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sci-biology/qrna: Remove last-rited pkg

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Signed-off-by: Michał Górny <mgorny@gentoo.org>
This commit is contained in:
Michał Górny
2026-03-28 11:51:39 +01:00
parent afd5b81ec2
commit 82141ca21a
9 changed files with 0 additions and 1216 deletions
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profiles/package.mask
-5
View File
@@ -279,11 +279,6 @@ net-mail/mailbox-count
dev-qt/qtlockedfile
dev-qt/qtsingleapplication
# David Seifert <soap@gentoo.org> (2026-02-11)
# No other distro packages this, last release over 12 years ago, C23 issues.
# Removal on 2026-03-13. Bug #944878.
sci-biology/qrna
# Sam James <sam@gentoo.org> (2026-02-09)
# This suite of packages is currently best placed in an overlay/external
# repository where users can more easily contribute. The ecosystem moves
sci-biology/qrna/Manifest
-2
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@@ -1,2 +0,0 @@
DIST qrna-2.0.3c.tar.bz2 6423705 BLAKE2B 42bb2f03bac4034da9bcdedcd7c09ce7d1892ceb14d5682745d77c7575a84ae1a6a598406895be2a844ceaffee045ec6357ad08cc0d67a1312458d11b6540fda SHA512 98710bcf8993e2c09ec1eb33632a18ac993ab817dc95a865200b0868f79b95ff61f5f7d3f0c1c33de6d26f674025ea11a8c7d8175b96071e4594daa252fa52b5
DIST qrna-2.0.4.tar.gz 3220929 BLAKE2B 77f1272ad9952a3b47142fe996e3838bf13d845e19753e73ad941c2a055e7cc1a714a41543097120d5e96aaa8d5d0394e7083413599f60dac21261b2e4071fd3 SHA512 9d2d697d537f9fb0dac374de1b80f6862630cea0bd7cd68f8c3fcf97457d393d2e38e709aac674f4e50d437d5ce11f0bf527c705c2bd28c3017894c11ea17222
sci-biology/qrna/files/26qrna
-1
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@@ -1 +0,0 @@
QRNADB="/usr/share/qrna/data"
sci-biology/qrna/files/qrna-2.0.3c-glibc-2.10.patch
-328
View File
@@ -1,328 +0,0 @@
diff -ur qrna-2.0.3c.orig/squid/sqio.c qrna-2.0.3c/squid/sqio.c
--- qrna-2.0.3c.orig/squid/sqio.c 2005-05-11 19:30:51.000000000 +0300
+++ qrna-2.0.3c/squid/sqio.c 2009-08-05 22:27:20.000000000 +0300
@@ -215,7 +215,7 @@
}
static void
-getline(struct ReadSeqVars *V)
+get_line(struct ReadSeqVars *V)
{
readline(V->f, V->sbuffer);
}
@@ -277,7 +277,7 @@
V->seqlen = 0;
if (addfirst) addseq(V->sbuffer, V);
do {
- getline(V);
+ get_line(V);
/* feof() alone is a bug; files not necessarily \n terminated */
if (*(V->sbuffer) == '\0' && feof(V->f))
done = TRUE;
@@ -305,7 +305,7 @@
char *sptr;
/* load first line of entry */
while (!feof(V->f) && strncmp(V->sbuffer, "ENTRY", 5) != 0)
- getline(V);
+ get_line(V);
if (feof(V->f)) return;
if ((sptr = strtok(V->sbuffer + 15, "\n\t ")) != NULL)
@@ -314,7 +314,7 @@
SetSeqinfoString(V->sqinfo, sptr, SQINFO_ID);
}
do {
- getline(V);
+ get_line(V);
if (!feof(V->f) && strncmp(V->sbuffer, "TITLE", 5) == 0)
SetSeqinfoString(V->sqinfo, V->sbuffer+15, SQINFO_DESC);
else if (!feof(V->f) && strncmp(V->sbuffer, "ACCESSION", 9) == 0)
@@ -323,7 +323,7 @@
SetSeqinfoString(V->sqinfo, sptr, SQINFO_ACC);
}
} while (! feof(V->f) && (strncmp(V->sbuffer,"SEQUENCE", 8) != 0));
- getline(V); /* skip next line, coords */
+ get_line(V); /* skip next line, coords */
readLoop(0, endPIR, V);
@@ -337,7 +337,7 @@
/* get next line
*/
while (!feof(V->f) && strncmp(V->sbuffer, "ENTRY", 5) != 0)
- getline(V);
+ get_line(V);
}
@@ -355,7 +355,7 @@
char *nm;
/* position past ';' comments */
do {
- getline(V);
+ get_line(V);
} while (! (feof(V->f) || ((*V->sbuffer != 0) && (*V->sbuffer != ';')) ));
if (!feof(V->f))
@@ -367,7 +367,7 @@
}
while (!(feof(V->f) || ((*V->sbuffer != '\0') && (*V->sbuffer == ';'))))
- getline(V);
+ get_line(V);
}
static int
@@ -389,7 +389,7 @@
if ((nm = strtok(V->sbuffer+16, ",\n\t ")) != NULL)
SetSeqinfoString(V->sqinfo, nm, SQINFO_NAME);
}
- getline(V);
+ get_line(V);
}
if (! feof(V->f))
@@ -398,7 +398,7 @@
/* load next line
*/
while ((!feof(V->f)) && (*V->sbuffer != ';'))
- getline(V);
+ get_line(V);
}
@@ -416,7 +416,7 @@
int in_definition;
while (strncmp(V->sbuffer, "LOCUS", 5) != 0)
- getline(V);
+ get_line(V);
if ((sptr = strtok(V->sbuffer+12, "\n\t ")) != NULL)
{
@@ -427,7 +427,7 @@
in_definition = FALSE;
while (! feof(V->f))
{
- getline(V);
+ get_line(V);
if (! feof(V->f) && strstr(V->sbuffer, "DEFINITION") == V->sbuffer)
{
if ((sptr = strtok(V->sbuffer+12, "\n")) != NULL)
