Created attachment 447054 [details] build log I am unable to build sci-chemistry/avogadro2 with vtk. Build attached. emerge --info Portage 2.3.1 (python 3.5.2-final-0, default/linux/amd64/13.0, gcc-5.4.0, glibc-2.23-r2, 4.7.4 x86_64) ================================================================= System uname: Linux-4.7.4-x86_64-AMD_A10-7700K_Radeon_R7,_10_Compute_Cores_4C+6G-with-gentoo-2.3 KiB Mem: 7143440 total, 1946764 free KiB Swap: 10485744 total, 10483224 free Timestamp of repository gentoo: Wed, 21 Sep 2016 09:15:01 +0000 sh bash 4.3_p46-r1 ld GNU ld (Gentoo 2.26.1 p1.0) 2.26.1 app-shells/bash: 4.3_p46-r1::gentoo dev-java/java-config: 2.2.0-r3::gentoo dev-lang/perl: 5.24.0-r1::gentoo dev-lang/python: 2.7.12::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: 1.12.6-r1::gentoo, 1.13.4-r1::gentoo, 1.14.1-r1::gentoo, 1.15-r2::gentoo sys-devel/binutils: 2.26.1::gentoo sys-devel/gcc: 5.4.0::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 Repositories: gentoo location: /usr/portage sync-type: rsync sync-uri: rsync://rsync.europe.gentoo.org/gentoo-portage priority: -1000 kernelpanic location: /usr/local/portage masters: gentoo libressl location: /var/lib/layman/libressl sync-type: laymansync sync-uri: https://github.com/gentoo/libressl.git masters: gentoo priority: 50 science location: /var/lib/layman/science sync-type: laymansync sync-uri: git://anongit.gentoo.org/proj/sci.git masters: gentoo priority: 50 ACCEPT_KEYWORDS="amd64 ~amd64" ACCEPT_LICENSE="* -@EULA @EULA" CBUILD="x86_64-pc-linux-gnu" CFLAGS="-march=native -mtune=native -O2 -pipe" CHOST="x86_64-pc-linux-gnu" CONFIG_PROTECT="/etc /usr/lib64/libreoffice/program/sofficerc /usr/share/config /usr/share/gnupg/qualified.txt" CONFIG_PROTECT_MASK="/etc/ca-certificates.conf /etc/dconf /etc/env.d /etc/fonts/fonts.conf /etc/gconf /etc/gentoo-release /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 -mtune=native -O2 -pipe" DISTDIR="/var/portage/distfiles" FCFLAGS="-march=native -mtune=native -O2 -pipe" FEATURES="assume-digests binpkg-logs clean-logs compress-build-logs config-protect-if-modified distlocks ebuild-locks fixlafiles merge-sync news parallel-fetch parallel-install preserve-libs protect-owned sandbox sfperms split-elog split-log strict unknown-features-warn unmerge-logs unmerge-orphans userfetch userpriv usersandbox usersync xattr" FFLAGS="-march=native -mtune=native -O2 -pipe" GENTOO_MIRRORS="http://distfiles.gentoo.org" INSTALL_MASK="/etc/systemd /usr/lib/systemd /usr/lib64/systemd" LANG="it_IT.UTF-8" LDFLAGS="-Wl,-O1 -Wl,--as-needed" MAKEOPTS="-j5" 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="X a52 aac acl alsa amd64 ao berkdb blas branding bzip2 cairo caps cdda cli cracklib crypt cups curl cxx dbus djvu dri dts dv dvb dvd encode exif ffmpeg fftw flac fontconfig fortran gcj gdbm gif gimp gmp gpm gsm gstreamer iconv icu inotify ipv6 jbig jpeg jpeg2k lame lapack latex lcms libass libnotify libressl lzma lzo mad matroska mmap mms mmx mmxext mng modplug modules mp3 mpeg mpi multilib ncurses nls nptl nsplugin offensive ogg openexr opengl openmp pam pcre pdf png postscript raw readline scanner seccomp session smp sndfile sound sox speex sse sse2 ssl startup-notification svg theora threads tiff truetype udev unicode usb v4l vaapi vdpau vim-syntax vorbis wavpack wmf