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Bug 913591 - sci-biology/clustalw-2.1-r2 - [slibtool] [clang] ./.../FileReader.h: error: no template named auto_ptr
Summary: sci-biology/clustalw-2.1-r2 - [slibtool] [clang] ./.../FileReader.h: error: n...
Status: CONFIRMED
Alias: None
Product: Gentoo Linux
Classification: Unclassified
Component: Current packages (show other bugs)
Hardware: All Linux
: Normal normal (vote)
Assignee: Gentoo Science Biology related packages
URL:
Whiteboard:
Keywords:
Depends on:
Blocks:
 
Reported: 2023-09-03 19:48 UTC by Toralf Förster
Modified: 2023-09-03 19:48 UTC (History)
0 users

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


Attachments
emerge-info.txt (emerge-info.txt,17.55 KB, text/plain)
2023-09-03 19:48 UTC, Toralf Förster
Details
emerge-history.txt (emerge-history.txt,104.99 KB, text/plain)
2023-09-03 19:48 UTC, Toralf Förster
Details
environment (environment,24.31 KB, text/plain)
2023-09-03 19:48 UTC, Toralf Förster
Details
etc.clang.tar.xz (etc.clang.tar.xz,792 bytes, application/x-xz)
2023-09-03 19:48 UTC, Toralf Förster
Details
etc.portage.tar.xz (etc.portage.tar.xz,9.65 KB, application/x-xz)
2023-09-03 19:48 UTC, Toralf Förster
Details
logs.tar.xz (logs.tar.xz,5.28 KB, application/x-xz)
2023-09-03 19:48 UTC, Toralf Förster
Details
sci-biology:clustalw-2.1-r2:20230903-191927.log (sci-biology:clustalw-2.1-r2:20230903-191927.log,9.50 KB, text/plain)
2023-09-03 19:48 UTC, Toralf Förster
Details
temp.tar.xz (temp.tar.xz,9.04 KB, application/x-xz)
2023-09-03 19:48 UTC, Toralf Förster
Details

Note You need to log in before you can comment on or make changes to this bug.
Description Toralf Förster gentoo-dev 2023-09-03 19:48:22 UTC
./fileInput/../alignment/../substitutionMatrix/SubMatrix.h:97:66: warning: ISO
      C++11 does not allow conversion from string literal to 'char *'
      [-Wwritable-strings]
        void printVectorToFile(vector<short>& temp, char* name = "tempfi...
                                                                 ^
In file included from ./fileInput/FileReader.cpp:29:
./fileInput/FileReader.h:42:38: error: no template named 'auto_ptr'
        void checkInfile(int* nseqs, auto_ptr<FileParser>& fileParser);
                                     ^

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

  This is an unstable amd64 chroot image at a tinderbox (==build bot)
  name: 17.1_clang-20230902-205829

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

gcc-config -l:
 [1] x86_64-pc-linux-gnu-13 *
clang/llvm (if any):
clang version 16.0.6
Target: x86_64-pc-linux-gnu
Thread model: posix
InstalledDir: /usr/lib/llvm/16/bin
Configuration file: /etc/clang/clang.cfg
/usr/lib/llvm/16
16.0.6+libcxx
Python 3.11.5
Available Ruby profiles:
  [1]   ruby31 (with Rubygems) *
Available Rust versions:
  [1]   rust-1.72.0 *
The following VMs are available for generation-2:
1)	Eclipse Temurin JDK 11.0.19_p7 [openjdk-bin-11]
*)	Eclipse Temurin JDK 17.0.7_p7 [openjdk-bin-17]
3)	Eclipse Temurin JDK 8.372_p07 [openjdk-bin-8]
Available Java Virtual Machines:
  [1]   openjdk-bin-8 
  [2]   openjdk-bin-11 
  [3]   openjdk-bin-17  system-vm

The Glorious Glasgow Haskell Compilation System, version 9.0.2
php cli (if any):
  [1]   php8.1 *
  [2]   php8.2
go version go1.21.0 linux/amd64

  HEAD of ::gentoo
commit 3a8790d092cd4d3d1a8fbb2b24bcb10a13d0cb5e
Author: Repository mirror & CI <repomirrorci@gentoo.org>
Date:   Sun Sep 3 17:46:59 2023 +0000

    2023-09-03 17:46:59 UTC

emerge -qpvO sci-biology/clustalw
[ebuild  N    ] sci-biology/clustalw-2.1-r2
Comment 1 Toralf Förster gentoo-dev 2023-09-03 19:48:23 UTC
Created attachment 869528 [details]
emerge-info.txt
Comment 2 Toralf Förster gentoo-dev 2023-09-03 19:48:24 UTC
Created attachment 869529 [details]
emerge-history.txt
Comment 3 Toralf Förster gentoo-dev 2023-09-03 19:48:25 UTC
Created attachment 869530 [details]
environment
Comment 4 Toralf Förster gentoo-dev 2023-09-03 19:48:26 UTC
Created attachment 869531 [details]
etc.clang.tar.xz
Comment 5 Toralf Förster gentoo-dev 2023-09-03 19:48:26 UTC
Created attachment 869532 [details]
etc.portage.tar.xz
Comment 6 Toralf Förster gentoo-dev 2023-09-03 19:48:27 UTC
Created attachment 869533 [details]
logs.tar.xz
Comment 7 Toralf Förster gentoo-dev 2023-09-03 19:48:28 UTC
Created attachment 869534 [details]
sci-biology:clustalw-2.1-r2:20230903-191927.log
Comment 8 Toralf Förster gentoo-dev 2023-09-03 19:48:29 UTC
Created attachment 869535 [details]
temp.tar.xz