@@ -460,11 +460,11 @@
while (!(feof(V->f) || ((*V->sbuffer!=0) && (strstr(V->sbuffer,"LOCUS") == V->sbuffer))))
- getline(V);
+ get_line(V);
/* SRE: V->s now holds "//", so sequential
reads are wedged: fixed Tue Jul 13 1993 */
while (!feof(V->f) && strstr(V->sbuffer, "LOCUS ") != V->sbuffer)
- getline(V);
+ get_line(V);
}
static int
@@ -494,12 +494,12 @@
if ((sptr = strtok(V->sbuffer+4, "\n\t ")) != NULL)
SetSeqinfoString(V->sqinfo, sptr, SQINFO_NAME);
- getline(V); /*skip title-junk line*/
+ get_line(V); /*skip title-junk line*/
readLoop(0, endNBRF, V);
while (!(feof(V->f) || (*V->sbuffer != 0 && *V->sbuffer == '>')))
- getline(V);
+ get_line(V);
}
@@ -529,7 +529,7 @@
Die("bogus GCGdata format? %s", V->sbuffer);
/* second line contains free text description */
- getline(V);
+ get_line(V);
SetSeqinfoString(V->sqinfo, V->sbuffer, SQINFO_DESC);
if (binary) {
@@ -549,7 +549,7 @@
else readLoop(0, endGCGdata, V);
while (!(feof(V->f) || ((*V->sbuffer != 0) && (*V->sbuffer == '>'))))
- getline(V);
+ get_line(V);
}
static int
@@ -571,7 +571,7 @@
readLoop(0, endPearson, V);
while (!(feof(V->f) || ((*V->sbuffer != 0) && (*V->sbuffer == '>'))))
- getline(V);
+ get_line(V);
}
@@ -598,7 +598,7 @@
/* make sure we have first line */
while (!feof(V->f) && strncmp(V->sbuffer, "ID ", 4) != 0)
- getline(V);
+ get_line(V);
if ((sptr = strtok(V->sbuffer+5, "\n\t ")) != NULL)
{
@@ -607,7 +607,7 @@
}
do {
- getline(V);
+ get_line(V);
if (!feof(V->f) && strstr(V->sbuffer, "AC ") == V->sbuffer)
{
if ((sptr = strtok(V->sbuffer+5, "; \t\n")) != NULL)
@@ -631,7 +631,7 @@
/* load next record's ID line */
while (!feof(V->f) && strncmp(V->sbuffer, "ID ", 4) != 0)
- getline(V);
+ get_line(V);
}
@@ -647,7 +647,7 @@
{
char *sptr;
- getline(V); /*s == "seqLen seqid string..."*/
+ get_line(V); /*s == "seqLen seqid string..."*/
if ((sptr = strtok(V->sbuffer+6, " \t\n")) != NULL)
SetSeqinfoString(V->sqinfo, sptr, SQINFO_NAME);
@@ -658,7 +658,7 @@
readLoop(0, endZuker, V);
while (!(feof(V->f) | ((*V->sbuffer != '\0') & (*V->sbuffer == '('))))
- getline(V);
+ get_line(V);
}
static void
@@ -680,7 +680,7 @@
do {
done = feof(V->f);
- getline(V);
+ get_line(V);
if (! done) addseq(V->sbuffer, V);
} while (!done);
}
@@ -692,7 +692,7 @@
char *sptr;
int dostruc = FALSE;
- while (strncmp(V->sbuffer, "NAM ", 4) != 0) getline(V);
+ while (strncmp(V->sbuffer, "NAM ", 4) != 0) get_line(V);
if ((sptr = strtok(V->sbuffer+4, "\n\t ")) != NULL)
SetSeqinfoString(V->sqinfo, sptr, SQINFO_NAME);
@@ -700,7 +700,7 @@
/*CONSTCOND*/
while (1)
{
- getline(V);
+ get_line(V);
if (feof(V->f)) {squid_errno = SQERR_FORMAT; return; }
if (strncmp(V->sbuffer, "SRC ", 4) == 0)
@@ -732,14 +732,14 @@
while (1)
{
/* sequence line */
- getline(V);
+ get_line(V);
if (feof(V->f) || strncmp(V->sbuffer, "++", 2) == 0)
break;
addseq(V->sbuffer, V);
/* structure line */
if (dostruc)
{
- getline(V);
+ get_line(V);
if (feof(V->f)) { squid_errno = SQERR_FORMAT; return; }
addstruc(V->sbuffer, V);
}
@@ -747,7 +747,7 @@
while (!feof(V->f) && strncmp(V->sbuffer, "NAM ", 4) != 0)
- getline(V);
+ get_line(V);
}
@@ -786,7 +786,7 @@
/* Load the first line.
*/
- getline(dbfp);
+ get_line(dbfp);
return dbfp;
}
@@ -800,7 +800,7 @@
SeqfilePosition(SQFILE *sqfp, long offset)
{
fseek(sqfp->f, offset, SEEK_SET);
- getline(sqfp);
+ get_line(sqfp);
}
@@ -817,7 +817,7 @@
if (sqfp->ali_aseqs != NULL) sqfp->ali_curridx = 0;
else {
rewind(sqfp->f);
- getline(sqfp);
+ get_line(sqfp);
}
}
@@ -912,7 +912,7 @@
do { /* skip leading comments on GCG file */
gotuw = (strstr(V->sbuffer,"..") != NULL);
if (gotuw) readUWGCG(V);
- getline(V);
+ get_line(V);
} while (! feof(V->f));
break;
@@ -991,7 +991,7 @@
do { /* skip leading comments on GCG file */
gotuw = (strstr(V->sbuffer,"..") != NULL);
if (gotuw) readUWGCG(V);
- getline(V);
+ get_line(V);
} while (! feof(V->f));
break;
@@ -1098,7 +1098,7 @@
do { /* skip leading comments on GCG file */
gotuw = (strstr(V->sbuffer,"..") != NULL);
if (gotuw) readUWGCG(V);
- getline(V);
+ get_line(V);
} while (! feof(V->f));
break;
@@ -1204,7 +1204,7 @@
do { /* skip leading comments on GCG file */
gotuw = (strstr(V->sbuffer,"..") != NULL);
if (gotuw) readUWGCG(V);
- getline(V);
+ get_line(V);
} while (! feof(V->f));
break;
