Bug 681640 – sci-biology/mothur-1.27.0-r1 : classifyseqscommand.cpp:571:17: error: MPI_MODE_CREATE was not declared in this scope

• Status: CONFIRMED
• Product: Gentoo Linux

[Description Toralf Förster 2019-03-24 10:44:20 UTC]

mpicxx -O2 -pipe -march=native -DRELEASE_DATE="\"8/8/2012\"" -DVERSION="\"1.27.0\"" -DUSE_READLINE -DUSE_MPI -I.  -DBIT_VERSION  -c -o classifyseqscommand.o classifyseqscommand.cpp
classifyseqscommand.cpp: In member function ‘virtual int ClassifySeqsCommand::execute()’:
classifyseqscommand.cpp:571:17: error: ‘MPI_MODE_CREATE’ was not declared in this scope
     int outMode=MPI_MODE_CREATE|MPI_MODE_WRONLY;
                 ^~~~~~~~~~~~~~~
classifyseqscommand.cpp:571:17: note: suggested alternative: ‘MPI_MODE_NOPUT’

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

  This is an unstable amd64 chroot image at a tinderbox (==build bot)
  name: 17.0-no-multilib_libressl_20190322-132156

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

gcc-config -l:
 [1] x86_64-pc-linux-gnu-7.3.1
 [2] x86_64-pc-linux-gnu-8.3.0 *

Available Python interpreters, in order of preference:
  [1]   python3.6
  [2]   python2.7 (fallback)
Available Ruby profiles:
  [1]   ruby24 (with Rubygems)
  [2]   ruby25 (with Rubygems)
  [3]   ruby26 (with Rubygems) *
Available Rust versions:
  [1]   rust-1.32.0 *



emerge -qpvO sci-biology/mothur
[ebuild  N    ] sci-biology/mothur-1.27.0-r1  USE="mpi readline"

[Comment 1 Toralf Förster 2019-03-24 10:44:23 UTC]

Created attachment 570574 [details]
emerge-info.txt

[Comment 2 Toralf Förster 2019-03-24 10:44:26 UTC]

Created attachment 570576 [details]
emerge-history.txt

[Comment 3 Toralf Förster 2019-03-24 10:44:28 UTC]

Created attachment 570578 [details]
environment

[Comment 4 Toralf Förster 2019-03-24 10:44:31 UTC]

Created attachment 570580 [details]
etc.portage.tbz2

[Comment 5 Toralf Förster 2019-03-24 10:44:34 UTC]

Created attachment 570582 [details]
sci-biology:mothur-1.27.0-r1:20190323-225202.log

[Comment 6 Toralf Förster 2019-03-24 10:44:37 UTC]

Created attachment 570584 [details]
temp.tbz2

[Comment 7 Toralf Förster 2021-12-27 10:15:38 UTC]

*** Bug 830079 has been marked as a duplicate of this bug. ***

[Comment 8 Martin Mokrejš 2022-02-16 21:18:11 UTC]

There used to be a newer version 1.36.1 in the tree:

https://cgit.gentoo.org/proj/sci.git/tree/sci-biology/mothur?id=d209b24ac3b9de78f7048fb76467c42bad604263

[Comment 9 Sam James 2024-03-22 07:41:56 UTC]

*** Bug 920269 has been marked as a duplicate of this bug. ***