wxwidgets x264 xattr xcb xml xmp xpm xscreensaver xv xvid zlib" ABI_X86="32 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 fma3 fma4 mmx mmxext popcnt sse sse2 sse3 sse4_1 sse4_2 sse4a ssse3 xop" CURL_SSL="libressl" 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="evdev" KERNEL="linux" L10N="it en" LCD_DEVICES="bayrad cfontz cfontz633 glk hd44780 lb216 lcdm001 mtxorb ncurses text" LIBREOFFICE_EXTENSIONS="presenter-console presenter-minimizer" LINGUAS="it en" OFFICE_IMPLEMENTATION="libreoffice" PHP_TARGETS="php5-6" PYTHON_SINGLE_TARGET="python2_7" PYTHON_TARGETS="python2_7 python3_5" QEMU_SOFTMMU_TARGETS="i386 x86_64" QEMU_USER_TARGETS="i386 x86_64" RUBY_TARGETS="ruby23" SANE_BACKENDS="hp" USERLAND="GNU" VIDEO_CARDS="amdgpu radeon radeonsi" 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, EMERGE_DEFAULT_OPTS, LC_ALL, PORTAGE_BUNZIP2_COMMAND, PORTAGE_COMPRESS, PORTAGE_COMPRESS_FLAGS, PORTAGE_RSYNC_EXTRA_OPTS, USE_PYTHON
Please try again with recently added: sci-libs/avogadrolibs-1.91.0_pre20180406-r1 sci-chemistry/avogadro2-1.90.0_p20180211
Yes, it now compiles. But... at he first attempt to drag'n drop -- let say, draw an atom, drag and drop to create a bond -- the program segfaults. From dmesg: avogadro2[12426]: segfault at 55e658926928 ip 00007f4f3cd719b1 sp 00007ffe4805f850 error 6 in libc-2.26.so[7f4f3cce9000+1be000] segfaults happen also without vtk. Besides, some dependencies are missing in the tree (pybind11, libmsym, cclib) and some other are maybe 'extra' (like molequeue). I'm not sure that removal of avogadro (bug #645030) is a good idea.
(In reply to Michelangelo Scopelliti from comment #2) > Yes, it now compiles. But... > > at he first attempt to drag'n drop -- let say, draw an atom, drag and drop > to create a bond -- the program segfaults. Please report that upstream. > Besides, some dependencies are missing in the tree (pybind11, libmsym, > cclib) and some other are maybe 'extra' (like molequeue). Those missing dependencies are optional, if old avogadro did not need them, it is functionality not lost. > I'm not sure that removal of avogadro (bug #645030) is a good idea. No way around that unless old avogadro learns Qt5. We should rather try to speed up upstream with bug reports such as yours so that it can be considered good enough an alternative.
Closing this bug as fixed then.
(In reply to Michelangelo Scopelliti from comment #2) > at he first attempt to drag'n drop -- let say, draw an atom, drag and drop > to create a bond -- the program segfaults. Sounds like the following issue? https://github.com/OpenChemistry/avogadroapp/issues/61 ftr, we can keep avogadro a bit longer masked in tree if there are bugs preventing proper use of avogadro2, but ultimately it will not block Qt4 removal. But this will probably not happen in the next 2 months.
(In reply to Andreas Sturmlechner from comment #5) [CUT] > Sounds like the following issue? > https://github.com/OpenChemistry/avogadroapp/issues/61 > > ftr, we can keep avogadro a bit longer masked in tree if there are bugs > preventing proper use of avogadro2, but ultimately it will not block Qt4 > removal. But this will probably not happen in the next 2 months. I really don't know, I've no error messages besides the reported dmesg. Thank you for the pointer, I'll look into it.
