gentoo resync : 31.08.2021

10 files changed, 0 insertions, 555 deletions

diff --git a/sci-biology/ncbi-tools/Manifest b/sci-biology/ncbi-tools/Manifest
deleted file mode 100644
index c32f0222f1b9..000000000000
--- a/sci-biology/ncbi-tools/Manifest
+++ /dev/null
@@ -1,10 +0,0 @@
-AUX 21ncbi-r1 232 BLAKE2B e56335a0cb2325e4874d097c85fde16c6c7362d0f5ce36bfdbb844c1c315122740ce77c69ae6fc787190039207fd81ebf7c8994141c70e19e5f65711019f84fa SHA512 cddde027eb42ce34862c35ad0d809de3738301ea57aec2f84a447efa00eeedbeb528df29390041a1f947dd955d43cabac525316d343aafef001f1de21f5da2d9
-AUX ncbi-tools-2.2.26-_DEFAULT_SOURCE.patch 2283 BLAKE2B f171abf1c2c55bed3bfaaf5018704914d0f57a002a252f0874e88397e0ae28eeab909edda7c6a6085dd3a65dda125604e4959fbf94d9eea782c16bd2bb8934af SHA512 87cc2442e65d6d3a0fedd2501324834461cfcbbfa9adf83b0f070d5f4d77a1a30c8b9fd22a35263b705c2baefd0dfc11f53d27683b0357d2cd6f74cf379b7979
-AUX ncbi-tools-2.2.26-bfr-overflow.patch 3712 BLAKE2B 30985ea911c4f139b9c94cfd4371f27179e8842cc03feaf4dafcf19b9e0c3c080716d4341d524d70631f8af63dcfac9f113119fa30cd934b8e8817ca9dbf1384 SHA512 f88ffb38ca70ffc200943ee9c44d0d3828eec2c681622c8a6eae90f0a59bf6de0e0f609b5a24b42803a39bf0b6d7d203a323a18cead749120e84affbe7405397
-AUX ncbi-tools-2.2.26-format-security.patch 6358 BLAKE2B 6b83568f9dd0aed216762212a4bdfbdb6979f2cfc9f2146a75f37bd427fd745d1d12b3b57188062b8b05af21b3119409a3a2c4b6f3cf646678a810cb4290d06f SHA512 9a33c19913bae7c91bb888177acc89f608c8fd6616c258c73a39ba7c69fa9a3e40d66578a4cf61410300c3d5be851890f2b110c2e6e4580ab71546993b6afcc4
-AUX ncbi-tools-extra_vib.patch 1393 BLAKE2B 3c9e0ffa614e7baccf87beea601561a8f6e1c760ccb1eb05e2158731ce2598ea28dc6b737598bc21a210df023ff86465ae7c9c1d019a60e82ca55e9489e74812 SHA512 faef4b98f7ec4ab842c8a0b99caaf47855f84c2c5f7b6a967bce05afc7d0cc69925a3867da2834778c980dd5b9f848d3ef969eb3be8ea0bac20e937127dcba00
-AUX ncbi-tools-lop.patch 701 BLAKE2B 9df2fd3ba86bc9a4f52d3c1809b4d795392666c601aa607d2377129c42562a99087387eaa69d9e9ae07545ea91808902db65718ccf3d671ca88f7255119b1028 SHA512 706dfb29f9b1eff1fcc7dc1df1d533563d9d12ead5b930930121ad92a3e8c159d1d7cf30acd9f4462772e8f27e6dcf45cd6125f2fa077b3902145f6faf1c8352
-AUX ncbirc 57 BLAKE2B 140c208cf1c7dbb6a204e58632c576e4edf0cd71d151b69f70839f1b06ae19db0d74d49179d2f0bc1320a40fabad49bed18a98a8bd2a75f6ecf068e647382c60 SHA512 0b9b68116b362ccc625623abf4e959abfb8555c31117216eefe3093fe2dd122c3ce508fe389c07a069d6f4322d889718e455de65dd3ab7d55a16d947ecb07cfd
-DIST ncbi-tools-2.2.26.tar.gz 68691452 BLAKE2B 21444227c6896c387f46a5490db1e4cf3ac437f94029c68f11ee3c5438bf2c34584d4b1b0ab18d3996f9c4e423a7e17fece510a96a1aa8be5dea6c5a2688f24c SHA512 da167216b56386b8c91a660e8ea0f3ac39b991d4519af9e02fc26aa16ed602eb3d9d874446f69a8f6840ae31a4d5a29da170e04e8a72b56f8c3ca038d1437014
