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Bug 594994

Summary: sci-biology/bedtools-2.20.1 : ../.../FileRecordTypeChecker.h:120:44: error: ‘constexpr’ needed for in-class initialization of static data member ‘const float FileRecordTypeChecker::PERCENTAGE_PRINTABLE’ of non-integral type [-fpermissive]
Product: Gentoo Linux Reporter: Toralf Förster <toralf>
Component: Current packagesAssignee: Martin Mokrejš <mmokrejs>
Severity: normal CC: proxy-maint, sci-biology
Priority: Normal    
Version: unspecified   
Hardware: All   
OS: Linux   
Package list:
Runtime testing required: ---
Bug Depends on:    
Bug Blocks: 582084    
Attachments: emerge-history.txt

Description Toralf Förster gentoo-dev 2016-09-24 07:59:56 UTC
                 from BinTree.h:19,
                 from BinTree.cpp:1:
../../utils//fileType/FileRecordTypeChecker.h:120:44: error: ‘constexpr’ needed for in-class initialization of static data member ‘const float FileRecordTypeChecker::PERCENTAGE_PRINTABLE’ of non-integral type [-fpermissive]
  static const float PERCENTAGE_PRINTABLE = .9;
make[1]: *** [Makefile:30: ../../../obj//BinTree.o] Error 1

$ cat emerge-info.txt

  This is an unstable amd64 chroot image (named amd64-13.0-no-multilib-unstable_20160920-101304) at a hardened host acting as a tinderbox.

  USE flags ...

  ... in make.conf:
USE="  pax_kernel xtpax -cdinstall -oci8 -bindist apache2 cgroups compat cups cxx dvb egl fontconfig freetds gles2 gpg graphtft gstreamer -gtkstyle gudev -haptic hdf5 help -hpn ithreads javascript lapack -latex -ldap libinput libkms libvirtd mdnsresponder-compat minizip modplug mpeg3 mpg123 mta nscd objc openexr -openssl pcre16 png -postproc -python qml server smpeg snmp sockets spice sqlite3 ssh ssh-askpass sslv2 -system-cairo system-ffmpeg system-jpeg szip tcpd theora tls ufed uml usbredir utils uxa vorbis wayland wma wxwidgets xetex xkb xml xmp xz zip zlib"

  ... in /etc/portage/package.use/*:
  mail-mta/ssmtp      ssl mta
  net-misc/wget       ssl
  app-crypt/pinentry  -qt4
  app-editors/emacs   -dbus -svg -ssl -gtk -gtk3
  app-text/xmlto      -latex
  dev-libs/boehm-gc   threads
  dev-libs/libpcre    pcre16
  dev-lang/python     threads
  dev-qt/qtgui        egl eglfs
  net-nds/openldap    -sasl
  dev-util/cmake      -qt4 -qt5
  dev-vcs/git         -perl
  gnome-base/librsvg  -tools
  media-libs/mesa     -vaapi
  sys-apps/kmod       tools
  <=net-misc/openssh-7.3_p1-r2    -hpn
  net-misc/iputils -caps -filecaps

  entries in /etc/portage/package.unmask/*:

gcc-config -l:
 [1] x86_64-pc-linux-gnu-4.9.3
 [2] x86_64-pc-linux-gnu-6.2.0 *
llvm-config --version:

Available Python interpreters, in order of preference:
  [1]   python2.7
  [2]   python3.4
  [3]   python3.5 (fallback)


