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-rw-r--r--sci-biology/ncbi-tools/files/21ncbi-r16
-rw-r--r--sci-biology/ncbi-tools/files/ncbi-tools-2.2.26-_DEFAULT_SOURCE.patch81
-rw-r--r--sci-biology/ncbi-tools/files/ncbi-tools-2.2.26-bfr-overflow.patch103
-rw-r--r--sci-biology/ncbi-tools/files/ncbi-tools-2.2.26-format-security.patch124
-rw-r--r--sci-biology/ncbi-tools/files/ncbi-tools-extra_vib.patch37
-rw-r--r--sci-biology/ncbi-tools/files/ncbi-tools-lop.patch15
-rw-r--r--sci-biology/ncbi-tools/files/ncbirc2
7 files changed, 0 insertions, 368 deletions
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
generated by cgit v1.2.3 (git 2.25.1) at 2024-06-18 02:42:41 +0000