Bug 583932 – sci-chemistry/ball-1.4.2 : /.../common.h:175:18: error: ‘isnan’ was not declared in this scope, and no declarations were found by argument-dependent lookup at the point of instantiation [-fpermissive]

• Status: RESOLVED FIXED
• Product: Gentoo Linux

[Description Toralf Förster 2016-05-24 07:42:12 UTC]

/var/tmp/portage/sci-chemistry/ball-1.4.2/work/BALL-1.4.2/include/BALL/MATHS/common.h: In instantiation of ‘bool BALL::Maths::isNan(const T&) [with T = double]’:
/var/tmp/portage/sci-chemistry/ball-1.4.2/work/BALL-1.4.2/source/MOLMEC/MINIMIZATION/steepestDescent.C:214:46:   required from here
/var/tmp/portage/sci-chemistry/ball-1.4.2/work/BALL-1.4.2/include/BALL/MATHS/common.h:175:18: error: ‘isnan’ was not declared in this scope, and no declarations were found by argument-dependent lookup at the point of instantiation [-fpermissive]
     return (isnan(t) != 0);
                  ^
In file included from /usr/lib/gcc/x86_64-pc-linux-gnu/5.3.0/include/g++-v5/random:38:0,


$ cat emerge-info.txt
  -----------------------------------------------------------------

  This is an unstable amd64 chroot image (named amd64-13.0-unstable_20160522-215403) at a hardened host acting as a tinderbox.

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

  make.conf: USE="mmx sse sse2 pax_kernel xtpax -cdinstall -oci8 -bindist aes-ni alsa apache avx2 corefonts csc custom-optimization -dot evdev gcj -gif gles2 gnomecanvas -haptic introspection -isag libkms mikmod mng mod nss opencv -openssl qt3support server ssh-askpass ssl threads tk vaapi video wav xinetd xvfb xvmc xz"

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

Portage 2.3.0_rc1 (python 3.4.3-final-0, default/linux/amd64/13.0, gcc-5.3.0, glibc-2.23-r2, 4.5.5-hardened x86_64)
=================================================================
System uname: Linux-4.5.5-hardened-x86_64-Intel-R-_Core-TM-_i7-3770_CPU_@_3.40GHz-with-gentoo-2.2
KiB Mem:    16157888 total,   2360440 free
KiB Swap:   16777212 total,  16723152 free
Timestamp of repository gentoo: Tue, 24 May 2016 01:04:16 +0000
sh bash 4.3_p42-r2
ld GNU ld (Gentoo 2.25.1 p1.1) 2.25.1
ccache version 3.2.5 [disabled]
app-shells/bash:          4.3_p42-r2::gentoo
dev-java/java-config:     2.2.0-r3::gentoo
dev-lang/perl:            5.24.0::gentoo
dev-lang/python:          2.7.11-r2::gentoo, 3.4.3-r7::gentoo
dev-util/ccache:          3.2.5::gentoo
dev-util/cmake:           3.5.2-r1::gentoo
dev-util/pkgconfig:       0.29.1::gentoo
sys-apps/baselayout:      2.2::gentoo
sys-apps/openrc:          0.20.5::gentoo
sys-apps/sandbox:         2.10-r2::gentoo
sys-devel/autoconf:       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
sys-devel/gcc:            5.3.0::gentoo
sys-devel/gcc-config:     1.8-r1::gentoo
sys-devel/libtool:        2.4.6-r2::gentoo
sys-devel/make:           4.2-r1::gentoo
sys-kernel/linux-headers: 4.6::gentoo (virtual/os-headers)
sys-libs/glibc:           2.23-r2::gentoo
Repositories:

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

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

ACCEPT_KEYWORDS="amd64 ~amd64"
ACCEPT_LICENSE="*"
CBUILD="x86_64-pc-linux-gnu"
CFLAGS="-march=native -O2 -pipe"
CHOST="x86_64-pc-linux-gnu"
CONFIG_PROTECT="/etc /usr/share/gnupg/qualified.txt /var/lib/hsqldb"
CONFIG_PROTECT_MASK="/etc/ca-certificates.conf /etc/env.d /etc/fonts/fonts.conf /etc/gconf /etc/gentoo-release /etc/php/apache2-php7.0/ext-active/ /etc/php/cgi-php7.0/ext-active/ /etc/php/cli-php7.0/ext-active/ /etc/revdep-rebuild /etc/sandbox.d /etc/terminfo /etc/texmf/language.dat.d /etc/texmf/language.def.d /etc/texmf/updmap.d /etc/texmf/web2c"
CXXFLAGS="-march=native -O2 -pipe"
DISTDIR="/var/tmp/distfiles"
EMERGE_DEFAULT_OPTS="--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 news parallel-fetch preserve-libs protect-owned sandbox sfperms strict unknown-features-warn unmerge-logs unmerge-orphans userfetch userpriv usersandbox usersync xattr"
FFLAGS="-O2 -pipe"
GENTOO_MIRRORS="http://ftp.uni-erlangen.de/pub/mirrors/gentoo rsync://mirror.netcologne.de/gentoo/ ftp://sunsite.informatik.rwth-aachen.de/pub/Linux/gor.bytemark.co.uk/gentoo/ rsync://ftp.snt.utwente.nl/gentoo"
LANG="en_US.utf8"
LDFLAGS="-Wl,-O1 -Wl,--as-needed"
MAKEOPTS="-j1"
PKGDIR="/usr/portage/packages"
PORTAGE_CONFIGROOT="/"
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"
PORTAGE_TMPDIR="/var/tmp"
USE="acl aes-ni alsa amd64 apache avx2 berkdb bzip2 cli corefonts cracklib crypt csc custom-optimization cxx dri evdev fortran gcj gdbm gles2 gnomecanvas iconv introspection ipv6 libkms mikmod mmx mmxext mng mod modules multilib ncurses nls nptl nss opencv openmp pam pax_kernel pcre qt3support readline seccomp server session sse sse2 ssh-askpass ssl tcpd threads tk unicode vaapi video wav xattr xinetd xtpax xvfb xvmc xz 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" LCD_DEVICES="bayrad cfontz cfontz633 glk hd44780 lb216 lcdm001 mtxorb ncurses text" LIBREOFFICE_EXTENSIONS="presenter-console presenter-minimizer" OFFICE_IMPLEMENTATION="libreoffice" PHP_TARGETS="php5-5" PYTHON_SINGLE_TARGET="python2_7" PYTHON_TARGETS="python2_7 python3_4" RUBY_TARGETS="ruby20 ruby21" USERLAND="GNU" VIDEO_CARDS="intel i965" 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"
Unset:  CC, CPPFLAGS, CTARGET, CXX, INSTALL_MASK, LC_ALL, PORTAGE_BUNZIP2_COMMAND, PORTAGE_COMPRESS, PORTAGE_COMPRESS_FLAGS, PORTAGE_RSYNC_EXTRA_OPTS, USE_PYTHON

[Comment 1 Toralf Förster 2016-05-24 07:42:15 UTC]

Created attachment 435174 [details]
emerge-history.txt

[Comment 2 Toralf Förster 2016-05-24 07:42:18 UTC]

Created attachment 435176 [details]
environment

[Comment 3 Toralf Förster 2016-05-24 07:42:20 UTC]

Created attachment 435178 [details]
sci-chemistry:ball-1.4.2:20160524-015236.log

[Comment 4 David Seifert 2016-06-05 15:24:21 UTC]

commit 0947afa365abf88670172058186a1ff22de84a07
Author: David Seifert <[e-mail]>
Date:   Sun Jun 5 17:18:04 2016 +0200

    sci-chemistry/ball: Fix Swig bug, qualify std::isnan
    
    Gentoo-Bug: 583932
    * EAPI=6
    * Also fix GCC warning pollution due to
      misplaced attributes
    * Add subslot operator for dev-libs/boost
    * Remove USE=webkit, as webkit is no longer supported