Your message dated Mon, 14 Mar 2022 19:00:12 +0000
with message-id <e1ntpvq-0003ag...@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.
(NB: If you are a system administrator and have no idea what this
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immediately.)
--
1006776: https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=1006776
Debian Bug Tracking System
Contact ow...@bugs.debian.org with problems
--- Begin Message ---
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: sramac...@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
signature.asc
Description: PGP signature
--- End Message ---
--- Begin Message ---
Source: pbbam
Source-Version: 2.0.0+dfsg-1
Done: Andreas Tille <ti...@debian.org>
We believe that the bug you reported is fixed in the latest version of
pbbam, which is due to be installed in the Debian FTP archive.
A summary of the changes between this version and the previous one is
attached.
Thank you for reporting the bug, which will now be closed. If you
have further comments please address them to 1006...@bugs.debian.org,
and the maintainer will reopen the bug report if appropriate.
Debian distribution maintenance software
pp.
Andreas Tille <ti...@debian.org> (supplier of updated pbbam package)
(This message was generated automatically at their request; if you
believe that there is a problem with it please contact the archive
administrators by mailing ftpmas...@ftp-master.debian.org)
-----BEGIN PGP SIGNED MESSAGE-----
Hash: SHA512
Format: 1.8
Date: Mon, 07 Mar 2022 15:26:06 +0100
Source: pbbam
Binary: libpbbam-dev libpbbam2.0.0 libpbbam2.0.0-dbgsym pbbamtools
pbbamtools-dbgsym
Architecture: source amd64
Version: 2.0.0+dfsg-1
Distribution: unstable
Urgency: medium
Maintainer: Debian Med Packaging Team
<debian-med-packag...@lists.alioth.debian.org>
Changed-By: Andreas Tille <ti...@debian.org>
Description:
libpbbam-dev - Pacific Biosciences binary alignment/map (BAM) library (headers)
libpbbam2.0.0 - Pacific Biosciences binary alignment/map (BAM) library
pbbamtools - processing Pacific Biosciences binary alignment/map files
Closes: 1006776
Changes:
pbbam (2.0.0+dfsg-1) unstable; urgency=medium
.
* New upstream version
Closes: #1006776
* Bump SONAME to 2.0.0
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Files:
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pbbam_2.0.0+dfsg.orig.tar.xz
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pbbam_2.0.0+dfsg-1.debian.tar.xz
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libpbbam-dev_2.0.0+dfsg-1_amd64.deb
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