sci-biology/qrna/files/qrna-2.0.3c-ldflags.patch
-375
View File
@@ -1,375 +0,0 @@
--- a/squid/Makefile
+++ b/squid/Makefile
@@ -19,7 +19,6 @@
# On an Alliant, use fxc.
#
#CC = cc
-CC = gcc
#CC = fxc
## Any special compiler flags you want.
@@ -37,7 +36,6 @@
# for instance. If the code builds cleanly but seg faults, try
# rebuilding without optimization.
#
-CFLAGS = -O
#CFLAGS = -g
#CFLAGS = -TARG:exc_max -64 -Ofast=ip27 #specific SGI Origin200 compiler#
@@ -47,8 +45,6 @@
# Don't worry. The Makefile tests for ranlib existence and will work
# fine on SGIs even if RANLIB is set.
#
-AR = ar rcv
-RANLIB = ranlib
## Machine specific definitions
#
@@ -108,41 +104,41 @@
all: $(LIBTARGET)
alistat: $(OBJ) alistat_main.o
- $(CC) $(CFLAGS) $(MDEFS) -o alistat $(OBJ) alistat_main.o $(LIBS)
+ $(CC) $(CFLAGS) $(LDFLAGS) $(MDEFS) -o alistat $(OBJ) alistat_main.o $(LIBS)
compalign: $(OBJ) compalign_main.o
- $(CC) $(CFLAGS) $(MDEFS) -o compalign $(OBJ) compalign_main.o $(LIBS)
+ $(CC) $(CFLAGS) $(LDFLAGS) $(MDEFS) -o compalign $(OBJ) compalign_main.o $(LIBS)
compstruct: $(OBJ) compstruct_main.o
- $(CC) $(CFLAGS) $(MDEFS) -o compstruct $(OBJ) compstruct_main.o $(LIBS)
+ $(CC) $(CFLAGS) $(LDFLAGS) $(MDEFS) -o compstruct $(OBJ) compstruct_main.o $(LIBS)
getseq: $(OBJ) getseq_main.o
- $(CC) $(CFLAGS) $(MDEFS) -o getseq $(OBJ) getseq_main.o $(LIBS)
+ $(CC) $(CFLAGS) $(LDFLAGS) $(MDEFS) -o getseq $(OBJ) getseq_main.o $(LIBS)
reformat: $(OBJ) reformat_main.o
- $(CC) $(CFLAGS) $(MDEFS) -o reformat $(OBJ) reformat_main.o $(LIBS)
+ $(CC) $(CFLAGS) $(LDFLAGS) $(MDEFS) -o reformat $(OBJ) reformat_main.o $(LIBS)
revcomp: $(OBJ) revcomp_main.o
- $(CC) $(CFLAGS) $(MDEFS) -o revcomp $(OBJ) revcomp_main.o $(LIBS)
+ $(CC) $(CFLAGS) $(LDFLAGS) $(MDEFS) -o revcomp $(OBJ) revcomp_main.o $(LIBS)
seqstat: $(OBJ) seqstat_main.o
- $(CC) $(CFLAGS) $(MDEFS) -o seqstat $(OBJ) seqstat_main.o $(LIBS)
+ $(CC) $(CFLAGS) $(LDFLAGS) $(MDEFS) -o seqstat $(OBJ) seqstat_main.o $(LIBS)
seqsplit: $(OBJ) seqsplit_main.o
- $(CC) $(CFLAGS) $(MDEFS) -o seqstat $(OBJ) seqsplit_main.o $(LIBS)
+ $(CC) $(CFLAGS) $(LDFLAGS) $(MDEFS) -o seqstat $(OBJ) seqsplit_main.o $(LIBS)
shuffle: $(OBJ) shuffle_main.o
- $(CC) $(CFLAGS) $(MDEFS) -o shuffle $(OBJ) shuffle_main.o $(LIBS)
+ $(CC) $(CFLAGS) $(LDFLAGS) $(MDEFS) -o shuffle $(OBJ) shuffle_main.o $(LIBS)
translate: $(OBJ) translate_main.o
- $(CC) $(CFLAGS) $(MDEFS) -o translate $(OBJ) translate_main.o $(LIBS)
+ $(CC) $(CFLAGS) $(LDFLAGS) $(MDEFS) -o translate $(OBJ) translate_main.o $(LIBS)
weight: $(OBJ) weight_main.o
- $(CC) $(CFLAGS) $(MDEFS) -o weight $(OBJ) weight_main.o $(LIBS)
+ $(CC) $(CFLAGS) $(LDFLAGS) $(MDEFS) -o weight $(OBJ) weight_main.o $(LIBS)
$(LIBTARGET): $(OBJ)
- $(AR) $(LIBTARGET) $(OBJ)
+ $(AR) rcv $(LIBTARGET) $(OBJ)
-if test -x /bin/ranlib; then /bin/ranlib $(LIBTARGET); else exit 0; fi
-if test -x /usr/bin/ranlib; then /usr/bin/ranlib $(LIBTARGET); else exit 0; fi
-if test -x $(RANLIB); then $(RANLIB) $(LIBTARGET); else exit 0; fi
@@ -182,4 +178,4 @@
etags -t $(SRC) $(HDRS)
.c.o:
- $(CC) $(CFLAGS) $(MDEFS) -c $<
+ $(CC) $(CFLAGS) $(CPPFLAGS) $(MDEFS) -c $<
--- a/squid02/Makefile
+++ b/squid02/Makefile
@@ -27,8 +27,6 @@
## your compiler and compiler flags
#
-CC = gcc
-CFLAGS = -g -O2
## other defined flags for machine-specific stuff
#
@@ -37,8 +35,6 @@
## Archiver command
#
-AR = ar rcv
-RANLIB = ranlib
## instructions for installing man pages
#
@@ -158,10 +154,10 @@
all: version.h $(PROGS) libsquid.a
$(PROGS): %: %_main.o version.h $(OBJS)
- $(CC) $(CFLAGS) $(MDEFS) $(PVMLIBDIR) -o $@ $@_main.o $(OBJS) $(PVMLIBS) $(LIBS)
+ $(CC) $(CFLAGS) $(LDFLAGS) $(MDEFS) $(PVMLIBDIR) -o $@ $@_main.o $(OBJS) $(PVMLIBS) $(LIBS)
.c.o:
- $(CC) $(CFLAGS) $(PVMFLAG) $(PVMINCDIR) $(MDEFS) -c $<
+ $(CC) $(CFLAGS) $(CPPFLAGS) $(PVMFLAG) $(PVMINCDIR) $(MDEFS) -c $<
################################################################
@@ -172,7 +168,7 @@
module: libsquid.a
libsquid.a: version.h $(OBJS)
- $(AR) libsquid.a $(OBJS)
+ $(AR) rcv libsquid.a $(OBJS)
$(RANLIB) libsquid.a
chmod 644 libsquid.a
#################################################################
--- a/src/Makefile
+++ b/src/Makefile
@@ -21,7 +21,6 @@
SQUIDSRCDIR02 = ../squid02
## your compiler
-CC = gcc
#CC = cc
## any special compiler flags you want
@@ -30,7 +29,6 @@
#CFLAGS = -g -Wall -pedantic
#CFLAGS = -TARG:exc_max
#CFLAGS = -g -fullwarn -wlint,-fviah
-CFLAGS = -O
#CFLAGS = -p # profiling #
#CFLAGS = -64 -Ofast=ip27 #specific warhorse compiler#
@@ -131,145 +129,145 @@
all: $(PROGS)
main: $(OBJ) main.o
- $(CC) $(CFLAGS) -o $@ -L$(SQUIDDIR) $@.o $(LIBS)
+ $(CC) $(CFLAGS) $(LDFLAGS) -o $@ -L$(SQUIDDIR) $@.o $(LIBS)
cfgbuild: $(OBJ) cfgbuild.o
- $(CC) $(CFLAGS) -o $@ -L$(SQUIDDIR) $@.o $(OBJ) $(LIBS)
+ $(CC) $(CFLAGS) $(LDFLAGS) -o $@ -L$(SQUIDDIR) $@.o $(OBJ) $(LIBS)
eqrna: $(OBJ) eqrna.o
- $(CC) $(CFLAGS) -o $@ -L$(SQUIDDIR) $@.o $(OBJ) $(LIBS)
+ $(CC) $(CFLAGS) $(LDFLAGS) -o $@ -L$(SQUIDDIR) $@.o $(OBJ) $(LIBS)
eqrna_sample: $(OBJ) eqrna_sample.o
- $(CC) $(CFLAGS) -o $@ -L$(SQUIDDIR) $@.o $(OBJ) $(LIBS)
+ $(CC) $(CFLAGS) $(LDFLAGS) -o $@ -L$(SQUIDDIR) $@.o $(OBJ) $(LIBS)
shuffle: $(OBJ) shuffle.o
- $(CC) $(CFLAGS) -o $@ -L$(SQUIDDIR) $@.o $(OBJ) $(LIBS)
+ $(CC) $(CFLAGS) $(LDFLAGS) -o $@ -L$(SQUIDDIR) $@.o $(OBJ) $(LIBS)
rnamat_main: $(OBJ2) rnamat_main.o
- $(CC) $(CFLAGS) -o $@ -L$(SQUIDDIR02) $@.o $(OBJ2) $(LIBS)
+ $(CC) $(CFLAGS) $(LDFLAGS) -o $@ -L$(SQUIDDIR02) $@.o $(OBJ2) $(LIBS)
main.o: ../src/main.c
- $(CC) $(CFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $?
