Dear Maintainer,
I tried to have a look at this hanging test and could
reproduce a hang at this backtrace [1].
The loop in [2] gets not left because the result of the fgetc call
gets stored in a variable of type char and later compared to EOF.
It seems to be an issue with not being explicit
about signed/unsigned char with this variable.
At least using the type int makes the test finish and pass,
when libgatbcore3 is built with attached patch.
Kind regards,
Bernhard
[1]
(gdb) bt
#0 gatb::core::system::impl::CommonFile::gets (this=0x55839ffbb0,
s=<optimized out>, size=<optimized out>) at
./gatb-core/src/gatb/system/impl/FileSystemCommon.hpp:103
#1 0x00000076c633ee38 in gatb::core::bank::impl::BankAlbum::BankAlbum
(this=this@entry=0x55839fc860,
name="/tmp/autopkgtest.iSjXKJ/autopkgtest_tmp/simka_temp_output/simka_output_temp//input/A",
deleteIfExists=deleteIfExists@entry=false, __in_chrg=<optimized out>,
__vtt_parm=<optimized out>) at ./gatb-core/src/gatb/bank/impl/BankAlbum.cpp:64
#2 0x00000076c633f6a4 in
gatb::core::bank::impl::BankAlbumFactory::createBank (this=<optimized out>,
uri="/tmp/autopkgtest.iSjXKJ/autopkgtest_tmp/simka_temp_output/simka_output_temp//input/A")
at ./gatb-core/src/gatb/bank/impl/BankAlbum.cpp:343
#3 0x00000076c633c1a8 in gatb::core::bank::impl::Bank::_open_
(this=this@entry=0x555bb42388
<gatb::core::bank::impl::Bank::singleton()::instance>,
uri="/tmp/autopkgtest.iSjXKJ/autopkgtest_tmp/simka_temp_output/simka_output_temp//input/A")
at ./gatb-core/src/gatb/bank/impl/Bank.cpp:150
#4 0x000000555bb0b704 in gatb::core::bank::impl::Bank::open
(uri="/tmp/autopkgtest.iSjXKJ/autopkgtest_tmp/simka_temp_output/simka_output_temp//input/A")
at /usr/include/gatb/bank/impl/Bank.hpp:135
#5 SimkaAlgorithm<32ul>::isInputValid (this=0x7fd3195140) at
/build/simka-C4DX5D/simka-1.5.2/src/core/SimkaAlgorithm.cpp:362
#6 0x000000555baf9264 in SimkaPotaraAlgorithm<32ul>::execute
(this=0x7fd3195140) at /build/simka-C4DX5D/simka-1.5.2/src/SimkaPotara.hpp:413
#7 0x000000555badc9e4 in Functor<32ul>::operator() (this=<optimized out>,
p=...) at /build/simka-C4DX5D/simka-1.5.2/src/SimkaPotara.cpp:111
#8
gatb::core::tools::math::IntegerTemplate<boost::mpl::vector4<mpl_::int_<32>,
mpl_::int_<64>, mpl_::int_<96>, mpl_::int_<128> > >::Apply<Functor, Parameter,
boost::mpl::vector4<mpl_::int_<32>, mpl_::int_<64>, mpl_::int_<96>,
mpl_::int_<128> >, false>::execute (params=..., kmerSize=<optimized out>) at
/usr/include/gatb/tools/math/Integer.hpp:463
#9
gatb::core::tools::math::IntegerTemplate<boost::mpl::vector4<mpl_::int_<32>,
mpl_::int_<64>, mpl_::int_<96>, mpl_::int_<128> > >::apply<Functor, Parameter>
