Your message dated Tue, 07 Nov 2023 20:47:36 +0000
with message-id <e1r0sz2-000z17...@fasolo.debian.org>
and subject line Bug#1054708: fixed in mecat2 0.0+git20200428.f54c542+ds-4
has caused the Debian Bug report #1054708,
regarding mecat2: FTBFS: app/fsa/simple_align.hpp:12:45: error: ‘uint8_t’ has
not been declared
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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--
1054708: https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=1054708
Debian Bug Tracking System
Contact ow...@bugs.debian.org with problems
--- Begin Message ---
Source: mecat2
Version: 0.0+git20200428.f54c542+ds-3
Severity: serious
Justification: FTBFS
Tags: trixie sid ftbfs
User: lu...@debian.org
Usertags: ftbfs-20231027 ftbfs-trixie
Hi,
During a rebuild of all packages in sid, your package failed to build
on amd64.
Relevant part (hopefully):
> g++ -o ../Linux-amd64/obj/libfsa.a/app/fsa/simple_align.o -c -MD
> -D_GLIBCXX_PARALLEL -pthread -O3 -Wall -std=c++11 -DNDEBUG -fopenmp
> -U_GLIBCXX_PARALLEL -std=c++11 -Wall -O3 -D_FILE_OFFSET_BITS=64 -Iapp/fsa
> app/fsa/simple_align.cpp
> In file included from app/fsa/simple_align.cpp:1:
> app/fsa/simple_align.hpp:12:45: error: ‘uint8_t’ has not been declared
> 12 | KmerList(const std::string& target, uint8_t k);
> | ^~~~~~~
> app/fsa/simple_align.hpp:21:30: error: ‘uint32_t’ has not been declared
> 21 | size_t FirstPosition(uint32_t bkmer) const {
> | ^~~~~~~~
> app/fsa/simple_align.hpp:28:21: error: ‘uint32_t’ has not been declared
> 28 | size_t Size(uint32_t bkmer) const {
> | ^~~~~~~~
> app/fsa/simple_align.hpp:37:28: error: ‘uint32_t’ was not declared in this
> scope
> 37 | std::unordered_map<uint32_t, Node> list;
> | ^~~~~~~~
> app/fsa/simple_align.hpp:8:1: note: ‘uint32_t’ is defined in header
> ‘<cstdint>’; did you forget to ‘#include <cstdint>’?
> 7 | #include <vector>
> +++ |+#include <cstdint>
> 8 |
> app/fsa/simple_align.hpp:37:42: error: template argument 1 is invalid
> 37 | std::unordered_map<uint32_t, Node> list;
> | ^
> app/fsa/simple_align.hpp:37:42: error: template argument 3 is invalid
> app/fsa/simple_align.hpp:37:42: error: template argument 4 is invalid
> app/fsa/simple_align.hpp:37:42: error: template argument 5 is invalid
> app/fsa/simple_align.hpp:74:44: error: ‘uint8_t’ has not been declared
> 74 | SimpleAlign(const std::string &target, uint8_t k);
> | ^~~~~~~
> app/fsa/simple_align.hpp:81:12: error: ‘uint32_t’ does not name a type
> 81 | static uint32_t KmerMask(const uint8_t k);
> | ^~~~~~~~
> app/fsa/simple_align.hpp:81:12: note: ‘uint32_t’ is defined in header
> ‘<cstdint>’; did you forget to ‘#include <cstdint>’?
> app/fsa/simple_align.hpp:82:12: error: ‘uint32_t’ does not name a type
> 82 | static uint32_t CalcKmer(const char* seq, size_t k);
> | ^~~~~~~~
> app/fsa/simple_align.hpp:82:12: note: ‘uint32_t’ is defined in header
> ‘<cstdint>’; did you forget to ‘#include <cstdint>’?
> app/fsa/simple_align.hpp:83:12: error: ‘uint32_t’ does not name a type
> 83 | static uint32_t MoveKmer(uint32_t bkmer, size_t k, char e);
> | ^~~~~~~~
> app/fsa/simple_align.hpp:83:12: note: ‘uint32_t’ is defined in header
> ‘<cstdint>’; did you forget to ‘#include <cstdint>’?
> app/fsa/simple_align.hpp:89:5: error: ‘uint8_t’ does not name a type
> 89 | uint8_t k_;
> | ^~~~~~~
> app/fsa/simple_align.hpp:89:5: note: ‘uint8_t’ is defined in header
> ‘<cstdint>’; did you forget to ‘#include <cstdint>’?
> app/fsa/simple_align.hpp:91:5: error: ‘uint8_t’ does not name a type
> 91 | uint8_t query_stride_;
> | ^~~~~~~
> app/fsa/simple_align.hpp:91:5: note: ‘uint8_t’ is defined in header
> ‘<cstdint>’; did you forget to ‘#include <cstdint>’?