+ $(CC) $(CFLAGS) $(CPPFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $?
cfgbuild.o: ../src/cfgbuild.c
- $(CC) $(CFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $?
+ $(CC) $(CFLAGS) $(CPPFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $?
eqrna.o: ../src/eqrna.c
- $(CC) $(CFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $?
+ $(CC) $(CFLAGS) $(CPPFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $?
eqrna_sample.o: ../src/eqrna_sample.c
- $(CC) $(CFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $?
+ $(CC) $(CFLAGS) $(CPPFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $?
shuffle.o: ../src/shuffle.c
- $(CC) $(CFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $?
+ $(CC) $(CFLAGS) $(CPPFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $?
rnamat_main.o: ../src/rnamat_main.c
- $(CC) $(CFLAGS) $(MDEFS) -I$(SQUIDDIR02) -c $?
+ $(CC) $(CFLAGS) $(CPPFLAGS) $(MDEFS) -I$(SQUIDDIR02) -c $?
cfgio.o: ../src/cfgio.c
- $(CC) $(CFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $?
+ $(CC) $(CFLAGS) $(CPPFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $?
cfgmodel.o: ../src/cfgmodel.c
- $(CC) $(CFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $?
+ $(CC) $(CFLAGS) $(CPPFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $?
cfgparse.o: ../src/cfgparse.c
- $(CC) $(CFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $?
+ $(CC) $(CFLAGS) $(CPPFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $?
codcreatealign.o: ../src/codcreatealign.c
- $(CC) $(CFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $?
+ $(CC) $(CFLAGS) $(CPPFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $?
coddp.o: ../src/coddp.c
- $(CC) $(CFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $?
+ $(CC) $(CFLAGS) $(CPPFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $?
coddpscanfast.o: ../src/coddpscanfast.c
- $(CC) $(CFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $?
+ $(CC) $(CFLAGS) $(CPPFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $?
codmodel.o: ../src/codmodel.c
- $(CC) $(CFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $?
+ $(CC) $(CFLAGS) $(CPPFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $?
codon.o: ../src/codon.c
- $(CC) $(CFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $?
+ $(CC) $(CFLAGS) $(CPPFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $?
codscorealign.o: ../src/codscorealign.c
- $(CC) $(CFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $?
+ $(CC) $(CFLAGS) $(CPPFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $?
er_math.o: ../src/er_math.c
- $(CC) $(CFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $?
+ $(CC) $(CFLAGS) $(CPPFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $?
er_vectop.o: ../src/er_vectop.c
- $(CC) $(CFLAGS) $(MDEFS) -I$(SQUIDDIR02) -c $?
+ $(CC) $(CFLAGS) $(CPPFLAGS) $(MDEFS) -I$(SQUIDDIR02) -c $?
evd.o: ../src/evd.c
- $(CC) $(CFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $?
+ $(CC) $(CFLAGS) $(CPPFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $?
evolcodmodel.o: ../src/evolcodmodel.c
- $(CC) $(CFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $?
+ $(CC) $(CFLAGS) $(CPPFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $?
evolemissions.o: ../src/evolemissions.c
- $(CC) $(CFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $?
+ $(CC) $(CFLAGS) $(CPPFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $?
evolmisc.o: ../src/evolmisc.c
- $(CC) $(CFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $?
+ $(CC) $(CFLAGS) $(CPPFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $?
evolnullmodel.o: ../src/evolnullmodel.c
- $(CC) $(CFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $?
+ $(CC) $(CFLAGS) $(CPPFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $?
evolothmodel.o: ../src/evolothmodel.c
- $(CC) $(CFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $?
+ $(CC) $(CFLAGS) $(CPPFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $?
evolqrnaversion.o: ../src/evolqrnaversion.c
- $(CC) $(CFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $?
+ $(CC) $(CFLAGS) $(CPPFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $?
evolscorewithmodels.o: ../src/evolscorewithmodels.c
- $(CC) $(CFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $?
+ $(CC) $(CFLAGS) $(CPPFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $?
evolscorewithmodelscanfast.o: ../src/evolscorewithmodelscanfast.c
- $(CC) $(CFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $?
+ $(CC) $(CFLAGS) $(CPPFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $?
evolriboprob.o: ../src/evolriboprob.c
- $(CC) $(CFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $?
+ $(CC) $(CFLAGS) $(CPPFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $?
evolrnadp.o: ../src/evolrnadp.c
- $(CC) $(CFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $?
+ $(CC) $(CFLAGS) $(CPPFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $?
evolrnadpscanfast.o: ../src/evolrnadpscanfast.c
- $(CC) $(CFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $?
+ $(CC) $(CFLAGS) $(CPPFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $?
evolrnamodel.o: ../src/evolrnamodel.c
- $(CC) $(CFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $?
+ $(CC) $(CFLAGS) $(CPPFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $?
evolrnascorealign.o: ../src/evolrnascorealign.c
- $(CC) $(CFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $?
+ $(CC) $(CFLAGS) $(CPPFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $?
evolve.o: ../src/evolve.c
- $(CC) $(CFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $?
+ $(CC) $(CFLAGS) $(CPPFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $?
globals.o: ../src/globals.c
- $(CC) $(CFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $?
+ $(CC) $(CFLAGS) $(CPPFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $?
hexamer.o: ../src/hexamer.c
- $(CC) $(CFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $?
+ $(CC) $(CFLAGS) $(CPPFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $?
matrix.o: ../src/matrix.c
- $(CC) $(CFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $?
+ $(CC) $(CFLAGS) $(CPPFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $?
misc.o: ../src/misc.c
- $(CC) $(CFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $?
+ $(CC) $(CFLAGS) $(CPPFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $?
nrnscfg.o: ../src/nrnscfg.c
- $(CC) $(CFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $?
+ $(CC) $(CFLAGS) $(CPPFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $?
nstack.o: ../src/nstack.c
- $(CC) $(CFLAGS) $(MDEFS) -I$(SQUIDDIR02) -c $?
+ $(CC) $(CFLAGS) $(CPPFLAGS) $(MDEFS) -I$(SQUIDDIR02) -c $?
nullmodel.o: ../src/nullmodel.c
- $(CC) $(CFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $?
+ $(CC) $(CFLAGS) $(CPPFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $?
othcreatealign.o: ../src/othcreatealign.c
- $(CC) $(CFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $?
