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sci-biology/ncbi-tools: Remove last-rited package

Browse Source 
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@gentoo.org>
This commit is contained in:
Jakov Smolić
2021-08-30 19:17:23 +02:00
parent 1d628ae01e
commit 59b2be273d
11 changed files with 0 additions and 552 deletions
Download Patch File Download Diff File Expand all files Collapse all files

6
profiles/package.mask
View File

@@ -280,12 +280,6 @@ sys-apps/habitat
# revdeps. Bug #790137, #792870, removal in 30 days.
sci-libs/sktime
# David Seifert <soap@gentoo.org> (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 Revdeps are unmaintained too and out of date.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 <dilfridge@gentoo.org> (2021-07-31)
# Obsolete; all versions in current Perl core distributions
# are newer, and no virtuals currently pull these packages.

1
sci-biology/ncbi-tools/Manifest
View File

@@ -1 +0,0 @@
DIST ncbi-tools-2.2.26.tar.gz 68691452 BLAKE2B 21444227c6896c387f46a5490db1e4cf3ac437f94029c68f11ee3c5438bf2c34584d4b1b0ab18d3996f9c4e423a7e17fece510a96a1aa8be5dea6c5a2688f24c SHA512 da167216b56386b8c91a660e8ea0f3ac39b991d4519af9e02fc26aa16ed602eb3d9d874446f69a8f6840ae31a4d5a29da170e04e8a72b56f8c3ca038d1437014

6
sci-biology/ncbi-tools/files/21ncbi-r1
View File

@@ -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

81
sci-biology/ncbi-tools/files/ncbi-tools-2.2.26-_DEFAULT_SOURCE.patch
View File

@@ -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

103
sci-biology/ncbi-tools/files/ncbi-tools-2.2.26-bfr-overflow.patch
View File

@@ -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';
}

124
sci-biology/ncbi-tools/files/ncbi-tools-2.2.26-format-security.patch
View File

@@ -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;

37
sci-biology/ncbi-tools/files/ncbi-tools-extra_vib.patch
View File

@@ -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

15
sci-biology/ncbi-tools/files/ncbi-tools-lop.patch
View File

@@ -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

2
sci-biology/ncbi-tools/files/ncbirc
View File

@@ -1,2 +0,0 @@
[NCBI]
Data=@GENTOO_PORTAGE_EPREFIX@/usr/share/ncbi/data

8
sci-biology/ncbi-tools/metadata.xml
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@@ -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>

169
sci-biology/ncbi-tools/ncbi-tools-2.2.26-r3.ebuild
View File

@@ -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
}