[Debian-med-packaging] Bug#1006732: ngs-sdk: autopkgtest failure: fatal error: atomic32.h: No such file or directory
Paul Gevers
elbrus at debian.org
Thu Mar 3 20:33:22 GMT 2022
Source: ngs-sdk
Version: 2.11.2-3
X-Debbugs-CC: debian-ci at lists.debian.org
Severity: serious
User: debian-ci at lists.debian.org
Usertags: fails-always
Dear maintainer(s),
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?
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
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/ilib
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
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make[2]: Leaving directory
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mkdir -p
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py_AlignmentItf.cpp -fPIC -DNDEBUG -O3 -I.
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py_AlignmentIteratorItf.cpp -fPIC -DNDEBUG -O3 -I.
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py_ReferenceSequenceItf.cpp -fPIC -DNDEBUG -O3 -I.
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-MD ar rc
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make[2]: Leaving directory
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-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'
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
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,
from ReadCollectionItf.cpp:27:
/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
35 | #include <atomic32.h>
| ^~~~~~~~~~~~
compilation terminated.
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
autopkgtest [11:23:34]: test run-unit-test
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