(params=..., kmerSize=<optimized out>) at
/usr/include/gatb/tools/math/Integer.hpp:84
#10 SimkaPotara::execute (this=<optimized out>) at
/build/simka-C4DX5D/simka-1.5.2/src/SimkaPotara.cpp:140
#11 0x00000076c6428020 in gatb::core::tools::misc::impl::Tool::run
(this=0x7fd31955d8, input=<optimized out>) at
./gatb-core/src/gatb/tools/misc/impl/Tool.cpp:158
#12 0x00000076c64277c8 in gatb::core::tools::misc::impl::Tool::run
(this=0x7fd31955d8, argc=7, argv=0x7fd3195848) at
./gatb-core/src/gatb/tools/misc/impl/Tool.cpp:112
#13 0x000000555bad97bc in main (argc=7, argv=0x7fd3195848) at
/usr/include/c++/10/ext/new_allocator.h:79
[2]
https://sources.debian.org/src/gatb-core/1.4.2+dfsg-5/gatb-core/src/gatb/system/impl/FileSystemCommon.hpp/#L103
Description: Use int as return of fgetc
Author: Bernhard Übelacker <[email protected]>
Bug-Debian: https://bugs.debian.org/954273
Forwarded: no
Last-Update: 2020-11-03
Index: gatb-core-1.4.2+dfsg/gatb-core/src/gatb/system/impl/FileSystemCommon.hpp
===================================================================
--- gatb-core-1.4.2+dfsg.orig/gatb-core/src/gatb/system/impl/FileSystemCommon.hpp
+++ gatb-core-1.4.2+dfsg/gatb-core/src/gatb/system/impl/FileSystemCommon.hpp
@@ -100,7 +100,7 @@ public:
result = strlen (tmp);
/** we skip all characters until we reach the next '\n'. */
- if (result > 0) { for (char c = tmp[result-1]; c !='\n' && c!=EOF; c = fgetc (getHandle())) {} }
+ if (result > 0) { for (int c = tmp[result-1]; c !='\n' && c!=EOF; c = fgetc (getHandle())) {} }
}
/** We return the result. */
# Unstable chroot 2020-11-03 running on Android/LineageOS kernel
root@localhost:~# lscpu
Architecture: aarch64
CPU op-mode(s): 32-bit, 64-bit
Byte Order: Little Endian
CPU(s): 8
On-line CPU(s) list: 4,5
Off-line CPU(s) list: 0-3,6,7
Thread(s) per core: 1
Core(s) per socket: 2
Socket(s): 1
Vendor ID: ARM
Model: 1
Model name: Cortex-A53
Stepping: r0p1
CPU max MHz: 1113,6000
CPU min MHz: 249,6000
Flags: fp asimd evtstrm aes pmull sha1 sha2 crc32
root@localhost:~# uname -a
Linux localhost 3.10.108-g5285e19 #1 SMP PREEMPT Fri Oct 26 18:55:56 CEST 2018
aarch64 GNU/Linux
apt update
apt dist-upgrade
apt install mc htop psmisc net-tools strace quilt autopkgtest gdb valgrind
simka simkamin simka-dbgsym libgatbcore3-dbgsym
apt build-dep simka
apt build-dep gatb-core
mkdir /home/media_rw/source/libgatbcore3/orig -p
cd /home/media_rw/source/libgatbcore3/orig
apt source libgatbcore3
cd
autopkgtest --shell-fail simka -- null
gdb -q --pid $(pidof simka)
set width 0
set pagination off
directory /home/media_rw/source/libgatbcore3/orig/gatb-core-1.4.2+dfsg
info thread
bt
...
