Bug 553104

Summary:	sci-chemistry/openbabel-2.3.2::gentoo failed (compile phase) - openbabel-2.3.2/include/openbabel/shared_ptr.h:27:14: error: ‘std::tr1’ has not been declared using std::tr1::shared_ptr;
Product:	Gentoo Linux	Reporter:	Piotr Szymaniak <bugzie>
Component:	Current packages	Assignee:	Gentoo Chemistry-Related Packages <sci-chemistry>
Status:	RESOLVED OBSOLETE
Severity:	normal	CC:	jlec, kredba
Priority:	Normal
Version:	unspecified
Hardware:	All
OS:	Linux
URL:	https://github.com/openbabel/openbabel/commit/04d0fe305c28965cafb252945d4afd23c2b98468
Whiteboard:
Package list:		Runtime testing required:	---
Attachments:	build.log

Description Piotr Szymaniak 2015-06-23 22:20:58 UTC

Created attachment 405614 [details]
build.log

Portage 2.2.20 (python 2.7.10-final-0, default/linux/amd64/13.0, gcc-5.1.0, glibc-2.20-r2, 4.0.0 x86_64)
=================================================================
                         System Settings
=================================================================
System uname: Linux-4.0.0-x86_64-Common_KVM_processor-with-gentoo-2.2
KiB Mem:    16446612 total,  11098680 free
KiB Swap:          0 total,         0 free
Timestamp of repository gentoo: Mon, 22 Jun 2015 12:15:01 +0000
sh bash 4.3_p39
ld GNU ld (Gentoo 2.25 p1.2) 2.25
app-shells/bash:          4.3_p39::gentoo
dev-lang/perl:            5.20.2-r1::gentoo
dev-lang/python:          2.7.10::gentoo, 3.3.5-r1::gentoo
dev-util/pkgconfig:       0.28-r3::gentoo
sys-apps/baselayout:      2.2::gentoo
sys-apps/openrc:          0.17::gentoo
sys-apps/sandbox:         2.6-r1::gentoo
sys-devel/autoconf:       2.69-r1::gentoo
sys-devel/automake:       1.14.1::gentoo, 1.15::gentoo
sys-devel/binutils:       2.25-r1::gentoo
sys-devel/gcc:            5.1.0::gentoo
sys-devel/gcc-config:     1.8::gentoo
sys-devel/libtool:        2.4.6-r1::gentoo
sys-devel/make:           4.1-r1::gentoo
sys-kernel/linux-headers: 4.0::gentoo (virtual/os-headers)
sys-libs/glibc:           2.20-r2::gentoo
Repositories:

gentoo
    location: /usr/portage
    sync-type: rsync
    sync-uri: rsync://rsync1.fi.gentoo.org/gentoo-portage
    priority: -1000

ACCEPT_KEYWORDS="amd64 ~amd64"
ACCEPT_LICENSE="* -@EULA"
CBUILD="x86_64-pc-linux-gnu"
CFLAGS="-march=nocona -mno-sse3 -O2 -pipe"
CHOST="x86_64-pc-linux-gnu"
CONFIG_PROTECT="/etc /usr/share/gnupg/qualified.txt"
CONFIG_PROTECT_MASK="/etc/ca-certificates.conf /etc/env.d /etc/gconf /etc/gentoo-release /etc/revdep-rebuild /etc/sandbox.d /etc/terminfo"
CXXFLAGS="-march=nocona -mno-sse3 -O2 -pipe"
DISTDIR="/usr/portage/distfiles"
FCFLAGS="-O2 -pipe"
FEATURES="assume-digests binpkg-logs config-protect-if-modified distlocks ebuild-locks fixlafiles merge-sync news parallel-fetch preserve-libs protect-owned sandbox sfperms strict unknown-features-warn unmerge-logs unmerge-orphans userfetch userpriv usersandbox usersync"
FFLAGS="-O2 -pipe"
GENTOO_MIRRORS="http://trumpetti.atm.tut.fi/gentoo/"
LANG="en_US.utf8"
LDFLAGS="-Wl,-O1 -Wl,--as-needed"
MAKEOPTS="-j25"
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"
PORTAGE_TMPDIR="/var/tmp"
USE="acl amd64 berkdb bindist bzip2 cli cracklib crypt cxx dri fortran gdbm iconv ipv6 mmx mmxext modules multilib ncurses nls nptl openmp pam pcre readline session sse sse2 ssl tcpd unicode 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="mmx mmxext sse sse2" 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_3" RUBY_TARGETS="ruby19 ruby20" USERLAND="GNU" VIDEO_CARDS="fbdev glint intel mach64 mga nouveau nv r128 radeon savage sis tdfx trident vesa via vmware 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"
Unset:  CPPFLAGS, CTARGET, EMERGE_DEFAULT_OPTS, INSTALL_MASK, LC_ALL, PORTAGE_BUNZIP2_COMMAND, PORTAGE_COMPRESS, PORTAGE_COMPRESS_FLAGS, PORTAGE_RSYNC_EXTRA_OPTS, USE_PYTHON

[ebuild  N    ] sci-libs/inchi-1.04  USE="-doc -static-libs" 
[ebuild  N    ] app-arch/libarchive-3.1.2-r1  USE="acl bzip2 e2fsprogs iconv lzma zlib -expat -lzo -nettle -static-libs -xattr" 
[ebuild  N    ] dev-util/cmake-3.2.3  USE="ncurses -doc -emacs -qt4 -qt5 -system-jsoncpp {-test}" 
[ebuild  N    ] dev-cpp/eigen-3.2.4  USE="-debug -doc" 
[ebuild  N    ] sci-chemistry/openbabel-2.3.2  USE="openmp -doc {-test} -wxwidgets"

Comment 1 Justin Lecher (RETIRED) gentoo-dev

2015-06-24 06:27:38 UTC

I cannot reproduce this with gcc-4.9 here, so it is probably a gcc-5.1 bug. Could you please report this upstream and add the link here?

Comment 2 Justin Lecher (RETIRED) gentoo-dev

2015-06-24 07:37:57 UTC

This patch probably helps.

https://github.com/openbabel/openbabel/commit/04d0fe305c28965cafb252945d4afd23c2b98468

Could you please test this?

Comment 3 David Kredba 2015-10-10 17:59:26 UTC

Patch works, gcc-5.2.0. Thank you.

Comment 4 Justin Lecher (RETIRED) gentoo-dev

2015-11-04 19:29:02 UTC

commit fddaa01871af3e465b9bc4833a0ad68a2b91ffbb
Author: Justin Lecher <jlec@gentoo.org>
Date:   Wed Nov 4 20:24:01 2015 +0100

    sci-chemistry/openbabel: Drop old

    obsoletes

    Gentoo-Bug: https://bugs.gentoo.org/show_bug.cgi?id=449852

    Gentoo-Bug: https://bugs.gentoo.org/show_bug.cgi?id=553104

    Package-Manager: portage-2.2.23
    Signed-off-by: Justin Lecher <jlec@gentoo.org>

    https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=fddaa01871af3e465b9bc4833a0ad68a2b91ffbb