Bug#959643: marked as done (pbbam: FTBFS: ../tests/src/test_BamWriter.cpp:40:34: error: call of overloaded ‘CigarData(const char [1])’ is ambiguous)

[Debian Bug Tracking System]

Your message dated Fri, 11 Sep 2020 10:00:21 +
with message-id 
and subject line Bug#959643: fixed in pbbam 1.3.0+dfsg-1
has caused the Debian Bug report #959643,
regarding pbbam: FTBFS: ../tests/src/test_BamWriter.cpp:40:34: error: call of 
overloaded ‘CigarData(const char [1])’ is ambiguous
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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-- 
959643: https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=959643
Debian Bug Tracking System
Contact ow...@bugs.debian.org with problems
--- Begin Message ---
Source: pbbam
Version: 1.0.6+dfsg-2
Severity: serious
Justification: FTBFS on amd64
Tags: bullseye sid ftbfs
Usertags: ftbfs-20200501 ftbfs-bullseye

Hi,

During a rebuild of all packages in sid, your package failed to build
on amd64.

Relevant part (hopefully):
> c++ -Itests/59830eb@@pbbam_test@exe -Itests -I../tests -Iinclude -I../include 
> -I/usr/include -fdiagnostics-color=always -DNDEBUG -pipe 
> -D_FILE_OFFSET_BITS=64 -std=c++14 -g -O2 
> -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat 
> -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DBOOST_ALL_NO_LIB 
> -DBOOST_ALL_DYN_LINK -Wl,--start-group -lpthread -Wl,--end-group 
> -DGTEST_HAS_PTHREAD=1 -Wduplicated-cond -Wduplicated-branches -Wlogical-op 
> -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow 
> -Wformat=1 -MD -MQ 'tests/59830eb@@pbbam_test@exe/src_test_BamWriter.cpp.o' 
> -MF 'tests/59830eb@@pbbam_test@exe/src_test_BamWriter.cpp.o.d' -o 
> 'tests/59830eb@@pbbam_test@exe/src_test_BamWriter.cpp.o' -c 
> ../tests/src/test_BamWriter.cpp
> ../tests/src/test_BamWriter.cpp: In function ‘void 
> BamWriterTests::checkSingleRecord(bool)’:
> ../tests/src/test_BamWriter.cpp:40:34: error: call of overloaded 
> ‘CigarData(const char [1])’ is ambiguous
>40 | bamRecord.Impl().CigarData("");
>   |  ^
> In file included from ../include/pbbam/BamRecord.h:24,
>  from ../tests/src/test_BamWriter.cpp:11:
> ../include/pbbam/BamRecordImpl.h:251:20: note: candidate: 
> ‘PacBio::BAM::BamRecordImpl& PacBio::BAM::BamRecordImpl::CigarData(const 
> Cigar&)’
>   251 | BamRecordImpl& CigarData(const Cigar& cigar);
>   |^
> ../include/pbbam/BamRecordImpl.h:258:20: note: candidate: 
> ‘PacBio::BAM::BamRecordImpl& PacBio::BAM::BamRecordImpl::CigarData(const 
> string&)’
>   258 | BamRecordImpl& CigarData(const std::string& cigarString);
>   |^
> [129/216] c++ -Itests/59830eb@@pbbam_test@exe -Itests -I../tests -Iinclude 
> -I../include -I/usr/include -fdiagnostics-color=always -DNDEBUG -pipe 
> -D_FILE_OFFSET_BITS=64 -std=c++14 -g -O2 
> -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat 
> -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DBOOST_ALL_NO_LIB 
> -DBOOST_ALL_DYN_LINK -Wl,--start-group -lpthread -Wl,--end-group 
> -DGTEST_HAS_PTHREAD=1 -Wduplicated-cond -Wduplicated-branches -Wlogical-op 
> -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow 
> -Wformat=1 -MD -MQ 
> 'tests/59830eb@@pbbam_test@exe/src_test_BamRecordMapping.cpp.o' -MF 
> 'tests/59830eb@@pbbam_test@exe/src_test_BamRecordMapping.cpp.o.d' -o 
> 'tests/59830eb@@pbbam_test@exe/src_test_BamRecordMapping.cpp.o' -c 
> ../tests/src/test_BamRecordMapping.cpp
> [130/216] c++ -Itests/59830eb@@pbbam_test@exe -Itests -I../tests -Iinclude 
> -I../include -I/usr/include -fdiagnostics-color=always -DNDEBUG -pipe 
> -D_FILE_OFFSET_BITS=64 -std=c++14 -g -O2 
> -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat 
> -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DBOOST_ALL_NO_LIB 
> -DBOOST_ALL_DYN_LINK -Wl,--start-group -lpthread -Wl,--end-group 
> -DGTEST_HAS_PTHREAD=1 -Wduplicated-cond -Wduplicated-branches -Wlogical-op 
> -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow 
> -Wformat=1 -MD -MQ 
> 'tests/59830eb@@pbbam_test@exe/src_test_BamRecordClipping.cpp.o' -MF 
> 'tests/59830eb@@pbbam_test@exe/src_test_BamRecordClipping.cpp.o.d' -o 
> 'tests/59830eb@@pbbam_test@exe/src_test_BamRecordClipping.cpp.o' -c 
> ../tests/src/test_BamRecordClipping.cpp
> [131/216] c++ -Itests/59830eb@@pbbam_test@exe -Itests -I../tests -Iinclude 
> -I../include -I/usr/include -fdiagnostics-color=always -DNDEBUG -pipe 
> -D_FILE_OFFSET_BITS=64 -std=c++14 -g -O2 
> -fdebug-prefix-map=/