kill
cd example
simka -in simka_input.txt -out ./simka_results/ -out-tmp ./simka_temp_output
gdb -q --args simka -in simka_input.txt -out ./simka_results/ -out-tmp
./simka_temp_output
set width 0
set pagination off
directory /home/media_rw/source/libgatbcore3/orig/gatb-core-1.4.2+dfsg
b gatb::core::system::impl::CommonFile::gets
y
run
display tmp
display/x result
display/x c
display/i $pc
media_rw@localhost:~$ autopkgtest --shell-fail simka -- null
autopkgtest [15:23:09]: starting date: 2020-11-03
autopkgtest [15:23:09]: version 5.15
autopkgtest [15:23:09]: host localhost; command line: /usr/bin/autopkgtest
--shell-fail simka -- null
autopkgtest [15:23:09]: testbed dpkg architecture: arm64
autopkgtest [15:23:09]: testbed running kernel: Linux 3.10.108-g5285e19 #1 SMP
PREEMPT Fri Oct 26 18:55:56 CEST 2018
autopkgtest [15:23:09]: @@@@@@@@@@@@@@@@@@@@ apt-source simka
gpgv: unknown type of key resource 'trustedkeys.kbx'
gpgv: keyblock resource '/tmp/dpkg-verify-sig.OlJ_8hJF/trustedkeys.kbx':
General error
gpgv: Signature made Di 28 Jul 2020 11:33:45 UTC
gpgv: using RSA key 0401A810A6F243031EA397596D7D441919D02395
gpgv: issuer "[email protected]"
gpgv: Can't check signature: No public key
dpkg-source: Warnung: Fehler beim Überprüfen der Signatur von
./simka_1.5.2-1.dsc
autopkgtest [15:23:13]: testing package simka version 1.5.2-1
autopkgtest [15:23:13]: build not needed
autopkgtest [15:23:13]: test run-unit-test: preparing testbed
autopkgtest [15:23:14]: test run-unit-test: [-----------------------
A.fasta
B.fasta
C.fasta
D_paired_1.fasta
D_paired_2.fasta
dataset_metadata.csv
potara_job
simkaMin
simka_input.txt
simple_test.py
simple_test.sh
truth
test_simkaMin.py
truth_simkaMin
truth_simkaMin_symetrical
Testing simka
Creating input
Nb input datasets: 5
(hangs)
media_rw@localhost:~$ pstree -p
?(1)─┬─?(7877)───bash(7878)
├─?(7873)───bash(7874)───pstree(8558)
└─?(7869)───bash(7870)───autopkgtest(8437)─┬─autopkgtest-vir(8438)
└─bash(8515)───run-unit-test(8523)─┬─bash(8524)───tee(8526)
├─bash(8525)───tee(8527)
└─bash(8540)───simka(8541)
$ ps aux | grep -i simka
media_rw 8541 14.1 0.2 19636 5200 pts/9 t+ 15:23 2:59 simka -in
simka_input.txt -out ./simka_results/ -out-tmp ./simka_temp_output
media_rw@localhost:~$ gdb -q --pid $(pidof simka)
Attaching to process 8541
Reading symbols from /usr/bin/simka...
Reading symbols from
/usr/lib/debug/.build-id/41/eccb19567866f26b2e5dc789a1119d65c92433.debug...
warning: Unable to determine the number of hardware watchpoints available.
warning: Unable to determine the number of hardware breakpoints available.
Reading symbols from /lib/aarch64-linux-gnu/libgatbcore.so.3...
(No debugging symbols found in /lib/aarch64-linux-gnu/libgatbcore.so.3)
Reading symbols from /lib/aarch64-linux-gnu/libhdf5_serial.so.103...
(No debugging symbols found in /lib/aarch64-linux-gnu/libhdf5_serial.so.103)
Reading symbols from /lib/aarch64-linux-gnu/libz.so.1...
(No debugging symbols found in /lib/aarch64-linux-gnu/libz.so.1)
Reading symbols from /lib/aarch64-linux-gnu/libstdc++.so.6...
(No debugging symbols found in /lib/aarch64-linux-gnu/libstdc++.so.6)
Reading symbols from /lib/aarch64-linux-gnu/libm.so.6...
Reading symbols from
/usr/lib/debug/.build-id/38/410433b4787bc47fec5d35756593902967251d.debug...
Reading symbols from /lib/aarch64-linux-gnu/libgcc_s.so.1...
(No debugging symbols found in /lib/aarch64-linux-gnu/libgcc_s.so.1)
Reading symbols from /lib/aarch64-linux-gnu/libc.so.6...
Reading symbols from
/usr/lib/debug/.build-id/1c/e3b34b868080593ed7faa924a1dca60047cc96.debug...
