Bug#1006732: marked as done (ngs-sdk: autopkgtest failure: fatal error: atomic32.h: No such file or directory)

[Debian Bug Tracking System]

Your message dated Tue, 03 May 2022 19:49:12 +0000
with message-id <e1nlywg-000ipp...@fasolo.debian.org>
and subject line Bug#1006732: fixed in ngs-sdk 2.11.2-4
has caused the Debian Bug report #1006732,
regarding ngs-sdk: autopkgtest failure: fatal error: atomic32.h: No such file 
or directory
to be marked as done.

This means that you claim that the problem has been dealt with.
If this is not the case it is now your responsibility to reopen the
Bug report if necessary, and/or fix the problem forthwith.

(NB: If you are a system administrator and have no idea what this
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-- 
1006732: https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=1006732
Debian Bug Tracking System
Contact ow...@bugs.debian.org with problems

--- Begin Message ---

Source: ngs-sdk
Version: 2.11.2-3
X-Debbugs-CC: debian...@lists.debian.org
Severity: serious
User: debian...@lists.debian.org
Usertags: fails-always

Dear maintainer(s),



I copied some of the output at the bottom of this report.

More information about this bug and the reason for filing it can be found on
https://wiki.debian.org/ContinuousIntegration/RegressionEmailInformation

Paul

[1] https://qa.debian.org/excuses.php?package=ngs-sdk

https://ci.debian.net/data/autopkgtest/testing/arm64/n/ngs-sdk/19355330/log.gz

run-unit-test: running configure
Configuring NGS-SDK package
checking system type... Linux
checking OS distributor... checking machine architecture... aarch64
checking for supported architecture... aarch64 (64
 bits) is supported
checking for supported OS... Linux (linux) is supported
checking for supported tool chain... gcc tool chain is supported
checking for gcc... gcc (Debian 11.2.0-16) 11.2.0
checking for g++... yes
checking for Python 3... /usr/bin/python3
checking whether gcc accepts -Wno-array-bounds... yes
checking whether g++ accepts -static-libstdc++... no

configure: creating 'ld.linux.exe_cmd.sh'
configure: creating 'Makefile.config.linux.arm64'
configure: creating 'Makefile.config'
configure: creating 'reconfigure'
build type: release
build prefix: /home/debci/ncbi-outdir/ngs-sdk
build output path: /home/debci/ncbi-outdir/ngs-sdk/linux/gcc/arm64/rel
includedir: /usr/local/ngs/ngs-sdk/include
bindir: /usr/local/ngs/ngs-sdk/bin
libdir: /usr/local/ngs/ngs-sdk/lib
sharedir: /usr/local/ngs/ngs-sdk/share
CC = gcc -c
CPP = g++
configured with: ""
run-unit-test: making test

mkdir -p /home/debci/ncbi-outdir/ngs-sdk/linux/gcc/arm64/rel/ilib

mkdir -p /home/debci/ncbi-outdir/ngs-sdk/linux/gcc/arm64/rel/obj/dispatch

mkdir -p /home/debci/ncbi-outdir/ngs-sdk/linux/gcc/arm64/rel/lib
mkdir -p /home/debci/ncbi-outdir/ngs-sdk/linux/gcc/arm64/rel/obj/adapter

                 from ReadCollectionItf.cpp:27:

   35 | #include <atomic32.h>
      |          ^~~~~~~~~~~~
compilation terminated.

