Source: pbbam Version: 1.7.0+dfsg-2 Severity: serious Tags: ftbfs sid bookworm Justification: fails to build from source (but built successfully in the past) X-Debbugs-Cc: [email protected]
pbbam FTBFS:
FAILED: src/libpbbam.so.1.7.0.p/AlignmentPrinter.cpp.o
c++ -Isrc/libpbbam.so.1.7.0.p -Isrc -I../src -Iinclude -I../include
-fdiagnostics-color=always -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch
-Wnon-virtual-dtor -Wextra -Wpedantic -std=c++14 -g -O2
-ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat
-Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC
-DBOOST_ALL_NO_LIB -pthread -Wduplicated-cond -Wduplicated-branches
-Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion
-Wshadow -Wformat=1 -MD -MQ src/libpbbam.so.1.7.0.p/AlignmentPrinter.cpp.o -MF
src/libpbbam.so.1.7.0.p/AlignmentPrinter.cpp.o.d -o
src/libpbbam.so.1.7.0.p/AlignmentPrinter.cpp.o -c ../src/AlignmentPrinter.cpp
In file included from /usr/include/pbcopper/data/Read.h:11,
from /usr/include/pbcopper/data/MappedRead.h:8,
from ../include/pbbam/BamRecord.h:14,
from ../include/pbbam/AlignmentPrinter.h:11,
from ../src/AlignmentPrinter.cpp:3:
/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 ../include/pbbam/BamRecord.h:14,
from ../include/pbbam/AlignmentPrinter.h:11,
from ../src/AlignmentPrinter.cpp:3:
/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 ../include/pbbam/BamRecord.h:14,
from ../include/pbbam/AlignmentPrinter.h:11,
from ../src/AlignmentPrinter.cpp:3:
/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=pbbam&arch=amd64&ver=1.7.0%2Bdfsg-2%2Bb1&stamp=1645916714&raw=0
Cheers
--
Sebastian Ramacher
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