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Bug#1006776: pbbam: FTBFS: error: ‘optional’ in namespace ‘std’ does not name a template type

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Sebastian Ramacher

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Mar 4, 2022, 3:30:02 PM3/4/22
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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: sram...@debian.org

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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Adrian Bunk

unread,
Mar 4, 2022, 3:40:03 PM3/4/22
to
Control: tags -1 patch

On Fri, Mar 04, 2022 at 09:16:45PM +0100, Sebastian Ramacher wrote:
> 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: sram...@debian.org
>
> 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
>...

The upstream fix is
https://github.com/PacificBiosciences/pbbam/commit/0c3da1ac49c42ca443592526a58ae94f2f05493e

The minimal fix would be cpp_std=c++17 in meson.build.

> Cheers

cu
Adrian

Debian Bug Tracking System

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Mar 4, 2022, 3:40:03 PM3/4/22
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Processing control commands:

> tags -1 patch
Bug #1006776 [src:pbbam] pbbam: FTBFS: error: ‘optional’ in namespace ‘std’ does not name a template type
Added tag(s) patch.

--
1006776: https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=1006776
Debian Bug Tracking System
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Debian Bug Tracking System

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Mar 14, 2022, 3:10:03 PM3/14/22
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Your message dated Mon, 14 Mar 2022 19:00:12 +0000
with message-id <E1nTpvQ-...@fasolo.debian.org>
and subject line Bug#1006776: fixed in pbbam 2.0.0+dfsg-1
has caused the Debian Bug report #1006776,
regarding pbbam: FTBFS: error: ‘optional’ in namespace ‘std’ does not name a template type
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.

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