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#1013030 rna-star: ftbfs with GCC-12 #1013030

Package:: src:rna-star

Source:: rna-star

Submitter:: Matthias Klose

Date:: 2022-06-24 20:48:05 UTC

Severity:: normal

Tags:

#1013030#5

Date:: 2022-06-16 12:13:26 UTC

From:

To:

[This bug is targeted to the upcoming bookworm release]

Please keep this issue open in the bug tracker for the package it
was filed for.  If a fix in another package is required, please
file a bug for the other package (or clone), and add a block in this
package. Please keep the issue open until the package can be built in
a follow-up test rebuild.

The package fails to build in a test rebuild on at least amd64 with
gcc-12/g++-12, but succeeds to build with gcc-11/g++-11. The
severity of this report will be raised before the bookworm release.

The full build log can be found at:
http://qa-logs.debian.net/2022/06/09/gcc12/rna-star_2.7.10a+dfsg-2_unstable_gcc12.log
The last lines of the build log are at the end of this report.

To build with GCC 11, either set CC=gcc-11 CXX=g++-11 explicitly,
or install the gcc, g++, gfortran, ... packages from experimental.

  apt-get -t=experimental install g++

Common build failures are new warnings resulting in build failures with
-Werror turned on, or new/dropped symbols in Debian symbols files.
For other C/C++ related build failures see the porting guide at
http://gcc.gnu.org/gcc-11/porting_to.html

GCC 11 defaults to the GNU++17 standard.  If your package installs
header files in /usr/include, please don't work around C++17 issues
by choosing a lower C++ standard for the package build, but fix these
issues to build with the C++17 standard.