Bug#959643: Any idea whether latest version of pbbam is 1.0.7 or rather 1.3.0 (Was: Bug#959643)

[Andreas Tille]

Hi Adrian,

On Sun, Jun 21, 2020 at 07:13:25PM +0300, Adrian Bunk wrote:
> On Wed, May 27, 2020 at 02:06:40PM +1200, Michael Hudson-Doyle wrote:
> > FWIW there is a new release (1.0.7) available and that seems to fix this
> > failure (in Ubuntu, anyway).
> 
> Andreas, after looking at the sources I would say upgrading pbbam like 
> Ubuntu has done (including a round through NEW for the changed soname) 
> is the best way to fix this FTBFS.
> 
> BTW: The watch feels seems to no longer work.

I intended to fix the watch file using

diff --git a/debian/watch b/debian/watch
index 1b64644..d6bee57 100644
--- a/debian/watch
+++ b/debian/watch
@@ -1,4 +1,4 @@
 version=4
 
 opts="repacksuffix=+dfsg,dversionmangle=s/\+dfsg//g,repack,compression=xz" \
-  https://github.com/PacificBiosciences/pbbam/releases 
.*/archive/@ANY_VERSION@@ARCHIVE_EXT@
+  https://github.com/PacificBiosciences/pbbam/releases 
.*/archive/v?@ANY_VERSION@@ARCHIVE_EXT@


and expected to get version 1.0.7 as result since this is the latest
version mentioned on the Releases page.  However, it returns 1.3.0
which is actually the latest tag.  I'm now wondering what we should
package.  Any user of pbbam here on the list to clarify?

Kind regards

  Andreas.

-- 
http://fam-tille.de

Bug#959643:

[Adrian Bunk]

On Wed, May 27, 2020 at 02:06:40PM +1200, Michael Hudson-Doyle wrote:
> FWIW there is a new release (1.0.7) available and that seems to fix this
> failure (in Ubuntu, anyway).

Andreas, after looking at the sources I would say upgrading pbbam like 
Ubuntu has done (including a round through NEW for the changed soname) 
is the best way to fix this FTBFS.

cu
Adrian

BTW: The watch feels seems to no longer work.

Bug#959643:

[Michael Hudson-Doyle]

FWIW there is a new release (1.0.7) available and that seems to fix this
failure (in Ubuntu, anyway).

Bug#959643: pbbam: FTBFS: ../tests/src/test_BamWriter.cpp:40:34: error: call of overloaded ‘CigarData(const char [1])’ is ambiguous

[Lucas Nussbaum]

Source: pbbam
Version: 1.0.6+dfsg-2
Severity: serious
Justification: FTBFS on amd64
Tags: bullseye sid ftbfs
Usertags: ftbfs-20200501 ftbfs-bullseye

Hi,

During a rebuild of all packages in sid, your package failed to build
on amd64.

