diff options
Diffstat (limited to 'sci-biology')
22 files changed, 0 insertions, 848 deletions
diff --git a/sci-biology/Manifest.gz b/sci-biology/Manifest.gz Binary files differindex ef5ed336ca9a..2b54cdaa898b 100644 --- a/sci-biology/Manifest.gz +++ b/sci-biology/Manifest.gz 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 -} diff --git a/sci-biology/njplot/Manifest b/sci-biology/njplot/Manifest deleted file mode 100644 index 22b172beb6c7..000000000000 --- a/sci-biology/njplot/Manifest +++ /dev/null @@ -1,5 +0,0 @@ -AUX njplot-2.3-buildsystem.patch 1688 BLAKE2B 06d03338d02efc2b13985148f784472afbe27855fc3a0da9e8194dcf16337a320ccacc2de43a9daf6eb2eb4df172fbde4ea4777caa4f5edf58ddc9234a022386 SHA512 af7f9c4e7e20f80e66e78eefb93dce0f99594987fc9ce04de0f447c03e2523b152bd5d32459ab075ca7a65da5d2fb4bb7624e7048f1d6a9ac7c3e1d4b28927b3 -AUX njplot-2.3-format-security.patch 366 BLAKE2B 63160d8d6774d8dd802118cb8e40849545dc6b7522afd539cbe8861bc52309e70e06969a5a35786671c2ee3da77850923e0d4651582050699ec5c7159cbf16eb SHA512 1a6a3d823eebca79da482c534f4c7e54e025900dd6f8407a9ae50e997c3585301762da1b0bdd2311f6b5698ba33d96a8fca6b8fada541323a97773146ef8e773 -DIST njplot-2.3.tar.gz 83641 BLAKE2B 3dd2798c190a103e88babb592cda184ae7ab4839cc779f739205480e2cce641bc9f8a57d20bd96ce8fc4a1e662a81de0bb13f2a4ffa9d03f8e0f286c762b993a SHA512 51e7d48187f88c4afb36d55cf8de98dad3cd4cd541137262885fe84bedff9db83224cdfa3c6a14518cd8170a06139b798518afe9fbadd89162986ed788355059 -EBUILD njplot-2.3-r2.ebuild 847 BLAKE2B c681b44afb880e275afef70df7b6d14a36853c49872be1296c639e7c0ae1a358f3ebdd76294dce86392d5c75f01bee19c075c2533ff3b21c12f5e4769f032c26 SHA512 8a67dfe8db133776ea7bec00d376c0b25e4044916b1d67659b1a3a8a80c68ef7a90d91005e009acb48fa3f486c7611352639f00067d514cca93a32227a243eb4 -MISC metadata.xml 616 BLAKE2B 6b63329645cb512061e44565357fa2339303f98ebd34b6c7d39159dd61cb1997401500ec5c7db82e7c8a0792e0fbc46bd92fb350c5cc711f076e4dceb5ddd1a5 SHA512 828535cff695925a319a6180a904ec8ad35c387e684e4fafd8d86e9978fcba8dc151e8a3e191b6f8b6b75d29ed3352cc34e2adf325dc5a663b170724df48b771 diff --git a/sci-biology/njplot/files/njplot-2.3-buildsystem.patch b/sci-biology/njplot/files/njplot-2.3-buildsystem.patch deleted file mode 100644 index 61f8b95ea160..000000000000 --- a/sci-biology/njplot/files/njplot-2.3-buildsystem.patch +++ /dev/null @@ -1,59 +0,0 @@ - makefile | 16 ++++++++-------- - 1 file changed, 8 insertions(+), 8 deletions(-) - -diff --git a/makefile b/makefile -index ccb7dc2..9488c2a 100644 ---- a/makefile -+++ b/makefile -@@ -7,10 +7,10 @@ NO_PDF = -DNO_PDF - #PDFLIB = -L$(PDF) -lpdf - - # c compiler and linker --CC = gcc -+CC ?