-EBUILD ncbi-tools-2.2.26-r3.ebuild 4660 BLAKE2B ef1a3d2e1751792d2726786309eab8b514c72391c2362ce4927659012c96a991531ff558916d69ab89745259bdaceb75a794cff850deec817a90a3c0c5752804 SHA512 7fbb34e5f2ff5f4615b3f41834643acb89e3f47378301f90a449bee6d8629be6c057c4a04c320c10cc2b867ab13b7eae187b73ff987abaf31e03729e2eca11c2
-MISC metadata.xml 267 BLAKE2B 7cf386952842945148119de3263231db4d1046d5f54811f7e303ed8ec4d27cbc1960b99c92daf6f32e5b981c2fb9f50ec666be6193865d6e18541b7427a152a9 SHA512 91ab266d9ab24401bc0fec759c5b6cfcf44a3c5669fc31c7301d79770839bb5dfa0e155d949392ef06176b4a0b2c32b91b1b54b0027f972db61f0a5e54644403
diff --git a/sci-biology/ncbi-tools/files/21ncbi-r1 b/sci-biology/ncbi-tools/files/21ncbi-r1
deleted file mode 100644
index d4de68e6081a..000000000000
--- a/sci-biology/ncbi-tools/files/21ncbi-r1
+++ /dev/null
@@ -1,6 +0,0 @@
-# Location of the formatdb data sets
-BLASTDB="/usr/share/ncbi/formatdb"
-# Location of the BLAST matrixes.
-BLASTMAT="/usr/share/ncbi/data"
-# Location of the ".ncbi.rc" file which sets the default path for shared data.
-NCBI=/etc/ncbi
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
deleted file mode 100644
index bbc4623609c8..000000000000
--- a/sci-biology/ncbi-tools/files/ncbi-tools-2.2.26-_DEFAULT_SOURCE.patch
+++ /dev/null
@@ -1,81 +0,0 @@
- 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
- 
- 
- 
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
deleted file mode 100644
index e6763214a6e5..000000000000
--- a/sci-biology/ncbi-tools/files/ncbi-tools-2.2.26-bfr-overflow.patch
+++ /dev/null
@@ -1,103 +0,0 @@
- cdromlib/cdnewlib.c | 6 +++---
- corelib/ncbierr.c   | 2 +-
- corelib/ncbisgml.c  | 8 ++++----
- demo/errhdr.c       | 2 +-
- 4 files changed, 9 insertions(+), 9 deletions(-)
-
-diff --git a/cdromlib/cdnewlib.c b/cdromlib/cdnewlib.c
-index 461292c..be4a2d6 100644
---- a/cdromlib/cdnewlib.c
-+++ b/cdromlib/cdnewlib.c
-@@ -2676,7 +2676,7 @@ static int CdDevice_FileBuildPath (CdDevice *cddev, char *fpath, const char *fdi
- 			char volname[16];
- 			volname[0] = '\0';
- 			if (cddev->volume != NULL)
--				strncat(volname,cddev->volume->volume_name,sizeof volname);
-+				strncat(volname,cddev->volume->volume_name,sizeof volname - 1);
- 			else
- 				sprintf(volname,"entrez%d",cddev->hint);
- 			if (!FileBuildPath(fpath,volname,NULL))
-@@ -2748,7 +2748,7 @@ static int CdDevice_Init (CdDevice *cddev)
- 	memset((void*)&info,0,sizeof info);
- 	fpath[0] = '\0';
- 	if (cddev->inf.root !=NULL)
--		strncat(fpath,cddev->inf.root,sizeof fpath);
-+		strncat(fpath,cddev->inf.root,sizeof fpath - 1);
- 		
- 	if (cddev->ins_volname)
- 	{
-@@ -2766,7 +2766,7 @@ static int CdDevice_Init (CdDevice *cddev)
- 			{
- 				fpath[0] = '\0';
- 				if (cddev->inf.root !=NULL)