Reading symbols from /lib/ld-linux-aarch64.so.1...
Reading symbols from
/usr/lib/debug/.build-id/a6/0678b72f65e85bbecaf6e217352b5dd97f1e76.debug...
Reading symbols from /lib/aarch64-linux-gnu/libpthread.so.0...
Reading symbols from
/usr/lib/debug/.build-id/ab/38fd580cd1bee3e74c4b199fed65a20ac61660.debug...
[Thread debugging using libthread_db enabled]
Using host libthread_db library "/lib/aarch64-linux-gnu/libthread_db.so.1".
Reading symbols from /lib/aarch64-linux-gnu/libsz.so.2...
(No debugging symbols found in /lib/aarch64-linux-gnu/libsz.so.2)
Reading symbols from /lib/aarch64-linux-gnu/libdl.so.2...
Reading symbols from
/usr/lib/debug/.build-id/ab/b9c8bf80b6ec92bedbcdabb5dd69f6f8100e75.debug...
Reading symbols from /lib/aarch64-linux-gnu/libaec.so.0...
(No debugging symbols found in /lib/aarch64-linux-gnu/libaec.so.0)
_IO_getc (fp=0x55a751a530) at getc.c:37
37 getc.c: Datei oder Verzeichnis nicht gefunden.
(gdb) set width 0
(gdb) set pagination off
(gdb) info thread
Id Target Id Frame
* 1 Thread 0x76a049f010 (LWP 8541) "simka" _IO_getc (fp=0x55a751a530) at
getc.c:37
(gdb) bt
#0 _IO_getc (fp=0x55a751a530) at getc.c:37
#1 0x000000769ff22c2c in gatb::core::system::impl::CommonFile::gets(char*,
int) () from /lib/aarch64-linux-gnu/libgatbcore.so.3
#2 0x000000769fe8ce38 in
gatb::core::bank::impl::BankAlbum::BankAlbum(std::__cxx11::basic_string<char,
std::char_traits<char>, std::allocator<char> > const&, bool) () from
/lib/aarch64-linux-gnu/libgatbcore.so.3
#3 0x000000769fe8d6a4 in
gatb::core::bank::impl::BankAlbumFactory::createBank(std::__cxx11::basic_string<char,
std::char_traits<char>, std::allocator<char> > const&) () from
/lib/aarch64-linux-gnu/libgatbcore.so.3
#4 0x000000769fe8a1a8 in
gatb::core::bank::impl::Bank::_open_(std::__cxx11::basic_string<char,
std::char_traits<char>, std::allocator<char> > const&) () from
/lib/aarch64-linux-gnu/libgatbcore.so.3
#5 0x0000005572c0a704 in gatb::core::bank::impl::Bank::open
(uri="/tmp/autopkgtest.fkUiEY/autopkgtest_tmp/simka_temp_output/simka_output_temp//input/A")
at /usr/include/gatb/bank/impl/Bank.hpp:135
#6 SimkaAlgorithm<32ul>::isInputValid (this=0x7fda3b05f0) at
/build/simka-C4DX5D/simka-1.5.2/src/core/SimkaAlgorithm.cpp:362
#7 0x0000005572bf8264 in SimkaPotaraAlgorithm<32ul>::execute
(this=0x7fda3b05f0) at /build/simka-C4DX5D/simka-1.5.2/src/SimkaPotara.hpp:413
#8 0x0000005572bdb9e4 in Functor<32ul>::operator() (this=<optimized out>,
p=...) at /build/simka-C4DX5D/simka-1.5.2/src/SimkaPotara.cpp:111
#9
gatb::core::tools::math::IntegerTemplate<boost::mpl::vector4<mpl_::int_<32>,
