[Debian-med-packaging] Bug#1006778: blasr: FTBFS: ‘optional’ in namespace ‘std’ does not name a template type
Sebastian Ramacher
sramacher at debian.org
Fri Mar 4 20:19:39 GMT 2022
Source: blasr
Version: 5.3.5+dfsg-2
Severity: serious
Tags: sid bookworm ftbfs
X-Debbugs-Cc: sramacher at 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
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