Package: libbioparser-dev
Version: 2.0.1-1
Severity: normal
Dear Maintainers,
While investigating the reasons of failure to build from source
by several packages with Gcc 10, I observed a reoccurring
pattern at least on #957747 and #957748, and also while having a
look at #957836 (but it is hidden by the first build error in
that particular case):
/usr/include/bioparser/bioparser.hpp:867:24: error: ‘invalid_argument’ is not a
member of ‘std’
867 | throw std::invalid_argument("[bioparser::SamParser] error: "
| ^~~~~~~~~~~~~~~~
/usr/include/bioparser/bioparser.hpp: In member function ‘bool
bioparser::SamParser<T>::parse(std::vector<std::unique_ptr<T> >&, uint64_t,
bool)’:
/usr/include/bioparser/bioparser.hpp:891:28: error: ‘invalid_argument’ is not a
member of ‘std’
891 | throw std::invalid_argument("[bioparser::SamParser]
error: "
| ^~~~~~~~~~~~~~~~
In file included from /<<PKGBUILDDIR>>/src/main.cpp:8:
/usr/include/bioparser/bioparser.hpp: In function
‘std::unique_ptr<bioparser::Parser<T> > bioparser::createParser(const string&)’:
/usr/include/bioparser/bioparser.hpp:189:20: error: ‘invalid_argument’ is not a
member of ‘std’
189 | throw std::invalid_argument("[bioparser::createParser] error: "
| ^~~~~~~~~~~~~~~~
/usr/include/bioparser/bioparser.hpp: In lambda function:
/usr/include/bioparser/bioparser.hpp:263:24: error: ‘invalid_argument’ is not a
member of ‘std’
263 | throw std::invalid_argument("[bioparser::FastaParser]
error: "
| ^~~~~~~~~~~~~~~~
/usr/include/bioparser/bioparser.hpp: In member function ‘bool
bioparser::FastaParser<T>::parse(std::vector<std::unique_ptr<T> >&, uint64_t,
bool)’:
/usr/include/bioparser/bioparser.hpp:287:28: error: ‘invalid_argument’ is not a
member of ‘std’
287 | throw std::invalid_argument("[bioparser::FastaParser]
error: "
| ^~~~~~~~~~~~~~~~
/usr/include/bioparser/bioparser.hpp: In lambda function:
/usr/include/bioparser/bioparser.hpp:381:24: error: ‘invalid_argument’ is not a
member of ‘std’
381 | throw std::invalid_argument("[bioparser::FastqParser]
error: "
| ^~~~~~~~~~~~~~~~
/usr/include/bioparser/bioparser.hpp: In member function ‘bool
bioparser::FastqParser<T>::parse(std::vector<std::unique_ptr<T> >&, uint64_t,
bool)’:
/usr/include/bioparser/bioparser.hpp:407:28: error: ‘invalid_argument’ is not a
member of ‘std’
407 | throw std::invalid_argument("[bioparser::FastqParser]
error: "
| ^~~~~~~~~~~~~~~~
/usr/include/bioparser/bioparser.hpp: In lambda function:
/usr/include/bioparser/bioparser.hpp:545:24: error: ‘invalid_argument’ is not a
member of ‘std’
545 | throw std::invalid_argument("[bioparser::MhapParser] error:
"
| ^~~~~~~~~~~~~~~~
/usr/include/bioparser/bioparser.hpp: In member function ‘bool
bioparser::MhapParser<T>::parse(std::vector<std::unique_ptr<T> >&, uint64_t,
bool)’:
/usr/include/bioparser/bioparser.hpp:567:28: error: ‘invalid_argument’ is not a
member of ‘std’
567 | throw std::invalid_argument("[bioparser::MhapParser]
error: "
| ^~~~~~~~~~~~~~~~
/usr/include/bioparser/bioparser.hpp: In lambda function:
/usr/include/bioparser/bioparser.hpp:675:24: error: ‘invalid_argument’ is not a
member of ‘std’
675 | throw std::invalid_argument("[bioparser::PafParser] error: "
| ^~~~~~~~~~~~~~~~
/usr/include/bioparser/bioparser.hpp:691:24: error: ‘invalid_argument’ is not a
member of ‘std’
691 | throw std::invalid_argument("[bioparser::PafParser] error: "
| ^~~~~~~~~~~~~~~~
/usr/include/bioparser/bioparser.hpp: In member function ‘bool
bioparser::PafParser<T>::parse(std::vector<std::unique_ptr<T> >&, uint64_t,
bool)’:
/usr/include/bioparser/bioparser.hpp:714:28: error: ‘invalid_argument’ is not a
member of ‘std’
714 | throw std::invalid_argument("[bioparser::PafParser]
error: "
| ^~~~~~~~~~~~~~~~
/usr/include/bioparser/bioparser.hpp: In lambda function:
/usr/include/bioparser/bioparser.hpp:839:24: error: ‘invalid_argument’ is not a
member of ‘std’
839 | throw std::invalid_argument("[bioparser::SamParser] error: "
| ^~~~~~~~~~~~~~~~
/usr/include/bioparser/bioparser.hpp:867:24: error: ‘invalid_argument’ is not a
member of ‘std’
867 | throw std::invalid_argument("[bioparser::SamParser] error: "
| ^~~~~~~~~~~~~~~~
/usr/include/bioparser/bioparser.hpp: In member function ‘bool
bioparser::SamParser<T>::parse(std::vector<std::unique_ptr<T> >&, uint64_t,
bool)’:
/usr/include/bioparser/bioparser.hpp:891:28: error: ‘invalid_argument’ is not a
member of ‘std’
891 | throw std::invalid_argument("[bioparser::SamParser]
error: "
| ^~~~~~~~~~~~~~~~
This /usr/include/bioparser/bioparser.hpp header file is part of
libbioparser-dev, and looks to be missing inclusion of
stdexcept, per Gnu instructions on how to move to Gcc 10:
https://gcc.gnu.org/gcc-10/porting_to.html
Putting it into the header helps moving forward with these build
errors. I took the liberty to inform upstream about this issue:
https://github.com/rvaser/bioparser/pull/7
I hope this helps,
Kind Regards,
Étienne Mollier.
-- System Information:
Debian Release: bullseye/sid
APT prefers unstable
APT policy: (500, 'unstable'), (1, 'experimental')
Architecture: amd64 (x86_64)
Foreign Architectures: i386, riscv64
Kernel: Linux 5.5.6 (SMP w/4 CPU cores; PREEMPT)
Locale: LANG=C.UTF-8, LC_CTYPE=C.UTF-8 (charmap=UTF-8), LANGUAGE=C.UTF-8
(charmap=UTF-8)
Shell: /bin/sh linked to /usr/bin/dash
Init: systemd (via /run/systemd/system)
LSM: AppArmor: enabled
Versions of packages libbioparser-dev depends on:
ii zlib1g-dev 1:1.2.11.dfsg-2
libbioparser-dev recommends no packages.
libbioparser-dev suggests no packages.
-- no debconf information