mpl_::int_<64>, mpl_::int_<96>, mpl_::int_<128> > >::Apply<Functor, Parameter,
boost::mpl::vector4<mpl_::int_<32>, mpl_::int_<64>, mpl_::int_<96>,
mpl_::int_<128> >, false>::execute (params=..., kmerSize=<optimized out>) at
/usr/include/gatb/tools/math/Integer.hpp:463
#10
gatb::core::tools::math::IntegerTemplate<boost::mpl::vector4<mpl_::int_<32>,
mpl_::int_<64>, mpl_::int_<96>, mpl_::int_<128> > >::apply<Functor, Parameter>
(params=..., kmerSize=<optimized out>) at
/usr/include/gatb/tools/math/Integer.hpp:84
#11 SimkaPotara::execute (this=<optimized out>) at
/build/simka-C4DX5D/simka-1.5.2/src/SimkaPotara.cpp:140
#12 0x000000769ff76020 in
gatb::core::tools::misc::impl::Tool::run(gatb::core::tools::misc::IProperties*)
() from /lib/aarch64-linux-gnu/libgatbcore.so.3
#13 0x000000769ff757c8 in gatb::core::tools::misc::impl::Tool::run(int, char**)
() from /lib/aarch64-linux-gnu/libgatbcore.so.3
#14 0x0000005572bd87bc in main (argc=7, argv=0x7fda3b0cf8) at
/usr/include/c++/10/ext/new_allocator.h:79
(gdb) finish
Run till exit from #0 _IO_getc (fp=0x55a751a530) at getc.c:37
0x000000769ff22c2c in gatb::core::system::impl::CommonFile::gets(char*, int) ()
from /lib/aarch64-linux-gnu/libgatbcore.so.3
Value returned is $1 = -1
(gdb)
Run till exit from #0 0x000000769ff22c2c in
gatb::core::system::impl::CommonFile::gets(char*, int) () from
/lib/aarch64-linux-gnu/libgatbcore.so.3
^C
Program received signal SIGINT, Interrupt.
0x000000769f3254c8 in IO_validate_vtable (vtable=0x769f420070 <_IO_file_jumps>)
at libioP.h:944
944 libioP.h: Datei oder Verzeichnis nicht gefunden.
(gdb) detach
Detaching from program: /usr/bin/simka, process 8541
[Inferior 1 (process 8541) detached]
(gdb) q
media_rw@localhost:~$ gdb -q --pid $(pidof simka)
Attaching to process 8541
...
media_rw@localhost:/tmp/autopkgtest.fkUiEY/build.akj/src/example$ gdb -q --args
simka -in simka_input.txt -out ./simka_results/ -out-tmp ./simka_temp_output
...
(gdb) cont
Continuing.
^C
Program received signal SIGINT, Interrupt.
0x0000007fb6e754e4 in __GI__IO_default_uflow (fp=0x55594545c0) at genops.c:363
363 genops.c: Datei oder Verzeichnis nicht gefunden.
5: x/i $pc
=> 0x7fb6e754e4 <__GI__IO_default_uflow+68>: b.eq 0x7fb6e754f8
<__GI__IO_default_uflow+88> // b.none
6: /x $x0 = 0xffffffff
7: /x $w0 = 0xffffffff
(gdb) b fgetc
Breakpoint 3 at 0x7fb6e6f500: file getc.c, line 37.
(gdb) cont
Continuing.
Breakpoint 3, _IO_getc (fp=0x55594545c0) at getc.c:37
37 getc.c: Datei oder Verzeichnis nicht gefunden.
5: x/i $pc
=> 0x7fb6e6f500 <_IO_getc>: stp x29, x30, [sp, #-48]!
