New Upstream Snapshot - fermi-lite
Ready changes
Summary
Merged new upstream version: 0.1+git20221215.85f159e (was: 0.1+git20190320.b499514).
Resulting package
Built on 2023-02-09T00:23 (took 2m41s)
The resulting binary packages can be installed (if you have the apt repository enabled) by running one of:
apt install -t fresh-snapshots fml-asm-dbgsymapt install -t fresh-snapshots fml-asmapt install -t fresh-snapshots libfml-devapt install -t fresh-snapshots libfml0-dbgsymapt install -t fresh-snapshots libfml0
Diff
diff --git a/.gitignore b/.gitignore
deleted file mode 100644
index 282c932..0000000
--- a/.gitignore
+++ /dev/null
@@ -1,3 +0,0 @@
-*.o
-*.a
-.*.swp
diff --git a/debian/changelog b/debian/changelog
index 758e510..07d0d40 100644
--- a/debian/changelog
+++ b/debian/changelog
@@ -1,3 +1,10 @@
+fermi-lite (0.1+git20221215.85f159e-1) UNRELEASED; urgency=low
+
+ * New upstream snapshot.
+ * Drop patch gcc10.patch, present upstream.
+
+ -- Debian Janitor <janitor@jelmer.uk> Thu, 09 Feb 2023 00:21:25 -0000
+
fermi-lite (0.1+git20190320.b499514-1) unstable; urgency=medium
[ Michael R. Crusoe ]
diff --git a/debian/patches/bcf_seqlib.patch b/debian/patches/bcf_seqlib.patch
index 1035478..f9078d2 100644
--- a/debian/patches/bcf_seqlib.patch
+++ b/debian/patches/bcf_seqlib.patch
@@ -5,8 +5,10 @@ Description: Try to take over patches from libSeqLib which needs separate bfc.h
Author: Andreas Tille <tille@debian.org>
Last-Update: Thu, 02 Feb 2017 10:57:56 +0100
---- a/bfc.c
-+++ b/bfc.c
+Index: fermi-lite.git/bfc.c
+===================================================================
+--- fermi-lite.git.orig/bfc.c
++++ fermi-lite.git/bfc.c
@@ -7,24 +7,12 @@
#include "kmer.h"
#include "internal.h"
@@ -188,8 +190,10 @@ Last-Update: Thu, 02 Feb 2017 10:57:56 +0100
float fml_correct(const fml_opt_t *opt, int n, fml_seq1_t *seq)
{
return fml_correct_core(opt, 0, n, seq);
+Index: fermi-lite.git/bfc.h
+===================================================================
--- /dev/null
-+++ b/bfc.h
++++ fermi-lite.git/bfc.h
@@ -0,0 +1,153 @@
+#ifndef AC_BFC_H__
+#define AC_BFC_H__
diff --git a/debian/patches/ensure-signed-comparison.patch b/debian/patches/ensure-signed-comparison.patch
index 3e3384c..be7ad98 100644
--- a/debian/patches/ensure-signed-comparison.patch
+++ b/debian/patches/ensure-signed-comparison.patch
@@ -7,11 +7,11 @@ Author: Steve Langasek <steve.langasek@ubuntu.com>
Last-Update: 2020-03-17
Bug-Debian: https://bugs.debian.org/954127
-Index: fermi-lite-0.1/mag.c
+Index: fermi-lite.git/mag.c
===================================================================
---- fermi-lite-0.1.orig/mag.c
-+++ fermi-lite-0.1/mag.c
-@@ -506,7 +506,7 @@
+--- fermi-lite.git.orig/mag.c
++++ fermi-lite.git/mag.c
+@@ -506,7 +506,7 @@ double mag_cal_rdist(mag_t *g)
for (j = 0; j < 2; ++j) {
sum_n = sum_l = 0;
diff --git a/debian/patches/gcc10.patch b/debian/patches/gcc10.patch
deleted file mode 100644
index 3e7f65f..0000000
--- a/debian/patches/gcc10.patch
+++ /dev/null
@@ -1,16 +0,0 @@
-Description: Fix package to build with GCC-10
-Bug-Debian: https://bugs.debian.org/957198
-Author: Nilesh Patra <npatra974@gmail.com>
-Last-Update: Sat, 18 Apr 2020 22:55:21 +0530
-
---- a/rle.h
-+++ b/rle.h
-@@ -30,7 +30,7 @@
- *** 43+3 codec ***
- ******************/
-
--const uint8_t rle_auxtab[8];
-+extern const uint8_t rle_auxtab[8];
-
- #define RLE_MIN_SPACE 18
- #define rle_nptr(block) ((uint16_t*)(block))
diff --git a/debian/patches/hardening b/debian/patches/hardening
index e416fe1..62c6a5f 100644
--- a/debian/patches/hardening
+++ b/debian/patches/hardening
@@ -2,8 +2,10 @@ Description: add hardening flags
Adds necessary build flags for hardening.