autopkgtest [11:23:34]: test run-unit-test

You recently added an autopkgtest to your package ngs-sdk, great. However, it fails on all but amd64. Currently this failure is blocking the migration to testing [1]. Can you please investigate the situation and fix it? make[1]: Entering directory '/tmp/autopkgtest-lxc.5m6nldbq/downtmp/build.gg3/src/ngs-sdk/language' make[2]: Entering directory '/tmp/autopkgtest-lxc.5m6nldbq/downtmp/build.gg3/src/ngs-sdk/language/c++' mkdir -p /home/debci/ncbi-outdir/ngs-sdk/linux/gcc/arm64/rel/obj/language/c++ g++ -c -std=c++11 -o /home/debci/ncbi-outdir/ngs-sdk/linux/gcc/arm64/rel/obj/language/c++/ReadCollection.pic.o ReadCollection.cpp -fPIC -DNDEBUG -O3 -I. -I/tmp/autopkgtest-lxc.5m6nldbq/downtmp/build.gg3/src/ngs-sdk/language/c++ -I/tmp/autopkgtest-lxc.5m6nldbq/downtmp/build.gg3/src/ngs-sdk -I/tmp/autopkgtest-lxc.5m6nldbq/downtmp/build.gg3/src/ngs-sdk/ngs/unix/generic -MD g++ -c -std=c++11 -o /home/debci/ncbi-outdir/ngs-sdk/linux/gcc/arm64/rel/obj/language/c++/ReferenceSequence.pic.o ReferenceSequence.cpp -fPIC -DNDEBUG -O3 -I. -I/tmp/autopkgtest-lxc.5m6nldbq/downtmp/build.gg3/src/ngs-sdk/language/c++ -I/tmp/autopkgtest-lxc.5m6nldbq/downtmp/build.gg3/src/ngs-sdk -I/tmp/autopkgtest-lxc.5m6nldbq/downtmp/build.gg3/src/ngs-sdk/ngs/unix/generic -MD g++ -c -std=c++11 -o /home/debci/ncbi-outdir/ngs-sdk/linux/gcc/arm64/rel/obj/language/c++/ReferenceIterator.pic.o ReferenceIterator.cpp -fPIC -DNDEBUG -O3 -I. -I/tmp/autopkgtest-lxc.5m6nldbq/downtmp/build.gg3/src/ngs-sdk/language/c++ -I/tmp/autopkgtest-lxc.5m6nldbq/downtmp/build.gg3/src/ngs-sdk -I/tmp/autopkgtest-lxc.5m6nldbq/downtmp/build.gg3/src/ngs-sdk/ngs/unix/generic -MD g++ -c -std=c++11 -o /home/debci/ncbi-outdir/ngs-sdk/linux/gcc/arm64/rel/obj/language/c++/Reference.pic.o Reference.cpp -fPIC -DNDEBUG -O3 -I. -I/tmp/autopkgtest-lxc.5m6nldbq/downtmp/build.gg3/src/ngs-sdk/language/c++ -I/tmp/autopkgtest-lxc.5m6nldbq/downtmp/build.gg3/src/ngs-sdk -I/tmp/autopkgtest-lxc.5m6nldbq/downtmp/build.gg3/src/ngs-sdk/ngs/unix/generic -MD g++ -c -std=c++11 -o /home/debci/ncbi-outdir/ngs-sdk/linux/gcc/arm64/rel/obj/language/c++/PileupIterator.pic.o PileupIterator.cpp -fPIC -DNDEBUG -O3 -I. -I/tmp/autopkgtest-lxc.5m6nldbq/downtmp/build.gg3/src/ngs-sdk/language/c++ -I/tmp/autopkgtest-lxc.5m6nldbq/downtmp/build.gg3/src/ngs-sdk -I/tmp/autopkgtest-lxc.5m6nldbq/downtmp/build.gg3/src/ngs-sdk/ngs/unix/generic -MD g++ -c -std=c++11 -o /home/debci/ncbi-outdir/ngs-sdk/linux/gcc/arm64/rel/obj/language/c++/Pileup.pic.o Pileup.cpp -fPIC -DNDEBUG -O3 -I. -I/tmp/autopkgtest-lxc.5m6nldbq/downtmp/build.gg3/src/ngs-sdk/language/c++ -I/tmp/autopkgtest-lxc.5m6nldbq/downtmp/build.gg3/src/ngs-sdk -I/tmp/autopkgtest-lxc.5m6nldbq/downtmp/build.gg3/src/ngs-sdk/ngs/unix/generic -MD g++ -c -std=c++11 -o /home/debci/ncbi-outdir/ngs-sdk/linux/gcc/arm64/rel/obj/language/c++/PileupEventIterator.pic.o PileupEventIterator.cpp -fPIC -DNDEBUG -O3 -I. -I/tmp/autopkgtest-lxc.5m6nldbq/downtmp/build.gg3/src/ngs-sdk/language/c++ -I/tmp/autopkgtest-lxc.5m6nldbq/downtmp/build.gg3/src/ngs-sdk -I/tmp/autopkgtest-lxc.5m6nldbq/downtmp/build.gg3/src/ngs-sdk/ngs/unix/generic -MD g++ -c -std=c++11 -o /home/debci/ncbi-outdir/ngs-sdk/linux/gcc/arm64/rel/obj/language/c++/PileupEvent.pic.o PileupEvent.cpp -fPIC -DNDEBUG -O3 -I. -I/tmp/autopkgtest-lxc.5m6nldbq/downtmp/build.gg3/src/ngs-sdk/language/c++ -I/tmp/autopkgtest-lxc.5m6nldbq/downtmp/build.gg3/src/ngs-sdk -I/tmp/autopkgtest-lxc.5m6nldbq/downtmp/build.gg3/src/ngs-sdk/ngs/unix/generic -MD g++ -c -std=c++11 -o /home/debci/ncbi-outdir/ngs-sdk/linux/gcc/arm64/rel/obj/language/c++/AlignmentIterator.pic.o AlignmentIterator.cpp -fPIC -DNDEBUG -O3 -I. -I/tmp/autopkgtest-lxc.5m6nldbq/downtmp/build.gg3/src/ngs-sdk/language/c++ -I/tmp/autopkgtest-lxc.5m6nldbq/downtmp/build.gg3/src/ngs-sdk -I/tmp/autopkgtest-lxc.5m6nldbq/downtmp/build.gg3/src/ngs-sdk/ngs/unix/generic -MD g++ -c -std=c++11 -o /home/debci/ncbi-outdir/ngs-sdk/linux/gcc/arm64/rel/obj/language/c++/Alignment.pic.o Alignment.cpp -fPIC -DNDEBUG -O3 -I. -I/tmp/autopkgtest-lxc.5m6nldbq/downtmp/build.gg3/src/ngs-sdk/language/c++ -I/tmp/autopkgtest-lxc.5m6nldbq/downtmp/build.gg3/src/ngs-sdk -I/tmp/autopkgtest-lxc.5m6nldbq/downtmp/build.gg3/src/ngs-sdk/ngs/unix/generic -MD g++ -c -std=c++11 -o /home/debci/ncbi-outdir/ngs-sdk/linux/gcc/arm64/rel/obj/language/c++/ReadGroupIterator.pic.o ReadGroupIterator.cpp -fPIC -DNDEBUG -O3 -I. -I/tmp/autopkgtest-lxc.5m6nldbq/downtmp/build.gg3/src/ngs-sdk/language/c++ -I/tmp/autopkgtest-lxc.5m6nldbq/downtmp/build.gg3/src/ngs-sdk -I/tmp/autopkgtest-lxc.5m6nldbq/downtmp/build.gg3/src/ngs-sdk/ngs/unix/generic -MD g++ -c -std=c++11 -o /home/debci/ncbi-outdir/ngs-sdk/linux/gcc/arm64/rel/obj/language/c++/ReadGroup.pic.o ReadGroup.cpp -fPIC -DNDEBUG -O3 -I. -I/tmp/autopkgtest-lxc.5m6nldbq/downtmp/build.gg3/src/ngs-sdk/language/c++ -I/tmp/autopkgtest-lxc.5m6nldbq/downtmp/build.gg3/src/ngs-sdk -I/tmp/autopkgtest-lxc.5m6nldbq/downtmp/build.gg3/src/ngs-sdk/ngs/unix/generic -MD g++ -c -std=c++11 -o /home/debci/ncbi-outdir/ngs-sdk/linux/gcc/arm64/rel/obj/language/c++/ReadIterator.pic.o ReadIterator.cpp -fPIC -DNDEBUG -O3 -I. -I/tmp/autopkgtest-lxc.5m6nldbq/downtmp/build.gg3/src/ngs-sdk/language/c++ -I/tmp/autopkgtest-lxc.5m6nldbq/downtmp/build.gg3/src/ngs-sdk -I/tmp/autopkgtest-lxc.5m6nldbq/downtmp/build.gg3/src/ngs-sdk/ngs/unix/generic -MD g++ -c -std=c++11 -o /home/debci/ncbi-outdir/ngs-sdk/linux/gcc/arm64/rel/obj/language/c++/Read.pic.o Read.cpp -fPIC -DNDEBUG -O3 -I. -I/tmp/autopkgtest-lxc.5m6nldbq/downtmp/build.gg3/src/ngs-sdk/language/c++ -I/tmp/autopkgtest-lxc.5m6nldbq/downtmp/build.gg3/src/ngs-sdk -I/tmp/autopkgtest-lxc.5m6nldbq/downtmp/build.gg3/src/ngs-sdk/ngs/unix/generic -MD g++ -c -std=c++11 -o /home/debci/ncbi-outdir/ngs-sdk/linux/gcc/arm64/rel/obj/language/c++/FragmentIterator.pic.o FragmentIterator.cpp -fPIC -DNDEBUG -O3 -I. -I/tmp/autopkgtest-lxc.5m6nldbq/downtmp/build.gg3/src/ngs-sdk/language/c++ -I/tmp/autopkgtest-lxc.5m6nldbq/downtmp/build.gg3/src/ngs-sdk -I/tmp/autopkgtest-lxc.5m6nldbq/downtmp/build.gg3/src/ngs-sdk/ngs/unix/generic -MD g++ -c -std=c++11 -o /home/debci/ncbi-outdir/ngs-sdk/linux/gcc/arm64/rel/obj/language/c++/Fragment.pic.o Fragment.cpp -fPIC -DNDEBUG -O3 -I. -I/tmp/autopkgtest-lxc.5m6nldbq/downtmp/build.gg3/src/ngs-sdk/language/c++ -I/tmp/autopkgtest-lxc.5m6nldbq/downtmp/build.gg3/src/ngs-sdk -I/tmp/autopkgtest-lxc.5m6nldbq/downtmp/build.gg3/src/ngs-sdk/ngs/unix/generic -MD g++ -c -std=c++11 -o /home/debci/ncbi-outdir/ngs-sdk/linux/gcc/arm64/rel/obj/language/c++/Statistics.pic.o Statistics.cpp -fPIC -DNDEBUG -O3 -I. -I/tmp/autopkgtest-lxc.5m6nldbq/downtmp/build.gg3/src/ngs-sdk/language/c++ -I/tmp/autopkgtest-lxc.5m6nldbq/downtmp/build.gg3/src/ngs-sdk -I/tmp/autopkgtest-lxc.5m6nldbq/downtmp/build.gg3/src/ngs-sdk/ngs/unix/generic -MD g++ -c -std=c++11 -o /home/debci/ncbi-outdir/ngs-sdk/linux/gcc/arm64/rel/obj/language/c++/StringRef.pic.o StringRef.cpp -fPIC -DNDEBUG -O3 -I. -I/tmp/autopkgtest-lxc.5m6nldbq/downtmp/build.gg3/src/ngs-sdk/language/c++ -I/tmp/autopkgtest-lxc.5m6nldbq/downtmp/build.gg3/src/ngs-sdk -I/tmp/autopkgtest-lxc.5m6nldbq/downtmp/build.gg3/src/ngs-sdk/ngs/unix/generic -MD ar rc /home/debci/ncbi-outdir/ngs-sdk/linux/gcc/arm64/rel/ilib/libngs-bind-c++.a /home/debci/ncbi-outdir/ngs-sdk/linux/gcc/arm64/rel/obj/language/c++/ReadCollection.pic.o /home/debci/ncbi-outdir/ngs-sdk/linux/gcc/arm64/rel/obj/language/c++/ReferenceSequence.pic.o /home/debci/ncbi-outdir/ngs-sdk/linux/gcc/arm64/rel/obj/language/c++/ReferenceIterator.pic.o /home/debci/ncbi-outdir/ngs-sdk/linux/gcc/arm64/rel/obj/language/c++/Reference.pic.o /home/debci/ncbi-outdir/ngs-sdk/linux/gcc/arm64/rel/obj/language/c++/PileupIterator.pic.o /home/debci/ncbi-outdir/ngs-sdk/linux/gcc/arm64/rel/obj/language/c++/Pileup.pic.o /home/debci/ncbi-outdir/ngs-sdk/linux/gcc/arm64/rel/obj/language/c++/PileupEventIterator.pic.o /home/debci/ncbi-outdir/ngs-sdk/linux/gcc/arm64/rel/obj/language/c++/PileupEvent.pic.o /home/debci/ncbi-outdir/ngs-sdk/linux/gcc/arm64/rel/obj/language/c++/AlignmentIterator.pic.o /home/debci/ncbi-outdir/ngs-sdk/linux/gcc/arm64/rel/obj/language/c++/Alignment.pic.o /home/debci/ncbi-outdir/ngs-sdk/linux/gcc/arm64/rel/obj/language/c++/ReadGroupIterator.pic.o /home/debci/ncbi-outdir/ngs-sdk/linux/gcc/arm64/rel/obj/language/c++/ReadGroup.pic.o /home/debci/ncbi-outdir/ngs-sdk/linux/gcc/arm64/rel/obj/language/c++/ReadIterator.pic.o /home/debci/ncbi-outdir/ngs-sdk/linux/gcc/arm64/rel/obj/language/c++/Read.pic.o /home/debci/ncbi-outdir/ngs-sdk/linux/gcc/arm64/rel/obj/language/c++/FragmentIterator.pic.o /home/debci/ncbi-outdir/ngs-sdk/linux/gcc/arm64/rel/obj/language/c++/Fragment.pic.o /home/debci/ncbi-outdir/ngs-sdk/linux/gcc/arm64/rel/obj/language/c++/Statistics.pic.o /home/debci/ncbi-outdir/ngs-sdk/linux/gcc/arm64/rel/obj/language/c++/StringRef.pic.o make[2]: Leaving directory '/tmp/autopkgtest-lxc.5m6nldbq/downtmp/build.gg3/src/ngs-sdk/language/c++' make[2]: Entering directory '/tmp/autopkgtest-lxc.5m6nldbq/downtmp/build.gg3/src/ngs-sdk/language/java' mkdir -p /home/debci/ncbi-outdir/ngs-sdk/linux/gcc/arm64/rel/obj/language/java g++ -c -std=c++11 -o /home/debci/ncbi-outdir/ngs-sdk/linux/gcc/arm64/rel/obj/language/java/jni_ReadCollectionItf.pic.o jni_ReadCollectionItf.cpp -fPIC -DNDEBUG -O3 -I. -I/tmp/autopkgtest-lxc.5m6nldbq/downtmp/build.gg3/src/ngs-sdk/language/java -I/tmp/autopkgtest-lxc.5m6nldbq/downtmp/build.gg3/src/ngs-sdk -I/tmp/autopkgtest-lxc.5m6nldbq/downtmp/build.gg3/src/ngs-sdk/ngs/unix/generic -MD g++ -c -std=c++11 -o /home/debci/ncbi-outdir/ngs-sdk/linux/gcc/arm64/rel/obj/language/java/jni_ReferenceIteratorItf.pic.o jni_ReferenceIteratorItf.cpp -fPIC -DNDEBUG -O3 -I. -I/tmp/autopkgtest-lxc.5m6nldbq/downtmp/build.gg3/src/ngs-sdk/language/java -I/tmp/autopkgtest-lxc.5m6nldbq/downtmp/build.gg3/src/ngs-sdk -I/tmp/autopkgtest-lxc.5m6nldbq/downtmp/build.gg3/src/ngs-sdk/ngs/unix/generic -MD g++ -c -std=c++11 -o /home/debci/ncbi-outdir/ngs-sdk/linux/gcc/arm64/rel/obj/language/java/jni_ReferenceItf.pic.o jni_ReferenceItf.cpp -fPIC -DNDEBUG -O3 -I. -I/tmp/autopkgtest-lxc.5m6nldbq/downtmp/build.gg3/src/ngs-sdk/language/java -I/tmp/autopkgtest-lxc.5m6nldbq/downtmp/build.gg3/src/ngs-sdk -I/tmp/autopkgtest-lxc.5m6nldbq/downtmp/build.gg3/src/ngs-sdk/ngs/unix/generic -MD g++ -c -std=c++11 -o /home/debci/ncbi-outdir/ngs-sdk/linux/gcc/arm64/rel/obj/language/java/jni_ReferenceSequenceItf.pic.o jni_ReferenceSequenceItf.cpp -fPIC -DNDEBUG -O3 -I. -I/tmp/autopkgtest-lxc.5m6nldbq/downtmp/build.gg3/src/ngs-sdk/language/java -I/tmp/autopkgtest-lxc.5m6nldbq/downtmp/build.gg3/src/ngs-sdk -I/tmp/autopkgtest-lxc.5m6nldbq/downtmp/build.gg3/src/ngs-sdk/ngs/unix/generic -MD g++ -c -std=c++11 -o /home/debci/ncbi-outdir/ngs-sdk/linux/gcc/arm64/rel/obj/language/java/jni_PileupIteratorItf.pic.o jni_PileupIteratorItf.cpp -fPIC -DNDEBUG -O3 -I. -I/tmp/autopkgtest-lxc.5m6nldbq/downtmp/build.gg3/src/ngs-sdk/language/java -I/tmp/autopkgtest-lxc.5m6nldbq/downtmp/build.gg3/src/ngs-sdk -I/tmp/autopkgtest-lxc.5m6nldbq/downtmp/build.gg3/src/ngs-sdk/ngs/unix/generic -MD g++ -c -std=c++11 -o /home/debci/ncbi-outdir/ngs-sdk/linux/gcc/arm64/rel/obj/language/java/jni_PileupItf.pic.o jni_PileupItf.cpp -fPIC -DNDEBUG -O3 -I. -I/tmp/autopkgtest-lxc.5m6nldbq/downtmp/build.gg3/src/ngs-sdk/language/java -I/tmp/autopkgtest-lxc.5m6nldbq/downtmp/build.gg3/src/ngs-sdk -I/tmp/autopkgtest-lxc.5m6nldbq/downtmp/build.gg3/src/ngs-sdk/ngs/unix/generic -MD g++ -c -std=c++11 -o /home/debci/ncbi-outdir/ngs-sdk/linux/gcc/arm64/rel/obj/language/java/jni_PileupEventIteratorItf.pic.o jni_PileupEventIteratorItf.cpp -fPIC -DNDEBUG -O3 -I. -I/tmp/autopkgtest-lxc.5m6nldbq/downtmp/build.gg3/src/ngs-sdk/language/java -I/tmp/autopkgtest-lxc.5m6nldbq/downtmp/build.gg3/src/ngs-sdk -I/tmp/autopkgtest-lxc.5m6nldbq/downtmp/build.gg3/src/ngs-sdk/ngs/unix/generic -MD g++ -c -std=c++11 -o /home/debci/ncbi-outdir/ngs-sdk/linux/gcc/arm64/rel/obj/language/java/jni_PileupEventItf.pic.o jni_PileupEventItf.cpp -fPIC -DNDEBUG -O3 -I. -I/tmp/autopkgtest-lxc.5m6nldbq/downtmp/build.gg3/src/ngs-sdk/language/java -I/tmp/autopkgtest-lxc.5m6nldbq/downtmp/build.gg3/src/ngs-sdk -I/tmp/autopkgtest-lxc.5m6nldbq/downtmp/build.gg3/src/ngs-sdk/ngs/unix/generic -MD g++ -c -std=c++11 -o /home/debci/ncbi-outdir/ngs-sdk/linux/gcc/arm64/rel/obj/language/java/jni_AlignmentIteratorItf.pic.o jni_AlignmentIteratorItf.cpp -fPIC -DNDEBUG -O3 -I. -I/tmp/autopkgtest-lxc.5m6nldbq/downtmp/build.gg3/src/ngs-sdk/language/java -I/tmp/autopkgtest-lxc.5m6nldbq/downtmp/build.gg3/src/ngs-sdk -I/tmp/autopkgtest-lxc.5m6nldbq/downtmp/build.gg3/src/ngs-sdk/ngs/unix/generic -MD g++ -c -std=c++11 -o /home/debci/ncbi-outdir/ngs-sdk/linux/gcc/arm64/rel/obj/language/java/jni_AlignmentItf.pic.o jni_AlignmentItf.cpp -fPIC -DNDEBUG -O3 -I. -I/tmp/autopkgtest-lxc.5m6nldbq/downtmp/build.gg3/src/ngs-sdk/language/java -I/tmp/autopkgtest-lxc.5m6nldbq/downtmp/build.gg3/src/ngs-sdk -I/tmp/autopkgtest-lxc.5m6nldbq/downtmp/build.gg3/src/ngs-sdk/ngs/unix/generic -MD g++ -c -std=c++11 -o /home/debci/ncbi-outdir/ngs-sdk/linux/gcc/arm64/rel/obj/language/java/jni_ReadGroupIteratorItf.pic.o jni_ReadGroupIteratorItf.cpp -fPIC -DNDEBUG -O3 -I. -I/tmp/autopkgtest-lxc.5m6nldbq/downtmp/build.gg3/src/ngs-sdk/language/java -I/tmp/autopkgtest-lxc.5m6nldbq/downtmp/build.gg3/src/ngs-sdk -I/tmp/autopkgtest-lxc.5m6nldbq/downtmp/build.gg3/src/ngs-sdk/ngs/unix/generic -MD g++ -c -std=c++11 -o /home/debci/ncbi-outdir/ngs-sdk/linux/gcc/arm64/rel/obj/language/java/jni_ReadGroupItf.pic.o jni_ReadGroupItf.cpp -fPIC -DNDEBUG -O3 -I. -I/tmp/autopkgtest-lxc.5m6nldbq/downtmp/build.gg3/src/ngs-sdk/language/java -I/tmp/autopkgtest-lxc.5m6nldbq/downtmp/build.gg3/src/ngs-sdk -I/tmp/autopkgtest-lxc.5m6nldbq/downtmp/build.gg3/src/ngs-sdk/ngs/unix/generic -MD g++ -c -std=c++11 -o /home/debci/ncbi-outdir/ngs-sdk/linux/gcc/arm64/rel/obj/language/java/jni_ReadIteratorItf.pic.o jni_ReadIteratorItf.cpp -fPIC -DNDEBUG -O3 -I. -I/tmp/autopkgtest-lxc.5m6nldbq/downtmp/build.gg3/src/ngs-sdk/language/java -I/tmp/autopkgtest-lxc.5m6nldbq/downtmp/build.gg3/src/ngs-sdk -I/tmp/autopkgtest-lxc.5m6nldbq/downtmp/build.gg3/src/ngs-sdk/ngs/unix/generic -MD g++ -c -std=c++11 -o /home/debci/ncbi-outdir/ngs-sdk/linux/gcc/arm64/rel/obj/language/java/jni_ReadItf.pic.o jni_ReadItf.cpp -fPIC -DNDEBUG -O3 -I. -I/tmp/autopkgtest-lxc.5m6nldbq/downtmp/build.gg3/src/ngs-sdk/language/java -I/tmp/autopkgtest-lxc.5m6nldbq/downtmp/build.gg3/src/ngs-sdk -I/tmp/autopkgtest-lxc.5m6nldbq/downtmp/build.gg3/src/ngs-sdk/ngs/unix/generic -MD g++ -c -std=c++11 -o /home/debci/ncbi-outdir/ngs-sdk/linux/gcc/arm64/rel/obj/language/java/jni_FragmentItf.pic.o jni_FragmentItf.cpp -fPIC -DNDEBUG -O3 -I. -I/tmp/autopkgtest-lxc.5m6nldbq/downtmp/build.gg3/src/ngs-sdk/language/java -I/tmp/autopkgtest-lxc.5m6nldbq/downtmp/build.gg3/src/ngs-sdk -I/tmp/autopkgtest-lxc.5m6nldbq/downtmp/build.gg3/src/ngs-sdk/ngs/unix/generic -MD g++ -c -std=c++11 -o /home/debci/ncbi-outdir/ngs-sdk/linux/gcc/arm64/rel/obj/language/java/jni_StatisticsItf.pic.o jni_StatisticsItf.cpp -fPIC -DNDEBUG -O3 -I. -I/tmp/autopkgtest-lxc.5m6nldbq/downtmp/build.gg3/src/ngs-sdk/language/java -I/tmp/autopkgtest-lxc.5m6nldbq/downtmp/build.gg3/src/ngs-sdk -I/tmp/autopkgtest-lxc.5m6nldbq/downtmp/build.gg3/src/ngs-sdk/ngs/unix/generic -MD g++ -c -std=c++11 -o /home/debci/ncbi-outdir/ngs-sdk/linux/gcc/arm64/rel/obj/language/java/jni_Package.pic.o jni_Package.cpp -fPIC -DNDEBUG -O3 -I. -I/tmp/autopkgtest-lxc.5m6nldbq/downtmp/build.gg3/src/ngs-sdk/language/java -I/tmp/autopkgtest-lxc.5m6nldbq/downtmp/build.gg3/src/ngs-sdk -I/tmp/autopkgtest-lxc.5m6nldbq/downtmp/build.gg3/src/ngs-sdk/ngs/unix/generic -MD g++ -c -std=c++11 -o /home/debci/ncbi-outdir/ngs-sdk/linux/gcc/arm64/rel/obj/language/java/jni_String.pic.o jni_String.cpp -fPIC -DNDEBUG -O3 -I. -I/tmp/autopkgtest-lxc.5m6nldbq/downtmp/build.gg3/src/ngs-sdk/language/java -I/tmp/autopkgtest-lxc.5m6nldbq/downtmp/build.gg3/src/ngs-sdk -I/tmp/autopkgtest-lxc.5m6nldbq/downtmp/build.gg3/src/ngs-sdk/ngs/unix/generic -MD g++ -c -std=c++11 -o /home/debci/ncbi-outdir/ngs-sdk/linux/gcc/arm64/rel/obj/language/java/jni_Refcount.pic.o jni_Refcount.cpp -fPIC -DNDEBUG -O3 -I. -I/tmp/autopkgtest-lxc.5m6nldbq/downtmp/build.gg3/src/ngs-sdk/language/java -I/tmp/autopkgtest-lxc.5m6nldbq/downtmp/build.gg3/src/ngs-sdk -I/tmp/autopkgtest-lxc.5m6nldbq/downtmp/build.gg3/src/ngs-sdk/ngs/unix/generic -MD g++ -c -std=c++11 -o /home/debci/ncbi-outdir/ngs-sdk/linux/gcc/arm64/rel/obj/language/java/jni_ErrorMsg.pic.o jni_ErrorMsg.cpp -fPIC -DNDEBUG -O3 -I. -I/tmp/autopkgtest-lxc.5m6nldbq/downtmp/build.gg3/src/ngs-sdk/language/java -I/tmp/autopkgtest-lxc.5m6nldbq/downtmp/build.gg3/src/ngs-sdk -I/tmp/autopkgtest-lxc.5m6nldbq/downtmp/build.gg3/src/ngs-sdk/ngs/unix/generic -MD ar rc /home/debci/ncbi-outdir/ngs-sdk/linux/gcc/arm64/rel/ilib/libngs-bind-java.a /home/debci/ncbi-outdir/ngs-sdk/linux/gcc/arm64/rel/obj/language/java/jni_ReadCollectionItf.pic.o /home/debci/ncbi-outdir/ngs-sdk/linux/gcc/arm64/rel/obj/language/java/jni_ReferenceIteratorItf.pic.o /home/debci/ncbi-outdir/ngs-sdk/linux/gcc/arm64/rel/obj/language/java/jni_ReferenceItf.pic.o /home/debci/ncbi-outdir/ngs-sdk/linux/gcc/arm64/rel/obj/language/java/jni_ReferenceSequenceItf.pic.o /home/debci/ncbi-outdir/ngs-sdk/linux/gcc/arm64/rel/obj/language/java/jni_PileupIteratorItf.pic.o /home/debci/ncbi-outdir/ngs-sdk/linux/gcc/arm64/rel/obj/language/java/jni_PileupItf.pic.o /home/debci/ncbi-outdir/ngs-sdk/linux/gcc/arm64/rel/obj/language/java/jni_PileupEventIteratorItf.pic.o /home/debci/ncbi-outdir/ngs-sdk/linux/gcc/arm64/rel/obj/language/java/jni_PileupEventItf.pic.o /home/debci/ncbi-outdir/ngs-sdk/linux/gcc/arm64/rel/obj/language/java/jni_AlignmentIteratorItf.pic.o /home/debci/ncbi-outdir/ngs-sdk/linux/gcc/arm64/rel/obj/language/java/jni_AlignmentItf.pic.o /home/debci/ncbi-outdir/ngs-sdk/linux/gcc/arm64/rel/obj/language/java/jni_ReadGroupIteratorItf.pic.o /home/debci/ncbi-outdir/ngs-sdk/linux/gcc/arm64/rel/obj/language/java/jni_ReadGroupItf.pic.o /home/debci/ncbi-outdir/ngs-sdk/linux/gcc/arm64/rel/obj/language/java/jni_ReadIteratorItf.pic.o /home/debci/ncbi-outdir/ngs-sdk/linux/gcc/arm64/rel/obj/language/java/jni_ReadItf.pic.o /home/debci/ncbi-outdir/ngs-sdk/linux/gcc/arm64/rel/obj/language/java/jni_FragmentItf.pic.o /home/debci/ncbi-outdir/ngs-sdk/linux/gcc/arm64/rel/obj/language/java/jni_StatisticsItf.pic.o /home/debci/ncbi-outdir/ngs-sdk/linux/gcc/arm64/rel/obj/language/java/jni_Package.pic.o /home/debci/ncbi-outdir/ngs-sdk/linux/gcc/arm64/rel/obj/language/java/jni_String.pic.o /home/debci/ncbi-outdir/ngs-sdk/linux/gcc/arm64/rel/obj/language/java/jni_Refcount.pic.o /home/debci/ncbi-outdir/ngs-sdk/linux/gcc/arm64/rel/obj/language/java/jni_ErrorMsg.pic.o make[2]: Leaving