6: /x $x0 = 0x55594545c0
7: /x $w0 = 0x55594545c0
(gdb) dele 3
(gdb) finish
Run till exit from #0 _IO_getc (fp=0x55594545c0) at getc.c:37
gatb::core::system::impl::CommonFile::gets (this=0x5559459440, s=<optimized
out>, size=<optimized out>) at
./gatb-core/src/gatb/system/impl/FileSystemCommon.hpp:103
103 if (result > 0) { for (char c = tmp[result-1]; c !='\n'
&& c!=EOF; c = fgetc (getHandle())) {} }
5: x/i $pc
=> 0x7fb7a72c2c <gatb::core::system::impl::CommonFile::gets(char*, int)+124>:
and w0, w0, #0xff
6: /x $x0 = 0xffffffff
7: /x $w0 = 0xffffffff
Value returned is $10 = -1
(gdb) nexti
0x0000007fb7a72c30 103 if (result > 0) { for (char c =
tmp[result-1]; c !='\n' && c!=EOF; c = fgetc (getHandle())) {} }
5: x/i $pc
=> 0x7fb7a72c30 <gatb::core::system::impl::CommonFile::gets(char*, int)+128>:
cmp w0, #0xa
6: /x $x0 = 0xff
7: /x $w0 = 0xff
(gdb)
0x0000007fb7a72c34 103 if (result > 0) { for (char c =
tmp[result-1]; c !='\n' && c!=EOF; c = fgetc (getHandle())) {} }
5: x/i $pc
=> 0x7fb7a72c34 <gatb::core::system::impl::CommonFile::gets(char*, int)+132>:
b.ne 0x7fb7a72c20 <gatb::core::system::impl::CommonFile::gets(char*,
int)+112> // b.any
6: /x $x0 = 0xff
7: /x $w0 = 0xff
(gdb)
gatb::core::system::impl::CommonFile::getHandle (this=0x5559459440) at
./gatb-core/src/gatb/system/impl/FileSystemCommon.hpp:157
157 if (_handle == 0) { throw Exception ("Bad handle"); }
5: x/i $pc
=> 0x7fb7a72c20 <gatb::core::system::impl::CommonFile::gets(char*, int)+112>:
ldr x0, [x19, #40]
6: /x $x0 = 0xff
7: /x $w0 = 0xff
(gdb)
0x0000007fb7a72c24 157 if (_handle == 0) { throw Exception
("Bad handle"); }
5: x/i $pc
=> 0x7fb7a72c24 <gatb::core::system::impl::CommonFile::gets(char*, int)+116>:
cbz x0, 0x7fb7a72c94 <gatb::core::system::impl::CommonFile::gets(char*,
int)+228>
6: /x $x0 = 0x55594545c0
7: /x $w0 = 0x55594545c0
(gdb)
gatb::core::system::impl::CommonFile::gets (this=0x5559459440, s=<optimized
out>, size=<optimized out>) at
./gatb-core/src/gatb/system/impl/FileSystemCommon.hpp:158
158 return _handle;
5: x/i $pc
=> 0x7fb7a72c28 <gatb::core::system::impl::CommonFile::gets(char*, int)+120>:
bl 0x7fb79d58d0 <fgetc@plt>
6: /x $x0 = 0x55594545c0
7: /x $w0 = 0x55594545c0
(gdb)
103 if (result > 0) { for (char c = tmp[result-1]; c !='\n'
&& c!=EOF; c = fgetc (getHandle())) {} }
5: x/i $pc
=> 0x7fb7a72c2c <gatb::core::system::impl::CommonFile::gets(char*, int)+124>:
and w0, w0, #0xff
6: /x $x0 = 0xffffffff
7: /x $w0 = 0xffffffff
(gdb) print c
$11 = 255 '\377'
(gdb) ptype c
type = char
(gdb) print (unsigned char)c
$12 = 255 '\377'
(gdb) print (signed char)c
$13 = -1 '\377'
(gdb) print EOF
No symbol "EOF" in current context.