+ $(CC) $(CFLAGS) $(CPPFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $?
othdp.o: ../src/othdp.c
- $(CC) $(CFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $?
+ $(CC) $(CFLAGS) $(CPPFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $?
othdpscanfast.o: ../src/othdpscanfast.c
- $(CC) $(CFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $?
+ $(CC) $(CFLAGS) $(CPPFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $?
othmodel.o: ../src/othmodel.c
- $(CC) $(CFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $?
+ $(CC) $(CFLAGS) $(CPPFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $?
othscorealign.o: ../src/othscorealign.c
- $(CC) $(CFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $?
+ $(CC) $(CFLAGS) $(CPPFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $?
posterior.o: ../src/posterior.c
- $(CC) $(CFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $?
+ $(CC) $(CFLAGS) $(CPPFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $?
qrnaversion.o: ../src/qrnaversion.c
- $(CC) $(CFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $?
+ $(CC) $(CFLAGS) $(CPPFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $?
riboprob.o: ../src/riboprob.c
- $(CC) $(CFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $?
+ $(CC) $(CFLAGS) $(CPPFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $?
rnacreatealign.o: ../src/rnacreatealign.c
- $(CC) $(CFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $?
+ $(CC) $(CFLAGS) $(CPPFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $?
rnadp.o: ../src/rnadp.c
- $(CC) $(CFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $?
+ $(CC) $(CFLAGS) $(CPPFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $?
rnadpscanfast.o: ../src/rnadpscanfast.c
- $(CC) $(CFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $?
+ $(CC) $(CFLAGS) $(CPPFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $?
rnaio.o: ../src/rnaio.c
- $(CC) $(CFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $?
+ $(CC) $(CFLAGS) $(CPPFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $?
rnamat.o: ../src/rnamat.c
- $(CC) $(CFLAGS) $(MDEFS) -I$(SQUIDDIR02) -c $?
+ $(CC) $(CFLAGS) $(CPPFLAGS) $(MDEFS) -I$(SQUIDDIR02) -c $?
rnamodel.o: ../src/rnamodel.c
- $(CC) $(CFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $?
+ $(CC) $(CFLAGS) $(CPPFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $?
rnaoutput.o: ../src/rnaoutput.c
- $(CC) $(CFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $?
+ $(CC) $(CFLAGS) $(CPPFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $?
rnascorealign.o: ../src/rnascorealign.c
- $(CC) $(CFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $?
+ $(CC) $(CFLAGS) $(CPPFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $?
rnascfg.o: ../src/rnascfg.c
- $(CC) $(CFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $?
+ $(CC) $(CFLAGS) $(CPPFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $?
rnascfgscanfast.o: ../src/rnascfgscanfast.c
- $(CC) $(CFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $?
+ $(CC) $(CFLAGS) $(CPPFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $?
scorewithmodels.o: ../src/scorewithmodels.c
- $(CC) $(CFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $?
+ $(CC) $(CFLAGS) $(CPPFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $?
scorewithmodelscanfast.o: ../src/scorewithmodelscanfast.c
- $(CC) $(CFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $?
+ $(CC) $(CFLAGS) $(CPPFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $?
seqio.o: ../src/seqio.c
- $(CC) $(CFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $?
+ $(CC) $(CFLAGS) $(CPPFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $?
trace.o: ../src/trace.c
- $(CC) $(CFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $?
+ $(CC) $(CFLAGS) $(CPPFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $?
traceSCFG.o: ../src/traceSCFG.c
- $(CC) $(CFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $?
+ $(CC) $(CFLAGS) $(CPPFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $?
tying.o: ../src/tying.c
- $(CC) $(CFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $?
+ $(CC) $(CFLAGS) $(CPPFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $?
install: $(PROGS)
@@ -313,10 +311,10 @@
/usr/lib/lint/llib-lm.ln
.c.o:
- $(CC) $(CFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $<
+ $(CC) $(CFLAGS) $(CPPFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $<
.m.o:
