Bug 629670 – sci-biology/pysam-0.12 : bcftools/vcfplugin.c.pysam.c:27:20: fatal error: config.h: No such file or directory

• Status: RESOLVED FIXED
• Product: Gentoo Linux

[Description Toralf Förster 2017-09-02 15:03:46 UTC]

x86_64-pc-linux-gnu-gcc -O2 -pipe -march=native -Wall -fPIC -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python2.7 -c bcftools/vcfquery.c.pysam.c -o /var/tmp/portage/sci-biology/pysam-0.12/work/pysam-0.12-python2_7/temp.linux-x86_64-2.7/bcftools/vcfquery.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
x86_64-pc-linux-gnu-gcc -O2 -pipe -march=native -Wall -fPIC -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python2.7 -c bcftools/vcfplugin.c.pysam.c -o /var/tmp/portage/sci-biology/pysam-0.12/work/pysam-0.12-python2_7/temp.linux-x86_64-2.7/bcftools/vcfplugin.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
bcftools/vcfplugin.c.pysam.c:27:20: fatal error: config.h: No such file or directory
 #include "config.h"
                    ^
compilation terminated.

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

  This is an unstable amd64 chroot image at a tinderbox (==build bot)
  name: 13.0-desktop-plasma-systemd_20170831-193500

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

gcc-config -l:
 [1] x86_64-pc-linux-gnu-6.4.0 *

Available Python interpreters, in order of preference:
  [1]   python3.4
  [2]   python2.7 (fallback)

java-config:
The following VMs are available for generation-2:
*)	IcedTea JDK 3.5.1 [icedtea-bin-8]
Available Java Virtual Machines:
  [1]   icedtea-bin-8  system-vm

emerge -qpv sci-biology/pysam
[ebuild     U ] sci-biology/pysam-0.12 [0.9.0] PYTHON_TARGETS="python2_7 python3_4 -python3_5 -python3_6%"

[Comment 1 Toralf Förster 2017-09-02 15:03:49 UTC]

Created attachment 491832 [details]
emerge-info.txt

[Comment 2 Toralf Förster 2017-09-02 15:03:52 UTC]

Created attachment 491834 [details]
emerge-history.txt

[Comment 3 Toralf Förster 2017-09-02 15:03:54 UTC]

Created attachment 491836 [details]
environment

[Comment 4 Toralf Förster 2017-09-02 15:03:58 UTC]

Created attachment 491838 [details]
etc.portage.tbz2

[Comment 5 Toralf Förster 2017-09-02 15:04:01 UTC]

Created attachment 491840 [details]
logs.tbz2

[Comment 6 Toralf Förster 2017-09-02 15:04:04 UTC]

Created attachment 491842 [details]
sci-biology:pysam-0.12:20170902-145716.log

[Comment 7 Toralf Förster 2017-09-02 15:04:07 UTC]

Created attachment 491844 [details]
temp.tbz2

[Comment 8 David Seifert 2017-09-02 18:36:31 UTC]

commit e4dbb5c139e2c3dfe8a7d6eaa7f19a08da9b88b0
Author:     David Seifert <[e-mail]>
AuthorDate: Sat Sep 2 20:34:46 2017 +0200
Commit:     David Seifert <[e-mail]>
CommitDate: Sat Sep 2 20:35:42 2017 +0200

    sci-biology/pysam: Fix broken relative -I
    
    Bug: https://bugs.gentoo.org/show_bug.cgi?id=629670

[Comment 9 Toralf Förster 2017-09-02 21:09:08 UTC]

fixed