Author: Sascha Steinbiss <sascha@steinbiss.name>
Last-Update: 2016-01-08
---- fermi-lite.orig/Makefile
-+++ fermi-lite/Makefile
+Index: fermi-lite.git/Makefile
+===================================================================
+--- fermi-lite.git.orig/Makefile
++++ fermi-lite.git/Makefile
@@ -1,30 +1,27 @@
-CC= gcc
-CFLAGS= -g -Wall -O2 -fPIC #-fno-inline-functions -fno-inline-functions-called-once
diff --git a/debian/patches/make_shared_lib b/debian/patches/make_shared_lib
index eec0747..a052c28 100644
--- a/debian/patches/make_shared_lib
+++ b/debian/patches/make_shared_lib
@@ -2,8 +2,10 @@ Description: build shared library
Upstream only builds a static library, this adds a shared one.
Author: Sascha Steinbiss <sascha@steinbiss.name>
Last-Update: 2016-01-08
---- a/Makefile
-+++ b/Makefile
+Index: fermi-lite.git/Makefile
+===================================================================
+--- fermi-lite.git.orig/Makefile
++++ fermi-lite.git/Makefile
@@ -1,5 +1,5 @@
CC= gcc
-CFLAGS= -g -Wall -O2 -Wno-unused-function #-fno-inline-functions -fno-inline-functions-called-once
@@ -11,7 +13,7 @@ Last-Update: 2016-01-08
CPPFLAGS=
INCLUDES=
OBJS= kthread.o misc.o \
-@@ -8,13 +8,14 @@
+@@ -8,13 +8,14 @@ OBJS= kthread.o misc.o \
unitig.o mag.o bubble.o ksw.o
PROG= fml-asm
LIBS= -lm -lz -lpthread
@@ -27,7 +29,7 @@ Last-Update: 2016-01-08
fml-asm:libfml.a example.o
$(CC) $(CFLAGS) $^ -o $@ -L. -lfml $(LIBS)
-@@ -22,6 +23,10 @@
+@@ -22,6 +23,10 @@ fml-asm:libfml.a example.o
libfml.a:$(OBJS)
$(AR) -csru $@ $(OBJS)
diff --git a/debian/patches/rename_bseq1_t.patch b/debian/patches/rename_bseq1_t.patch
index 412eb33..ed24cd0 100644
--- a/debian/patches/rename_bseq1_t.patch
+++ b/debian/patches/rename_bseq1_t.patch
@@ -3,8 +3,10 @@ Bug-Upstream: https://github.com/lh3/fermi-lite/issues/5
Author: Andreas Tille <tille@debian.org>
Last-Update: Thu, 02 Feb 2017 10:57:56 +0100
---- a/bfc.c
-+++ b/bfc.c
+Index: fermi-lite.git/bfc.c
+===================================================================
+--- fermi-lite.git.orig/bfc.c
++++ fermi-lite.git/bfc.c
@@ -60,7 +60,7 @@ typedef struct { // cache to reduce lock
typedef struct {
int k, q;
@@ -78,8 +80,10 @@ Last-Update: Thu, 02 Feb 2017 10:57:56 +0100
{
return fml_correct_core(opt, 1, n, seq);
}
---- a/bseq.c
-+++ b/bseq.c
+Index: fermi-lite.git/bseq.c
+===================================================================
+--- fermi-lite.git.orig/bseq.c
++++ fermi-lite.git/bseq.c
@@ -6,10 +6,10 @@
#include "kseq.h"
KSEQ_INIT(gzFile, gzread)
@@ -106,8 +110,10 @@ Last-Update: Thu, 02 Feb 2017 10:57:56 +0100
}
s = &seqs[n];
s->seq = strdup(ks->seq.s);
---- a/misc.c
-+++ b/misc.c
+Index: fermi-lite.git/misc.c
+===================================================================
+--- fermi-lite.git.orig/misc.c
++++ fermi-lite.git/misc.c
@@ -40,7 +40,7 @@ void fml_opt_init(fml_opt_t *opt)
opt->mag_opt.flag = MAG_F_NO_SIMPL | MAG_F_POPOPEN;
}
@@ -153,8 +159,10 @@ Last-Update: Thu, 02 Feb 2017 10:57:56 +0100
{
rld_t *e;
mag_t *g;
---- a/example.c
-+++ b/example.c
+Index: fermi-lite.git/example.c
+===================================================================
+--- fermi-lite.git.orig/example.c
++++ fermi-lite.git/example.c
@@ -7,7 +7,7 @@ int main(int argc, char *argv[])
{
fml_opt_t opt;
@@ -173,8 +181,10 @@ Last-Update: Thu, 02 Feb 2017 10:57:56 +0100
utg = fml_assemble(&opt, n_seqs, seqs, &n_utg);
if (!gfa_out) fml_utg_print(n_utg, utg);
else fml_utg_print_gfa(n_utg, utg);
---- a/internal.h
-+++ b/internal.h
+Index: fermi-lite.git/internal.h
+===================================================================
+--- fermi-lite.git.orig/internal.h
++++ fermi-lite.git/internal.h
@@ -12,7 +12,7 @@ extern "C" {
void kt_for(int n_threads, void (*func)(void*,long,int), void *data, long n);
void seq_reverse(int l, unsigned char *s);
@@ -184,8 +194,10 @@ Last-Update: Thu, 02 Feb 2017 10:57:56 +0100
#ifdef __cplusplus
}
