commit: 59b2be273d92b67c4c7f581657151a5e7cbb63ae Author: Jakov Smolić <jsmolic <AT> gentoo <DOT> org> AuthorDate: Mon Aug 30 17:17:23 2021 +0000 Commit: Jakov Smolić <jsmolic <AT> gentoo <DOT> org> CommitDate: Mon Aug 30 17:38:50 2021 +0000 URL: https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=59b2be27
sci-biology/ncbi-tools: Remove last-rited package Closes: https://bugs.gentoo.org/649930 Closes: https://bugs.gentoo.org/782790 Closes: https://bugs.gentoo.org/741188 Closes: https://bugs.gentoo.org/715636 Closes: https://bugs.gentoo.org/710338 Closes: https://bugs.gentoo.org/701340 Closes: https://bugs.gentoo.org/586982 Closes: https://bugs.gentoo.org/295584 Signed-off-by: Jakov Smolić <jsmolic <AT> gentoo.org> profiles/package.mask | 6 - sci-biology/ncbi-tools/Manifest | 1 - sci-biology/ncbi-tools/files/21ncbi-r1 | 6 - .../files/ncbi-tools-2.2.26-_DEFAULT_SOURCE.patch | 81 ---------- .../files/ncbi-tools-2.2.26-bfr-overflow.patch | 103 ------------- .../files/ncbi-tools-2.2.26-format-security.patch | 124 --------------- .../ncbi-tools/files/ncbi-tools-extra_vib.patch | 37 ----- sci-biology/ncbi-tools/files/ncbi-tools-lop.patch | 15 -- sci-biology/ncbi-tools/files/ncbirc | 2 - sci-biology/ncbi-tools/metadata.xml | 8 - sci-biology/ncbi-tools/ncbi-tools-2.2.26-r3.ebuild | 169 --------------------- 11 files changed, 552 deletions(-) diff --git a/profiles/package.mask b/profiles/package.mask index a91a2a5b53e..05bca5f6c4a 100644 --- a/profiles/package.mask +++ b/profiles/package.mask @@ -280,12 +280,6 @@ sys-apps/habitat # revdeps. Bug #790137, #792870, removal in 30 days. sci-libs/sktime -# David Seifert <[email protected]> (2021-08-01) -# Last release 10 years ago, EOL upstream, no other distro packages this -# anymore, tons of bugs. Revdeps are unmaintained too and out of date. -# Bug #798015, removal in 30 days. -sci-biology/ncbi-tools - # Andreas K. Hüttel <[email protected]> (2021-07-31) # Obsolete; all versions in current Perl core distributions # are newer, and no virtuals currently pull these packages. diff --git a/sci-biology/ncbi-tools/Manifest b/sci-biology/ncbi-tools/Manifest deleted file mode 100644 index 3513d8ffc44..00000000000 --- a/sci-biology/ncbi-tools/Manifest +++ /dev/null @@ -1 +0,0 @@ -DIST ncbi-tools-2.2.26.tar.gz 68691452 BLAKE2B 21444227c6896c387f46a5490db1e4cf3ac437f94029c68f11ee3c5438bf2c34584d4b1b0ab18d3996f9c4e423a7e17fece510a96a1aa8be5dea6c5a2688f24c SHA512 da167216b56386b8c91a660e8ea0f3ac39b991d4519af9e02fc26aa16ed602eb3d9d874446f69a8f6840ae31a4d5a29da170e04e8a72b56f8c3ca038d1437014 diff --git a/sci-biology/ncbi-tools/files/21ncbi-r1 b/sci-biology/ncbi-tools/files/21ncbi-r1 deleted file mode 100644 index d4de68e6081..00000000000 --- 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 bbc4623609c..00000000000 --- 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 e6763214a6e..00000000000 --- 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 c12feff51af..00000000000 --- 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 cb7d1adf920..00000000000 --- 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 867b203aecb..00000000000 --- 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 dd77b452fe7..00000000000 --- 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 959160fe46b..00000000000 --- 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>[email protected]</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 cec2f688b66..00000000000 --- 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 -}