= gcc - - # Vibrant top directory --VIBRANT = /banques0/ncbiJun04 -+VIBRANT = /usr/include/ncbi - - - # X11 include directory -@@ -24,15 +24,15 @@ OBJECTS = njplot-vib.o - OBJUNROOTED = unrooted-vib.o preptree.o - - --CFLAGS = -c -DWIN_MOTIF -Dunix -I$(VIBRANT)/include -I$(VIBRANT)/vibrant -I$(VIBRANT)/corelib \ -+CFLAGS += -c -DWIN_MOTIF -Dunix -I$(VIBRANT)/include -I$(VIBRANT)/vibrant -I$(VIBRANT)/corelib \ - -I$(VIBRANT) -I$(PDF) -I$(X11INCL) -I$(MOTIFINCL) $(HELPFILENAME) $(NO_PDF) \ -- -Wimplicit-function-declaration -g -+ -Wimplicit-function-declaration - - all: njplot unrooted newicktops newicktotxt - - - njplot : $(OBJECTS) -- $(CC) -g -o njplot $(OBJECTS) \ -+ $(CC) $(LDFLAGS) -o njplot $(OBJECTS) \ - -L$(VIBRANT)/lib \ - -lvibrant -lncbi \ - $(PDFLIB) \ -@@ -40,16 +40,16 @@ njplot : $(OBJECTS) - -L/usr/X11R6/lib -lXmu -lXt -lX11 -lm - - unrooted : $(OBJUNROOTED) -- $(CC) -g -o unrooted $(OBJUNROOTED) \ -+ $(CC) $(LDFLAGS) -o unrooted $(OBJUNROOTED) \ - -L$(VIBRANT)/lib -lvibrant -lncbi \ - -L$(MOTIFLIB) -lXm \ - -L/usr/X11R6/lib -lXmu -lXt -lX11 -lm - - newicktops: njplot-vib.c -- $(CC) -DNO_GUI -DNO_PDF -o $@ njplot-vib.c -lm -+ $(CC) $(LDFLAGS) $(CFLAGS) -DNO_GUI -DNO_PDF -o $@ njplot-vib.c -lm - - newicktotxt: njplot-vib.c -- $(CC) -DTTY -o $@ njplot-vib.c -lm -+ $(CC) -DTTY $(LDFLAGS) $(CFLAGS) -o $@ njplot-vib.c -lm - - - .c.o : diff --git a/sci-biology/njplot/files/njplot-2.3-format-security.patch b/sci-biology/njplot/files/njplot-2.3-format-security.patch deleted file mode 100644 index 686b8475e9ed..000000000000 --- a/sci-biology/njplot/files/njplot-2.3-format-security.patch +++ /dev/null @@ -1,16 +0,0 @@ - njplot-vib.c | 2 +- - 1 file changed, 1 insertion(+), 1 deletion(-) - -diff --git a/njplot-vib.c b/njplot-vib.c -index fe55609..63fd3b6 100644 ---- a/njplot-vib.c -+++ b/njplot-vib.c -@@ -1976,7 +1976,7 @@ PDFONLY" no window interface, just write the PDF/PostScript tree plot\n" - #else - fprintf(stderr, - #endif -- message); -+ "%s", message); - exit(0); - } - } diff --git a/sci-biology/njplot/metadata.xml b/sci-biology/njplot/metadata.xml deleted file mode 100644 index 2a3eb3140966..000000000000 --- a/sci-biology/njplot/metadata.xml +++ /dev/null @@ -1,15 +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> - <longdescription> - NJplot is a tree drawing program able to draw any phylogenetic tree - expressed in the Newick phylogenetic tree format (e.g., the format used - by the PHYLIP package). NJplot is especially convenient for rooting the - unrooted trees obtained from parsimony, distance or maximum likelihood - tree-building methods. - </longdescription> -</pkgmetadata> diff --git a/sci-biology/njplot/njplot-2.3-r2.ebuild b/sci-biology/njplot/njplot-2.3-r2.ebuild deleted file mode 100644 index 420861dac42b..000000000000 --- a/sci-biology/njplot/njplot-2.3-r2.ebuild +++ /dev/null @@ -1,38 +0,0 @@ -# Copyright 1999-2017 Gentoo Foundation -# Distributed under the terms of the GNU General Public License v2 - -EAPI=6 - -inherit toolchain-funcs - -DESCRIPTION="A phylogenetic tree drawing program which supports tree rooting" -HOMEPAGE="http://pbil.univ-lyon1.fr/software/njplot.html" -SRC_URI="ftp://pbil.univ-lyon1.fr/pub/mol_phylogeny/njplot/archive/njplot-${PV}.tar.gz" - -LICENSE="public-domain" -SLOT="0" -KEYWORDS="~amd64 ~x86" -IUSE="" - -RDEPEND=" - sci-biology/ncbi-tools[X,static-libs] - x11-libs/libXmu" -DEPEND="${RDEPEND}" - -PATCHES=( - "${FILESDIR}"/${P}-format-security.patch - "${FILESDIR}"/${P}-buildsystem.patch -) - -src_prepare() { - default - sed -i -e "s:njplot.help:${EPREFIX}/usr/share/doc/${PF}/njplot.help:" njplot-vib.c || die - - tc-export CC -} - -src_install() { - dobin newicktops newicktotxt njplot unrooted - doman *.1 - dodoc README njplot.help -} diff --git a/sci-biology/psipred/Manifest b/sci-biology/psipred/Manifest deleted file mode 100644 index ae2d7f82a568..000000000000 --- a/sci-biology/psipred/Manifest +++ /dev/null @@ -1,7 +0,0 @@ -AUX 3.1-Makefile.patch 1103 BLAKE2B ba9c5a7f60d62d66d1cd5a5e9b0a68ffe5c99124d02eae1924ffe92ecb2d24d7224e5bd0b37db3cf17da4f39d3c8b6b53e04466da8976e71910b9dcea9bc59ab SHA512 6e0daf4478b5b992ed1647bf653320b18cd2582ca69ebe761654bd4bd9c9c46b7de183ae84a28582cb5543603362eb7eb6c306ff562c3ec18c292d89480fd127 -AUX 3.1-path.patch 1128 BLAKE2B ea445427fe2ff574028b3d82ae353da5a1dfe3f5c7fade419287f6dc2e819471b4ec007dfee7cf71a1c958082a8dfa83acd5046208e0a7b16c07d90cdd68073f SHA512 e6201669db910f074bb13d1b781416d8d99300f328147cccd7755d5d6595b25aa45353f6da6566f225a067e94ab8ee41ea89bfd75cf2cdf2c076481707acf88c -AUX 3.2-fgets.patch 427 BLAKE2B dba911ef9d28c230e38d326336fa7adfae31ffafd225d525968f58b1013df2f5812b0c678f37576714c7bfa396c7378b2e1201f8c6b2bea844c2e042eea7c0ec SHA512 a8a59a765057e20b9c606b8e4d76b5657a9a06150247b426d939805547148ddc8a1cb4282e04bcdcd756bfa6df7bebffcc77b84f62c86be2f643069d2ff913bb -DIST psipred3.5.tar.gz 1101579 BLAKE2B 2fd86841cbc4bb86045b51f8283550832df8356ee88a6ef2c85281b5810debb23ac53652ddc5ffc9bd6f8e9e7248ce39ccee23400ff8fb49cd05b877d730b553 SHA512 a7b3f7d149f6a29cf0b48bdb900f6983d42af01132d8b54a7be88994d09fcf27dbe57115d41ec9654da6daf6898d5986d08fbdcefa3a4c81af0d358500cd40c2 -DIST tdbdata.tar.gz 40241247 BLAKE2B c85a2fde9b29a14e1da27be1a7ea5fe1704f72b66cd79514dd50a3a0d2d8aab9341f7d5075f6d1896cefa54ca83948387b902b38780181777dc505a9a15b4aab SHA512 f96d7ffbb77e129251e27f62b7f099d944bacd14935e03fc52c9f0b262cce1ad477ad43520a93b407951fb8f5dd3ba2e27ff6b5ae8a637ec03bc02f8c7c3990c -EBUILD psipred-3.5.ebuild 1215 BLAKE2B b51ae7660ff58dd8d8c738b0019cf935afa8e4049af536065348a5afdf4ac8bba3e8d49fbd456de633a6ab471a3a4c4dee126e213c3b76a8ca75401dbbc0be2c SHA512 dc506a260d7cefb6b632dae25410860c9efc2561581735eabdbf321c635b4347f1a8ba911abb326c7bf80d85b3ae945b483d538e12f21ef3255c5b3edc8a4e17 -MISC metadata.xml 