncbi-tools-2.2.26-bfr-overflow.patch |
| 161 |
deleted file mode 100644 |
| 162 |
index e6763214a6e..00000000000 |
| 163 |
--- a/sci-biology/ncbi-tools/files/ncbi-tools-2.2.26-bfr-overflow.patch |
| 164 |
+++ /dev/null |
| 165 |
@@ -1,103 +0,0 @@ |
| 166 |
- cdromlib/cdnewlib.c | 6 +++--- |
| 167 |
- corelib/ncbierr.c | 2 +- |
| 168 |
- corelib/ncbisgml.c | 8 ++++---- |
| 169 |
- demo/errhdr.c | 2 +- |
| 170 |
- 4 files changed, 9 insertions(+), 9 deletions(-) |
| 171 |
- |
| 172 |
-diff --git a/cdromlib/cdnewlib.c b/cdromlib/cdnewlib.c |
| 173 |
-index 461292c..be4a2d6 100644 |
| 174 |
---- a/cdromlib/cdnewlib.c |
| 175 |
-+++ b/cdromlib/cdnewlib.c |
| 176 |
-@@ -2676,7 +2676,7 @@ static int CdDevice_FileBuildPath (CdDevice *cddev, char *fpath, const char *fdi |
| 177 |
- char volname[16]; |
| 178 |
- volname[0] = '\0'; |
| 179 |
- if (cddev->volume != NULL) |
| 180 |
-- strncat(volname,cddev->volume->volume_name,sizeof volname); |
| 181 |
-+ strncat(volname,cddev->volume->volume_name,sizeof volname - 1); |
| 182 |
- else |
| 183 |
- sprintf(volname,"entrez%d",cddev->hint); |
| 184 |
- if (!FileBuildPath(fpath,volname,NULL)) |
| 185 |
-@@ -2748,7 +2748,7 @@ static int CdDevice_Init (CdDevice *cddev) |
| 186 |
- memset((void*)&info,0,sizeof info); |
| 187 |
- fpath[0] = '\0'; |
| 188 |
- if (cddev->inf.root !=NULL) |
| 189 |
-- strncat(fpath,cddev->inf.root,sizeof fpath); |
| 190 |
-+ strncat(fpath,cddev->inf.root,sizeof fpath - 1); |
| 191 |
- |
| 192 |
- if (cddev->ins_volname) |
| 193 |
- { |
| 194 |
-@@ -2766,7 +2766,7 @@ static int CdDevice_Init (CdDevice *cddev) |
| 195 |
- { |
| 196 |
- fpath[0] = '\0'; |
| 197 |
- if (cddev->inf.root !=NULL) |
| 198 |
-- strncat(fpath,cddev->inf.root,sizeof fpath); |
| 199 |
-+ strncat(fpath,cddev->inf.root,sizeof fpath - 1); |
| 200 |
- sprintf(volname,"entrez%d",j+1); |
| 201 |
- FileBuildPath(fpath,volname,NULL); |
| 202 |
- if (CdTestPath(fpath,&info)) |
| 203 |
-diff --git a/corelib/ncbierr.c b/corelib/ncbierr.c |
| 204 |
-index 0429d86..7b96a2e 100644 |
| 205 |
---- a/corelib/ncbierr.c |
| 206 |
-+++ b/corelib/ncbierr.c |
| 207 |
-@@ -952,7 +952,7 @@ static FILE * ErrMsgRoot_fopen (ErrMsgRoot *ctx) |
| 208 |
- if (FileLength(file)==0 || (fd = FileOpen(file,s_msg_mode)) == NULL) |
| 209 |
- { |
| 210 |
- strcpy(path,info->msgpath); |
| 211 |
-- strncat(path,file,sizeof(path)); |
| 212 |
-+ strncat(path,file,sizeof(path) - 1); |
| 213 |
- fd = FileOpen(path,s_msg_mode); |
| 214 |
- } |
| 215 |
- |
| 216 |
-diff --git a/corelib/ncbisgml.c b/corelib/ncbisgml.c |
| 217 |
-index 99412be..a653aef 100644 |
| 218 |
---- a/corelib/ncbisgml.c |
| 219 |
-+++ b/corelib/ncbisgml.c |
| 220 |
-@@ -260,7 +260,7 @@ NLM_EXTERN char * LIBCALL Nlm_Sgml2Ascii (const char *sgml, char *ascii, size_t |
| 221 |