---- a/fml.h
-+++ b/fml.h
+Index: fermi-lite.git/fml.h
+===================================================================
+--- fermi-lite.git.orig/fml.h
++++ fermi-lite.git/fml.h
@@ -8,7 +8,7 @@
typedef struct {
int32_t l_seq;
@@ -242,8 +254,10 @@ Last-Update: Thu, 02 Feb 2017 10:57:56 +0100
/**
* Generate initial overlap graph
---- a/README.md
-+++ b/README.md
+Index: fermi-lite.git/README.md
+===================================================================
+--- fermi-lite.git.orig/README.md
++++ fermi-lite.git/README.md
@@ -34,11 +34,11 @@ sketch of the example:
int main(int argc, char *argv[])
{
diff --git a/debian/patches/series b/debian/patches/series
index 54b3bdd..a596184 100644
--- a/debian/patches/series
+++ b/debian/patches/series
@@ -5,4 +5,3 @@ bcf_seqlib.patch
simde
ensure-signed-comparison.patch
sync_instead_of_atomic
-gcc10.patch
diff --git a/debian/patches/simde b/debian/patches/simde
index 869771e..b25ac3e 100644
--- a/debian/patches/simde
+++ b/debian/patches/simde
@@ -1,7 +1,9 @@
Author: Michael R. Crusoe <michael.crusoe@gmail.com>
Description: use the simde header library for greater compatibility
---- fermi-lite.orig/ksw.c
-+++ fermi-lite/ksw.c
+Index: fermi-lite.git/ksw.c
+===================================================================
+--- fermi-lite.git.orig/ksw.c
++++ fermi-lite.git/ksw.c
@@ -25,7 +25,8 @@
#include <stdlib.h>
diff --git a/debian/patches/sync_instead_of_atomic b/debian/patches/sync_instead_of_atomic
index ef57148..afa46aa 100644
--- a/debian/patches/sync_instead_of_atomic
+++ b/debian/patches/sync_instead_of_atomic
@@ -1,9 +1,11 @@
From: Michael R. Crusoe <michael.crusoe@gmail.com>
Subject: fix compatibility on mipsel
Forwarded: https://github.com/lh3/fermi-lite/pull/13
---- fermi-lite.orig/unitig.c
-+++ fermi-lite/unitig.c
-@@ -71,7 +71,7 @@
+Index: fermi-lite.git/unitig.c
+===================================================================
+--- fermi-lite.git.orig/unitig.c
++++ fermi-lite.git/unitig.c
+@@ -71,7 +71,7 @@ static inline void set_bit(uint64_t *bit
{
uint64_t *p = bits + (x>>6);
uint64_t z = 1LLU<<(x&0x3f);
@@ -12,7 +14,7 @@ Forwarded: https://github.com/lh3/fermi-lite/pull/13
}
static inline void set_bits(uint64_t *bits, const rldintv_t *p)
-@@ -389,7 +389,7 @@
+@@ -389,7 +389,7 @@ static void worker(void *data, long _i,
magv_t *q;
p[0] = w->visited + (d->z.k[0]>>6); x[0] = 1LLU<<(d->z.k[0]&0x3f);
p[1] = w->visited + (d->z.k[1]>>6); x[1] = 1LLU<<(d->z.k[1]&0x3f);
diff --git a/rle.h b/rle.h
index 0d59484..4f8946d 100644
--- a/rle.h
+++ b/rle.h
@@ -30,7 +30,7 @@ extern "C" {
*** 43+3 codec ***
******************/
-const uint8_t rle_auxtab[8];
+extern const uint8_t rle_auxtab[8];
#define RLE_MIN_SPACE 18
#define rle_nptr(block) ((uint16_t*)(block))
Debdiff
[The following lists of changes regard files as different if they have different names, permissions or owners.]
Files in second set of .debs but not in first
-rw-r--r-- root/root /usr/lib/debug/.build-id/cf/f83e21d26b0a5a1aa78aced796362b2db8506c.debug -rw-r--r-- root/root /usr/lib/debug/.build-id/e9/79914cd9a3364825b639e1779d3c8ca75807de.debug
Files in first set of .debs but not in second
-rw-r--r-- root/root /usr/lib/debug/.build-id/7f/1db725c091c17bcb0faeb93590ca78745a4913.debug -rw-r--r-- root/root /usr/lib/debug/.build-id/fb/5270c80b0038642b875b3b59e3f79cf54b6fb6.debug
No differences were encountered between the control files of package fml-asm
Control files of package fml-asm-dbgsym: lines which differ (wdiff format)
Build-Ids: fb5270c80b0038642b875b3b59e3f79cf54b6fb6 e979914cd9a3364825b639e1779d3c8ca75807de
No differences were encountered between the control files of package libfml-dev
No differences were encountered between the control files of package libfml0
Control files of package libfml0-dbgsym: lines which differ (wdiff format)
Build-Ids: 7f1db725c091c17bcb0faeb93590ca78745a4913 cff83e21d26b0a5a1aa78aced796362b2db8506c