--					strncat(fpath,cddev->inf.root,sizeof fpath);
-+					strncat(fpath,cddev->inf.root,sizeof fpath - 1);
- 				sprintf(volname,"entrez%d",j+1);
- 				FileBuildPath(fpath,volname,NULL);
- 				if (CdTestPath(fpath,&info))
-diff --git a/corelib/ncbierr.c b/corelib/ncbierr.c
-index 0429d86..7b96a2e 100644
---- a/corelib/ncbierr.c
-+++ b/corelib/ncbierr.c
-@@ -952,7 +952,7 @@ static FILE * ErrMsgRoot_fopen (ErrMsgRoot *ctx)
- 	if (FileLength(file)==0 || (fd = FileOpen(file,s_msg_mode)) == NULL)
-           {
-             strcpy(path,info->msgpath);
--            strncat(path,file,sizeof(path));
-+            strncat(path,file,sizeof(path) - 1);
-             fd = FileOpen(path,s_msg_mode);
-           }
- 
-diff --git a/corelib/ncbisgml.c b/corelib/ncbisgml.c
-index 99412be..a653aef 100644
---- a/corelib/ncbisgml.c
-+++ b/corelib/ncbisgml.c
-@@ -260,7 +260,7 @@ NLM_EXTERN char * LIBCALL  Nlm_Sgml2Ascii (const char *sgml, char *ascii, size_t
- 			}
- 			if (i >= num_sgml_entity)
- 			{
--				char bad[SGML_ERROR_MSG_LIM];
-+				char bad[SGML_ERROR_MSG_LIM + 2];
- 				bad[0] = '\0';
- 				strncat(bad,sgml,SGML_ERROR_MSG_LIM);
- 				ErrPostEx(SEV_ERROR,E_SGML,3,"Unrecognized SGML entity &%s in [%s]",tbuf,bad);
-@@ -279,7 +279,7 @@ NLM_EXTERN char * LIBCALL  Nlm_Sgml2Ascii (const char *sgml, char *ascii, size_t
- 				from++;
- 			if (*from == '\0')
- 			{
--				char bad[SGML_ERROR_MSG_LIM];
-+				char bad[SGML_ERROR_MSG_LIM + 2];
- 				bad[0] = '\0';
- 				strncat(bad,sgml,SGML_ERROR_MSG_LIM);
- 				ErrPostEx(SEV_ERROR,E_SGML,2, "Unbalanced <> in SGML [%s]",bad);
-@@ -335,7 +335,7 @@ NLM_EXTERN size_t LIBCALL  Nlm_Sgml2AsciiLen (const char *sgml)
- 			}
- 			if (i >= num_sgml_entity)
- 			{
--				char bad[SGML_ERROR_MSG_LIM];
-+				char bad[SGML_ERROR_MSG_LIM + 2];
- 				bad[0] = '\0';
- 				strncat(bad,sgml,SGML_ERROR_MSG_LIM);
- 				ErrPostEx(SEV_ERROR,E_SGML,3,"Unrecognized SGML entity &%s in [%s]",tbuf,bad);
-@@ -349,7 +349,7 @@ NLM_EXTERN size_t LIBCALL  Nlm_Sgml2AsciiLen (const char *sgml)
- 				from++;
- 			if (*from == '\0')
- 			{
--				char bad[SGML_ERROR_MSG_LIM];
-+				char bad[SGML_ERROR_MSG_LIM + 2];
- 				bad[0] = '\0';
- 				strncat(bad,sgml,SGML_ERROR_MSG_LIM);
- 				ErrPostEx(SEV_ERROR,E_SGML,2,"Unbalanced <> in SGML [%s]",bad);
-diff --git a/demo/errhdr.c b/demo/errhdr.c
-index 01cd955..5081489 100644
---- a/demo/errhdr.c
-+++ b/demo/errhdr.c
-@@ -41,7 +41,7 @@ int main (int argc, char **argv)
- 		else if (mod[0] == '\0')
- 		{
- 			char *p;
--			strncat(mod,argv[i],sizeof mod);
-+			strncat(mod,argv[i],sizeof mod - 1);
- 			if ((p = strstr(argv[i],".msg")) != NULL)
- 				*p = '\0';
- 		}
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
deleted file mode 100644
index c12feff51af1..000000000000