directory '/tmp/autopkgtest-lxc.5m6nldbq/downtmp/build.gg3/src/ngs-sdk/language/java' make[2]: Entering directory '/tmp/autopkgtest-lxc.5m6nldbq/downtmp/build.gg3/src/ngs-sdk/language/python' mkdir -p /home/debci/ncbi-outdir/ngs-sdk/linux/gcc/arm64/rel/obj/language/python g++ -c -std=c++11 -o /home/debci/ncbi-outdir/ngs-sdk/linux/gcc/arm64/rel/obj/language/python/py_AlignmentItf.pic.o py_AlignmentItf.cpp -fPIC -DNDEBUG -O3 -I. -I/tmp/autopkgtest-lxc.5m6nldbq/downtmp/build.gg3/src/ngs-sdk/language/python -I/tmp/autopkgtest-lxc.5m6nldbq/downtmp/build.gg3/src/ngs-sdk -I/tmp/autopkgtest-lxc.5m6nldbq/downtmp/build.gg3/src/ngs-sdk/ngs/unix/generic -MD g++ -c -std=c++11 -o /home/debci/ncbi-outdir/ngs-sdk/linux/gcc/arm64/rel/obj/language/python/py_AlignmentIteratorItf.pic.o py_AlignmentIteratorItf.cpp -fPIC -DNDEBUG -O3 -I. -I/tmp/autopkgtest-lxc.5m6nldbq/downtmp/build.gg3/src/ngs-sdk/language/python -I/tmp/autopkgtest-lxc.5m6nldbq/downtmp/build.gg3/src/ngs-sdk -I/tmp/autopkgtest-lxc.5m6nldbq/downtmp/build.gg3/src/ngs-sdk/ngs/unix/generic -MD g++ -c -std=c++11 -o /home/debci/ncbi-outdir/ngs-sdk/linux/gcc/arm64/rel/obj/language/python/py_FragmentItf.pic.o py_FragmentItf.cpp -fPIC -DNDEBUG -O3 -I. -I/tmp/autopkgtest-lxc.5m6nldbq/downtmp/build.gg3/src/ngs-sdk/language/python -I/tmp/autopkgtest-lxc.5m6nldbq/downtmp/build.gg3/src/ngs-sdk -I/tmp/autopkgtest-lxc.5m6nldbq/downtmp/build.gg3/src/ngs-sdk/ngs/unix/generic -MD g++ -c -std=c++11 -o /home/debci/ncbi-outdir/ngs-sdk/linux/gcc/arm64/rel/obj/language/python/py_FragmentIteratorItf.pic.o py_FragmentIteratorItf.cpp -fPIC -DNDEBUG -O3 -I. -I/tmp/autopkgtest-lxc.5m6nldbq/downtmp/build.gg3/src/ngs-sdk/language/python -I/tmp/autopkgtest-lxc.5m6nldbq/downtmp/build.gg3/src/ngs-sdk -I/tmp/autopkgtest-lxc.5m6nldbq/downtmp/build.gg3/src/ngs-sdk/ngs/unix/generic -MD g++ -c -std=c++11 -o /home/debci/ncbi-outdir/ngs-sdk/linux/gcc/arm64/rel/obj/language/python/py_PackageItf.pic.o py_PackageItf.cpp -fPIC -DNDEBUG -O3 -I. -I/tmp/autopkgtest-lxc.5m6nldbq/downtmp/build.gg3/src/ngs-sdk/language/python -I/tmp/autopkgtest-lxc.5m6nldbq/downtmp/build.gg3/src/ngs-sdk -I/tmp/autopkgtest-lxc.5m6nldbq/downtmp/build.gg3/src/ngs-sdk/ngs/unix/generic -MD g++ -c -std=c++11 -o /home/debci/ncbi-outdir/ngs-sdk/linux/gcc/arm64/rel/obj/language/python/py_PileupEventItf.pic.o py_PileupEventItf.cpp -fPIC -DNDEBUG -O3 -I. -I/tmp/autopkgtest-lxc.5m6nldbq/downtmp/build.gg3/src/ngs-sdk/language/python -I/tmp/autopkgtest-lxc.5m6nldbq/downtmp/build.gg3/src/ngs-sdk -I/tmp/autopkgtest-lxc.5m6nldbq/downtmp/build.gg3/src/ngs-sdk/ngs/unix/generic -MD g++ -c -std=c++11 -o /home/debci/ncbi-outdir/ngs-sdk/linux/gcc/arm64/rel/obj/language/python/py_PileupEventIteratorItf.pic.o py_PileupEventIteratorItf.cpp -fPIC -DNDEBUG -O3 -I. -I/tmp/autopkgtest-lxc.5m6nldbq/downtmp/build.gg3/src/ngs-sdk/language/python -I/tmp/autopkgtest-lxc.5m6nldbq/downtmp/build.gg3/src/ngs-sdk -I/tmp/autopkgtest-lxc.5m6nldbq/downtmp/build.gg3/src/ngs-sdk/ngs/unix/generic -MD g++ -c -std=c++11 -o /home/debci/ncbi-outdir/ngs-sdk/linux/gcc/arm64/rel/obj/language/python/py_PileupItf.pic.o py_PileupItf.cpp -fPIC -DNDEBUG -O3 -I. -I/tmp/autopkgtest-lxc.5m6nldbq/downtmp/build.gg3/src/ngs-sdk/language/python -I/tmp/autopkgtest-lxc.5m6nldbq/downtmp/build.gg3/src/ngs-sdk -I/tmp/autopkgtest-lxc.5m6nldbq/downtmp/build.gg3/src/ngs-sdk/ngs/unix/generic -MD g++ -c -std=c++11 -o /home/debci/ncbi-outdir/ngs-sdk/linux/gcc/arm64/rel/obj/language/python/py_PileupIteratorItf.pic.o py_PileupIteratorItf.cpp -fPIC -DNDEBUG -O3 -I. -I/tmp/autopkgtest-lxc.5m6nldbq/downtmp/build.gg3/src/ngs-sdk/language/python -I/tmp/autopkgtest-lxc.5m6nldbq/downtmp/build.gg3/src/ngs-sdk -I/tmp/autopkgtest-lxc.5m6nldbq/downtmp/build.gg3/src/ngs-sdk/ngs/unix/generic -MD g++ -c -std=c++11 -o /home/debci/ncbi-outdir/ngs-sdk/linux/gcc/arm64/rel/obj/language/python/py_ReadCollectionItf.pic.o py_ReadCollectionItf.cpp -fPIC -DNDEBUG -O3 -I. -I/tmp/autopkgtest-lxc.5m6nldbq/downtmp/build.gg3/src/ngs-sdk/language/python -I/tmp/autopkgtest-lxc.5m6nldbq/downtmp/build.gg3/src/ngs-sdk -I/tmp/autopkgtest-lxc.5m6nldbq/downtmp/build.gg3/src/ngs-sdk/ngs/unix/generic -MD g++ -c -std=c++11 -o /home/debci/ncbi-outdir/ngs-sdk/linux/gcc/arm64/rel/obj/language/python/py_ReadGroupItf.pic.o py_ReadGroupItf.cpp -fPIC -DNDEBUG -O3 -I. -I/tmp/autopkgtest-lxc.5m6nldbq/downtmp/build.gg3/src/ngs-sdk/language/python -I/tmp/autopkgtest-lxc.5m6nldbq/downtmp/build.gg3/src/ngs-sdk -I/tmp/autopkgtest-lxc.5m6nldbq/downtmp/build.gg3/src/ngs-sdk/ngs/unix/generic -MD g++ -c -std=c++11 -o /home/debci/ncbi-outdir/ngs-sdk/linux/gcc/arm64/rel/obj/language/python/py_ReadGroupIteratorItf.pic.o py_ReadGroupIteratorItf.cpp -fPIC -DNDEBUG -O3 -I. -I/tmp/autopkgtest-lxc.5m6nldbq/downtmp/build.gg3/src/ngs-sdk/language/python -I/tmp/autopkgtest-lxc.5m6nldbq/downtmp/build.gg3/src/ngs-sdk -I/tmp/autopkgtest-lxc.5m6nldbq/downtmp/build.gg3/src/ngs-sdk/ngs/unix/generic -MD g++ -c -std=c++11 -o /home/debci/ncbi-outdir/ngs-sdk/linux/gcc/arm64/rel/obj/language/python/py_ReadItf.pic.o py_ReadItf.cpp -fPIC -DNDEBUG -O3 -I. -I/tmp/autopkgtest-lxc.5m6nldbq/downtmp/build.gg3/src/ngs-sdk/language/python -I/tmp/autopkgtest-lxc.5m6nldbq/downtmp/build.gg3/src/ngs-sdk -I/tmp/autopkgtest-lxc.5m6nldbq/downtmp/build.gg3/src/ngs-sdk/ngs/unix/generic -MD g++ -c -std=c++11 -o /home/debci/ncbi-outdir/ngs-sdk/linux/gcc/arm64/rel/obj/language/python/py_ReadIteratorItf.pic.o py_ReadIteratorItf.cpp -fPIC -DNDEBUG -O3 -I. -I/tmp/autopkgtest-lxc.5m6nldbq/downtmp/build.gg3/src/ngs-sdk/language/python -I/tmp/autopkgtest-lxc.5m6nldbq/downtmp/build.gg3/src/ngs-sdk -I/tmp/autopkgtest-lxc.5m6nldbq/downtmp/build.gg3/src/ngs-sdk/ngs/unix/generic -MD g++ -c -std=c++11 -o /home/debci/ncbi-outdir/ngs-sdk/linux/gcc/arm64/rel/obj/language/python/py_ReferenceItf.pic.o py_ReferenceItf.cpp -fPIC -DNDEBUG -O3 -I. -I/tmp/autopkgtest-lxc.5m6nldbq/downtmp/build.gg3/src/ngs-sdk/language/python -I/tmp/autopkgtest-lxc.5m6nldbq/downtmp/build.gg3/src/ngs-sdk -I/tmp/autopkgtest-lxc.5m6nldbq/downtmp/build.gg3/src/ngs-sdk/ngs/unix/generic -MD g++ -c -std=c++11 -o /home/debci/ncbi-outdir/ngs-sdk/linux/gcc/arm64/rel/obj/language/python/py_ReferenceIteratorItf.pic.o py_ReferenceIteratorItf.cpp -fPIC -DNDEBUG -O3 -I. -I/tmp/autopkgtest-lxc.5m6nldbq/downtmp/build.gg3/src/ngs-sdk/language/python -I/tmp/autopkgtest-lxc.5m6nldbq/downtmp/build.gg3/src/ngs-sdk -I/tmp/autopkgtest-lxc.5m6nldbq/downtmp/build.gg3/src/ngs-sdk/ngs/unix/generic -MD g++ -c -std=c++11 -o /home/debci/ncbi-outdir/ngs-sdk/linux/gcc/arm64/rel/obj/language/python/py_ReferenceSequenceItf.pic.o py_ReferenceSequenceItf.cpp -fPIC -DNDEBUG -O3 -I. -I/tmp/autopkgtest-lxc.5m6nldbq/downtmp/build.gg3/src/ngs-sdk/language/python -I/tmp/autopkgtest-lxc.5m6nldbq/downtmp/build.gg3/src/ngs-sdk -I/tmp/autopkgtest-lxc.5m6nldbq/downtmp/build.gg3/src/ngs-sdk/ngs/unix/generic -MD g++ -c -std=c++11 -o /home/debci/ncbi-outdir/ngs-sdk/linux/gcc/arm64/rel/obj/language/python/py_StatisticsItf.pic.o py_StatisticsItf.cpp -fPIC -DNDEBUG -O3 -I. -I/tmp/autopkgtest-lxc.5m6nldbq/downtmp/build.gg3/src/ngs-sdk/language/python -I/tmp/autopkgtest-lxc.5m6nldbq/downtmp/build.gg3/src/ngs-sdk -I/tmp/autopkgtest-lxc.5m6nldbq/downtmp/build.gg3/src/ngs-sdk/ngs/unix/generic -MD g++ -c -std=c++11 -o /home/debci/ncbi-outdir/ngs-sdk/linux/gcc/arm64/rel/obj/language/python/py_Refcount.pic.o py_Refcount.cpp -fPIC -DNDEBUG -O3 -I. -I/tmp/autopkgtest-lxc.5m6nldbq/downtmp/build.gg3/src/ngs-sdk/language/python -I/tmp/autopkgtest-lxc.5m6nldbq/downtmp/build.gg3/src/ngs-sdk -I/tmp/autopkgtest-lxc.5m6nldbq/downtmp/build.gg3/src/ngs-sdk/ngs/unix/generic -MD g++ -c -std=c++11 -o /home/debci/ncbi-outdir/ngs-sdk/linux/gcc/arm64/rel/obj/language/python/py_StringItf.pic.o py_StringItf.cpp -fPIC -DNDEBUG -O3 -I. -I/tmp/autopkgtest-lxc.5m6nldbq/downtmp/build.gg3/src/ngs-sdk/language/python -I/tmp/autopkgtest-lxc.5m6nldbq/downtmp/build.gg3/src/ngs-sdk -I/tmp/autopkgtest-lxc.5m6nldbq/downtmp/build.gg3/src/ngs-sdk/ngs/unix/generic -MD ar rc /home/debci/ncbi-outdir/ngs-sdk/linux/gcc/arm64/rel/ilib/libngs-bind-python.a /home/debci/ncbi-outdir/ngs-sdk/linux/gcc/arm64/rel/obj/language/python/py_AlignmentItf.pic.o /home/debci/ncbi-outdir/ngs-sdk/linux/gcc/arm64/rel/obj/language/python/py_AlignmentIteratorItf.pic.o /home/debci/ncbi-outdir/ngs-sdk/linux/gcc/arm64/rel/obj/language/python/py_FragmentItf.pic.o /home/debci/ncbi-outdir/ngs-sdk/linux/gcc/arm64/rel/obj/language/python/py_FragmentIteratorItf.pic.o /home/debci/ncbi-outdir/ngs-sdk/linux/gcc/arm64/rel/obj/language/python/py_PackageItf.pic.o /home/debci/ncbi-outdir/ngs-sdk/linux/gcc/arm64/rel/obj/language/python/py_PileupEventItf.pic.o /home/debci/ncbi-outdir/ngs-sdk/linux/gcc/arm64/rel/obj/language/python/py_PileupEventIteratorItf.pic.o /home/debci/ncbi-outdir/ngs-sdk/linux/gcc/arm64/rel/obj/language/python/py_PileupItf.pic.o /home/debci/ncbi-outdir/ngs-sdk/linux/gcc/arm64/rel/obj/language/python/py_PileupIteratorItf.pic.o /home/debci/ncbi-outdir/ngs-sdk/linux/gcc/arm64/rel/obj/language/python/py_ReadCollectionItf.pic.o /home/debci/ncbi-outdir/ngs-sdk/linux/gcc/arm64/rel/obj/language/python/py_ReadGroupItf.pic.o /home/debci/ncbi-outdir/ngs-sdk/linux/gcc/arm64/rel/obj/language/python/py_ReadGroupIteratorItf.pic.o /home/debci/ncbi-outdir/ngs-sdk/linux/gcc/arm64/rel/obj/language/python/py_ReadItf.pic.o /home/debci/ncbi-outdir/ngs-sdk/linux/gcc/arm64/rel/obj/language/python/py_ReadIteratorItf.pic.o /home/debci/ncbi-outdir/ngs-sdk/linux/gcc/arm64/rel/obj/language/python/py_ReferenceItf.pic.o /home/debci/ncbi-outdir/ngs-sdk/linux/gcc/arm64/rel/obj/language/python/py_ReferenceIteratorItf.pic.o /home/debci/ncbi-outdir/ngs-sdk/linux/gcc/arm64/rel/obj/language/python/py_ReferenceSequenceItf.pic.o /home/debci/ncbi-outdir/ngs-sdk/linux/gcc/arm64/rel/obj/language/python/py_StatisticsItf.pic.o /home/debci/ncbi-outdir/ngs-sdk/linux/gcc/arm64/rel/obj/language/python/py_Refcount.pic.o /home/debci/ncbi-outdir/ngs-sdk/linux/gcc/arm64/rel/obj/language/python/py_StringItf.pic.o make[2]: Leaving directory '/tmp/autopkgtest-lxc.5m6nldbq/downtmp/build.gg3/src/ngs-sdk/language/python' make[1]: Leaving directory '/tmp/autopkgtest-lxc.5m6nldbq/downtmp/build.gg3/src/ngs-sdk/language' make[1]: Entering directory '/tmp/autopkgtest-lxc.5m6nldbq/downtmp/build.gg3/src/ngs-sdk/dispatch' g++ -c -std=c++11 -o /home/debci/ncbi-outdir/ngs-sdk/linux/gcc/arm64/rel/obj/dispatch/ReadCollectionItf.pic.o ReadCollectionItf.cpp -fPIC -DNDEBUG -O3 -I. -I/tmp/autopkgtest-lxc.5m6nldbq/downtmp/build.gg3/src/ngs-sdk/dispatch -I/tmp/autopkgtest-lxc.5m6nldbq/downtmp/build.gg3/src/ngs-sdk -I/tmp/autopkgtest-lxc.5m6nldbq/downtmp/build.gg3/src/ngs-sdk/ngs/unix/generic -MD g++ -c -std=c++11 -o /home/debci/ncbi-outdir/ngs-sdk/linux/gcc/arm64/rel/obj/dispatch/ReferenceItf.pic.o ReferenceItf.cpp -fPIC -DNDEBUG -O3 -I. -I/tmp/autopkgtest-lxc.5m6nldbq/downtmp/build.gg3/src/ngs-sdk/dispatch -I/tmp/autopkgtest-lxc.5m6nldbq/downtmp/build.gg3/src/ngs-sdk -I/tmp/autopkgtest-lxc.5m6nldbq/downtmp/build.gg3/src/ngs-sdk/ngs/unix/generic -MD g++ -c -std=c++11 -o /home/debci/ncbi-outdir/ngs-sdk/linux/gcc/arm64/rel/obj/dispatch/ReferenceSequenceItf.pic.o ReferenceSequenceItf.cpp -fPIC -DNDEBUG -O3 -I. -I/tmp/autopkgtest-lxc.5m6nldbq/downtmp/build.gg3/src/ngs-sdk/dispatch -I/tmp/autopkgtest-lxc.5m6nldbq/downtmp/build.gg3/src/ngs-sdk -I/tmp/autopkgtest-lxc.5m6nldbq/downtmp/build.gg3/src/ngs-sdk/ngs/unix/generic -MD g++ -c -std=c++11 -o /home/debci/ncbi-outdir/ngs-sdk/linux/gcc/arm64/rel/obj/dispatch/PileupItf.pic.o PileupItf.cpp -fPIC -DNDEBUG -O3 -I. -I/tmp/autopkgtest-lxc.5m6nldbq/downtmp/build.gg3/src/ngs-sdk/dispatch -I/tmp/autopkgtest-lxc.5m6nldbq/downtmp/build.gg3/src/ngs-sdk -I/tmp/autopkgtest-lxc.5m6nldbq/downtmp/build.gg3/src/ngs-sdk/ngs/unix/generic -MD g++ -c -std=c++11 -o /home/debci/ncbi-outdir/ngs-sdk/linux/gcc/arm64/rel/obj/dispatch/PileupEventItf.pic.o PileupEventItf.cpp -fPIC -DNDEBUG -O3 -I. -I/tmp/autopkgtest-lxc.5m6nldbq/downtmp/build.gg3/src/ngs-sdk/dispatch -I/tmp/autopkgtest-lxc.5m6nldbq/downtmp/build.gg3/src/ngs-sdk -I/tmp/autopkgtest-lxc.5m6nldbq/downtmp/build.gg3/src/ngs-sdk/ngs/unix/generic -MD g++ -c -std=c++11 -o /home/debci/ncbi-outdir/ngs-sdk/linux/gcc/arm64/rel/obj/dispatch/AlignmentItf.pic.o AlignmentItf.cpp -fPIC -DNDEBUG -O3 -I. -I/tmp/autopkgtest-lxc.5m6nldbq/downtmp/build.gg3/src/ngs-sdk/dispatch -I/tmp/autopkgtest-lxc.5m6nldbq/downtmp/build.gg3/src/ngs-sdk -I/tmp/autopkgtest-lxc.5m6nldbq/downtmp/build.gg3/src/ngs-sdk/ngs/unix/generic -MD g++ -c -std=c++11 -o /home/debci/ncbi-outdir/ngs-sdk/linux/gcc/arm64/rel/obj/dispatch/ReadGroupItf.pic.o ReadGroupItf.cpp -fPIC -DNDEBUG -O3 -I. -I/tmp/autopkgtest-lxc.5m6nldbq/downtmp/build.gg3/src/ngs-sdk/dispatch -I/tmp/autopkgtest-lxc.5m6nldbq/downtmp/build.gg3/src/ngs-sdk -I/tmp/autopkgtest-lxc.5m6nldbq/downtmp/build.gg3/src/ngs-sdk/ngs/unix/generic -MD g++ -c -std=c++11 -o /home/debci/ncbi-outdir/ngs-sdk/linux/gcc/arm64/rel/obj/dispatch/ReadItf.pic.o ReadItf.cpp -fPIC -DNDEBUG -O3 -I. -I/tmp/autopkgtest-lxc.5m6nldbq/downtmp/build.gg3/src/ngs-sdk/dispatch -I/tmp/autopkgtest-lxc.5m6nldbq/downtmp/build.gg3/src/ngs-sdk -I/tmp/autopkgtest-lxc.5m6nldbq/downtmp/build.gg3/src/ngs-sdk/ngs/unix/generic -MD g++ -c -std=c++11 -o /home/debci/ncbi-outdir/ngs-sdk/linux/gcc/arm64/rel/obj/dispatch/FragmentItf.pic.o FragmentItf.cpp -fPIC -DNDEBUG -O3 -I. -I/tmp/autopkgtest-lxc.5m6nldbq/downtmp/build.gg3/src/ngs-sdk/dispatch -I/tmp/autopkgtest-lxc.5m6nldbq/downtmp/build.gg3/src/ngs-sdk -I/tmp/autopkgtest-lxc.5m6nldbq/downtmp/build.gg3/src/ngs-sdk/ngs/unix/generic -MD g++ -c -std=c++11 -o /home/debci/ncbi-outdir/ngs-sdk/linux/gcc/arm64/rel/obj/dispatch/StatisticsItf.pic.o StatisticsItf.cpp -fPIC -DNDEBUG -O3 -I. -I/tmp/autopkgtest-lxc.5m6nldbq/downtmp/build.gg3/src/ngs-sdk/dispatch -I/tmp/autopkgtest-lxc.5m6nldbq/downtmp/build.gg3/src/ngs-sdk -I/tmp/autopkgtest-lxc.5m6nldbq/downtmp/build.gg3/src/ngs-sdk/ngs/unix/generic -MD g++ -c -std=c++11 -o /home/debci/ncbi-outdir/ngs-sdk/linux/gcc/arm64/rel/obj/dispatch/PackageItf.pic.o PackageItf.cpp -fPIC -DNDEBUG -O3 -I. -I/tmp/autopkgtest-lxc.5m6nldbq/downtmp/build.gg3/src/ngs-sdk/dispatch -I/tmp/autopkgtest-lxc.5m6nldbq/downtmp/build.gg3/src/ngs-sdk -I/tmp/autopkgtest-lxc.5m6nldbq/downtmp/build.gg3/src/ngs-sdk/ngs/unix/generic -MD g++ -c -std=c++11 -o /home/debci/ncbi-outdir/ngs-sdk/linux/gcc/arm64/rel/obj/dispatch/StringItf.pic.o StringItf.cpp -fPIC -DNDEBUG -O3 -I. -I/tmp/autopkgtest-lxc.5m6nldbq/downtmp/build.gg3/src/ngs-sdk/dispatch -I/tmp/autopkgtest-lxc.5m6nldbq/downtmp/build.gg3/src/ngs-sdk -I/tmp/autopkgtest-lxc.5m6nldbq/downtmp/build.gg3/src/ngs-sdk/ngs/unix/generic -MD g++ -c -std=c++11 -o /home/debci/ncbi-outdir/ngs-sdk/linux/gcc/arm64/rel/obj/dispatch/Refcount.pic.o Refcount.cpp -fPIC -DNDEBUG -O3 -I. -I/tmp/autopkgtest-lxc.5m6nldbq/downtmp/build.gg3/src/ngs-sdk/dispatch -I/tmp/autopkgtest-lxc.5m6nldbq/downtmp/build.gg3/src/ngs-sdk -I/tmp/autopkgtest-lxc.5m6nldbq/downtmp/build.gg3/src/ngs-sdk/ngs/unix/generic -MD g++ -c -std=c++11 -o /home/debci/ncbi-outdir/ngs-sdk/linux/gcc/arm64/rel/obj/dispatch/VTable.pic.o VTable.cpp -fPIC -DNDEBUG -O3 -I. -I/tmp/autopkgtest-lxc.5m6nldbq/downtmp/build.gg3/src/ngs-sdk/dispatch -I/tmp/autopkgtest-lxc.5m6nldbq/downtmp/build.gg3/src/ngs-sdk -I/tmp/autopkgtest-lxc.5m6nldbq/downtmp/build.gg3/src/ngs-sdk/ngs/unix/generic -MD g++ -c -std=c++11 -o /home/debci/ncbi-outdir/ngs-sdk/linux/gcc/arm64/rel/obj/dispatch/ErrBlock.pic.o ErrBlock.cpp -fPIC -DNDEBUG -O3 -I. -I/tmp/autopkgtest-lxc.5m6nldbq/downtmp/build.gg3/src/ngs-sdk/dispatch -I/tmp/autopkgtest-lxc.5m6nldbq/downtmp/build.gg3/src/ngs-sdk -I/tmp/autopkgtest-lxc.5m6nldbq/downtmp/build.gg3/src/ngs-sdk/ngs/unix/generic -MD g++ -c -std=c++11 -o /home/debci/ncbi-outdir/ngs-sdk/linux/gcc/arm64/rel/obj/dispatch/ErrorMsg.pic.o ErrorMsg.cpp -fPIC -DNDEBUG -O3 -I. -I/tmp/autopkgtest-lxc.5m6nldbq/downtmp/build.gg3/src/ngs-sdk/dispatch -I/tmp/autopkgtest-lxc.5m6nldbq/downtmp/build.gg3/src/ngs-sdk -I/tmp/autopkgtest-lxc.5m6nldbq/downtmp/build.gg3/src/ngs-sdk/ngs/unix/generic -MD ar rc /home/debci/ncbi-outdir/ngs-sdk/linux/gcc/arm64/rel/ilib/libngs-disp.a /home/debci/ncbi-outdir/ngs-sdk/linux/gcc/arm64/rel/obj/dispatch/ReadCollectionItf.pic.o /home/debci/ncbi-outdir/ngs-sdk/linux/gcc/arm64/rel/obj/dispatch/ReferenceItf.pic.o /home/debci/ncbi-outdir/ngs-sdk/linux/gcc/arm64/rel/obj/dispatch/ReferenceSequenceItf.pic.o /home/debci/ncbi-outdir/ngs-sdk/linux/gcc/arm64/rel/obj/dispatch/PileupItf.pic.o /home/debci/ncbi-outdir/ngs-sdk/linux/gcc/arm64/rel/obj/dispatch/PileupEventItf.pic.o /home/debci/ncbi-outdir/ngs-sdk/linux/gcc/arm64/rel/obj/dispatch/AlignmentItf.pic.o /home/debci/ncbi-outdir/ngs-sdk/linux/gcc/arm64/rel/obj/dispatch/ReadGroupItf.pic.o /home/debci/ncbi-outdir/ngs-sdk/linux/gcc/arm64/rel/obj/dispatch/ReadItf.pic.o /home/debci/ncbi-outdir/ngs-sdk/linux/gcc/arm64/rel/obj/dispatch/FragmentItf.pic.o /home/debci/ncbi-outdir/ngs-sdk/linux/gcc/arm64/rel/obj/dispatch/StatisticsItf.pic.o /home/debci/ncbi-outdir/ngs-sdk/linux/gcc/arm64/rel/obj/dispatch/PackageItf.pic.o /home/debci/ncbi-outdir/ngs-sdk/linux/gcc/arm64/rel/obj/dispatch/StringItf.pic.o /home/debci/ncbi-outdir/ngs-sdk/linux/gcc/arm64/rel/obj/dispatch/Refcount.pic.o /home/debci/ncbi-outdir/ngs-sdk/linux/gcc/arm64/rel/obj/dispatch/VTable.pic.o /home/debci/ncbi-outdir/ngs-sdk/linux/gcc/arm64/rel/obj/dispatch/ErrBlock.pic.o /home/debci/ncbi-outdir/ngs-sdk/linux/gcc/arm64/rel/obj/dispatch/ErrorMsg.pic.o make[1]: Leaving directory '/tmp/autopkgtest-lxc.5m6nldbq/downtmp/build.gg3/src/ngs-sdk/dispatch' make[1]: Entering directory '/tmp/autopkgtest-lxc.5m6nldbq/downtmp/build.gg3/src/ngs-sdk/adapter' g++ -c -std=c++11 -o /home/debci/ncbi-outdir/ngs-sdk/linux/gcc/arm64/rel/obj/adapter/ReadCollectionItf.pic.o ReadCollectionItf.cpp -fPIC -DNDEBUG -O3 -I. -I/tmp/autopkgtest-lxc.5m6nldbq/downtmp/build.gg3/src/ngs-sdk/adapter -I/tmp/autopkgtest-lxc.5m6nldbq/downtmp/build.gg3/src/ngs-sdk -I/tmp/autopkgtest-lxc.5m6nldbq/downtmp/build.gg3/src/ngs-sdk/ngs/unix/generic -MD In file included from /tmp/autopkgtest-lxc.5m6nldbq/downtmp/build.gg3/src/ngs-sdk/ngs/adapter/Refcount.hpp:35, from /tmp/autopkgtest-lxc.5m6nldbq/downtmp/build.gg3/src/ngs-sdk/ngs/adapter/ReadCollectionItf.hpp:31, /tmp/autopkgtest-lxc.5m6nldbq/downtmp/build.gg3/src/ngs-sdk/ngs/adapter/defs.h:35:10: fatal error: atomic32.h: No such file or directory make[1]: *** [/tmp/autopkgtest-lxc.5m6nldbq/downtmp/build.gg3/src/ngs-sdk/./Makefile.config.linux.arm64:110: /home/debci/ncbi-outdir/ngs-sdk/linux/gcc/arm64/rel/obj/adapter/ReadCollectionItf.pic.o] Error 1 make[1]: Leaving directory '/tmp/autopkgtest-lxc.5m6nldbq/downtmp/build.gg3/src/ngs-sdk/adapter' make: *** [/tmp/autopkgtest-lxc.5m6nldbq/downtmp/build.gg3/src/ngs-sdk/Makefile.rules:31: adapter] Error 2