Portage 2.3.1 (python 2.7.12-final-0, default/linux/amd64/13.0/no-multilib, gcc-6.2.0, glibc-2.23-r2, 4.7.4-hardened-r1 x86_64)
                         System Settings
System uname: Linux-4.7.4-hardened-r1-x86_64-Intel-R-_Core-TM-_i7-3930K_CPU_@_3.20GHz-with-gentoo-2.3
KiB Mem:    65285480 total,   1216684 free
KiB Swap:   67108860 total,  67108752 free
Timestamp of repository gentoo: Sat, 24 Sep 2016 01:19:42 +0000
sh bash 4.3_p46-r1
ld GNU ld (Gentoo 2.25.1 p1.1) 2.25.1
app-shells/bash:          4.3_p46-r1::gentoo
dev-lang/perl:            5.24.0-r1::gentoo
dev-lang/python:          2.7.12::gentoo, 3.4.5::gentoo, 3.5.2::gentoo
dev-util/cmake:           3.6.2::gentoo
dev-util/pkgconfig:       0.29.1::gentoo
sys-apps/baselayout:      2.3::gentoo
sys-apps/openrc:          0.21.7::gentoo
sys-apps/sandbox:         2.10-r2::gentoo
sys-devel/autoconf:       2.13::gentoo, 2.69-r2::gentoo
sys-devel/automake:       1.11.6-r2::gentoo, 1.13.4-r1::gentoo, 1.14.1-r1::gentoo, 1.15-r2::gentoo
sys-devel/binutils:       2.25.1-r1::gentoo, 2.26.1::gentoo
sys-devel/gcc:            4.9.3::gentoo, 6.2.0-r1::gentoo
sys-devel/gcc-config:     1.8-r1::gentoo
sys-devel/libtool:        2.4.6-r2::gentoo
sys-devel/make:           4.2.1::gentoo
sys-kernel/linux-headers: 4.7::gentoo (virtual/os-headers)
sys-libs/glibc:           2.23-r2::gentoo

    location: /usr/portage
    sync-type: rsync
    sync-uri: rsync://
    priority: 1

    location: /usr/local/portage
    masters: gentoo
    priority: 2

ACCEPT_KEYWORDS="amd64 ~amd64"
CFLAGS="-march=native -O2 -pipe"
CONFIG_PROTECT="/etc /etc/stunnel/stunnel.conf /usr/lib64/tomoyo/conf /usr/share/config /usr/share/gnupg/qualified.txt /var/rancid/.cloginrc /var/yp/Makefile"
CONFIG_PROTECT_MASK="/etc/ca-certificates.conf /etc/dconf /etc/env.d /etc/fonts/fonts.conf /etc/gconf /etc/gentoo-release /etc/php/apache2-php5.6/ext-active/ /etc/php/apache2-php7.0/ext-active/ /etc/php/cgi-php5.6/ext-active/ /etc/php/cgi-php7.0/ext-active/ /etc/php/cli-php5.6/ext-active/ /etc/php/cli-php7.0/ext-active/ /etc/revdep-rebuild /etc/sandbox.d /etc/terminfo"
CXXFLAGS="-march=native -O2 -pipe"
EMERGE_DEFAULT_OPTS="--verbose --verbose-conflicts --color=n --nospinner --tree --quiet-build"
FCFLAGS="-O2 -pipe"
FEATURES="assume-digests binpkg-logs config-protect-if-modified distlocks ebuild-locks fixlafiles ipc-sandbox merge-sync network-sandbox parallel-fetch preserve-libs protect-owned sandbox sfperms strict test-fail-continue unknown-features-warn unmerge-logs unmerge-orphans userfetch userpriv usersandbox usersync xattr"
FFLAGS="-O2 -pipe"
GENTOO_MIRRORS=" rsync:// rsync://"
LDFLAGS="-Wl,-O1 -Wl,--as-needed"
PORTAGE_RSYNC_OPTS="--recursive --links --safe-links --perms --times --omit-dir-times --compress --force --whole-file --delete --stats --human-readable --timeout=180 --exclude=/distfiles --exclude=/local --exclude=/packages --exclude=/.git"
USE="acl amd64 apache2 berkdb bzip2 cgroups cli compat cracklib crypt cups cxx dri dvb egl fontconfig fortran freetds gdbm gles2 gpg graphtft gstreamer gudev hdf5 help iconv ipv6 ithreads javascript lapack libinput libkms libvirtd mdnsresponder-compat minizip mmx mmxext modplug modules mpeg3 mpg123 mta ncurses nls nptl nscd objc openexr openmp pam pax_kernel pcre pcre16 png qml readline seccomp server session smpeg snmp sockets spice sqlite3 sse sse2 ssh ssh-askpass ssl sslv2 system-ffmpeg system-jpeg szip tcpd theora tls ufed uml unicode usbredir utils uxa vorbis wayland wma wxwidgets xattr xetex xkb xml xmp xtpax xz zip zlib" ABI_X86="64" ALSA_CARDS="ali5451 als4000 atiixp atiixp-modem bt87x ca0106 cmipci emu10k1x ens1370 ens1371 es1938 es1968 fm801 hda-intel intel8x0 intel8x0m maestro3 trident usb-audio via82xx via82xx-modem ymfpci" APACHE2_MODULES="authn_core authz_core socache_shmcb unixd actions alias auth_basic authn_alias authn_anon authn_dbm authn_default authn_file authz_dbm authz_default authz_groupfile authz_host authz_owner authz_user autoindex cache cgi cgid dav dav_fs dav_lock deflate dir disk_cache env expires ext_filter file_cache filter headers include info log_config logio mem_cache mime mime_magic negotiation rewrite setenvif speling status unique_id userdir usertrack vhost_alias" CALLIGRA_FEATURES="kexi words flow plan sheets stage tables krita karbon braindump author" CAMERAS="ptp2" COLLECTD_PLUGINS="df interface irq load memory rrdtool swap syslog" CPU_FLAGS_X86="aes avx mmx mmxext popcnt sse sse2 sse3 sse4_1 sse4_2 ssse3" ELIBC="glibc" GPSD_PROTOCOLS="ashtech aivdm earthmate evermore fv18 garmin garmintxt gpsclock itrax mtk3301 nmea ntrip navcom oceanserver oldstyle oncore rtcm104v2 rtcm104v3 sirf superstar2 timing tsip tripmate tnt ublox ubx" INPUT_DEVICES="keyboard mouse evdev" KERNEL="linux" L10N="bs" LCD_DEVICES="bayrad cfontz cfontz633 glk hd44780 lb216 lcdm001 mtxorb ncurses text" LIBREOFFICE_EXTENSIONS="presenter-console presenter-minimizer" OFFICE_IMPLEMENTATION="libreoffice" PHP_TARGETS="php5-6" PYTHON_SINGLE_TARGET="python2_7" PYTHON_TARGETS="python2_7 python3_4" RUBY_TARGETS="ruby20 ruby21" USERLAND="GNU" VIDEO_CARDS="amdgpu fbdev intel nouveau radeon radeonsi vesa dummy v4l" XTABLES_ADDONS="quota2 psd pknock lscan length2 ipv4options ipset ipp2p iface geoip fuzzy condition tee tarpit sysrq steal rawnat logmark ipmark dhcpmac delude chaos account"
Comment 1 Toralf Förster gentoo-dev 2016-09-24 08:00:03 UTC
Created attachment 447708 [details]
Comment 2 Toralf Förster gentoo-dev 2016-09-24 08:00:06 UTC
Created attachment 447710 [details]
Comment 3 Toralf Förster gentoo-dev 2016-09-24 08:00:09 UTC
Created attachment 447712 [details]
Comment 4 Martin Mokrejš 2016-09-24 09:01:11 UTC
Hi Toralf,
  incidentally I brought a new version to sci overlay:

commit 459c9ffc65063046c8954391cc3904bfdffdf084
Author: Martin Mokrejš <>
Date:   Tue Sep 20 17:28:04 2016 +0200

    sci-biology/bedtools: version bump
    Package-Manager: portage-2.3.0

  I cannot really comment on the compile issue, I could only re-report to upstream.
Comment 5 Toralf Förster gentoo-dev 2016-09-24 09:13:14 UTC
(In reply to Martin Mokrejš from comment #4)
>  incidentally I brought a new version to sci overlay:

hhm,the tinderbox doesn't use any overlay usually.
Comment 6 David Seifert gentoo-dev 2016-09-24 23:09:55 UTC
commit c8c95dc5616fe51e1fffe9f875556a5ff14be39e
Author: David Seifert <>
Date:   Sun Sep 25 00:47:39 2016 +0200

    sci-biology/bedtools: Version bump to 2.26.0
    Gentoo-bug: 594994
    * EAPI=6
    * Make buildsystem output verbose
    * Inherit 'python-any-r1', due to python script
    * Add dependencies for test suite
    * Properly set CXX and CXXFLAGS
Comment 7 Martin Mokrejš 2016-10-03 17:48:26 UTC
Wow, thank you David, the ebuild file looks quite different now. I just kept what used to be inside so far. Thank you. Dropping the package from sci overlay now to avoid collision.

commit 29f09c80275e0e14527e2e45e91f9aaed8f2af2b
Author: Martin Mokrejš <>
Date:   Mon Oct 3 19:47:40 2016 +0200

    sci-biology/bedtools: rewritten ebuild landed now in main tree (bug #594994)