[...]
      |       ^~~~~~
/usr/include/c++/12/bits/unordered_map.h:438:7: note:   conversion of argument 1 would be ill-formed:
SoloCommon.h:59:44: error: invalid user-defined conversion from ‘<brace-enclosed initializer list>’ to ‘std::unordered_map<long long unsigned int, std::array<long long unsigned int, 15> >::node_type&&’ {aka ‘std::_Hashtable<long long unsigned int, std::pair<const long long unsigned int, std::array<long long unsigned int, 15> >, std::allocator<std::pair<const long long unsigned int, std::array<long long unsigned int, 15> > >, std::__detail::_Select1st, std::equal_to<long long unsigned int>, std::hash<long long unsigned int>, std::__detail::_Mod_range_hashing, std::__detail::_Default_ranged_hash, std::__detail::_Prime_rehash_policy, std::__detail::_Hashtable_traits<false, false, true> >::node_type&&’} [-fpermissive]
   59 |         auto cbInserted = flagCounts.insert({cb, {} });
      |                           ~~~~~~~~~~~~~~~~~^~~~~~~~~~~
In file included from /usr/include/c++/12/bits/hashtable.h:38:
/usr/include/c++/12/bits/node_handle.h:283:7: note: candidate is: ‘std::_Node_handle<_Key, _Value, _NodeAlloc>::_Node_handle(typename _AllocTraits::pointer, const _NodeAlloc&) [with _Key = long long unsigned int; _Value = std::pair<const long long unsigned int, std::array<long long unsigned int, 15> >; _NodeAlloc = std::allocator<std::__detail::_Hash_node<std::pair<const long long unsigned int, std::array<long long unsigned int, 15> >, false> >; typename _AllocTraits::pointer = std::__detail::_Hash_node<std::pair<const long long unsigned int, std::array<long long unsigned int, 15> >, false>*; _AllocTraits = std::allocator_traits<std::allocator<std::__detail::_Hash_node<std::pair<const long long unsigned int, std::array<long long unsigned int, 15> >, false> > >]’ (near match)
  283 |       _Node_handle(typename _AllocTraits::pointer __ptr,
      |       ^~~~~~~~~~~~
/usr/include/c++/12/bits/node_handle.h:283:7: note:   conversion of argument 1 would be ill-formed:
SoloCommon.h:59:46: error: invalid conversion from ‘uintCB’ {aka ‘long long unsigned int’} to ‘std::allocator_traits<std::allocator<std::__detail::_Hash_node<std::pair<const long long unsigned int, std::array<long long unsigned int, 15> >, false> > >::pointer’ {aka ‘std::__detail::_Hash_node<std::pair<const long long unsigned int, std::array<long long unsigned int, 15> >, false>*’} [-fpermissive]
   59 |         auto cbInserted = flagCounts.insert({cb, {} });
      |                                              ^~
      |                                              |
      |                                              uintCB {aka long long unsigned int}
SoloCommon.h:59:44: error: ‘std::_Node_handle<_Key, _Value, _NodeAlloc>::_Node_handle(typename _AllocTraits::pointer, const _NodeAlloc&) [with _Key = long long unsigned int; _Value = std::pair<const long long unsigned int, std::array<long long unsigned int, 15> >; _NodeAlloc = std::allocator<std::__detail::_Hash_node<std::pair<const long long unsigned int, std::array<long long unsigned int, 15> >, false> >; typename _AllocTraits::pointer = std::__detail::_Hash_node<std::pair<const long long unsigned int, std::array<long long unsigned int, 15> >, false>*; _AllocTraits = std::allocator_traits<std::allocator<std::__detail::_Hash_node<std::pair<const long long unsigned int, std::array<long long unsigned int, 15> >, false> > >]’ is private within this context
   59 |         auto cbInserted = flagCounts.insert({cb, {} });
      |                           ~~~~~~~~~~~~~~~~~^~~~~~~~~~~
/usr/include/c++/12/bits/node_handle.h:283:7: note: declared private here
  283 |       _Node_handle(typename _AllocTraits::pointer __ptr,
      |       ^~~~~~~~~~~~
SoloCommon.h:59:46: error: invalid conversion from ‘uintCB’ {aka ‘long long unsigned int’} to ‘std::allocator_traits<std::allocator<std::__detail::_Hash_node<std::pair<const long long unsigned int, std::array<long long unsigned int, 15> >, false> > >::pointer’ {aka ‘std::__detail::_Hash_node<std::pair<const long long unsigned int, std::array<long long unsigned int, 15> >, false>*’} [-fpermissive]