- } |
| 222 |
- if (i >= num_sgml_entity) |
| 223 |
- { |
| 224 |
-- char bad[SGML_ERROR_MSG_LIM]; |
| 225 |
-+ char bad[SGML_ERROR_MSG_LIM + 2]; |
| 226 |
- bad[0] = '\0'; |
| 227 |
- strncat(bad,sgml,SGML_ERROR_MSG_LIM); |
| 228 |
- ErrPostEx(SEV_ERROR,E_SGML,3,"Unrecognized SGML entity &%s in [%s]",tbuf,bad); |
| 229 |
-@@ -279,7 +279,7 @@ NLM_EXTERN char * LIBCALL Nlm_Sgml2Ascii (const char *sgml, char *ascii, size_t |
| 230 |
- from++; |
| 231 |
- if (*from == '\0') |
| 232 |
- { |
| 233 |
-- char bad[SGML_ERROR_MSG_LIM]; |
| 234 |
-+ char bad[SGML_ERROR_MSG_LIM + 2]; |
| 235 |
- bad[0] = '\0'; |
| 236 |
- strncat(bad,sgml,SGML_ERROR_MSG_LIM); |
| 237 |
- ErrPostEx(SEV_ERROR,E_SGML,2, "Unbalanced <> in SGML [%s]",bad); |
| 238 |
-@@ -335,7 +335,7 @@ NLM_EXTERN size_t LIBCALL Nlm_Sgml2AsciiLen (const char *sgml) |
| 239 |
- } |
| 240 |
- if (i >= num_sgml_entity) |
| 241 |
- { |
| 242 |
-- char bad[SGML_ERROR_MSG_LIM]; |
| 243 |
-+ char bad[SGML_ERROR_MSG_LIM + 2]; |
| 244 |
- bad[0] = '\0'; |
| 245 |
- strncat(bad,sgml,SGML_ERROR_MSG_LIM); |
| 246 |
- ErrPostEx(SEV_ERROR,E_SGML,3,"Unrecognized SGML entity &%s in [%s]",tbuf,bad); |
| 247 |
-@@ -349,7 +349,7 @@ NLM_EXTERN size_t LIBCALL Nlm_Sgml2AsciiLen (const char *sgml) |
| 248 |
- from++; |
| 249 |
- if (*from == '\0') |
| 250 |
- { |
| 251 |
-- char bad[SGML_ERROR_MSG_LIM]; |
| 252 |
-+ char bad[SGML_ERROR_MSG_LIM + 2]; |
| 253 |
- bad[0] = '\0'; |
| 254 |
- strncat(bad,sgml,SGML_ERROR_MSG_LIM); |
| 255 |
- ErrPostEx(SEV_ERROR,E_SGML,2,"Unbalanced <> in SGML [%s]",bad); |
| 256 |
-diff --git a/demo/errhdr.c b/demo/errhdr.c |
| 257 |
-index 01cd955..5081489 100644 |
| 258 |
---- a/demo/errhdr.c |
| 259 |
-+++ b/demo/errhdr.c |
| 260 |
-@@ -41,7 +41,7 @@ int main (int argc, char **argv) |
| 261 |
- else if (mod[0] == '\0') |
| 262 |
- { |
| 263 |
- char *p; |
| 264 |
-- strncat(mod,argv[i],sizeof mod); |
| 265 |
-+ strncat(mod,argv[i],sizeof mod - 1); |
| 266 |
- if ((p = strstr(argv[i],".msg")) != NULL) |
| 267 |
- *p = '\0'; |
| 268 |
- } |
| 269 |
|
| 270 |
diff --git a/sci-biology/ncbi-tools/files/ncbi-tools-2.2.26-format-security.patch b/sci-biology/ncbi-tools/files/ncbi-tools-2.2.26-format-security.patch |
| 271 |
deleted file mode 100644 |
| 272 |
index c12feff51af..00000000000 |
| 273 |
--- a/sci-biology/ncbi-tools/files/ncbi-tools-2.2.26-format-security.patch |
| 274 |
+++ /dev/null |
| 275 |
@@ -1,124 +0,0 @@ |
| 276 |
- api/alignmgr2.c | 2 +- |
| 277 |
- api/pgppop.c | 2 +- |
| 278 |
- api/txalign.c | 10 +++++----- |
| 279 |
- desktop/seqpanel.c | 4 ++-- |
| 280 |
- tools/spidey.c | 4 ++-- |
| 281 |
- 5 files changed, 11 insertions(+), 11 deletions(-) |
| 282 |
- |
| 283 |
-diff --git a/api/alignmgr2.c b/api/alignmgr2.c |
| 284 |
-index 5b43ef3..4b9007e 100644 |
