Bug#940564: racon: FTBFS against libspoa3

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Bug#940564: racon: FTBFS against libspoa3

Graham Inggs-3
Source: racon
Version: 1.3.2-1
Severity: serious

Hi Maintainer

In a recent binNMU against libspoa3 [1], racon FTBFS with the errors below.

Regards
Graham


[1]
https://buildd.debian.org/status/fetch.php?pkg=racon&arch=amd64&ver=1.3.2-1%2Bb2&stamp=1566980028&raw=0


/usr/bin/c++   -I/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/config
-I/<<PKGBUILDDIR>>/src  -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=.
-fstack-protector-strong -Wformat -Werror=format-security -Wdate-time
-D_FORTIFY_SOURCE=2 -Wall -Wextra -pedantic   -std=gnu++11 -o
CMakeFiles/racon.dir/src/main.cpp.o -c /<<PKGBUILDDIR>>/src/main.cpp
/<<PKGBUILDDIR>>/src/polisher.cpp: In member function ‘void
racon::Polisher::initialize()’:
/<<PKGBUILDDIR>>/src/polisher.cpp:169:15: error: ‘class
bioparser::Parser<racon::Sequence>’ has no member named ‘parse_objects’
   169 |     tparser_->parse_objects(sequences_, -1);
       |               ^~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/polisher.cpp:196:33: error: ‘class
bioparser::Parser<racon::Sequence>’ has no member named ‘parse_objects’
   196 |         auto status = sparser_->parse_objects(sequences_,
kChunkSize);
       |                                 ^~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/polisher.cpp:277:33: error: ‘class
bioparser::Parser<racon::Overlap>’ has no member named ‘parse_objects’
   277 |         auto status = oparser_->parse_objects(overlaps,
kChunkSize);
       |                                 ^~~~~~~~~~~~~
...
/<<PKGBUILDDIR>>/src/window.cpp: In member function ‘bool
racon::Window::generate_consensus(std::shared_ptr<spoa::AlignmentEngine>)’:
/<<PKGBUILDDIR>>/src/window.cpp:89:43: error: ‘using element_type =
class spoa::AlignmentEngine’ {aka ‘class spoa::AlignmentEngine’} has no
member named ‘align_sequence_with_graph’
    89 |             alignment =
alignment_engine->align_sequence_with_graph(
       |                                           ^~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/window.cpp:95:43: error: ‘using element_type =
class spoa::AlignmentEngine’ {aka ‘class spoa::AlignmentEngine’} has no
member named ‘align_sequence_with_graph’
    95 |             alignment =
alignment_engine->align_sequence_with_graph(
       |                                           ^~~~~~~~~~~~~~~~~~~~~~~~~
make[3]: *** [CMakeFiles/racon.dir/build.make:118:
CMakeFiles/racon.dir/src/window.cpp.o] Error 1

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Bug#940564: racon: FTBFS against libspoa3

Andreas Tille-2
Latest upstream needs liblogger[1] which needs to be packaged new.
I'm working on this (Python3 migration drained to many resources,
sorry)

[1]  https://salsa.debian.org/med-team/liblogger

--
http://fam-tille.de

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Bug#940564: racon: FTBFS against libspoa3

Andreas Tille-5
In reply to this post by Graham Inggs-3
Control: tags -1 upstream
Control: forwarded -1 https://github.com/lbcb-sci/racon/issues/6

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Processed: Re: Bug#940564: racon: FTBFS against libspoa3

Debian Bug Tracking System
In reply to this post by Graham Inggs-3
Processing control commands:

> tags -1 upstream
Bug #940564 [src:racon] racon: FTBFS against libspoa3
Added tag(s) upstream.
> forwarded -1 https://github.com/lbcb-sci/racon/issues/6
Bug #940564 [src:racon] racon: FTBFS against libspoa3
Set Bug forwarded-to-address to 'https://github.com/lbcb-sci/racon/issues/6'.

--
940564: https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=940564
Debian Bug Tracking System
Contact [hidden email] with problems

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Bug#940564: Upstream tries to find a solution without liblogger

Andreas Tille-5
In reply to this post by Graham Inggs-3
The current racon needs an extra dependency from liblogger (#940585).
Upstream is working on a solution without this since it was rejected.

--
http://fam-tille.de

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Bug#940564: [lbcb-sci/racon] Incompatible with latest spoa release (#6)

Andreas Tille-5
In reply to this post by Graham Inggs-3
On Tue, Oct 08, 2019 at 03:51:47AM -0700, Robert Vaser wrote:
> Hi Andreas, yes I have a plan how to deal with it but I am not available for a week or more. Will let you know.
Thanks a lot.  Just take your time until end of October since I'll be not available until then. ;-)

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Bug#940564: marked as done (racon: FTBFS against libspoa3)

Debian Bug Tracking System
In reply to this post by Graham Inggs-3
Your message dated Tue, 12 Nov 2019 17:22:24 +0000
with message-id <[hidden email]>
and subject line Bug#940564: fixed in racon 1.4.10-1
has caused the Debian Bug report #940564,
regarding racon: FTBFS against libspoa3
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.

(NB: If you are a system administrator and have no idea what this
message is talking about, this may indicate a serious mail system
misconfiguration somewhere. Please contact [hidden email]
immediately.)


--
940564: https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=940564
Debian Bug Tracking System
Contact [hidden email] with problems

Source: racon
Version: 1.3.2-1
Severity: serious

Hi Maintainer

In a recent binNMU against libspoa3 [1], racon FTBFS with the errors below.

