Source: pbseqlib Version: 5.3.5+dfsg-3 Severity: serious Tags: ftbfs sid bookworm Justification: fails to build from source (but built successfully in the past) X-Debbugs-Cc: sramac...@debian.org
pbseqlib FTBFS:
FAILED: libblasr.so.5.3.5.p/hdf_HDFAlnGroupGroup.cpp.o
c++ -Ilibblasr.so.5.3.5.p -I. -I.. -I/usr/include/hdf5/serial
-fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch
-Wnon-virtual-dtor -Wextra -Wpedantic -std=c++17 -g -O2
-ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat
-Werror=format-security -O3 -std=c++14 -Wdate-time -D_FORTIFY_SOURCE=2
-DHAVE_HDF5_1_10_1 -O3 -fPIC -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor
-Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ
libblasr.so.5.3.5.p/hdf_HDFAlnGroupGroup.cpp.o -MF
libblasr.so.5.3.5.p/hdf_HDFAlnGroupGroup.cpp.o.d -o
libblasr.so.5.3.5.p/hdf_HDFAlnGroupGroup.cpp.o -c ../hdf/HDFAlnGroupGroup.cpp
In file included from /usr/include/pbcopper/data/Read.h:11,
from /usr/include/pbcopper/data/MappedRead.h:8,
from /usr/include/pbbam/BamRecord.h:14,
from ../pbdata/DNASequence.hpp:17,
from ../hdf/BufferedHDFArray.hpp:19,
from ../hdf/HDFArray.hpp:9,
from ../hdf/HDFAlnGroupGroup.hpp:6,
from ../hdf/HDFAlnGroupGroup.cpp:1:
/usr/include/pbcopper/data/ReadId.h:22:10: error: ‘optional’ in namespace ‘std’
does not name a template type
22 | std::optional<Interval> ZmwInterval;
| ^~~~~~~~
/usr/include/pbcopper/data/ReadId.h:22:5: note: ‘std::optional’ is only
available from C++17 onwards
22 | std::optional<Interval> ZmwInterval;
| ^~~
In file included from /usr/include/pbcopper/data/MappedRead.h:8,
from /usr/include/pbbam/BamRecord.h:14,
from ../pbdata/DNASequence.hpp:17,
from ../hdf/BufferedHDFArray.hpp:19,
from ../hdf/HDFArray.hpp:9,
from ../hdf/HDFAlnGroupGroup.hpp:6,
from ../hdf/HDFAlnGroupGroup.cpp:1:
/usr/include/pbcopper/data/Read.h:28:49: error: ‘std::optional’ has not been
declared
28 | Read(Data::ReadId id, std::string seq, std::optional<Frames> pw,
std::optional<Frames> ipd,
| ^~~~~~~~
/usr/include/pbcopper/data/Read.h:28:57: error: expected ‘,’ or ‘...’ before
‘<’ token
28 | Read(Data::ReadId id, std::string seq, std::optional<Frames> pw,
std::optional<Frames> ipd,
| ^
/usr/include/pbcopper/data/Read.h:40:10: error: ‘optional’ in namespace ‘std’
does not name a template type
40 | std::optional<Frames> PulseWidth;
| ^~~~~~~~
/usr/include/pbcopper/data/Read.h:40:5: note: ‘std::optional’ is only available
from C++17 onwards
40 | std::optional<Frames> PulseWidth;
| ^~~
/usr/include/pbcopper/data/Read.h:42:10: error: ‘optional’ in namespace ‘std’
does not name a template type
42 | std::optional<Frames> IPD;
| ^~~~~~~~
/usr/include/pbcopper/data/Read.h:42:5: note: ‘std::optional’ is only available
from C++17 onwards
42 | std::optional<Frames> IPD;
| ^~~
In file included from /usr/include/pbbam/BamRecord.h:14,
from ../pbdata/DNASequence.hpp:17,
from ../hdf/BufferedHDFArray.hpp:19,
from ../hdf/HDFArray.hpp:9,
from ../hdf/HDFAlnGroupGroup.hpp:6,
from ../hdf/HDFAlnGroupGroup.cpp:1:
/usr/include/pbcopper/data/MappedRead.h:63:10: error: ‘optional’ in namespace
‘std’ does not name a template type
63 | std::optional<Frames> AlignedIPD(
| ^~~~~~~~
/usr/include/pbcopper/data/MappedRead.h:63:5: note: ‘std::optional’ is only
available from C++17 onwards
63 | std::optional<Frames> AlignedIPD(
| ^~~
/usr/include/pbcopper/data/MappedRead.h:68:10: error: ‘optional’ in namespace
‘std’ does not name a template type
68 | std::optional<Frames> AlignedPulseWidth(
| ^~~~~~~~
/usr/include/pbcopper/data/MappedRead.h:68:5: note: ‘std::optional’ is only
available from C++17 onwards
68 | std::optional<Frames> AlignedPulseWidth(
| ^~~
See
https://buildd.debian.org/status/fetch.php?pkg=pbseqlib&arch=amd64&ver=5.3.5%2Bdfsg-3%2Bb1&stamp=1645916767&raw=0
Cheers
--
Sebastian Ramacher
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