755791 – [science overlay] sci-biology/verifyBamID-1.1.3 : VcfRecordDiscardRules.h: error: unordered_set in namespace std does not name a template type

Bug 755791 - [science overlay] sci-biology/verifyBamID-1.1.3 : VcfRecordDiscardRules.h: error: unordered_set in namespace std does not name a template type

Summary: [science overlay] sci-biology/verifyBamID-1.1.3 : VcfRecordDiscardRules.h: er...

Status:	RESOLVED FIXED

Alias:	None

Product:	Gentoo Linux
Classification:	Unclassified
Component:	Current packages (show other bugs)
Hardware:	All Linux

Importance:	Normal normal (vote)
Assignee:	Gentoo Science Related Packages

URL:
Whiteboard:
Keywords:

Depends on:
Blocks:

Reported:	2020-11-20 15:56 UTC by Toralf Förster
Modified:	2021-05-05 18:44 UTC (History)
CC List:	2 users (show)

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

Attachments
emerge-info.txt (emerge-info.txt,17.61 KB, text/plain) 2020-11-20 15:56 UTC, Toralf Förster	Details
emerge-history.txt (emerge-history.txt,58.46 KB, text/plain) 2020-11-20 15:56 UTC, Toralf Förster	Details
environment (environment,49.74 KB, text/plain) 2020-11-20 15:56 UTC, Toralf Förster	Details
etc.portage.tbz2 (etc.portage.tbz2,16.59 KB, application/x-bzip) 2020-11-20 15:56 UTC, Toralf Förster	Details
logs.tbz2 (logs.tbz2,1.20 KB, application/x-bzip) 2020-11-20 15:56 UTC, Toralf Förster	Details
sci-biology:verifyBamID-1.1.3:20201120-070229.log (sci-biology:verifyBamID-1.1.3:20201120-070229.log,32.75 KB, text/plain) 2020-11-20 15:56 UTC, Toralf Förster	Details
temp.tbz2 (temp.tbz2,16.01 KB, application/x-bzip) 2020-11-20 15:56 UTC, Toralf Förster	Details
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Description Toralf Förster gentoo-dev

2020-11-20 15:56:20 UTC

                 from VcfFileReader.h:24,
                 from VcfFileReader.cpp:20:
VcfRecordDiscardRules.h:72:18: error: ‘unordered_set’ in namespace ‘std’ does not name a template type
   72 |     typedef std::unordered_set<vcfIDtype> IDList;
      |                  ^~~~~~~~~~~~~
VcfRecordDiscardRules.h:1:1: note: ‘std::unordered_set’ is defined in header ‘<unordered_set>’; did you forget to ‘#include <unordered_set>’?

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

  This is an unstable amd64 chroot image at a tinderbox (==build bot)
  name: 17.1_no-multilib-libressl_science-20201116-220441

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

gcc-config -l:
 [1] x86_64-pc-linux-gnu-10.2.0 *
/usr/lib/llvm/11
11.0.0
Available Python interpreters, in order of preference:
  [1]   python3.7
  [2]   python3.9 (fallback)
  [3]   python3.8 (fallback)
  [4]   python2.7 (fallback)
The following VMs are available for generation-2:
*)	AdoptOpenJDK 8.272_p10 [openjdk-bin-8]
Available Java Virtual Machines:
  [1]   openjdk-bin-8  system-vm

The Glorious Glasgow Haskell Compilation System, version 8.8.4

  timestamp(s) of HEAD at this tinderbox image:
/var/db/repos/gentoo	Fri Nov 20 05:46:41 AM UTC 2020
/var/db/repos/libressl	Sat Nov  7 03:06:11 PM UTC 2020

emerge -qpvO sci-biology/verifyBamID
[ebuild  N    ] sci-biology/verifyBamID-1.1.3

Comment 1 Toralf Förster gentoo-dev

2020-11-20 15:56:21 UTC

Created attachment 673735 [details]
emerge-info.txt

Comment 2 Toralf Förster gentoo-dev

2020-11-20 15:56:23 UTC

Created attachment 673738 [details]
emerge-history.txt

Comment 3 Toralf Förster gentoo-dev

2020-11-20 15:56:24 UTC

Created attachment 673741 [details]
environment

Comment 4 Toralf Förster gentoo-dev

2020-11-20 15:56:25 UTC

Created attachment 673744 [details]
etc.portage.tbz2

Comment 5 Toralf Förster gentoo-dev

2020-11-20 15:56:26 UTC

Created attachment 673747 [details]
logs.tbz2

Comment 6 Toralf Förster gentoo-dev

2020-11-20 15:56:28 UTC

Created attachment 673750 [details]
sci-biology:verifyBamID-1.1.3:20201120-070229.log

Comment 7 Toralf Förster gentoo-dev

2020-11-20 15:56:29 UTC

Created attachment 673753 [details]
temp.tbz2