> app/fsa/simple_align.hpp: In member function ‘size_t
> SimpleAlign::KmerList::FirstPosition(int) const’:
> app/fsa/simple_align.hpp:22:28: error: request for member ‘find’ in ‘((const
> SimpleAlign::KmerList*)this)->SimpleAlign::KmerList::list’, which is of
> non-class type ‘const int’
> 22 | auto it = list.find(bkmer);
> | ^~~~
> app/fsa/simple_align.hpp:23:31: error: request for member ‘end’ in ‘((const
> SimpleAlign::KmerList*)this)->SimpleAlign::KmerList::list’, which is of
> non-class type ‘const int’
> 23 | return it != list.end() ? it->second.head :
> next_same.size();
> | ^~~
> app/fsa/simple_align.hpp: In member function ‘size_t
> SimpleAlign::KmerList::Size(int) const’:
> app/fsa/simple_align.hpp:29:28: error: request for member ‘find’ in ‘((const
> SimpleAlign::KmerList*)this)->SimpleAlign::KmerList::list’, which is of
> non-class type ‘const int’
> 29 | auto it = list.find(bkmer);
> | ^~~~
> app/fsa/simple_align.hpp:30:31: error: request for member ‘end’ in ‘((const
> SimpleAlign::KmerList*)this)->SimpleAlign::KmerList::list’, which is of
> non-class type ‘const int’
> 30 | return it != list.end() ? it->second.count : 0;
> | ^~~
> app/fsa/simple_align.cpp: At global scope:
> app/fsa/simple_align.cpp:19:1: error: no declaration matches
> ‘SimpleAlign::KmerList::KmerList(const std::string&, uint8_t)’
> 19 | SimpleAlign::KmerList::KmerList(const std::string &target, uint8_t k)
> {
> | ^~~~~~~~~~~
> app/fsa/simple_align.hpp:11:12: note: candidates are:
> ‘SimpleAlign::KmerList::KmerList(SimpleAlign::KmerList&&)’
> 11 | struct KmerList {
> | ^~~~~~~~
> app/fsa/simple_align.hpp:11:12: note:
> ‘SimpleAlign::KmerList::KmerList(const SimpleAlign::KmerList&)’
> app/fsa/simple_align.hpp:12:9: note:
> ‘SimpleAlign::KmerList::KmerList(const std::string&, int)’
> 12 | KmerList(const std::string& target, uint8_t k);
> | ^~~~~~~~
> app/fsa/simple_align.hpp:11:12: note: ‘struct SimpleAlign::KmerList’ defined
> here
> 11 | struct KmerList {
> | ^~~~~~~~
> app/fsa/simple_align.cpp:54:1: error: no declaration matches
> ‘SimpleAlign::SimpleAlign(const std::string&, uint8_t)’
> 54 | SimpleAlign::SimpleAlign(const std::string &target, uint8_t k)
> | ^~~~~~~~~~~
> app/fsa/simple_align.hpp:9:7: note: candidates are:
> ‘SimpleAlign::SimpleAlign(SimpleAlign&&)’
> 9 | class SimpleAlign {
> | ^~~~~~~~~~~
> app/fsa/simple_align.hpp:9:7: note:
> ‘SimpleAlign::SimpleAlign(const SimpleAlign&)’
> app/fsa/simple_align.hpp:74:5: note:
> ‘SimpleAlign::SimpleAlign(const std::string&, int)’
> 74 | SimpleAlign(const std::string &target, uint8_t k);
> | ^~~~~~~~~~~
> app/fsa/simple_align.hpp:9:7: note: ‘class SimpleAlign’ defined here
> 9 | class SimpleAlign {
> | ^~~~~~~~~~~
> app/fsa/simple_align.cpp: In member function ‘SimpleAlign::KmerMatch
> SimpleAlign::FindKmerMatch(const std::string&, size_t)’:
> app/fsa/simple_align.cpp:64:39: error: ‘k_’ was not declared in this scope
> 64 | for (size_t i=0; i<query.size() - k_ + 1; i += stride) {
> | ^~
> app/fsa/simple_align.cpp:65:22: error: ‘CalcKmer’ was not declared in this
> scope
> 65 | auto bkmer = CalcKmer(query.c_str()+i, k_);
> | ^~~~~~~~
> app/fsa/simple_align.cpp: In member function ‘SimpleAlign::Result
> SimpleAlign::Align(const std::string&, int, bool)’:
> app/fsa/simple_align.cpp:78:44: error: ‘query_stride_’ was not declared in
> this scope
> 78 | KmerMatch match = FindKmerMatch(query, query_stride_);
> | ^~~~~~~~~~~~~
> app/fsa/simple_align.cpp:79:44: error: ‘k_’ was not declared in this scope
> 79 | auto range = FindCandidateRange(match, k_*5, 12);
> | ^~
> app/fsa/simple_align.cpp: In member function ‘SimpleAlign::Result
> SimpleAlign::Align(const std::string&, const std::string&, int, bool)’:
> app/fsa/simple_align.cpp:153:37: warning: comparison of integer expressions
> of different signedness: ‘int’ and
