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

More details

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