Regards
Graham


[1]
https://buildd.debian.org/status/fetch.php?pkg=racon&arch=amd64&ver=1.3.2-1%2Bb2&stamp=1566980028&raw=0


/usr/bin/c++   -I/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/config
-I/<<PKGBUILDDIR>>/src  -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=.
-fstack-protector-strong -Wformat -Werror=format-security -Wdate-time
-D_FORTIFY_SOURCE=2 -Wall -Wextra -pedantic   -std=gnu++11 -o
CMakeFiles/racon.dir/src/main.cpp.o -c /<<PKGBUILDDIR>>/src/main.cpp
/<<PKGBUILDDIR>>/src/polisher.cpp: In member function ‘void
racon::Polisher::initialize()’:
/<<PKGBUILDDIR>>/src/polisher.cpp:169:15: error: ‘class
bioparser::Parser<racon::Sequence>’ has no member named ‘parse_objects’
   169 |     tparser_->parse_objects(sequences_, -1);
       |               ^~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/polisher.cpp:196:33: error: ‘class
bioparser::Parser<racon::Sequence>’ has no member named ‘parse_objects’
   196 |         auto status = sparser_->parse_objects(sequences_,
kChunkSize);
       |                                 ^~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/polisher.cpp:277:33: error: ‘class
bioparser::Parser<racon::Overlap>’ has no member named ‘parse_objects’
   277 |         auto status = oparser_->parse_objects(overlaps,
kChunkSize);
       |                                 ^~~~~~~~~~~~~
...
/<<PKGBUILDDIR>>/src/window.cpp: In member function ‘bool
racon::Window::generate_consensus(std::shared_ptr<spoa::AlignmentEngine>)’:
/<<PKGBUILDDIR>>/src/window.cpp:89:43: error: ‘using element_type =
class spoa::AlignmentEngine’ {aka ‘class spoa::AlignmentEngine’} has no
member named ‘align_sequence_with_graph’
    89 |             alignment =
alignment_engine->align_sequence_with_graph(
       |                                           ^~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/window.cpp:95:43: error: ‘using element_type =
class spoa::AlignmentEngine’ {aka ‘class spoa::AlignmentEngine’} has no
member named ‘align_sequence_with_graph’
    95 |             alignment =
alignment_engine->align_sequence_with_graph(
       |                                           ^~~~~~~~~~~~~~~~~~~~~~~~~
make[3]: *** [CMakeFiles/racon.dir/build.make:118:
CMakeFiles/racon.dir/src/window.cpp.o] Error 1

Source: racon
Source-Version: 1.4.10-1

We believe that the bug you reported is fixed in the latest version of
racon, 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 [hidden email],
and the maintainer will reopen the bug report if appropriate.

Debian distribution maintenance software
pp.
Michael R. Crusoe <[hidden email]> (supplier of updated racon 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 [hidden email])


-----BEGIN PGP SIGNED MESSAGE-----
Hash: SHA512

Format: 1.8
Date: Tue, 12 Nov 2019 14:43:58 +0100
Source: racon
Architecture: source
Version: 1.4.10-1
Distribution: unstable
Urgency: medium
Maintainer: Debian Med Packaging Team <[hidden email]>
Changed-By: Michael R. Crusoe <[hidden email]>
Closes: 940564
Changes:
 racon (1.4.10-1) unstable; urgency=medium
 .
   * Team upload.
 .
   [ Andreas Tille ]
   * New upstream version
   * debhelper-compat 12
   * Standards-Version: 4.4.0
   * Point watch file to new location
   * New homepage
   * Versioned Build-Depends: libthread-pool-dev (>= 2)
 .
   [ Michael Crusoe ]
   * New upstream version Closes: #940564
   * Run the tests during the build
   * Run the tests as part of 'autopkgtest'ing
   * Set the racon_wrapper to use /usr/bin/rampler
Checksums-Sha1:
 9a6b5263176599e585eb4afe2766311c8cb50869 2052 racon_1.4.10-1.dsc
 009b3965f14da0e4d435f2795cc87290df088945 3078510 racon_1.4.10.orig.tar.gz
 58443fb94a827e577c63b2634f68ae50ee5e591a 5636 racon_1.4.10-1.debian.tar.xz
 a4638dca079629b33fc54a7f386964ad7149bd0d 9235 racon_1.4.10-1_source.buildinfo
Checksums-Sha256:
 9bed66ff63b8327f5078024480631b7fc483d1dc60504ab592c9935a27dd4622 2052 racon_1.4.10-1.dsc
 101c1ba967eda296fea6f88c7ee7b01eb5c912b253dd0b0fdd80399b504808cb 3078510 racon_1.4.10.orig.tar.gz
 b82dff885b70b7ceee64456d50acedfb9db433bb95879aa83d71e6ee836e0e61 5636 racon_1.4.10-1.debian.tar.xz
 7fe65dcda937db680a2344b54f3cb4e69585b4b2caea4eb8fa0e1eafd795a10d 9235 racon_1.4.10-1_source.buildinfo
Files:
 e1b5e674f564f60b1bcf7237e7ef2143 2052 science optional racon_1.4.10-1.dsc
 5dfc8faa3089477f60682977d1ccf7ee 3078510 science optional racon_1.4.10.orig.tar.gz
 ae4a44305fbee3f54fde16de6099478f 5636 science optional racon_1.4.10-1.debian.tar.xz
 a539209be03b31f05bbc51c1db95e76e 9235 science optional racon_1.4.10-1_source.buildinfo

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