| 285 |
---- a/api/alignmgr2.c |
| 286 |
-+++ b/api/alignmgr2.c |
| 287 |
-@@ -5616,7 +5616,7 @@ NLM_EXTERN void AlnMgr2PrintSeqAlign(SeqAlignPtr sap, Int4 linesize, Boolean isn |
| 288 |
- spp = SeqPortNew(bsp, amp->from_row, amp->to_row, amp->strand, seqcode); |
| 289 |
- ctr = SeqPortRead(spp, (Uint1Ptr)buf, amp->to_row-amp->from_row+1); |
| 290 |
- buf[ctr] = '\0'; |
| 291 |
-- fprintf(ofp, buf); |
| 292 |
-+ fprintf(ofp, "%s", buf); |
| 293 |
- SeqPortFree(spp); |
| 294 |
- } |
| 295 |
- } |
| 296 |
-diff --git a/api/pgppop.c b/api/pgppop.c |
| 297 |
-index d16d79d..b359378 100644 |
| 298 |
---- a/api/pgppop.c |
| 299 |
-+++ b/api/pgppop.c |
| 300 |
-@@ -2994,7 +2994,7 @@ Char DefLine[255]; |
| 301 |
- if (szSeq){ |
| 302 |
- if (!DDV_GetSequenceFromParaG(pgp,&szSeq,bspLength,IsAA,NULL, |
| 303 |
- NULL,NULL)) continue; |
| 304 |
-- fprintf(fp,szSeq); |
| 305 |
-+ fprintf(fp, "%s", szSeq); |
| 306 |
- fprintf(fp,"\n"); |
| 307 |
- MemFree(szSeq); |
| 308 |
- } |
| 309 |
-diff --git a/api/txalign.c b/api/txalign.c |
| 310 |
-index 5877f9c..cb35fbc 100644 |
| 311 |
---- a/api/txalign.c |
| 312 |
-+++ b/api/txalign.c |
| 313 |
-@@ -1767,13 +1767,13 @@ static CharPtr DrawTextToBuffer(ValNodePtr tdp_list, CharPtr PNTR m_buf, Boolean |
| 314 |
- if(options&TXALIGN_HTML&&options&TXALIGN_MASTER&&DbHasGi&&(options&TXALIGN_GET_SEQUENCE)){ |
| 315 |
- Char checkboxBuf[200]; |
| 316 |
- sprintf(checkboxBuf, "<input type=\"checkbox\" name=\"getSeqGi\" value=\"%ld\" onClick=\"synchronizeCheck(this.value, 'getSeqAlignment%ld', 'getSeqGi', this.checked)\">", sip->data.intvalue, query_number_glb); |
| 317 |
-- sprintf(docbuf+pos,checkboxBuf); |
| 318 |
-+ sprintf(docbuf+pos,"%s", checkboxBuf); |
| 319 |
- |
| 320 |
- pos += StringLen(checkboxBuf); |
| 321 |
- } |
| 322 |
- |
| 323 |
- html_len = StringLen(HTML_buffer); |
| 324 |
-- sprintf(docbuf+pos, HTML_buffer); |
| 325 |
-+ sprintf(docbuf+pos, "%s", HTML_buffer); |
| 326 |
- pos += html_len; |
| 327 |
- |
| 328 |
- pos += print_label_to_buffer_all_ex(docbuf+pos, tdp->label, tdp->pos, |
| 329 |
-@@ -1790,7 +1790,7 @@ static CharPtr DrawTextToBuffer(ValNodePtr tdp_list, CharPtr PNTR m_buf, Boolean |
| 330 |
- 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); |
| 331 |
- |
| 332 |
- html_len = StringLen(HTML_buffer); |
| 333 |
-- sprintf(docbuf+pos, HTML_buffer); |
| 334 |
-+ sprintf(docbuf+pos, "%s", HTML_buffer); |
| 335 |
- pos += html_len; |
| 336 |
- pos += print_label_to_buffer_all_ex(docbuf+pos, tdp->label, tdp->pos, |
| 337 |
- tdp->strand, FALSE, TRUE, label_size, num_size, show_strand, strip_semicolon); |
| 338 |
-@@ -1799,7 +1799,7 @@ static CharPtr DrawTextToBuffer(ValNodePtr tdp_list, CharPtr PNTR m_buf, Boolean |
| 339 |
- 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); |
| 340 |
- |
| 341 |
- html_len = StringLen(HTML_buffer); |
| 342 |
-- sprintf(docbuf+pos, HTML_buffer); |
| 343 |
-+ sprintf(docbuf+pos, "%s", HTML_buffer); |
| 344 |
- pos += html_len; |
| 345 |
- pos += print_label_to_buffer_all_ex(docbuf+pos, tdp->label, tdp->pos, |
| 346 |
- tdp->strand, FALSE, TRUE, label_size, num_size, show_strand, strip_semicolon); |
| 347 |
-@@ -1816,7 +1816,7 @@ static CharPtr DrawTextToBuffer(ValNodePtr tdp_list, CharPtr PNTR m_buf, Boolean |
| 348 |
- if(options&TXALIGN_HTML&&options&TXALIGN_MASTER&&DbHasGi&&(options&TXALIGN_GET_SEQUENCE)){ |
| 349 |
- Char checkboxBuf[200]; |
| 350 |
- sprintf(checkboxBuf, "<input type=\"checkbox\" name=\"getSeqMaster\" value=\"\" onClick=\"uncheckable('getSeqAlignment%ld', 'getSeqMaster')\">", query_number_glb); |
| 351 |
-- sprintf(docbuf+pos,checkboxBuf); |
| 352 |
-+ sprintf(docbuf+pos,"%s",checkboxBuf); |
| 353 |
- |
| 354 |
- pos += StringLen(checkboxBuf); |
| 355 |
- } |
| 356 |
-diff --git a/desktop/seqpanel.c b/desktop/seqpanel.c |
| 357 |
-index 2e78e13..c7538aa 100644 |
| 358 |
---- a/desktop/seqpanel.c |
| 359 |
-+++ b/desktop/seqpanel.c |
| 360 |
-@@ -8661,7 +8661,7 @@ WriteAlignmentInterleaveToFileEx |
| 361 |
- seqbuf, alnbuf, &alnbuf_len, |
| 362 |
- show_substitutions); |
| 363 |
- MemCpy (printed_line + label_len + 1 + coord_len, alnbuf, alnbuf_len); |
| 364 |
-- fprintf (fp, printed_line); |
| 365 |
-+ fprintf (fp, "%s", printed_line); |
| 366 |
- } |
| 367 |
- fprintf (fp, "\n"); |
| 368 |
- start = stop + 1; |
| 369 |
-@@ -8757,7 +8757,7 @@ extern void WriteAlignmentContiguousToFile |
| 370 |
- seqbuf, alnbuf, &alnbuf_len, |
| 371 |
- show_substitutions); |
| 372 |
- MemCpy (printed_line, alnbuf, alnbuf_len); |
| 373 |
-- fprintf (fp, printed_line); |
| 374 |
-+ fprintf (fp, "%s", printed_line); |
| 375 |
- start = stop + 1; |
| 376 |
- stop += seq_chars_per_row; |
| 377 |
- } |
| 378 |
-diff --git a/tools/spidey.c b/tools/spidey.c |
| 379 |
-index d6ce62d..ac9f59a 100644 |
| 380 |
---- a/tools/spidey.c |
| 381 |
-+++ b/tools/spidey.c |
| 382 |
-@@ -2088,7 +2088,7 @@ static void SPI_PrintResult(FILE *ofp, FILE *ofp2, SPI_RegionInfoPtr srip, Biose |
| 383 |
- fprintf(ofp2, " "); |
| 384 |
- ctr++; |
| 385 |
- } |
| 386 |
-- fprintf(ofp2, buf); |
| 387 |
-+ fprintf(ofp2, "%s", buf); |
| 388 |
- if (spp){ |
| 389 |
- SeqPortFree(spp); |
| 390 |
- } |
| 391 |
-@@ -2417,7 +2417,7 @@ static void SPI_PrintHerdResult(FILE *ofp, FILE *ofp2, SPI_mRNAToHerdPtr herd, S |
| 392 |
- ctr = SeqPortRead(spp, (Uint1Ptr)buf, 10); |
| 393 |
- if (ctr > 0) |
| 394 |
- buf[ctr] = '\0'; |
| 395 |
-- fprintf(ofp2, buf); |
| 396 |
-+ fprintf(ofp2, "%s", buf); |
| 397 |
- SeqPortFree(spp); |
| 398 |
- } |
| 399 |
- done = TRUE; |
| 400 |
|
| 401 |
diff --git a/sci-biology/ncbi-tools/files/ncbi-tools-extra_vib.patch b/sci-biology/ncbi-tools/files/ncbi-tools-extra_vib.patch |
| 402 |
deleted file mode 100644 |
| 403 |
index cb7d1adf920..00000000000 |
| 404 |
--- a/sci-biology/ncbi-tools/files/ncbi-tools-extra_vib.patch |
| 405 |
+++ /dev/null |
| 406 |
@@ -1,37 +0,0 @@ |
| 407 |
---- ncbi-20061015/make/makedis.csh 2006-09-14 17:37:03.000000000 +0200 |
| 408 |
-+++ ncbi/make/makedis.csh 2007-03-07 21:00:36.090836460 +0100 |
| 409 |
-@@ -485,6 +485,34 @@ |
| 410 |
- |
| 411 |
- set net_stat = $status |
| 412 |
- |
| 413 |
-+if ( $net_stat == 0 ) then |
| 414 |
-+ # Compile additional tools, usually hidden |
| 415 |
-+ if ( ! $?EXTRA_VIB ) then |
| 416 |
-+ set EXTRA_VIB = ( asn2all ) |
| 417 |
-+ endif |
| 418 |
-+ |
| 419 |
-+ if ("$?NCBI_MT_OTHERLIBS" == "1") then |
| 420 |
-+ set CMD='make $MFLG -f makenet.unx \ |
| 421 |
-+ CFLAGS1=\"$NCBI_OPTFLAG $NCBI_CFLAGS1 $OGL_INCLUDE\" \ |
| 422 |
-+ LDFLAGS1=\"$NCBI_LDFLAGS1\" SHELL=\"$NCBI_MAKE_SHELL\" \ |
| 423 |
-+ AR=\"$NCBI_AR\" CC=\"$NCBI_CC\" RAN=\"$NCBI_RANLIB\" OTHERLIBS=\"$NCBI_OTHERLIBS\" \ |
| 424 |
-+ THREAD_OBJ=$NCBI_THREAD_OBJ \ |
| 425 |
-+ THREAD_OTHERLIBS=\"$NCBI_MT_OTHERLIBS\" \ |
| 426 |
-+ NETENTREZVERSION=\"$NETENTREZVERSION\" $NET_VIB $EXTRA_VIB' |
| 427 |
-+ else |
| 428 |
-+ set CMD='make $MFLG -f makenet.unx \ |
| 429 |
-+ CFLAGS1=\"$NCBI_OPTFLAG $NCBI_CFLAGS1 $OGL_INCLUDE\" \ |
| 430 |
-+ LDFLAGS1=\"$NCBI_LDFLAGS1\" SHELL=\"$NCBI_MAKE_SHELL\" \ |
| 431 |
-+ AR=\"$NCBI_AR\" CC=\"$NCBI_CC\" RAN=\"$NCBI_RANLIB\" OTHERLIBS=\"$NCBI_OTHERLIBS\" \ |
| 432 |
-+ NETENTREZVERSION=\"$NETENTREZVERSION\" $NET_VIB $EXTRA_VIB' |
| 433 |
-+ endif |
| 434 |
-+ eval echo $CMD |
| 435 |
-+ eval echo $CMD | sh |
| 436 |
-+ |
| 437 |
-+ set net_stat = $status |
| 438 |
-+ |
| 439 |
-+endif |
| 440 |
-+ |
| 441 |
- if ($make_stat != 0 || $demo_stat != 0 || $threaded_demo_stat != 0 || $net_stat != 0) then |
| 442 |
- echo FAILURE primary make status = $make_stat, demo = $demo_stat, threaded_demo = $threaded_demo_stat, net = $net_stat |
| 443 |
- cat <<EOF |
| 444 |
|
| 445 |
diff --git a/sci-biology/ncbi-tools/files/ncbi-tools-lop.patch b/sci-biology/ncbi-tools/files/ncbi-tools-lop.patch |
| 446 |
deleted file mode 100644 |
| 447 |
index 867b203aecb..00000000000 |
| 448 |
--- a/sci-biology/ncbi-tools/files/ncbi-tools-lop.patch |
| 449 |
+++ /dev/null |
| 450 |
@@ -1,15 +0,0 @@ |
| 451 |
---- platform/linux-power.ncbi.mk.bak 2005-08-04 22:45:13.000000000 -0500 |
| 452 |
-+++ platform/linux-power.ncbi.mk 2005-08-04 22:45:35.000000000 -0500 |
| 453 |
-@@ -9,10 +9,10 @@ |
| 454 |
- #it appears the flags above do not work anymore with newer libc, |
| 455 |
- #the new flags should work. Dima. 08/23/01 |
| 456 |
- NCBI_AR=ar |
| 457 |
