[Debian-med-packaging] Bug#954273: simka: arm64 autopkgtest time out

Wed Nov 4 16:47:09 GMT 2020

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 at entry=0x55839fc860, name="/tmp/autopkgtest.iSjXKJ/autopkgtest_tmp/simka_temp_output/simka_output_temp//input/A", deleteIfExists=deleteIfExists at 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 at 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

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# Unstable chroot 2020-11-03 running on Android/LineageOS kernel

root at 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 at 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 at 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 "s.doust at student.liverpool.ac.uk"
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 at 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 at 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 $1 = -1
(gdb) 
Run till exit from #0  0x000000769ff22c2c in gatb::core::system::impl::CommonFile::gets(char*, int) () from /lib/aarch64-linux-gnu/libgatbcore.so.3
^C
Program received signal SIGINT, Interrupt.
0x000000769f3254c8 in IO_validate_vtable (vtable=0x769f420070 <_IO_file_jumps>) at libioP.h:944
944     libioP.h: Datei oder Verzeichnis nicht gefunden.
(gdb) detach
Detaching from program: /usr/bin/simka, process 8541
[Inferior 1 (process 8541) detached]
(gdb) q
media_rw at localhost:~$ gdb -q --pid $(pidof simka)
Attaching to process 8541
...

media_rw at 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 at 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 at entry=0x55839fc860, name="/tmp/autopkgtest.iSjXKJ/autopkgtest_tmp/simka_temp_output/simka_output_temp//input/A", deleteIfExists=deleteIfExists at 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 at 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