Relevant part (hopefully):
> c++ -Itests/59830eb@@pbbam_test@exe -Itests -I../tests -Iinclude -I../include 
> -I/usr/include -fdiagnostics-color=always -DNDEBUG -pipe 
> -D_FILE_OFFSET_BITS=64 -std=c++14 -g -O2 
> -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat 
> -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DBOOST_ALL_NO_LIB 
> -DBOOST_ALL_DYN_LINK -Wl,--start-group -lpthread -Wl,--end-group 
> -DGTEST_HAS_PTHREAD=1 -Wduplicated-cond -Wduplicated-branches -Wlogical-op 
> -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow 
> -Wformat=1 -MD -MQ 'tests/59830eb@@pbbam_test@exe/src_test_BamWriter.cpp.o' 
> -MF 'tests/59830eb@@pbbam_test@exe/src_test_BamWriter.cpp.o.d' -o 
> 'tests/59830eb@@pbbam_test@exe/src_test_BamWriter.cpp.o' -c 
> ../tests/src/test_BamWriter.cpp
> ../tests/src/test_BamWriter.cpp: In function ‘void 
> BamWriterTests::checkSingleRecord(bool)’:
> ../tests/src/test_BamWriter.cpp:40:34: error: call of overloaded 
> ‘CigarData(const char [1])’ is ambiguous
>40 | bamRecord.Impl().CigarData("");
>   |  ^
> In file included from ../include/pbbam/BamRecord.h:24,
>  from ../tests/src/test_BamWriter.cpp:11:
> ../include/pbbam/BamRecordImpl.h:251:20: note: candidate: 
> ‘PacBio::BAM::BamRecordImpl& PacBio::BAM::BamRecordImpl::CigarData(const 
> Cigar&)’
>   251 | BamRecordImpl& CigarData(const Cigar& cigar);
>   |^
> ../include/pbbam/BamRecordImpl.h:258:20: note: candidate: 
> ‘PacBio::BAM::BamRecordImpl& PacBio::BAM::BamRecordImpl::CigarData(const 
> string&)’
>   258 | BamRecordImpl& CigarData(const std::string& cigarString);
>   |^
> [129/216] c++ -Itests/59830eb@@pbbam_test@exe -Itests -I../tests -Iinclude 
> -I../include -I/usr/include -fdiagnostics-color=always -DNDEBUG -pipe 
> -D_FILE_OFFSET_BITS=64 -std=c++14 -g -O2 
> -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat 
> -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DBOOST_ALL_NO_LIB 
> -DBOOST_ALL_DYN_LINK -Wl,--start-group -lpthread -Wl,--end-group 
> -DGTEST_HAS_PTHREAD=1 -Wduplicated-cond -Wduplicated-branches -Wlogical-op 
> -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow 
> -Wformat=1 -MD -MQ 
> 'tests/59830eb@@pbbam_test@exe/src_test_BamRecordMapping.cpp.o' -MF 
> 'tests/59830eb@@pbbam_test@exe/src_test_BamRecordMapping.cpp.o.d' -o 
> 'tests/59830eb@@pbbam_test@exe/src_test_BamRecordMapping.cpp.o' -c 
> ../tests/src/test_BamRecordMapping.cpp
> [130/216] c++ -Itests/59830eb@@pbbam_test@exe -Itests -I../tests -Iinclude 
> -I../include -I/usr/include -fdiagnostics-color=always -DNDEBUG -pipe 
> -D_FILE_OFFSET_BITS=64 -std=c++14 -g -O2 
> -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat 
> -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DBOOST_ALL_NO_LIB 
> -DBOOST_ALL_DYN_LINK -Wl,--start-group -lpthread -Wl,--end-group 
> -DGTEST_HAS_PTHREAD=1 -Wduplicated-cond -Wduplicated-branches -Wlogical-op 
> -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow 
> -Wformat=1 -MD -MQ 
> 'tests/59830eb@@pbbam_test@exe/src_test_BamRecordClipping.cpp.o' -MF 
> 'tests/59830eb@@pbbam_test@exe/src_test_BamRecordClipping.cpp.o.d' -o 
> 'tests/59830eb@@pbbam_test@exe/src_test_BamRecordClipping.cpp.o' -c 
> ../tests/src/test_BamRecordClipping.cpp
> [131/216] c++ -Itests/59830eb@@pbbam_test@exe -Itests -I../tests -Iinclude 
> -I../include -I/usr/include -fdiagnostics-color=always -DNDEBUG -pipe 
> -D_FILE_OFFSET_BITS=64 -std=c++14 -g -O2 
> -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat 
> -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DBOOST_ALL_NO_LIB 
> -DBOOST_ALL_DYN_LINK -Wl,--start-group -lpthread -Wl,--end-group 
> -DGTEST_HAS_PTHREAD=1 -Wduplicated-cond -Wduplicated-branches -Wlogical-op 
> -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow 
> -Wformat=1 -MD -MQ 
> 'tests/59830eb@@pbbam_test@exe/src_test_BamRecordImplVariableData.cpp.o' -MF 
> 'tests/59830eb@@pbbam_test@exe/src_test_BamRecordImplVariableData.cpp.o.d' -o 
> 'tests/59830eb@@pbbam_test@exe/src_test_BamRecordImplVariableData.cpp.o' -c 
> ../tests/src/test_BamRecordImplVariableData.cpp
> ninja: build stopped: subcommand failed.
> dh_auto_build: error: cd obj-x86_64-linux-gnu && LC_ALL=C.UTF-8 ninja -j4 -v 
> returned exit code 1
> make: *** [debian/rules:13: build] Error 25

The full build log is available from:
   http://qa-logs.debian.net/2020/05/01/pbbam_1.0.6+dfsg-2_unstable.log

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!

About the archive rebuild: