Your message dated Tue, 08 Mar 2022 11:33:43 +0000
with message-id <e1nry63-0003xv...@fasolo.debian.org>
and subject line Bug#1006778: fixed in blasr 5.3.5+dfsg-3
has caused the Debian Bug report #1006778,
regarding blasr: FTBFS: ‘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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--
1006778: https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=1006778
Debian Bug Tracking System
Contact ow...@bugs.debian.org with problems
--- Begin Message ---
Source: blasr
Version: 5.3.5+dfsg-2
Severity: serious
Tags: sid bookworm ftbfs
X-Debbugs-Cc: sramac...@debian.org
blasr FTBFS:
FAILED: libblasr_impl.a.p/extrautils_SuffixArrayToBWT.cpp.o
c++ -Ilibblasr_impl.a.p -I. -I.. -I/usr/include/libblasr
-I/usr/include/hdf5/serial -I/usr/include/pbseq -fdiagnostics-color=always
-D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra
-Wpedantic -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2
-ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat
-Werror=format-security -DHAVE_HDF5_1_10_1 -std=c++14 -isystem
/usr/include/hdf5/serial -fPIC -DBOOST_ALL_NO_LIB -pthread
-Wno-delete-non-virtual-dtor -Wno-non-virtual-dtor -Wno-unused-but-set-variable
-Wno-unused-variable -MD -MQ
libblasr_impl.a.p/extrautils_SuffixArrayToBWT.cpp.o -MF
libblasr_impl.a.p/extrautils_SuffixArrayToBWT.cpp.o.d -o
libblasr_impl.a.p/extrautils_SuffixArrayToBWT.cpp.o -c
../extrautils/SuffixArrayToBWT.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 /usr/include/pbseq/pbdata/DNASequence.hpp:17,
from /usr/include/pbseq/alignment/bwt/Occ.hpp:8,
from /usr/include/pbseq/alignment/bwt/BWT.hpp:7,
from ../extrautils/SuffixArrayToBWT.cpp:4:
/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 /usr/include/pbseq/pbdata/DNASequence.hpp:17,
from /usr/include/pbseq/alignment/bwt/Occ.hpp:8,
from /usr/include/pbseq/alignment/bwt/BWT.hpp:7,
from ../extrautils/SuffixArrayToBWT.cpp:4:
/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 /usr/include/pbseq/pbdata/DNASequence.hpp:17,
from /usr/include/pbseq/alignment/bwt/Occ.hpp:8,
from /usr/include/pbseq/alignment/bwt/BWT.hpp:7,
from ../extrautils/SuffixArrayToBWT.cpp:4:
/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(
| ^~~
In file included from ../extrautils/SuffixArrayToBWT.cpp:4:
/usr/include/pbseq/alignment/bwt/BWT.hpp: In member function ‘void
Bwt<T_BWT_Sequence, T_DNASequence>::InitializeDNACharacterCount() [with
T_BWT_Sequence = PackedDNASequence; T_DNASequence = FASTASequence]’:
/usr/include/pbseq/alignment/bwt/BWT.hpp:192:21: warning: this statement may
fall through [-Wimplicit-fallthrough=]
192 | charCount[0]++;
| ^~~~~~~~~
/usr/include/pbseq/alignment/bwt/BWT.hpp:193:17: note: here
193 | case 0: //A
| ^~~~
/usr/include/pbseq/alignment/bwt/BWT.hpp:194:21: warning: this statement may
fall through [-Wimplicit-fallthrough=]
194 | charCount[1]++;
| ^~~~~~~~~
/usr/include/pbseq/alignment/bwt/BWT.hpp:195:17: note: here
195 | case 1: //C
| ^~~~
/usr/include/pbseq/alignment/bwt/BWT.hpp:196:21: warning: this statement may
fall through [-Wimplicit-fallthrough=]
196 | charCount[2]++;
| ^~~~~~~~~
/usr/include/pbseq/alignment/bwt/BWT.hpp:197:17: note: here
197 | case 2: //G
| ^~~~
/usr/include/pbseq/alignment/bwt/BWT.hpp:198:21: warning: this statement may
fall through [-Wimplicit-fallthrough=]
198 | charCount[3]++;
| ^~~~~~~~~
/usr/include/pbseq/alignment/bwt/BWT.hpp:199:17: note: here
199 | case 3: //T
| ^~~~
/usr/include/pbseq/alignment/bwt/BWT.hpp:200:21: warning: this statement may
fall through [-Wimplicit-fallthrough=]
200 | charCount[4]++;
| ^~~~~~~~~
/usr/include/pbseq/alignment/bwt/BWT.hpp:201:17: note: here
201 | case 4: //N
| ^~~~
See
https://buildd.debian.org/status/fetch.php?pkg=blasr&arch=amd64&ver=5.3.5%2Bdfsg-2%2Bb1&stamp=1645915394&raw=0
Cheers
--
Sebastian Ramacher
signature.asc
Description: PGP signature
--- End Message ---
--- Begin Message ---
Source: blasr
Source-Version: 5.3.5+dfsg-3
Done: Andreas Tille <ti...@debian.org>
We believe that the bug you reported is fixed in the latest version of
blasr, 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 blasr 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: Tue, 08 Mar 2022 11:56:33 +0100
Source: blasr
Architecture: source
Version: 5.3.5+dfsg-3
Distribution: unstable
Urgency: medium
Maintainer: Debian Med Packaging Team
<debian-med-packag...@lists.alioth.debian.org>
Changed-By: Andreas Tille <ti...@debian.org>
Closes: 1006778
Changes:
blasr (5.3.5+dfsg-3) unstable; urgency=medium
.
* d/rules: Drop -std=c++14 from DEB_CXXFLAGS_MAINT_APPEND
Closes: #1006778
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