[Debian-med-packaging] Bug#1006777: pbseqlib: FTBFS: error: ‘optional’ in namespace ‘std’ does not name a template type

[Sebastian Ramacher]

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: sramacher at 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
-------------- next part --------------
A non-text attachment was scrubbed...
Name: signature.asc
Type: application/pgp-signature
Size: 833 bytes
Desc: not available
URL: <http://alioth-lists.debian.net/pipermail/debian-med-packaging/attachments/20220304/ffe3cb38/attachment-0001.sig>