(gdb) bt
#0 gatb::core::system::impl::CommonFile::gets (this=0x55839ffbb0, s=<optimized
out>, size=<optimized out>) at
./gatb-core/src/gatb/system/impl/FileSystemCommon.hpp:103
#1 0x00000076c633ee38 in gatb::core::bank::impl::BankAlbum::BankAlbum
(this=this@entry=0x55839fc860,
name="/tmp/autopkgtest.iSjXKJ/autopkgtest_tmp/simka_temp_output/simka_output_temp//input/A",
deleteIfExists=deleteIfExists@entry=false, __in_chrg=<optimized out>,
__vtt_parm=<optimized out>) at ./gatb-core/src/gatb/bank/impl/BankAlbum.cpp:64
#2 0x00000076c633f6a4 in gatb::core::bank::impl::BankAlbumFactory::createBank
(this=<optimized out>,
uri="/tmp/autopkgtest.iSjXKJ/autopkgtest_tmp/simka_temp_output/simka_output_temp//input/A")
at ./gatb-core/src/gatb/bank/impl/BankAlbum.cpp:343
#3 0x00000076c633c1a8 in gatb::core::bank::impl::Bank::_open_
(this=this@entry=0x555bb42388
<gatb::core::bank::impl::Bank::singleton()::instance>,
uri="/tmp/autopkgtest.iSjXKJ/autopkgtest_tmp/simka_temp_output/simka_output_temp//input/A")
at ./gatb-core/src/gatb/bank/impl/Bank.cpp:150
#4 0x000000555bb0b704 in gatb::core::bank::impl::Bank::open
(uri="/tmp/autopkgtest.iSjXKJ/autopkgtest_tmp/simka_temp_output/simka_output_temp//input/A")
at /usr/include/gatb/bank/impl/Bank.hpp:135
#5 SimkaAlgorithm<32ul>::isInputValid (this=0x7fd3195140) at
/build/simka-C4DX5D/simka-1.5.2/src/core/SimkaAlgorithm.cpp:362
#6 0x000000555baf9264 in SimkaPotaraAlgorithm<32ul>::execute
(this=0x7fd3195140) at /build/simka-C4DX5D/simka-1.5.2/src/SimkaPotara.hpp:413
#7 0x000000555badc9e4 in Functor<32ul>::operator() (this=<optimized out>,
p=...) at /build/simka-C4DX5D/simka-1.5.2/src/SimkaPotara.cpp:111
#8
gatb::core::tools::math::IntegerTemplate<boost::mpl::vector4<mpl_::int_<32>,
mpl_::int_<64>, mpl_::int_<96>, mpl_::int_<128> > >::Apply<Functor, Parameter,
boost::mpl::vector4<mpl_::int_<32>, mpl_::int_<64>, mpl_::int_<96>,
mpl_::int_<128> >, false>::execute (params=..., kmerSize=<optimized out>) at
/usr/include/gatb/tools/math/Integer.hpp:463
#9
gatb::core::tools::math::IntegerTemplate<boost::mpl::vector4<mpl_::int_<32>,
mpl_::int_<64>, mpl_::int_<96>, mpl_::int_<128> > >::apply<Functor, Parameter>
(params=..., kmerSize=<optimized out>) at
/usr/include/gatb/tools/math/Integer.hpp:84
#10 SimkaPotara::execute (this=<optimized out>) at
/build/simka-C4DX5D/simka-1.5.2/src/SimkaPotara.cpp:140
#11 0x00000076c6428020 in gatb::core::tools::misc::impl::Tool::run
(this=0x7fd31955d8, input=<optimized out>) at
./gatb-core/src/gatb/tools/misc/impl/Tool.cpp:158
#12 0x00000076c64277c8 in gatb::core::tools::misc::impl::Tool::run
(this=0x7fd31955d8, argc=7, argv=0x7fd3195848) at
./gatb-core/src/gatb/tools/misc/impl/Tool.cpp:112
#13 0x000000555bad97bc in main (argc=7, argv=0x7fd3195848) at
/usr/include/c++/10/ext/new_allocator.h:79
cd /home/media_rw/source/libgatbcore3
cp orig try3 -a
dpkg-buildpackage -uc -j2
adb pull
/storage/emulated/0/debian-11-bullseye-arm64-chroot/chroot/home/media_rw/source/libgatbcore3/try3/gatb-core-1.4.2+dfsg/debian/patches/use-int-as-return-of-fgetc.patch