--- a/sci-biology/ncbi-tools/files/ncbi-tools-2.2.26-format-security.patch
+++ /dev/null
@@ -1,124 +0,0 @@
- 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;
diff --git a/sci-biology/ncbi-tools/files/ncbi-tools-extra_vib.patch b/sci-biology/ncbi-tools/files/ncbi-tools-extra_vib.patch
deleted file mode 100644
index cb7d1adf9208..000000000000
--- a/sci-biology/ncbi-tools/files/ncbi-tools-extra_vib.patch
+++ /dev/null
@@ -1,37 +0,0 @@
---- ncbi-20061015/make/makedis.csh	2006-09-14 17:37:03.000000000 +0200
-+++ ncbi/make/makedis.csh	2007-03-07 21:00:36.090836460 +0100
-@@ -485,6 +485,34 @@
- 
- set net_stat = $status
- 
-+if ( $net_stat == 0 ) then
-+	# Compile additional tools, usually hidden
-+	if ( ! $?EXTRA_VIB ) then
-+		set EXTRA_VIB = ( asn2all )
-+	endif
-+	
-+	if ("$?NCBI_MT_OTHERLIBS" == "1") then
-+		set CMD='make $MFLG -f makenet.unx \
-+			CFLAGS1=\"$NCBI_OPTFLAG $NCBI_CFLAGS1 $OGL_INCLUDE\" \
-+			LDFLAGS1=\"$NCBI_LDFLAGS1\" SHELL=\"$NCBI_MAKE_SHELL\" \
-+			AR=\"$NCBI_AR\" CC=\"$NCBI_CC\" RAN=\"$NCBI_RANLIB\" OTHERLIBS=\"$NCBI_OTHERLIBS\" \
-+			THREAD_OBJ=$NCBI_THREAD_OBJ \
-+			THREAD_OTHERLIBS=\"$NCBI_MT_OTHERLIBS\" \
-+			NETENTREZVERSION=\"$NETENTREZVERSION\" $NET_VIB $EXTRA_VIB'
-+	else
-+		set CMD='make $MFLG -f makenet.unx \
-+			CFLAGS1=\"$NCBI_OPTFLAG $NCBI_CFLAGS1 $OGL_INCLUDE\" \
-+			LDFLAGS1=\"$NCBI_LDFLAGS1\" SHELL=\"$NCBI_MAKE_SHELL\" \
-+			AR=\"$NCBI_AR\" CC=\"$NCBI_CC\" RAN=\"$NCBI_RANLIB\" OTHERLIBS=\"$NCBI_OTHERLIBS\" \
-+			NETENTREZVERSION=\"$NETENTREZVERSION\" $NET_VIB $EXTRA_VIB'
-+	endif
-+	eval echo $CMD
-+	eval echo $CMD | sh
-+	
-+	set net_stat = $status
-+	
-+endif
-+
- if ($make_stat != 0 || $demo_stat != 0 || $threaded_demo_stat != 0 || $net_stat != 0) then
-    echo FAILURE primary make status = $make_stat, demo = $demo_stat, threaded_demo = $threaded_demo_stat, net = $net_stat
- 	cat <<EOF
diff --git a/sci-biology/ncbi-tools/files/ncbi-tools-lop.patch b/sci-biology/ncbi-tools/files/ncbi-tools-lop.patch
deleted file mode 100644
index 867b203aecb1..000000000000
--- a/sci-biology/ncbi-tools/files/ncbi-tools-lop.patch
+++ /dev/null
@@ -1,15 +0,0 @@
---- platform/linux-power.ncbi.mk.bak	2005-08-04 22:45:13.000000000 -0500
-+++ platform/linux-power.ncbi.mk	2005-08-04 22:45:35.000000000 -0500
-@@ -9,10 +9,10 @@
- #it appears the flags above do not work anymore with newer libc,
- #the new flags should work. Dima. 08/23/01
- NCBI_AR=ar
--NCBI_CC = xlc_r -w -qcpluscmt -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE
-+NCBI_CC = gcc -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE
- NCBI_CFLAGS1 = -c 
- NCBI_LDFLAGS1 = -O3 -D_LARGE_FILES 
--NCBI_OPTFLAG = -O3 -qmaxmem=-1 -D_LARGE_FILE
-+NCBI_OPTFLAG = -O3  -D_LARGE_FILE
- NCBI_BIN_MASTER = /vol/stcfs/rchen/LoP/ncbi/bin