OpenPGP_signature
Description: OpenPGP digital signature

--- End Message ---

--- Begin Message ---

Source: ngs-sdk
Source-Version: 2.11.2-4
Done: Pierre Gruet <p...@debian.org>

We believe that the bug you reported is fixed in the latest version of
ngs-sdk, which is due to be installed in the Debian FTP archive.

A summary of the changes between this version and the previous one is
attached.

Thank you for reporting the bug, which will now be closed.  If you
have further comments please address them to 1006...@bugs.debian.org,
and the maintainer will reopen the bug report if appropriate.

Debian distribution maintenance software
pp.
Pierre Gruet <p...@debian.org> (supplier of updated ngs-sdk package)

(This message was generated automatically at their request; if you
believe that there is a problem with it please contact the archive
administrators by mailing ftpmas...@ftp-master.debian.org)


-----BEGIN PGP SIGNED MESSAGE-----
Hash: SHA512

Format: 1.8
Date: Tue, 03 May 2022 21:17:32 +0200
Source: ngs-sdk
Architecture: source
Version: 2.11.2-4
Distribution: unstable
Urgency: medium
Maintainer: Debian Med Packaging Team 
<debian-med-packag...@lists.alioth.debian.org>
Changed-By: Pierre Gruet <p...@debian.org>
Closes: 1006732
Changes:
 ngs-sdk (2.11.2-4) unstable; urgency=medium
 .
   * Team upload
   * Rewriting the autopkgtest to test the package as-installed
     (Closes: #1006732)
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ngs-sdk_2.11.2-4_source.buildinfo
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ngs-sdk_2.11.2-4.debian.tar.xz
 8c3650b8797eccb21027be9f95805042 10886 science optional 
ngs-sdk_2.11.2-4_source.buildinfo

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--- End Message ---