267 BLAKE2B 7cf386952842945148119de3263231db4d1046d5f54811f7e303ed8ec4d27cbc1960b99c92daf6f32e5b981c2fb9f50ec666be6193865d6e18541b7427a152a9 SHA512 91ab266d9ab24401bc0fec759c5b6cfcf44a3c5669fc31c7301d79770839bb5dfa0e155d949392ef06176b4a0b2c32b91b1b54b0027f972db61f0a5e54644403 diff --git a/sci-biology/psipred/files/3.1-Makefile.patch b/sci-biology/psipred/files/3.1-Makefile.patch deleted file mode 100644 index 0c70b6868565..000000000000 --- a/sci-biology/psipred/files/3.1-Makefile.patch +++ /dev/null @@ -1,38 +0,0 @@ -diff --git a/src/Makefile b/src/Makefile -index abed8af..26061fa 100644 ---- a/src/Makefile -+++ b/src/Makefile -@@ -6,9 +6,9 @@ - #### CFLAGS Flags to pass to C compiler. - - INCDIR = . --CC = cc -+CC ?= gcc - --CFLAGS = -O -+CFLAGS ?= -O2 - LIBS = -lm - - all: psipred psipass2 chkparse seq2mtx pfilt -@@ -20,16 +20,16 @@ clean: - /bin/rm -f psipred psipass2 chkparse seq2mtx pfilt - - psipred: sspred_avpred.c ssdefs.h sspred_net.h -- $(CC) $(CFLAGS) sspred_avpred.c $(LIBS) -o psipred -+ $(CC) $(CFLAGS) $(LDFLAGS) sspred_avpred.c $(LIBS) -o psipred - - psipass2: sspred_hmulti.c ssdefs.h sspred_net2.h -- $(CC) $(CFLAGS) sspred_hmulti.c $(LIBS) -o psipass2 -+ $(CC) $(CFLAGS) $(LDFLAGS) sspred_hmulti.c $(LIBS) -o psipass2 - - chkparse: chkparse.c -- $(CC) $(CFLAGS) chkparse.c $(LIBS) -o chkparse -+ $(CC) $(CFLAGS) $(LDFLAGS) chkparse.c $(LIBS) -o chkparse - - seq2mtx: seq2mtx.c -- $(CC) $(CFLAGS) seq2mtx.c $(LIBS) -o seq2mtx -+ $(CC) $(CFLAGS) $(LDFLAGS) seq2mtx.c $(LIBS) -o seq2mtx - - pfilt: pfilt.c -- $(CC) $(CFLAGS) pfilt.c $(LIBS) -o pfilt -+ $(CC) $(CFLAGS) $(LDFLAGS) pfilt.c $(LIBS) -o pfilt diff --git a/sci-biology/psipred/files/3.1-path.patch b/sci-biology/psipred/files/3.1-path.patch deleted file mode 100644 index 564e9c8a1ef9..000000000000 --- a/sci-biology/psipred/files/3.1-path.patch +++ /dev/null @@ -1,38 +0,0 @@ -diff --git a/runpsipred b/runpsipred -index 4ccf44e..34dee99 100755 ---- a/runpsipred -+++ b/runpsipred -@@ -14,13 +14,13 @@ - set dbname = uniref90filt - - # Where the NCBI programs have been installed --set ncbidir = /usr/local/bin -+set ncbidir = @GENTOO_PORTAGE_EPREFIX@/usr/bin - - # Where the PSIPRED V2 programs have been installed --set execdir = ./bin -+set execdir = @GENTOO_PORTAGE_EPREFIX@/usr/bin - - # Where the PSIPRED V2 data files have been installed --set datadir = ./data -+set datadir = @GENTOO_PORTAGE_EPREFIX@/usr/share/psipred/data - - set basename = $1:r - set rootname = $basename:t -diff --git a/runpsipred_single b/runpsipred_single -index 1f7680b..7bd5bc3 100755 ---- a/runpsipred_single -+++ b/runpsipred_single -@@ -10,10 +10,10 @@ - # NOTE: Script modified to be more cluster friendly (DTJ April 2008) - - # Where the PSIPRED V3 programs have been installed --set execdir = ./bin -+set execdir = @GENTOO_PORTAGE_EPREFIX@/usr/bin - - # Where the PSIPRED V3 data files have been installed --set datadir = ./data -+set datadir = @GENTOO_PORTAGE_EPREFIX@/usr/share/psipred/data - - set basename = $1:r - set rootname = $basename:t diff --git a/sci-biology/psipred/files/3.2-fgets.patch b/sci-biology/psipred/files/3.2-fgets.patch deleted file mode 100644 index ec06d141ee34..000000000000 --- a/sci-biology/psipred/files/3.2-fgets.patch +++ /dev/null @@ -1,13 +0,0 @@ -diff --git a/src/sspred_avpred.c b/src/sspred_avpred.c -index 37b1332..4f04ab6 100644 ---- a/src/sspred_avpred.c -+++ b/src/sspred_avpred.c -@@ -223,7 +223,7 @@ predict(int argc, char **argv) - int getmtx(FILE *lfil) - { - int aa, i, j, naa; -- char buf[256], *p; -+ char buf[65536], *p; - - if (fscanf(lfil, "%d", &naa) != 1) - fail("Bad mtx file - no sequence length!"); diff --git a/sci-biology/psipred/metadata.xml b/sci-biology/psipred/metadata.xml deleted file mode 100644 index 959160fe46b1..000000000000 --- a/sci-biology/psipred/metadata.xml +++ /dev/null @@ -1,8 +0,0 @@ -<?xml version="1.0" encoding="UTF-8"?> -<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> -<pkgmetadata> - <maintainer type="project"> - <email>sci-biology@gentoo.org</email> - <name>Gentoo Biology Project</name> - </maintainer> -</pkgmetadata> diff --git a/sci-biology/psipred/psipred-3.5.ebuild b/sci-biology/psipred/psipred-3.5.ebuild deleted file mode 100644 index f5619ef4b544..000000000000 --- a/sci-biology/psipred/psipred-3.5.ebuild +++ /dev/null @@ -1,56 +0,0 @@ -# Copyright 1999-2021 Gentoo Authors -# Distributed under the terms of the GNU General Public License v2 - -EAPI=5 - -inherit epatch prefix toolchain-funcs versionator - -#MY_P="${PN}$(delete_all_version_separators)" -MY_P="${PN}${PV}" - -DESCRIPTION="Protein Secondary Structure Prediction" -HOMEPAGE="http://bioinf.cs.ucl.ac.uk/psipred/" -SRC_URI=" - http://bioinf.cs.ucl.ac.uk/downloads/${PN}/${MY_P}.tar.gz - test? ( http://bioinfadmin.cs.ucl.ac.uk/downloads/psipred/old/data/tdbdata.tar.gz )" - -LICENSE="psipred" -SLOT="0" -KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux" -IUSE="test" -RESTRICT="!test? ( test )" - -RDEPEND=" - app-shells/tcsh - sci-biology/ncbi-tools - sci-biology/update-blastdb" -DEPEND="" - -S="${WORKDIR}"/${PN} - -src_prepare() { - rm -f bin/* - epatch \ - "${FILESDIR}"/3.1-Makefile.patch \ - "${FILESDIR}"/3.1-path.patch \ - "${FILESDIR}"/3.2-fgets.patch - eprefixify runpsipred* - emake -C src clean -} - -src_compile() { - emake -C src CC=$(tc-getCC) -} - -src_install() { - emake -C src DESTDIR="${D}" install - dobin runpsipred* bin/* BLAST+/runpsipred* - insinto /usr/share/${PN} - doins -r data - dodoc README -} - -pkg_postinst() { - elog "Please use the update_blastdb.pl in order to" - elog "maintain your own local blastdb" -} |