Bug 238471 - biology/ncbi-blast+ fails to build with current GCC: seqdb_reader/test/seqdb_perf.cpp:152:34: error: 'kScanUncompressed' not specified in enclosing 'parallel'
Summary: biology/ncbi-blast+ fails to build with current GCC: seqdb_reader/test/seqdb_...
Status: Closed FIXED
Alias: None
Product: Ports & Packages
Classification: Unclassified
Component: Individual Port(s) (show other bugs)
Version: Latest
Hardware: Any Any
: --- Affects Some People
Assignee: Jason W. Bacon
URL:
Keywords:
Depends on:
Blocks: 238330
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Reported: 2019-06-10 20:50 UTC by Gerald Pfeifer
Modified: 2019-06-13 06:21 UTC (History)
0 users

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Description Gerald Pfeifer freebsd_committer 2019-06-10 20:50:55 UTC
See PR 238330 for details, which is about updating the default version of
GCC from 8 to 9. 

Detailed logs at:

http://pb2.nyi.freebsd.org/data/120i386-default-PR238330/2019-06-09_20h27m22s/logs/errors/ncbi-blast+-2.8.1_2.log
http://package22.nyi.freebsd.org/data/112amd64-default-PR238330/2019-06-09_20h29m30s/logs/errors/ncbi-blast+-2.8.1_2.log
http://package18.nyi.freebsd.org/data/120amd64-default-PR238330/2019-06-09_20h26m27s/logs/errors/ncbi-blast+-2.8.1_2.log


The update to a newer version of GCC is blocked by this issue which 
appears to be about improper use of GOMP:

                            ~~^~~~~~~~~~~~~~~~~~~~~
/wrkdirs/usr/ports/biology/ncbi-blast+/work/ncbi-blast-2.8.1+-src/c++/src/objtools/blast/seqdb_reader/test/seqdb_perf.cpp:152:34: error: 'kScanUncompressed' not specified in enclosing 'parallel'
  152 |             if (m_DbIsProtein || kScanUncompressed) {
      |                                  ^~~~~~~~~~~~~~~~~
/wrkdirs/usr/ports/biology/ncbi-blast+/work/ncbi-blast-2.8.1+-src/c++/src/objtools/blast/seqdb_reader/test/seqdb_perf.cpp:140:13: error: enclosing 'parallel'
  140 |     #pragma omp parallel default(none) num_threads(m_DbHandles.size()) \
      |             ^~~
gmake[7]: *** [/wrkdirs/usr/ports/biology/ncbi-blast+/work/ncbi-blast-2.8.1+-src/c++/ReleaseMT/build/Makefile.rules:88: seqdb_perf.o] Error 1
Comment 1 Gerald Pfeifer freebsd_committer 2019-06-10 20:54:47 UTC
Reassigning to maintainer.
Comment 2 Jason W. Bacon freebsd_committer 2019-06-11 23:49:40 UTC
Looking into it.
Comment 3 Jason W. Bacon freebsd_committer 2019-06-12 16:42:18 UTC
2.9.0 builds fine with GCC 9.

https://github.com/outpaddling/freebsd-ports-wip/tree/master/ncbi-blast%2B

I'll commit an update following full testing.
Comment 4 commit-hook freebsd_committer 2019-06-12 23:54:29 UTC
A commit references this bug:

Author: jwb
Date: Wed Jun 12 23:53:33 UTC 2019
New revision: 504047
URL: https://svnweb.freebsd.org/changeset/ports/504047

Log:
  biology/ncbi-blast+: Upgrade to 2.9.0

  Fixes build issue with gcc9

  PR:             238471
  Reported by:    gerald

Changes:
  head/biology/ncbi-blast+/Makefile
  head/biology/ncbi-blast+/distinfo
  head/biology/ncbi-blast+/pkg-plist
Comment 5 Gerald Pfeifer freebsd_committer 2019-06-13 06:21:32 UTC
Great, thank you, Jason!