- $(CC) $(CFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $<
+ $(CC) $(CFLAGS) $(CPPFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $<
sci-biology/qrna/files/qrna-2.0.4-ldflags.patch
-381
View File
@@ -1,381 +0,0 @@
diff --git a/squid/Makefile b/squid/Makefile
index fafab4c..8c329b3 100644
--- a/squid/Makefile
+++ b/squid/Makefile
@@ -19,7 +19,6 @@ MANDIR = $(HOME)/man
# On an Alliant, use fxc.
#
#CC = cc
-CC = gcc
#CC = fxc
## Any special compiler flags you want.
@@ -37,7 +36,6 @@ CC = gcc
# for instance. If the code builds cleanly but seg faults, try
# rebuilding without optimization.
#
-CFLAGS = -O -m32
#CFLAGS = -g
#CFLAGS = -TARG:exc_max -64 -Ofast=ip27 #specific SGI Origin200 compiler#
@@ -47,8 +45,6 @@ CFLAGS = -O -m32
# Don't worry. The Makefile tests for ranlib existence and will work
# fine on SGIs even if RANLIB is set.
#
-AR = ar rcv
-RANLIB = ranlib
## Machine specific definitions
#
@@ -108,41 +104,41 @@ DIST = $(SRC) $(HDRS) $(READMES) Makefile
all: $(LIBTARGET)
alistat: $(OBJ) alistat_main.o
- $(CC) $(CFLAGS) $(MDEFS) -o alistat $(OBJ) alistat_main.o $(LIBS)
+ $(CC) $(CFLAGS) $(LDFLAGS) $(MDEFS) -o alistat $(OBJ) alistat_main.o $(LIBS)
compalign: $(OBJ) compalign_main.o
- $(CC) $(CFLAGS) $(MDEFS) -o compalign $(OBJ) compalign_main.o $(LIBS)
+ $(CC) $(CFLAGS) $(LDFLAGS) $(MDEFS) -o compalign $(OBJ) compalign_main.o $(LIBS)
compstruct: $(OBJ) compstruct_main.o
- $(CC) $(CFLAGS) $(MDEFS) -o compstruct $(OBJ) compstruct_main.o $(LIBS)
+ $(CC) $(CFLAGS) $(LDFLAGS) $(MDEFS) -o compstruct $(OBJ) compstruct_main.o $(LIBS)
getseq: $(OBJ) getseq_main.o
- $(CC) $(CFLAGS) $(MDEFS) -o getseq $(OBJ) getseq_main.o $(LIBS)
+ $(CC) $(CFLAGS) $(LDFLAGS) $(MDEFS) -o getseq $(OBJ) getseq_main.o $(LIBS)
reformat: $(OBJ) reformat_main.o
- $(CC) $(CFLAGS) $(MDEFS) -o reformat $(OBJ) reformat_main.o $(LIBS)
+ $(CC) $(CFLAGS) $(LDFLAGS) $(MDEFS) -o reformat $(OBJ) reformat_main.o $(LIBS)
revcomp: $(OBJ) revcomp_main.o
- $(CC) $(CFLAGS) $(MDEFS) -o revcomp $(OBJ) revcomp_main.o $(LIBS)
+ $(CC) $(CFLAGS) $(LDFLAGS) $(MDEFS) -o revcomp $(OBJ) revcomp_main.o $(LIBS)
seqstat: $(OBJ) seqstat_main.o
- $(CC) $(CFLAGS) $(MDEFS) -o seqstat $(OBJ) seqstat_main.o $(LIBS)
+ $(CC) $(CFLAGS) $(LDFLAGS) $(MDEFS) -o seqstat $(OBJ) seqstat_main.o $(LIBS)
seqsplit: $(OBJ) seqsplit_main.o
- $(CC) $(CFLAGS) $(MDEFS) -o seqstat $(OBJ) seqsplit_main.o $(LIBS)
+ $(CC) $(CFLAGS) $(LDFLAGS) $(MDEFS) -o seqstat $(OBJ) seqsplit_main.o $(LIBS)
shuffle: $(OBJ) shuffle_main.o
- $(CC) $(CFLAGS) $(MDEFS) -o shuffle $(OBJ) shuffle_main.o $(LIBS)
+ $(CC) $(CFLAGS) $(LDFLAGS) $(MDEFS) -o shuffle $(OBJ) shuffle_main.o $(LIBS)
translate: $(OBJ) translate_main.o
- $(CC) $(CFLAGS) $(MDEFS) -o translate $(OBJ) translate_main.o $(LIBS)
+ $(CC) $(CFLAGS) $(LDFLAGS) $(MDEFS) -o translate $(OBJ) translate_main.o $(LIBS)
weight: $(OBJ) weight_main.o
- $(CC) $(CFLAGS) $(MDEFS) -o weight $(OBJ) weight_main.o $(LIBS)
+ $(CC) $(CFLAGS) $(LDFLAGS) $(MDEFS) -o weight $(OBJ) weight_main.o $(LIBS)
$(LIBTARGET): $(OBJ)
- $(AR) $(LIBTARGET) $(OBJ)
+ $(AR) rcv $(LIBTARGET) $(OBJ)
-if test -x /bin/ranlib; then /bin/ranlib $(LIBTARGET); else exit 0; fi
-if test -x /usr/bin/ranlib; then /usr/bin/ranlib $(LIBTARGET); else exit 0; fi
-if test -x $(RANLIB); then $(RANLIB) $(LIBTARGET); else exit 0; fi
@@ -182,4 +178,4 @@ tags:
etags -t $(SRC) $(HDRS)
.c.o:
- $(CC) $(CFLAGS) $(MDEFS) -c $<
+ $(CC) $(CFLAGS) $(CPPFLAGS) $(MDEFS) -c $<
diff --git a/squid02/Makefile b/squid02/Makefile
index d32240f..757e0dd 100644
--- a/squid02/Makefile
+++ b/squid02/Makefile
@@ -27,8 +27,6 @@ SCRIPTDIR = ${exec_prefix}/bin
## your compiler and compiler flags
#
-CC = gcc
-CFLAGS = -g -O2 -m32
## other defined flags for machine-specific stuff
#
@@ -37,8 +35,6 @@ LIBS = -lm
## Archiver command
#
-AR = ar rcv
-RANLIB = ranlib
## instructions for installing man pages
#
@@ -158,10 +154,10 @@ OBJS = a2m.o\
all: version.h $(PROGS) libsquid.a
$(PROGS): %: %_main.o version.h $(OBJS)
- $(CC) $(CFLAGS) $(MDEFS) $(PVMLIBDIR) -o $@ $@_main.o $(OBJS) $(PVMLIBS) $(LIBS)
+ $(CC) $(CFLAGS) $(LDFLAGS) $(MDEFS) $(PVMLIBDIR) -o $@ $@_main.o $(OBJS) $(PVMLIBS) $(LIBS)
.c.o:
- $(CC) $(CFLAGS) $(PVMFLAG) $(PVMINCDIR) $(MDEFS) -c $<
+ $(CC) $(CFLAGS) $(CPPFLAGS) $(PVMFLAG) $(PVMINCDIR) $(MDEFS) -c $<
################################################################
@@ -172,7 +168,7 @@ $(PROGS): %: %_main.o version.h $(OBJS)
module: libsquid.a
libsquid.a: version.h $(OBJS)
- $(AR) libsquid.a $(OBJS)
+ $(AR) rcv libsquid.a $(OBJS)
$(RANLIB) libsquid.a
chmod 644 libsquid.a
#################################################################
diff --git a/src/Makefile b/src/Makefile
index d93182b..35c8b3d 100644
--- a/src/Makefile
+++ b/src/Makefile
@@ -21,7 +21,6 @@ SQUIDDIR02 = ../squid02
SQUIDSRCDIR02 = ../squid02
## your compiler
-CC = gcc
#CC = cc
## any special compiler flags you want
@@ -30,7 +29,6 @@ CC = gcc
#CFLAGS = -g -Wall -pedantic
#CFLAGS = -TARG:exc_max
#CFLAGS = -g -fullwarn -wlint,-fviah
-CFLAGS = -O -m32
#CFLAGS = -p # profiling #
#CFLAGS = -64 -Ofast=ip27 #specific warhorse compiler#
@@ -131,145 +129,145 @@ DEMOS =
all: $(PROGS)
main: $(OBJ) main.o
- $(CC) $(CFLAGS) -o $@ -L$(SQUIDDIR) $@.o $(LIBS)
+ $(CC) $(CFLAGS) $(LDFLAGS) -o $@ -L$(SQUIDDIR) $@.o $(LIBS)
cfgbuild: $(OBJ) cfgbuild.o
- $(CC) $(CFLAGS) -o $@ -L$(SQUIDDIR) $@.o $(OBJ) $(LIBS)
+ $(CC) $(CFLAGS) $(LDFLAGS) -o $@ -L$(SQUIDDIR) $@.o $(OBJ) $(LIBS)
eqrna: $(OBJ) eqrna.o
- $(CC) $(CFLAGS) -o $@ -L$(SQUIDDIR) $@.o $(OBJ) $(LIBS)
+ $(CC) $(CFLAGS) $(LDFLAGS) -o $@ -L$(SQUIDDIR) $@.o $(OBJ) $(LIBS)
eqrna_sample: $(OBJ) eqrna_sample.o
- $(CC) $(CFLAGS) -o $@ -L$(SQUIDDIR) $@.o $(OBJ) $(LIBS)
+ $(CC) $(CFLAGS) $(LDFLAGS) -o $@ -L$(SQUIDDIR) $@.o $(OBJ) $(LIBS)
shuffle: $(OBJ) shuffle.o
- $(CC) $(CFLAGS) -o $@ -L$(SQUIDDIR) $@.o $(OBJ) $(LIBS)
+ $(CC) $(CFLAGS) $(LDFLAGS) -o $@ -L$(SQUIDDIR) $@.o $(OBJ) $(LIBS)
rnamat_main: $(OBJ2) rnamat_main.o
- $(CC) $(CFLAGS) -o $@ -L$(SQUIDDIR02) $@.o $(OBJ2) $(LIBS)
+ $(CC) $(CFLAGS) $(LDFLAGS) -o $@ -L$(SQUIDDIR02) $@.o $(OBJ2) $(LIBS)
main.o: ../src/main.c
- $(CC) $(CFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $?