--NCBI_CC = xlc_r -w -qcpluscmt -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE |
| 458 |
-+NCBI_CC = gcc -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE |
| 459 |
- NCBI_CFLAGS1 = -c |
| 460 |
- NCBI_LDFLAGS1 = -O3 -D_LARGE_FILES |
| 461 |
--NCBI_OPTFLAG = -O3 -qmaxmem=-1 -D_LARGE_FILE |
| 462 |
-+NCBI_OPTFLAG = -O3 -D_LARGE_FILE |
| 463 |
- NCBI_BIN_MASTER = /vol/stcfs/rchen/LoP/ncbi/bin |
| 464 |
- NCBI_BIN_COPY = /vol/stcfs/rchen/LoP/ncbi/bin |
| 465 |
- NCBI_INCDIR = /vol/stcfs/rchen/LoP/ncbi/include |
| 466 |
|
| 467 |
diff --git a/sci-biology/ncbi-tools/files/ncbirc b/sci-biology/ncbi-tools/files/ncbirc |
| 468 |
deleted file mode 100644 |
| 469 |
index dd77b452fe7..00000000000 |
| 470 |
--- a/sci-biology/ncbi-tools/files/ncbirc |
| 471 |
+++ /dev/null |
| 472 |
@@ -1,2 +0,0 @@ |
| 473 |
-[NCBI] |
| 474 |
-Data=@GENTOO_PORTAGE_EPREFIX@/usr/share/ncbi/data |
| 475 |
|
| 476 |
diff --git a/sci-biology/ncbi-tools/metadata.xml b/sci-biology/ncbi-tools/metadata.xml |
| 477 |
deleted file mode 100644 |
| 478 |
index 959160fe46b..00000000000 |
| 479 |
--- a/sci-biology/ncbi-tools/metadata.xml |
| 480 |
+++ /dev/null |
| 481 |
@@ -1,8 +0,0 @@ |
| 482 |
-<?xml version="1.0" encoding="UTF-8"?> |
| 483 |
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> |
| 484 |
-<pkgmetadata> |
| 485 |
- <maintainer type="project"> |
| 486 |
- <email>sci-biology@g.o</email> |
| 487 |
- <name>Gentoo Biology Project</name> |
| 488 |
- </maintainer> |
| 489 |
-</pkgmetadata> |
| 490 |
|
| 491 |
diff --git a/sci-biology/ncbi-tools/ncbi-tools-2.2.26-r3.ebuild b/sci-biology/ncbi-tools/ncbi-tools-2.2.26-r3.ebuild |
| 492 |
deleted file mode 100644 |
| 493 |
index cec2f688b66..00000000000 |
| 494 |
--- a/sci-biology/ncbi-tools/ncbi-tools-2.2.26-r3.ebuild |
| 495 |
+++ /dev/null |
| 496 |
@@ -1,169 +0,0 @@ |
| 497 |
-# Copyright 1999-2021 Gentoo Authors |
| 498 |
-# Distributed under the terms of the GNU General Public License v2 |
| 499 |
- |
| 500 |
-EAPI=5 |
| 501 |
- |
| 502 |
-inherit epatch flag-o-matic prefix toolchain-funcs |
| 503 |
- |
| 504 |
-DESCRIPTION="Development toolkit and applications for computational biology, including BLAST" |
| 505 |
-HOMEPAGE="https://www.ncbi.nlm.nih.gov/" |
| 506 |
-SRC_URI="ftp://ftp.ncbi.nlm.nih.gov/blast/executables/release/${PV}/ncbi.tar.gz -> ${P}.tar.gz" |
| 507 |
- |
| 508 |
-SLOT="0" |
| 509 |
-LICENSE="public-domain" |
| 510 |
-KEYWORDS="~alpha amd64 ppc64 x86 ~amd64-linux ~x86-linux ~ppc-macos" |
| 511 |
-IUSE="doc static-libs X" |
| 512 |
- |
| 513 |
-RDEPEND=" |
| 514 |
- app-shells/tcsh |
| 515 |
- dev-lang/perl |
| 516 |
- media-libs/libpng:0= |
| 517 |
- virtual/glu |
| 518 |
- virtual/opengl |
| 519 |
- X? ( |
| 520 |
- media-libs/fontconfig |
| 521 |
- x11-libs/motif:0= |
| 522 |
- x11-libs/libICE |