- NCBI_BIN_COPY = /vol/stcfs/rchen/LoP/ncbi/bin
- NCBI_INCDIR = /vol/stcfs/rchen/LoP/ncbi/include
diff --git a/sci-biology/ncbi-tools/files/ncbirc b/sci-biology/ncbi-tools/files/ncbirc
deleted file mode 100644
index dd77b452fe74..000000000000
--- a/sci-biology/ncbi-tools/files/ncbirc
+++ /dev/null
@@ -1,2 +0,0 @@
-[NCBI]
-Data=@GENTOO_PORTAGE_EPREFIX@/usr/share/ncbi/data
diff --git a/sci-biology/ncbi-tools/metadata.xml b/sci-biology/ncbi-tools/metadata.xml
deleted file mode 100644
index 959160fe46b1..000000000000
--- a/sci-biology/ncbi-tools/metadata.xml
+++ /dev/null
@@ -1,8 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
-  <maintainer type="project">
-    <email>sci-biology@gentoo.org</email>
-    <name>Gentoo Biology Project</name>
-  </maintainer>
-</pkgmetadata>
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
deleted file mode 100644
index cec2f688b661..000000000000
--- a/sci-biology/ncbi-tools/ncbi-tools-2.2.26-r3.ebuild
+++ /dev/null
@@ -1,169 +0,0 @@
-# Copyright 1999-2021 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=5
-
-inherit epatch flag-o-matic prefix toolchain-funcs
-
-DESCRIPTION="Development toolkit and applications for computational biology, including BLAST"
-HOMEPAGE="https://www.ncbi.nlm.nih.gov/"
-SRC_URI="ftp://ftp.ncbi.nlm.nih.gov/blast/executables/release/${PV}/ncbi.tar.gz -> ${P}.tar.gz"
-
-SLOT="0"
-LICENSE="public-domain"
-KEYWORDS="~alpha amd64 ppc64 x86 ~amd64-linux ~x86-linux ~ppc-macos"
-IUSE="doc static-libs X"
-
-RDEPEND="
-	app-shells/tcsh
-	dev-lang/perl
-	media-libs/libpng:0=
-	virtual/glu
-	virtual/opengl
-	X? (
-		media-libs/fontconfig
-		x11-libs/motif:0=
-		x11-libs/libICE
-		x11-libs/libX11
-		x11-libs/libXft
-		x11-libs/libXmu
-		x11-libs/libXt
-		)"
-DEPEND="
-	${RDEPEND}
-	virtual/pkgconfig
-"
-
-S="${WORKDIR}/ncbi"
-
-EXTRA_VIB="asn2all asn2asn"
-
-pkg_setup() {
-	echo
-	ewarn 'Please note that the NCBI toolkit (and especially the X'
-	ewarn 'applications) are known to have compilation and run-time'
-	ewarn 'problems when compiled with agressive compilation flags. The'
-	ewarn '"-O3" flag is filtered by the ebuild on the x86 architecture if'
-	ewarn 'X support is enabled.'
-	echo
-}
-
-src_prepare() {
-	epatch \
-		"${FILESDIR}"/${PN}-extra_vib.patch \
-		"${FILESDIR}"/${P}-bfr-overflow.patch \
-		"${FILESDIR}"/${P}-format-security.patch \
-		"${FILESDIR}"/${P}-_DEFAULT_SOURCE.patch
-
-	if use ppc || use ppc64; then
-		epatch "${FILESDIR}"/${PN}-lop.patch
-	fi
-
-	if ! use X; then
-		sed \
-			-e "s:\#set HAVE_OGL=0:set HAVE_OGL=0:" \
-			-e "s:\#set HAVE_MOTIF=0:set HAVE_MOTIF=0:" \
-			-i "${S}"/make/makedis.csh || die
-	else
-		# X applications segfault on startup on x86 with -O3.
-		use x86 || replace-flags '-O3' '-O2'
-	fi
-
-	# Apply user C flags...