   59 |         auto cbInserted = flagCounts.insert({cb, {} });
      |                                              ^~
      |                                              |
      |                                              uintCB {aka long long unsigned int}
/usr/include/c++/12/bits/node_handle.h:283:51: note:   initializing argument 1 of ‘std::_Node_handle<_Key, _Value, _NodeAlloc>::_Node_handle(typename _AllocTraits::pointer, const _NodeAlloc&) [with _Key = long long unsigned int; _Value = std::pair<const long long unsigned int, std::array<long long unsigned int, 15> >; _NodeAlloc = std::allocator<std::__detail::_Hash_node<std::pair<const long long unsigned int, std::array<long long unsigned int, 15> >, false> >; typename _AllocTraits::pointer = std::__detail::_Hash_node<std::pair<const long long unsigned int, std::array<long long unsigned int, 15> >, false>*; _AllocTraits = std::allocator_traits<std::allocator<std::__detail::_Hash_node<std::pair<const long long unsigned int, std::array<long long unsigned int, 15> >, false> > >]’
  283 |       _Node_handle(typename _AllocTraits::pointer __ptr,
      |                    ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~
/usr/include/c++/12/bits/unordered_map.h:443:7: note: candidate: ‘std::unordered_map<_Key, _Tp, _Hash, _Pred, _Alloc>::iterator std::unordered_map<_Key, _Tp, _Hash, _Pred, _Alloc>::insert(const_iterator, node_type&&) [with _Key = long long unsigned int; _Tp = std::array<long long unsigned int, 15>; _Hash = std::hash<long long unsigned int>; _Pred = std::equal_to<long long unsigned int>; _Alloc = std::allocator<std::pair<const long long unsigned int, std::array<long long unsigned int, 15> > >; iterator = std::__detail::_Insert_base<long long unsigned int, std::pair<const long long unsigned int, std::array<long long unsigned int, 15> >, std::allocator<std::pair<const long long unsigned int, std::array<long long unsigned int, 15> > >, std::__detail::_Select1st, std::equal_to<long long unsigned int>, std::hash<long long unsigned int>, std::__detail::_Mod_range_hashing, std::__detail::_Default_ranged_hash, std::__detail::_Prime_rehash_policy, std::__detail::_Hashtable_traits<false, false, true> >::iterator; const_iterator = std::__detail::_Insert_base<long long unsigned int, std::pair<const long long unsigned int, std::array<long long unsigned int, 15> >, std::allocator<std::pair<const long long unsigned int, std::array<long long unsigned int, 15> > >, std::__detail::_Select1st, std::equal_to<long long unsigned int>, std::hash<long long unsigned int>, std::__detail::_Mod_range_hashing, std::__detail::_Default_ranged_hash, std::__detail::_Prime_rehash_policy, std::__detail::_Hashtable_traits<false, false, true> >::const_iterator; node_type = std::_Hashtable<long long unsigned int, std::pair<const long long unsigned int, std::array<long long unsigned int, 15> >, std::allocator<std::pair<const long long unsigned int, std::array<long long unsigned int, 15> > >, std::__detail::_Select1st, std::equal_to<long long unsigned int>, std::hash<long long unsigned int>, std::__detail::_Mod_range_hashing, std::__detail::_Default_ranged_hash, std::__detail::_Prime_rehash_policy, std::__detail::_Hashtable_traits<false, false, true> >::node_type]’
  443 |       insert(const_iterator, node_type&& __nh)
      |       ^~~~~~
/usr/include/c++/12/bits/unordered_map.h:443:7: note:   candidate expects 2 arguments, 1 provided
/usr/include/c++/12/bits/unordered_map.h:551:7: note: candidate: ‘std::pair<typename std::_Hashtable<_Key, std::pair<const _Key, _Val>, _Alloc, std::__detail::_Select1st, _Pred, _Hash, std::__detail::_Mod_range_hashing, std::__detail::_Default_ranged_hash, std::__detail::_Prime_rehash_policy, std::__detail::_Hashtable_traits<std::__not_<std::__and_<std::__is_fast_hash<_Hash>, std::__is_nothrow_invocable<const _Hash&, const _Key&> > >::value, false, true> >::iterator, bool> std::unordered_map<_Key, _Tp, _Hash, _Pred, _Alloc>::insert(const value_type&) [with _Key = long long unsigned int; _Tp = std::array<long long unsigned int, 15>; _Hash = std::hash<long long unsigned int>; _Pred = std::equal_to<long long unsigned int>; _Alloc = std::allocator<std::pair<const long long unsigned int, std::array<long long unsigned int, 15> > >; typename std::_Hashtable<_Key, std::pair<const _Key, _Val>, _Alloc, std::__detail::_Select1st, _Pred, _Hash, std::__detail::_Mod_range_hashing, std::__detail::_Default_ranged_hash, std::__detail::_Prime_rehash_policy, std::__detail::_Hashtable_traits<std::__not_<std::__and_<std::__is_fast_hash<_Hash>, std::__is_nothrow_invocable<const _Hash&, const _Key&> > >::value, false, true> >::iterator = std::__detail::_Insert_base<long long unsigned int, std::pair<const long long unsigned int, std::array<long long unsigned int, 15> >, std::allocator<std::pair<const long long unsigned int, std::array<long long unsigned int, 15> > >, std::__detail::_Select1st, std::equal_to<long long unsigned int>, std::hash<long long unsigned int>, std::__detail::_Mod_range_hashing, std::__detail::_Default_ranged_hash, std::__detail::_Prime_rehash_policy, std::__detail::_Hashtable_traits<false, false, true> >::iterator; value_type = std::pair<const long long unsigned int, std::array<long long unsigned int, 15> >]’
  551 |       insert(const value_type& __x)
      |       ^~~~~~
/usr/include/c++/12/bits/unordered_map.h:551:32: note:   no known conversion for argument 1 from ‘<brace-enclosed initializer list>’ to ‘const std::unordered_map<long long unsigned int, std::array<long long unsigned int, 15> >::value_type&’ {aka ‘const std::pair<const long long unsigned int, std::array<long long unsigned int, 15> >&’}
  551 |       insert(const value_type& __x)
      |              ~~~~~~~~~~~~~~~~~~^~~
/usr/include/c++/12/bits/unordered_map.h:557:7: note: candidate: ‘std::pair<typename std::_Hashtable<_Key, std::pair<const _Key, _Val>, _Alloc, std::__detail::_Select1st, _Pred, _Hash, std::__detail::_Mod_range_hashing, std::__detail::_Default_ranged_hash, std::__detail::_Prime_rehash_policy, std::__detail::_Hashtable_traits<std::__not_<std::__and_<std::__is_fast_hash<_Hash>, std::__is_nothrow_invocable<const _Hash&, const _Key&> > >::value, false, true> >::iterator, bool> std::unordered_map<_Key, _Tp, _Hash, _Pred, _Alloc>::insert(value_type&&) [with _Key = long long unsigned int; _Tp = std::array<long long unsigned int, 15>; _Hash = std::hash<long long unsigned int>; _Pred = std::equal_to<long long unsigned int>; _Alloc = std::allocator<std::pair<const long long unsigned int, std::array<long long unsigned int, 15> > >; typename std::_Hashtable<_Key, std::pair<const _Key, _Val>, _Alloc, std::__detail::_Select1st, _Pred, _Hash, std::__detail::_Mod_range_hashing, std::__detail::_Default_ranged_hash, std::__detail::_Prime_rehash_policy, std::__detail::_Hashtable_traits<std::__not_<std::__and_<std::__is_fast_hash<_Hash>, std::__is_nothrow_invocable<const _Hash&, const _Key&> > >::value, false, true> >::iterator = std::__detail::_Insert_base<long long unsigned int, std::pair<const long long unsigned int, std::array<long long unsigned int, 15> >, std::allocator<std::pair<const long long unsigned int, std::array<long long unsigned int, 15> > >, std::__detail::_Select1st, std::equal_to<long long unsigned int>, std::hash<long long unsigned int>, std::__detail::_Mod_range_hashing, std::__detail::_Default_ranged_hash, std::__detail::_Prime_rehash_policy, std::__detail::_Hashtable_traits<false, false, true> >::iterator; value_type = std::pair<const long long unsigned int, std::array<long long unsigned int, 15> >]’
  557 |       insert(value_type&& __x)
      |       ^~~~~~
/usr/include/c++/12/bits/unordered_map.h:557:27: note:   no known conversion for argument 1 from ‘<brace-enclosed initializer list>’ to ‘std::unordered_map<long long unsigned int, std::array<long long unsigned int, 15> >::value_type&&’ {aka ‘std::pair<const long long unsigned int, std::array<long long unsigned int, 15> >&&’}
  557 |       insert(value_type&& __x)
      |              ~~~~~~~~~~~~~^~~
/usr/include/c++/12/bits/unordered_map.h:590:7: note: candidate: ‘std::unordered_map<_Key, _Tp, _Hash, _Pred, _Alloc>::iterator std::unordered_map<_Key, _Tp, _Hash, _Pred, _Alloc>::insert(const_iterator, const value_type&) [with _Key = long long unsigned int; _Tp = std::array<long long unsigned int, 15>; _Hash = std::hash<long long unsigned int>; _Pred = std::equal_to<long long unsigned int>; _Alloc = std::allocator<std::pair<const long long unsigned int, std::array<long long unsigned int, 15> > >; iterator = std::__detail::_Insert_base<long long unsigned int, std::pair<const long long unsigned int, std::array<long long unsigned int, 15> >, std::allocator<std::pair<const long long unsigned int, std::array<long long unsigned int, 15> > >, std::__detail::_Select1st, std::equal_to<long long unsigned int>, std::hash<long long unsigned int>, std::__detail::_Mod_range_hashing, std::__detail::_Default_ranged_hash, std::__detail::_Prime_rehash_policy, std::__detail::_Hashtable_traits<false, false, true> >::iterator; const_iterator = std::__detail::_Insert_base<long long unsigned int, std::pair<const long long unsigned int, std::array<long long unsigned int, 15> >, std::allocator<std::pair<const long long unsigned int, std::array<long long unsigned int, 15> > >, std::__detail::_Select1st, std::equal_to<long long unsigned int>, std::hash<long long unsigned int>, std::__detail::_Mod_range_hashing, std::__detail::_Default_ranged_hash, std::__detail::_Prime_rehash_policy, std::__detail::_Hashtable_traits<false, false, true> >::const_iterator; value_type = std::pair<const long long unsigned int, std::array<long long unsigned int, 15> >]’
  590 |       insert(const_iterator __hint, const value_type& __x)
      |       ^~~~~~
/usr/include/c++/12/bits/unordered_map.h:590:7: note:   candidate expects 2 arguments, 1 provided
/usr/include/c++/12/bits/unordered_map.h:596:7: note: candidate: ‘std::unordered_map<_Key, _Tp, _Hash, _Pred, _Alloc>::iterator std::unordered_map<_Key, _Tp, _Hash, _Pred, _Alloc>::insert(const_iterator, value_type&&) [with _Key = long long unsigned int; _Tp = std::array<long long unsigned int, 15>; _Hash = std::hash<long long unsigned int>; _Pred = std::equal_to<long long unsigned int>; _Alloc = std::allocator<std::pair<const long long unsigned int, std::array<long long unsigned int, 15> > >; iterator = std::__detail::_Insert_base<long long unsigned int, std::pair<const long long unsigned int, std::array<long long unsigned int, 15> >, std::allocator<std::pair<const long long unsigned int, std::array<long long unsigned int, 15> > >, std::__detail::_Select1st, std::equal_to<long long unsigned int>, std::hash<long long unsigned int>, std::__detail::_Mod_range_hashing, std::__detail::_Default_ranged_hash, std::__detail::_Prime_rehash_policy, std::__detail::_Hashtable_traits<false, false, true> >::iterator; const_iterator = std::__detail::_Insert_base<long long unsigned int, std::pair<const long long unsigned int, std::array<long long unsigned int, 15> >, std::allocator<std::pair<const long long unsigned int, std::array<long long unsigned int, 15> > >, std::__detail::_Select1st, std::equal_to<long long unsigned int>, std::hash<long long unsigned int>, std::__detail::_Mod_range_hashing, std::__detail::_Default_ranged_hash, std::__detail::_Prime_rehash_policy, std::__detail::_Hashtable_traits<false, false, true> >::const_iterator; value_type = std::pair<const long long unsigned int, std::array<long long unsigned int, 15> >]’
  596 |       insert(const_iterator __hint, value_type&& __x)
      |       ^~~~~~
/usr/include/c++/12/bits/unordered_map.h:596:7: note:   candidate expects 2 arguments, 1 provided
/usr/include/c++/12/bits/unordered_map.h:627:7: note: candidate: ‘void std::unordered_map<_Key, _Tp, _Hash, _Pred, _Alloc>::insert(std::initializer_list<typename std::_Hashtable<_Key, std::pair<const _Key, _Val>, _Alloc, std::__detail::_Select1st, _Pred, _Hash, std::__detail::_Mod_range_hashing, std::__detail::_Default_ranged_hash, std::__detail::_Prime_rehash_policy, std::__detail::_Hashtable_traits<std::__not_<std::__and_<std::__is_fast_hash<_Hash>, std::__is_nothrow_invocable<const _Hash&, const _Key&> > >::value, false, true> >::value_type>) [with _Key = long long unsigned int; _Tp = std::array<long long unsigned int, 15>; _Hash = std::hash<long long unsigned int>; _Pred = std::equal_to<long long unsigned int>; _Alloc = std::allocator<std::pair<const long long unsigned int, std::array<long long unsigned int, 15> > >; typename std::_Hashtable<_Key, std::pair<const _Key, _Val>, _Alloc, std::__detail::_Select1st, _Pred, _Hash, std::__detail::_Mod_range_hashing, std::__detail::_Default_ranged_hash, std::__detail::_Prime_rehash_policy, std::__detail::_Hashtable_traits<std::__not_<std::__and_<std::__is_fast_hash<_Hash>, std::__is_nothrow_invocable<const _Hash&, const _Key&> > >::value, false, true> >::value_type = std::pair<const long long unsigned int, std::array<long long unsigned int, 15> >]’
  627 |       insert(initializer_list<value_type> __l)
      |       ^~~~~~
/usr/include/c++/12/bits/unordered_map.h:627:43: note:   no known conversion for argument 1 from ‘<brace-enclosed initializer list>’ to ‘std::initializer_list<std::pair<const long long unsigned int, std::array<long long unsigned int, 15> > >’
  627 |       insert(initializer_list<value_type> __l)
      |              ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~
SoloCommon.h: In member function ‘void SoloReadFlagClass::countsAddNoCBarray(std::array<long long unsigned int, 15>&)’:
SoloCommon.h:74:42: error: no match for ‘operator[]’ (operand types are ‘std::array<long long unsigned int, 15>’ and ‘unsigned int’)
   74 |             flagCountsNoCB[ibit] += arrIn[ibit];
      |                                          ^
make[2]: *** [Makefile:96: SoloBarcode.o] Error 1
make[2]: Leaving directory '/<<PKGBUILDDIR>>/source'
dh_auto_build: error: cd source && make -j8 "INSTALL=install --strip-program=true" SFX=-sse3 "CCFLAGS_common_add=-flto -flto -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x" "CXXFLAGS=-g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse3" "LDFLAGS_add=-Wl,-z,relro -Wl,-z,now" STAR-sse3 STARlong-sse3 returned exit code 2
make[1]: *** [debian/rules:26: override_dh_auto_build] Error 25
make[1]: Leaving directory '/<<PKGBUILDDIR>>'
make: *** [debian/rules:21: binary] Error 2
dpkg-buildpackage: error: debian/rules binary subprocess returned exit status 2

#1013030#10

Date:: 2022-06-24 20:45:01 UTC

From:

To:

We believe that the bug you reported is fixed in the latest version of
rna-star, 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 1013030@bugs.debian.org,
and the maintainer will reopen the bug report if appropriate.

Debian distribution maintenance software
pp.
Nilesh Patra <nilesh@debian.org> (supplier of updated rna-star 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 ftpmaster@ftp-master.debian.org)
Format: 1.8
Date: Fri, 24 Jun 2022 19:46:55 +0000
Source: rna-star
Architecture: source
Version: 2.7.10a+dfsg-3
Distribution: unstable
Urgency: medium
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Changed-By: Nilesh Patra <nilesh@debian.org>
Closes: 1013030
Changes:
 rna-star (2.7.10a+dfsg-3) unstable; urgency=medium
 .
   * Add patch to fix gcc-12 FTBFS (Closes: #1013030)
Checksums-Sha1:
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Checksums-Sha256:
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Files:
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#1013030 rna-star: ftbfs with GCC-12 #1013030

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