| 523 |
- x11-libs/libX11 |
| 524 |
- x11-libs/libXft |
| 525 |
- x11-libs/libXmu |
| 526 |
- x11-libs/libXt |
| 527 |
- )" |
| 528 |
-DEPEND=" |
| 529 |
- ${RDEPEND} |
| 530 |
- virtual/pkgconfig |
| 531 |
-" |
| 532 |
- |
| 533 |
-S="${WORKDIR}/ncbi" |
| 534 |
- |
| 535 |
-EXTRA_VIB="asn2all asn2asn" |
| 536 |
- |
| 537 |
-pkg_setup() { |
| 538 |
- echo |
| 539 |
- ewarn 'Please note that the NCBI toolkit (and especially the X' |
| 540 |
- ewarn 'applications) are known to have compilation and run-time' |
| 541 |
- ewarn 'problems when compiled with agressive compilation flags. The' |
| 542 |
- ewarn '"-O3" flag is filtered by the ebuild on the x86 architecture if' |
| 543 |
- ewarn 'X support is enabled.' |
| 544 |
- echo |
| 545 |
-} |
| 546 |
- |
| 547 |
-src_prepare() { |
| 548 |
- epatch \ |
| 549 |
- "${FILESDIR}"/${PN}-extra_vib.patch \ |
| 550 |
- "${FILESDIR}"/${P}-bfr-overflow.patch \ |
| 551 |
- "${FILESDIR}"/${P}-format-security.patch \ |
| 552 |
- "${FILESDIR}"/${P}-_DEFAULT_SOURCE.patch |
| 553 |
- |
| 554 |
- if use ppc || use ppc64; then |
| 555 |
- epatch "${FILESDIR}"/${PN}-lop.patch |
| 556 |
- fi |
| 557 |
- |
| 558 |
- if ! use X; then |
| 559 |
- sed \ |
| 560 |
- -e "s:\#set HAVE_OGL=0:set HAVE_OGL=0:" \ |
| 561 |
- -e "s:\#set HAVE_MOTIF=0:set HAVE_MOTIF=0:" \ |
| 562 |
- -i "${S}"/make/makedis.csh || die |
| 563 |
- else |
| 564 |
- # X applications segfault on startup on x86 with -O3. |
| 565 |
- use x86 || replace-flags '-O3' '-O2' |
| 566 |
- fi |
| 567 |
- |
| 568 |
- # Apply user C flags... |
| 569 |
- cd "${S}"/platform |
| 570 |
- sed \ |
| 571 |
- -e "s:-O[s0-9]\?::g" \ |
| 572 |
- -e 's:-m\(cpu\|arch\)=[a-zA-Z0-9]*::g' \ |
| 573 |
- -e 's:-x[A-Z]*::g' \ |
| 574 |
- -e 's:-pipe::g' \ |
| 575 |
- -e "/NCBI_MAKE_SHELL *=/s:=.*:= \"${EPREFIX}/bin/sh\":g" \ |
| 576 |
- -e "/NCBI_AR *=/s:ar:$(tc-getAR):g" \ |
| 577 |
- -e "/NCBI_RANLIB *=/s:ranlib:$(tc-getRANLIB):g" \ |
| 578 |
- -e "/NCBI_CC *=/s:= [a-zA-Z0-9]* := $(tc-getCC) :g" \ |
| 579 |
- -e "/NCBI_OPTFLAG *=/s:$: ${CFLAGS}:g" \ |
| 580 |
- -e "/NCBI_LDFLAGS1 *=/s:$: ${CFLAGS} ${LDFLAGS}:g" \ |
| 581 |
- -e "/NCBI_OGLLIBS *=/s:=.*:= $($(tc-getPKG_CONFIG) --cflags gl glu 2>/dev/null):g" \ |
| 582 |
- -e "/OPENGL_LIBS *=/s:=.*:= $($(tc-getPKG_CONFIG) --libs gl glu 2>/dev/null):g" \ |
| 583 |
- -e "/NCBI_OGLLIBS *=/s:=.*:= $($(tc-getPKG_CONFIG) --libs gl glu 2>/dev/null):g" \ |
| 584 |
- -i * || die |
| 585 |
- |
| 586 |
- # We use dynamic libraries |
| 587 |
- sed -i -e "s/-Wl,-Bstatic//" *linux*.ncbi.mk || die |
| 588 |
- |
| 589 |
- sed \ |
| 590 |
- -re "s:/usr(/bin/.*sh):\1:g" \ |
| 591 |
- -e "s:(/bin/.*sh):${EPREFIX}\1:g" \ |
| 592 |
- -i $(find "${S}" -type f) || die |
| 593 |
-} |
| 594 |
- |
| 595 |
-src_compile() { |
| 596 |