-	cd "${S}"/platform
-	sed \
-		-e "s:-O[s0-9]\?::g" \
-		-e 's:-m\(cpu\|arch\)=[a-zA-Z0-9]*::g' \
-		-e 's:-x[A-Z]*::g' \
-		-e 's:-pipe::g' \
-		-e "/NCBI_MAKE_SHELL *=/s:=.*:= \"${EPREFIX}/bin/sh\":g" \
-		-e "/NCBI_AR *=/s:ar:$(tc-getAR):g" \
-		-e "/NCBI_RANLIB *=/s:ranlib:$(tc-getRANLIB):g" \
-		-e "/NCBI_CC *=/s:= [a-zA-Z0-9]* := $(tc-getCC) :g" \
-		-e "/NCBI_OPTFLAG *=/s:$: ${CFLAGS}:g" \
-		-e "/NCBI_LDFLAGS1 *=/s:$: ${CFLAGS} ${LDFLAGS}:g" \
-		-e "/NCBI_OGLLIBS *=/s:=.*:= $($(tc-getPKG_CONFIG) --cflags gl glu 2>/dev/null):g" \
-		-e "/OPENGL_LIBS *=/s:=.*:= $($(tc-getPKG_CONFIG) --libs gl glu 2>/dev/null):g" \
-		-e "/NCBI_OGLLIBS *=/s:=.*:= $($(tc-getPKG_CONFIG) --libs gl glu 2>/dev/null):g" \
-		-i * || die
-
-	# We use dynamic libraries
-	sed -i -e "s/-Wl,-Bstatic//" *linux*.ncbi.mk || die
-
-	sed \
-		-re "s:/usr(/bin/.*sh):\1:g" \
-		-e "s:(/bin/.*sh):${EPREFIX}\1:g" \
-		-i $(find "${S}" -type f) || die
-}
-
-src_compile() {
-	export EXTRA_VIB
-	cd "${WORKDIR}"
-	csh ncbi/make/makedis.csh || die
-	mkdir "${S}"/cgi "${S}"/real || die
-	mv "${S}"/bin/*.cgi "${S}"/cgi || die
-	mv "${S}"/bin/*.REAL "${S}"/real || die
-	cd "${S}"/demo
-	emake \
-		-f ../make/makenet.unx \
-		CC="$(tc-getCC) ${CFLAGS} -I../include  -L../lib" \
-		LDFLAGS="${LDFLAGS}" \
-		spidey
-	cp spidey ../bin/ || die
-}
-
-src_install() {
-	#sci-geosciences/cdat-lite
-	mv "${S}"/bin/cdscan "${S}"/bin/cdscan-ncbi || die
-
-	dobin "${S}"/bin/*
-
-	for i in ${EXTRA_VIB}; do
-		dobin "${S}"/build/${i}
-	done
-	use static-libs && dolib.a "${S}"/lib/*.a
-	mkdir -p "${ED}"/usr/include/ncbi
-	cp -RL "${S}"/include/* "${ED}"/usr/include/ncbi || \
-		die "Failed to install headers."
-
-	# TODO: wwwblast with webapps
-	#insinto /usr/share/ncbi/lib/cgi
-	#doins ${S}/cgi/*
-	#insinto /usr/share/ncbi/lib/real
-	#doins ${S}/real/*
-
-	# Basic documentation
-	dodoc "${S}"/{README,VERSION,doc/{*.txt,README.*}}
-	newdoc "${S}"/doc/fa2htgs/README README.fa2htgs
-	newdoc "${S}"/config/README README.config
-	newdoc "${S}"/network/encrypt/README README.encrypt
-	newdoc "${S}"/network/nsclilib/readme README.nsclilib
-	newdoc "${S}"/sequin/README README.sequin
-	mv "${S}"/doc/man/fmerge{,-ncbi}.1 || die
-	doman "${S}"/doc/man/*
-
-	# Hypertext user documentation
-	dohtml "${S}"/{README.htm,doc/{*.html,*.htm,*.gif}}
-	insinto /usr/share/doc/${PF}/html
-	doins -r "${S}"/doc/blast "${S}"/doc/images "${S}"/doc/seq_install
-
-	# Developer documentation
-	if use doc; then
-		# Demo programs
-		mkdir "${ED}"/usr/share/ncbi
-		mv "${S}"/demo "${ED}"/usr/share/ncbi/demo || die
-	fi
-
-	# Shared data (similarity matrices and such) and database directory.
-	insinto /usr/share/ncbi
-	doins -r "${S}"/data
-	dodir /usr/share/ncbi/formatdb
-
-	# Default config file to set the path for shared data.
-	insinto /etc/ncbi
-	newins "${FILESDIR}"/ncbirc .ncbirc
-	eprefixify "${ED}"/etc/ncbi/.ncbirc
-
-	# Env file to set the location of the config file and BLAST databases.
-	newenvd "${FILESDIR}"/21ncbi-r1 21ncbi
-}