+ $(CC) $(CFLAGS) $(CPPFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $?
cfgbuild.o: ../src/cfgbuild.c
- $(CC) $(CFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $?
+ $(CC) $(CFLAGS) $(CPPFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $?
eqrna.o: ../src/eqrna.c
- $(CC) $(CFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $?
+ $(CC) $(CFLAGS) $(CPPFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $?
eqrna_sample.o: ../src/eqrna_sample.c
- $(CC) $(CFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $?
+ $(CC) $(CFLAGS) $(CPPFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $?
shuffle.o: ../src/shuffle.c
- $(CC) $(CFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $?
+ $(CC) $(CFLAGS) $(CPPFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $?
rnamat_main.o: ../src/rnamat_main.c
- $(CC) $(CFLAGS) $(MDEFS) -I$(SQUIDDIR02) -c $?
+ $(CC) $(CFLAGS) $(CPPFLAGS) $(MDEFS) -I$(SQUIDDIR02) -c $?
cfgio.o: ../src/cfgio.c
- $(CC) $(CFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $?
+ $(CC) $(CFLAGS) $(CPPFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $?
cfgmodel.o: ../src/cfgmodel.c
- $(CC) $(CFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $?
+ $(CC) $(CFLAGS) $(CPPFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $?
cfgparse.o: ../src/cfgparse.c
- $(CC) $(CFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $?
+ $(CC) $(CFLAGS) $(CPPFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $?
codcreatealign.o: ../src/codcreatealign.c
- $(CC) $(CFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $?
+ $(CC) $(CFLAGS) $(CPPFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $?
coddp.o: ../src/coddp.c
- $(CC) $(CFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $?
+ $(CC) $(CFLAGS) $(CPPFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $?
coddpscanfast.o: ../src/coddpscanfast.c
- $(CC) $(CFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $?
+ $(CC) $(CFLAGS) $(CPPFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $?
codmodel.o: ../src/codmodel.c
- $(CC) $(CFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $?
+ $(CC) $(CFLAGS) $(CPPFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $?
codon.o: ../src/codon.c
- $(CC) $(CFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $?
+ $(CC) $(CFLAGS) $(CPPFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $?
codscorealign.o: ../src/codscorealign.c
- $(CC) $(CFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $?
+ $(CC) $(CFLAGS) $(CPPFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $?
er_math.o: ../src/er_math.c
- $(CC) $(CFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $?
+ $(CC) $(CFLAGS) $(CPPFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $?
er_vectop.o: ../src/er_vectop.c
- $(CC) $(CFLAGS) $(MDEFS) -I$(SQUIDDIR02) -c $?
+ $(CC) $(CFLAGS) $(CPPFLAGS) $(MDEFS) -I$(SQUIDDIR02) -c $?
evd.o: ../src/evd.c
- $(CC) $(CFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $?
+ $(CC) $(CFLAGS) $(CPPFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $?
evolcodmodel.o: ../src/evolcodmodel.c
- $(CC) $(CFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $?
+ $(CC) $(CFLAGS) $(CPPFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $?
evolemissions.o: ../src/evolemissions.c
- $(CC) $(CFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $?
+ $(CC) $(CFLAGS) $(CPPFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $?
evolmisc.o: ../src/evolmisc.c
- $(CC) $(CFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $?
+ $(CC) $(CFLAGS) $(CPPFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $?
evolnullmodel.o: ../src/evolnullmodel.c
- $(CC) $(CFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $?
+ $(CC) $(CFLAGS) $(CPPFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $?
evolothmodel.o: ../src/evolothmodel.c
- $(CC) $(CFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $?
+ $(CC) $(CFLAGS) $(CPPFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $?
evolqrnaversion.o: ../src/evolqrnaversion.c
- $(CC) $(CFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $?
+ $(CC) $(CFLAGS) $(CPPFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $?
evolscorewithmodels.o: ../src/evolscorewithmodels.c
- $(CC) $(CFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $?
+ $(CC) $(CFLAGS) $(CPPFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $?
evolscorewithmodelscanfast.o: ../src/evolscorewithmodelscanfast.c
- $(CC) $(CFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $?
+ $(CC) $(CFLAGS) $(CPPFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $?
evolriboprob.o: ../src/evolriboprob.c
- $(CC) $(CFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $?
+ $(CC) $(CFLAGS) $(CPPFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $?
evolrnadp.o: ../src/evolrnadp.c
- $(CC) $(CFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $?
+ $(CC) $(CFLAGS) $(CPPFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $?
evolrnadpscanfast.o: ../src/evolrnadpscanfast.c
- $(CC) $(CFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $?
+ $(CC) $(CFLAGS) $(CPPFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $?
evolrnamodel.o: ../src/evolrnamodel.c
- $(CC) $(CFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $?
+ $(CC) $(CFLAGS) $(CPPFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $?
evolrnascorealign.o: ../src/evolrnascorealign.c
- $(CC) $(CFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $?
+ $(CC) $(CFLAGS) $(CPPFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $?
evolve.o: ../src/evolve.c
- $(CC) $(CFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $?
+ $(CC) $(CFLAGS) $(CPPFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $?
globals.o: ../src/globals.c
- $(CC) $(CFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $?
+ $(CC) $(CFLAGS) $(CPPFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $?
hexamer.o: ../src/hexamer.c
- $(CC) $(CFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $?
+ $(CC) $(CFLAGS) $(CPPFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $?
matrix.o: ../src/matrix.c
- $(CC) $(CFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $?
+ $(CC) $(CFLAGS) $(CPPFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $?
misc.o: ../src/misc.c
- $(CC) $(CFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $?
+ $(CC) $(CFLAGS) $(CPPFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $?
nrnscfg.o: ../src/nrnscfg.c
- $(CC) $(CFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $?
+ $(CC) $(CFLAGS) $(CPPFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $?
nstack.o: ../src/nstack.c
- $(CC) $(CFLAGS) $(MDEFS) -I$(SQUIDDIR02) -c $?
+ $(CC) $(CFLAGS) $(CPPFLAGS) $(MDEFS) -I$(SQUIDDIR02) -c $?
nullmodel.o: ../src/nullmodel.c
- $(CC) $(CFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $?
+ $(CC) $(CFLAGS) $(CPPFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $?
othcreatealign.o: ../src/othcreatealign.c
- $(CC) $(CFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $?
+ $(CC) $(CFLAGS) $(CPPFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $?
othdp.o: ../src/othdp.c
- $(CC) $(CFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $?
+ $(CC) $(CFLAGS) $(CPPFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $?
othdpscanfast.o: ../src/othdpscanfast.c
- $(CC) $(CFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $?
+ $(CC) $(CFLAGS) $(CPPFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $?
othmodel.o: ../src/othmodel.c
- $(CC) $(CFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $?