- export EXTRA_VIB |
| 597 |
- cd "${WORKDIR}" |
| 598 |
- csh ncbi/make/makedis.csh || die |
| 599 |
- mkdir "${S}"/cgi "${S}"/real || die |
| 600 |
- mv "${S}"/bin/*.cgi "${S}"/cgi || die |
| 601 |
- mv "${S}"/bin/*.REAL "${S}"/real || die |
| 602 |
- cd "${S}"/demo |
| 603 |
- emake \ |
| 604 |
- -f ../make/makenet.unx \ |
| 605 |
- CC="$(tc-getCC) ${CFLAGS} -I../include -L../lib" \ |
| 606 |
- LDFLAGS="${LDFLAGS}" \ |
| 607 |
- spidey |
| 608 |
- cp spidey ../bin/ || die |
| 609 |
-} |
| 610 |
- |
| 611 |
-src_install() { |
| 612 |
- #sci-geosciences/cdat-lite |
| 613 |
- mv "${S}"/bin/cdscan "${S}"/bin/cdscan-ncbi || die |
| 614 |
- |
| 615 |
- dobin "${S}"/bin/* |
| 616 |
- |
| 617 |
- for i in ${EXTRA_VIB}; do |
| 618 |
- dobin "${S}"/build/${i} |
| 619 |
- done |
| 620 |
- use static-libs && dolib.a "${S}"/lib/*.a |
| 621 |
- mkdir -p "${ED}"/usr/include/ncbi |
| 622 |
- cp -RL "${S}"/include/* "${ED}"/usr/include/ncbi || \ |
| 623 |
- die "Failed to install headers." |
| 624 |
- |
| 625 |
- # TODO: wwwblast with webapps |
| 626 |
- #insinto /usr/share/ncbi/lib/cgi |
| 627 |
- #doins ${S}/cgi/* |
| 628 |
- #insinto /usr/share/ncbi/lib/real |
| 629 |
- #doins ${S}/real/* |
| 630 |
- |
| 631 |
- # Basic documentation |
| 632 |
- dodoc "${S}"/{README,VERSION,doc/{*.txt,README.*}} |
| 633 |
- newdoc "${S}"/doc/fa2htgs/README README.fa2htgs |
| 634 |
- newdoc "${S}"/config/README README.config |
| 635 |
- newdoc "${S}"/network/encrypt/README README.encrypt |
| 636 |
- newdoc "${S}"/network/nsclilib/readme README.nsclilib |
| 637 |
- newdoc "${S}"/sequin/README README.sequin |
| 638 |
- mv "${S}"/doc/man/fmerge{,-ncbi}.1 || die |
| 639 |
- doman "${S}"/doc/man/* |
| 640 |
- |
| 641 |
- # Hypertext user documentation |
| 642 |
- dohtml "${S}"/{README.htm,doc/{*.html,*.htm,*.gif}} |
| 643 |
- insinto /usr/share/doc/${PF}/html |
| 644 |
- doins -r "${S}"/doc/blast "${S}"/doc/images "${S}"/doc/seq_install |
| 645 |
- |
| 646 |
- # Developer documentation |
| 647 |
- if use doc; then |
| 648 |
- # Demo programs |
| 649 |
- mkdir "${ED}"/usr/share/ncbi |
| 650 |
- mv "${S}"/demo "${ED}"/usr/share/ncbi/demo || die |
| 651 |
- fi |
| 652 |
- |
| 653 |
- # Shared data (similarity matrices and such) and database directory. |
| 654 |
- insinto /usr/share/ncbi |
| 655 |
- doins -r "${S}"/data |
| 656 |
- dodir /usr/share/ncbi/formatdb |
| 657 |
- |
| 658 |
- # Default config file to set the path for shared data. |
| 659 |
- insinto /etc/ncbi |
| 660 |
- newins "${FILESDIR}"/ncbirc .ncbirc |
| 661 |
- eprefixify "${ED}"/etc/ncbi/.ncbirc |
| 662 |
- |
| 663 |
- # Env file to set the location of the config file and BLAST databases. |
| 664 |
- newenvd "${FILESDIR}"/21ncbi-r1 21ncbi |
| 665 |
-} |
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