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Bug 664700 - sci-biology/vaal-46233-r2 : ./.../KmerShape.h:566:49: error: could not convert kmer_shape_zebra<K>::getStringId() from String {aka FeudalString<char> } to KmerShapeId
Summary: sci-biology/vaal-46233-r2 : ./.../KmerShape.h:566:49: error: could not conver...
Status: RESOLVED WONTFIX
Alias: None
Product: Gentoo Linux
Classification: Unclassified
Component: Current packages (show other bugs)
Hardware: All Linux
: Normal normal
Assignee: Gentoo Science Biology related packages
URL:
Whiteboard:
Keywords:
Depends on:
Blocks:
 
Reported: 2018-08-27 16:48 UTC by Toralf Förster
Modified: 2019-07-22 10:07 UTC (History)
0 users

See Also:
Package list:
Runtime testing required: ---


Attachments
emerge-info.txt (emerge-info.txt,16.84 KB, text/plain)
2018-08-27 16:48 UTC, Toralf Förster
Details
emerge-history.txt (emerge-history.txt,229.73 KB, text/plain)
2018-08-27 16:49 UTC, Toralf Förster
Details
environment (environment,57.78 KB, text/plain)
2018-08-27 16:49 UTC, Toralf Förster
Details
etc.portage.tbz2 (etc.portage.tbz2,13.05 KB, application/x-bzip)
2018-08-27 16:49 UTC, Toralf Förster
Details
logs.tbz2 (logs.tbz2,8.26 KB, application/x-bzip)
2018-08-27 16:49 UTC, Toralf Förster
Details
sci-biology:vaal-46233-r2:20180827-080342.log (sci-biology:vaal-46233-r2:20180827-080342.log,30.50 KB, text/plain)
2018-08-27 16:49 UTC, Toralf Förster
Details
temp.tbz2 (temp.tbz2,22.06 KB, application/x-bzip)
2018-08-27 16:49 UTC, Toralf Förster
Details

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Description Toralf Förster gentoo-dev 2018-08-27 16:48:54 UTC
                 from pairwise_aligners/PerfectAlignerLG.cc:11:
./kmers/KmerShape.h: In static member function ‘static KmerShapeId kmer_shape_zebra<K>::getId()’:
./kmers/KmerShape.h:566:49: error: could not convert ‘kmer_shape_zebra<K>::getStringId()’ from ‘String’ {aka ‘FeudalString<char>’} to ‘KmerShapeId’
  static KmerShapeId getId() { return getStringId(); }
                                      ~~~~~~~~~~~^~
make[2]: *** [Makefile:1653: PerfectAlignerLG.o] Error 1

  -------------------------------------------------------------------

  This is an unstable amd64 chroot image at a tinderbox (==build bot)
  name: 17.0-desktop_libressl_20180820-195837

  -------------------------------------------------------------------

gcc-config -l:
 [1] x86_64-pc-linux-gnu-7.3.1
 [2] x86_64-pc-linux-gnu-8.2.0 *

Available Python interpreters, in order of preference:
  [1]   python3.7
  [2]   python3.6
  [3]   python2.7 (fallback)
Available Ruby profiles:
  [1]   ruby23 (with Rubygems)
  [2]   ruby25 (with Rubygems) *
java-config:
The following VMs are available for generation-2:
*)	IcedTea JDK 3.8.0 [icedtea-8]
2)	IcedTea JDK 3.8.0 [icedtea-bin-8]
Available Java Virtual Machines:
  [1]   icedtea-8  system-vm
  [2]   icedtea-bin-8 

emerge -qpv sci-biology/vaal
[ebuild  N    ] sci-biology/vaal-46233-r2  USE="openmp"
Comment 1 Toralf Förster gentoo-dev 2018-08-27 16:48:57 UTC
Created attachment 545198 [details]
emerge-info.txt
Comment 2 Toralf Förster gentoo-dev 2018-08-27 16:49:00 UTC
Created attachment 545200 [details]
emerge-history.txt
Comment 3 Toralf Förster gentoo-dev 2018-08-27 16:49:03 UTC
Created attachment 545202 [details]
environment
Comment 4 Toralf Förster gentoo-dev 2018-08-27 16:49:06 UTC
Created attachment 545204 [details]
etc.portage.tbz2
Comment 5 Toralf Förster gentoo-dev 2018-08-27 16:49:09 UTC
Created attachment 545206 [details]
logs.tbz2
Comment 6 Toralf Förster gentoo-dev 2018-08-27 16:49:12 UTC
Created attachment 545208 [details]
sci-biology:vaal-46233-r2:20180827-080342.log
Comment 7 Toralf Förster gentoo-dev 2018-08-27 16:49:15 UTC
Created attachment 545210 [details]
temp.tbz2
Comment 8 Larry the Git Cow gentoo-dev 2019-06-22 10:05:32 UTC
The bug has been referenced in the following commit(s):

https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=c8b947e648fdb093108496df8f8dfe5468ec0630

commit c8b947e648fdb093108496df8f8dfe5468ec0630
Author:     David Seifert <soap@gentoo.org>
AuthorDate: 2019-06-22 10:05:04 +0000
Commit:     David Seifert <soap@gentoo.org>
CommitDate: 2019-06-22 10:05:04 +0000

    package.mask: Last rite sci-biology/vaal
    
    Bug: https://bugs.gentoo.org/664700
    Bug: https://bugs.gentoo.org/685980
    Signed-off-by: David Seifert <soap@gentoo.org>

 profiles/package.mask | 7 +++++++
 1 file changed, 7 insertions(+)
Comment 9 Mikle Kolyada (RETIRED) archtester Gentoo Infrastructure gentoo-dev Security 2019-07-22 10:07:28 UTC
Gone.