> ‘std::__cxx11::basic_string<char>::size_type’ {aka ‘long unsigned int’}
> [-Wsign-compare]
> 153 | if ( node.x + node.len >= query.size() || node.y +
> node.len >= target_.size()) {
> | ~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~
> app/fsa/simple_align.cpp:153:75: warning: comparison of integer expressions
> of different signedness: ‘int’ and
> ‘std::__cxx11::basic_string<char>::size_type’ {aka ‘long unsigned int’}
> [-Wsign-compare]
> 153 | if ( node.x + node.len >= query.size() || node.y +
> node.len >= target_.size()) {
> |
> ~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~
> app/fsa/simple_align.cpp: At global scope:
> app/fsa/simple_align.cpp:297:10: error: no declaration matches ‘uint32_t
> SimpleAlign::KmerMask(uint8_t)’
> 297 | uint32_t SimpleAlign::KmerMask(uint8_t k) {
> | ^~~~~~~~~~~
> app/fsa/simple_align.cpp:297:10: note: no functions named ‘uint32_t
> SimpleAlign::KmerMask(uint8_t)’
> app/fsa/simple_align.hpp:9:7: note: ‘class SimpleAlign’ defined here
> 9 | class SimpleAlign {
> | ^~~~~~~~~~~
> app/fsa/simple_align.cpp:308:10: error: no declaration matches ‘uint32_t
> SimpleAlign::CalcKmer(const char*, size_t)’
> 308 | uint32_t SimpleAlign::CalcKmer(const char* seq, size_t k) {
> | ^~~~~~~~~~~
> app/fsa/simple_align.cpp:308:10: note: no functions named ‘uint32_t
> SimpleAlign::CalcKmer(const char*, size_t)’
> app/fsa/simple_align.hpp:9:7: note: ‘class SimpleAlign’ defined here
> 9 | class SimpleAlign {
> | ^~~~~~~~~~~
> app/fsa/simple_align.cpp:321:10: error: no declaration matches ‘uint32_t
> SimpleAlign::MoveKmer(uint32_t, size_t, char)’
> 321 | uint32_t SimpleAlign::MoveKmer(uint32_t bkmer, size_t k, char e) {
> | ^~~~~~~~~~~
> app/fsa/simple_align.cpp:321:10: note: no functions named ‘uint32_t
> SimpleAlign::MoveKmer(uint32_t, size_t, char)’
> app/fsa/simple_align.hpp:9:7: note: ‘class SimpleAlign’ defined here
> 9 | class SimpleAlign {
> | ^~~~~~~~~~~
> make[2]: *** [Makefile:411:
> ../Linux-amd64/obj/libfsa.a/app/fsa/simple_align.o] Error 1
The full build log is available from:
http://qa-logs.debian.net/2023/10/27/mecat2_0.0+git20200428.f54c542+ds-3_unstable.log
All bugs filed during this archive rebuild are listed at:
https://bugs.debian.org/cgi-bin/pkgreport.cgi?tag=ftbfs-20231027;users=lu...@debian.org
or:
https://udd.debian.org/bugs/?release=na&merged=ign&fnewerval=7&flastmodval=7&fusertag=only&fusertagtag=ftbfs-20231027&fusertaguser=lu...@debian.org&allbugs=1&cseverity=1&ctags=1&caffected=1#results
A list of current common problems and possible solutions is available at
http://wiki.debian.org/qa.debian.org/FTBFS . You're welcome to contribute!
If you reassign this bug to another package, please mark it as 'affects'-ing
this package. See https://www.debian.org/Bugs/server-control#affects
If you fail to reproduce this, please provide a build log and diff it with mine
so that we can identify if something relevant changed in the meantime.
--- End Message ---
--- Begin Message ---
Source: mecat2
Source-Version: 0.0+git20200428.f54c542+ds-4
Done: Andreas Tille <ti...@debian.org>
We believe that the bug you reported is fixed in the latest version of
mecat2, 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 1054...@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 mecat2 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: SHA256
Format: 1.8
Date: Tue, 07 Nov 2023 08:44:12 +0100
Source: mecat2
Architecture: source
Version: 0.0+git20200428.f54c542+ds-4
Distribution: unstable
Urgency: medium
Maintainer: Debian Med Packaging Team
<debian-med-packag...@lists.alioth.debian.org>
Changed-By: Andreas Tille <ti...@debian.org>
Closes: 1054708
Changes:
mecat2 (0.0+git20200428.f54c542+ds-4) unstable; urgency=medium
.
* Team upload.
* Add patch to fix FTBFS with gcc-13
Closes: #1054708
* Standards-Version: 4.6.2 (routine-update)
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