+ $(CC) $(CFLAGS) $(CPPFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $?
othscorealign.o: ../src/othscorealign.c
- $(CC) $(CFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $?
+ $(CC) $(CFLAGS) $(CPPFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $?
posterior.o: ../src/posterior.c
- $(CC) $(CFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $?
+ $(CC) $(CFLAGS) $(CPPFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $?
qrnaversion.o: ../src/qrnaversion.c
- $(CC) $(CFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $?
+ $(CC) $(CFLAGS) $(CPPFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $?
riboprob.o: ../src/riboprob.c
- $(CC) $(CFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $?
+ $(CC) $(CFLAGS) $(CPPFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $?
rnacreatealign.o: ../src/rnacreatealign.c
- $(CC) $(CFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $?
+ $(CC) $(CFLAGS) $(CPPFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $?
rnadp.o: ../src/rnadp.c
- $(CC) $(CFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $?
+ $(CC) $(CFLAGS) $(CPPFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $?
rnadpscanfast.o: ../src/rnadpscanfast.c
- $(CC) $(CFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $?
+ $(CC) $(CFLAGS) $(CPPFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $?
rnaio.o: ../src/rnaio.c
- $(CC) $(CFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $?
+ $(CC) $(CFLAGS) $(CPPFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $?
rnamat.o: ../src/rnamat.c
- $(CC) $(CFLAGS) $(MDEFS) -I$(SQUIDDIR02) -c $?
+ $(CC) $(CFLAGS) $(CPPFLAGS) $(MDEFS) -I$(SQUIDDIR02) -c $?
rnamodel.o: ../src/rnamodel.c
- $(CC) $(CFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $?
+ $(CC) $(CFLAGS) $(CPPFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $?
rnaoutput.o: ../src/rnaoutput.c
- $(CC) $(CFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $?
+ $(CC) $(CFLAGS) $(CPPFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $?
rnascorealign.o: ../src/rnascorealign.c
- $(CC) $(CFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $?
+ $(CC) $(CFLAGS) $(CPPFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $?
rnascfg.o: ../src/rnascfg.c
- $(CC) $(CFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $?
+ $(CC) $(CFLAGS) $(CPPFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $?
rnascfgscanfast.o: ../src/rnascfgscanfast.c
- $(CC) $(CFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $?
+ $(CC) $(CFLAGS) $(CPPFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $?
scorewithmodels.o: ../src/scorewithmodels.c
- $(CC) $(CFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $?
+ $(CC) $(CFLAGS) $(CPPFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $?
scorewithmodelscanfast.o: ../src/scorewithmodelscanfast.c
- $(CC) $(CFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $?
+ $(CC) $(CFLAGS) $(CPPFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $?
seqio.o: ../src/seqio.c
- $(CC) $(CFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $?
+ $(CC) $(CFLAGS) $(CPPFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $?
trace.o: ../src/trace.c
- $(CC) $(CFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $?
+ $(CC) $(CFLAGS) $(CPPFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $?
traceSCFG.o: ../src/traceSCFG.c
- $(CC) $(CFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $?
+ $(CC) $(CFLAGS) $(CPPFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $?
tying.o: ../src/tying.c
- $(CC) $(CFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $?
+ $(CC) $(CFLAGS) $(CPPFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $?
install: $(PROGS)
@@ -313,10 +311,10 @@ lint:
/usr/lib/lint/llib-lm.ln
.c.o:
- $(CC) $(CFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $<
+ $(CC) $(CFLAGS) $(CPPFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $<
.m.o:
- $(CC) $(CFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $<
+ $(CC) $(CFLAGS) $(CPPFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $<
sci-biology/qrna/metadata.xml
-8
View File
@@ -1,8 +0,0 @@
<?xml version="1.0" encoding="UTF-8"?>
<!DOCTYPE pkgmetadata SYSTEM "https://www.gentoo.org/dtd/metadata.dtd">
<pkgmetadata>
<maintainer type="project">
<email>sci-biology@gentoo.org</email>
<name>Gentoo Biology Project</name>
</maintainer>
</pkgmetadata>
sci-biology/qrna/qrna-2.0.3c-r3.ebuild
-55
View File
@@ -1,55 +0,0 @@
# Copyright 1999-2020 Gentoo Authors
# Distributed under the terms of the GNU General Public License v2
EAPI=7
inherit toolchain-funcs
DESCRIPTION="Prototype ncRNA genefinder"
HOMEPAGE="http://selab.janelia.org/software.html"
SRC_URI="mirror://gentoo/${P}.tar.bz2"
LICENSE="GPL-2"
SLOT="0"
KEYWORDS="~amd64 ~x86"
RDEPEND="
dev-lang/perl
sci-biology/hmmer:2"
DEPEND="${RDEPEND}"
PATCHES=(
"${FILESDIR}"/${P}-glibc-2.10.patch
"${FILESDIR}"/${P}-ldflags.patch
)
src_prepare() {
default
rm -v squid*/*.a || die
}
src_configure() {
tc-export AR CC RANLIB
}
src_compile() {
local d
for d in squid squid02 src; do
emake -C ${d}
done
}
src_install() {
dobin src/{cfgbuild,eqrna,eqrna_sample,rnamat_main} scripts/*
newdoc 00README README
dodoc -r documentation/.
insinto /usr/share/${PN}/data
doins -r lib/.
insinto /usr/share/${PN}/demos
doins -r Demos/.
# Sets the path to the QRNA data files
doenvd "${FILESDIR}"/26qrna
}
sci-biology/qrna/qrna-2.0.4.ebuild
-61
View File
@@ -1,61 +0,0 @@
# Copyright 1999-2024 Gentoo Authors
# Distributed under the terms of the GNU General Public License v2
EAPI=8
inherit toolchain-funcs vcs-clean
DESCRIPTION="Prototype ncRNA genefinder"
HOMEPAGE="http://eddylab.org/software.html"
SRC_URI="
http://eddylab.org/software/qrna/qrna.tar.gz -> ${P}.tar.gz
examples? ( mirror://gentoo/qrna-2.0.3c.tar.bz2 )
"
LICENSE="GPL-2"
SLOT="0"
KEYWORDS="~amd64 ~x86"
IUSE="examples"
RDEPEND="
dev-lang/perl
sci-biology/hmmer:2"
DEPEND="${RDEPEND}"
PATCHES=(
"${FILESDIR}"/${P}-ldflags.patch
)
src_prepare() {
default
esvn_clean
rm -v squid*/*.a || die
}
src_configure() {
tc-export AR CC RANLIB
}
src_compile() {
local d
for d in squid squid02 src; do
emake -C ${d}
done
}
src_install() {
dobin src/{cfgbuild,eqrna,eqrna_sample,rnamat_main} scripts/*
newdoc 00README README
dodoc -r documentation/.
insinto /usr/share/${PN}/data
doins -r lib/.
if use examples; then
insinto /usr/share/${PN}/demos
doins -r "${WORKDIR}"/qrna-2.0.3c/Demos/.
fi
# Sets the path to the QRNA data files
doenvd "${FILESDIR}"/26qrna
}