After upgrading to =dev-python/sip-4.11 =kde-base/pykde4-4.4.5 and =sci-chemistry/avogadro-1.0.1 don't compile. With =dev-python/sip-4.10.5 =kde-base/pykde4-4.4.5 and =sci-chemistry/avogadro-1.0.1 compile successfully. Reproducible: Always Steps to Reproduce: 1. Upgrade to =dev-python/sip-4.11 2. Recompile packages which depends on sip and PyQt4 3. =sci-chemistry/avogadro-1.0.1 and =kde-base/pykde4-4.4.5 compile failed emerge --info Portage 2.2_rc72 (default/linux/amd64/10.0/desktop/kde, gcc-4.4.4, glibc-2.12.1-r1, 2.6.35-gentoo-r5 x86_64) ================================================================= System uname: Linux-2.6.35-gentoo-r5-x86_64-Intel-R-_Core-TM-2_Duo_CPU_E7500_@_2.93GHz-with-gentoo-2.0.1 Timestamp of tree: Wed, 01 Sep 2010 23:00:01 +0000 ccache version 2.4 [enabled] app-shells/bash: 4.1_p7 dev-java/java-config: 2.1.11 dev-lang/python: 2.6.5-r3 dev-util/ccache: 2.4-r8 dev-util/cmake: 2.8.1-r2 sys-apps/baselayout: 2.0.1 sys-apps/openrc: 0.6.2 sys-apps/sandbox: 2.3-r1 sys-devel/autoconf: 2.13, 2.65-r1 sys-devel/automake: 1.9.6-r3, 1.10.3, 1.11.1 sys-devel/binutils: 2.20.1-r1 sys-devel/gcc: 4.4.4-r1 sys-devel/gcc-config: 1.4.1 sys-devel/libtool: 2.2.10 sys-devel/make: 3.81-r2 virtual/os-headers: 2.6.35 (sys-kernel/linux-headers) ACCEPT_KEYWORDS="amd64 ~amd64" ACCEPT_LICENSE="* -@EULA PUEL sun-prerelease-jdk7 dlj-1.1 googleearth AdobeFlash-10.1" CBUILD="x86_64-pc-linux-gnu" CFLAGS="-O2 -pipe -march=nocona" CHOST="x86_64-pc-linux-gnu" CONFIG_PROTECT="/etc /usr/kde/3.5/env /usr/kde/3.5/share/config /usr/kde/3.5/shutdown /usr/share/X11/xkb /usr/share/config /var/lib/hsqldb" CONFIG_PROTECT_MASK="/etc/ca-certificates.conf /etc/env.d /etc/env.d/java/ /etc/fonts/fonts.conf /etc/gconf /etc/gentoo-release /etc/portage /etc/revdep-rebuild /etc/sandbox.d /etc/splash /etc/terminfo /etc/texmf/language.dat.d /etc/texmf/language.def.d /etc/texmf/updmap.d /etc/texmf/web2c" CXXFLAGS="-O2 -pipe -march=nocona" DISTDIR="/usr/portage/distfiles" FEATURES="assume-digests buildpkg ccache collision-protect distlocks fixlafiles fixpackages metadata-transfer news parallel-fetch preserve-libs protect-owned sandbox sfperms strict unknown-features-warn unmerge-logs unmerge-orphans userfetch" GENTOO_MIRRORS="http://ash.catalysis.ru/gentoo/ http://linux.nsu.ru/gentoo-distfiles http://mirror.yandex.ru/gentoo-distfiles/ http://trumpetti.atm.tut.fi/gentoo http://oschtan.academ.org/" LANG="ru_RU.UTF-8" LC_ALL="" LDFLAGS="-Wl,-O1 -Wl,--as-needed" LINGUAS="ru" MAKEOPTS="-j3" PKGDIR="/usr/portage/packages" PORTAGE_CONFIGROOT="/" PORTAGE_RSYNC_OPTS="--recursive --links --safe-links --perms --times --compress --force --whole-file --delete --stats --timeout=180 --exclude=/distfiles --exclude=/local --exclude=/packages" PORTAGE_TMPDIR="/var/tmp" PORTDIR="/usr/portage" PORTDIR_OVERLAY="/var/lib/layman/oschtan /var/lib/layman/mozilla /var/lib/layman/sci /var/lib/layman/x11 /var/lib/layman/flying" SYNC="rsync://ash.catalysis.ru/gentoo-portage/" USE="7zip X a52 aac aalib acl acpi additions alsa amd64 amr amrnb amrwb ao apm applet audiofile bash-completion bdf berkdb branding bs2b bzip2 cairo cdda cdparanoia cdr cgi cjk clamav cleartype cli color-console consolekit cracklib cups cvs cxx dbus divx djvu dri drm dts dvd dvdr dvdread emboss emerald emf enca encode examples exceptions exif extensions faac faad fam fbcondecor ffmpeg firefox firefox3 flac fortran ftp fuse gd gecko gif gimp glitz gmedia gphoto2 gpm graphviz hal handbook hddtemp hdri htmlhandbook icons iconv icq imagemagick imlib java javascript jbig jingle jpeg jpeg2k kde lame latex lcms libnotify libsamplerate lm_sensors lzma mad mdnsresponder-compat midi mikmod mime mjpeg mmx mng modplug modules motif mozilla mp2 mp3 mp4 mpeg mplayer mudflap multilib multitarget musepack musicbrainz ncurses network nls nova npp nptl nptlonly nsplugin oav objc objc++ objc-gc ogg openexr opengl openmp oscar pam pango pcre pdf perl pertty plotutils png povray ppds pppd projectm python qt3 qt3support qt4 quicktime rar rcc readline realmedia reflection rtc samba scrobbler sdl sensord session sndfile sound source spell spl sqlite srt sse sse2 ssl ssse3 startup-notification subversion suid svg symlink sysfs syslog system-sqlite szip taglib tcpd templates theora threads thumbnail tidy tiff truetype type1 unicode unsupported usb userlocales utempter vcd visualization vorbis wavpack wma wmf wmp x264 x264-svn-encoder xattr xcb xcomposite xml xorg xpm xscreensaver xulrunner xv xvid zip zlib" ALSA_CARDS="intel-hda" ALSA_PCM_PLUGINS="adpcm alaw asym copy dmix dshare dsnoop empty extplug file hooks iec958 ioplug ladspa lfloat linear meter mmap_emul mulaw multi null plug rate route share shm softvol" CAMERAS="adc65 agfa_cl20 aox barbie canon casio_qv clicksmart310 digigr8 digita dimagev dimera3500 directory enigma13 fuji gsmart300 hp215 iclick jamcam jd11 kodak_dc120 kodak_dc210 kodak_dc240 kodak_dc3200 kodak_ez200 konica konica_qm150 largan lg_gsm mars mustek panasonic_coolshot panasonic_dc1000 panasonic_dc1580 panasonic_l859 pccam300 pccam600 polaroid_pdc320 polaroid_pdc640 polaroid_pdc700 ptp2 ricoh ricoh_g3 samsung sierra sipix_blink sipix_blink2 sipix_web2 smal sonix sony_dscf1 sony_dscf55 soundvision spca50x sq905 stv0674 stv0680 sx330z template toshiba_pdrm11 jl2005a topfield ax203 st2205" ELIBC="glibc" INPUT_DEVICES="evdev" KERNEL="linux" LCD_DEVICES="bayrad cfontz cfontz633 glk hd44780 lb216 lcdm001 mtxorb ncurses text" LINGUAS="ru" RUBY_TARGETS="ruby18" SANE_BACKENDS="abaton agfafocus apple artec artec_eplus48u as6e avision bh canon canon630u canon_dr canon_pp cardscan coolscan coolscan2 coolscan3 dc210 dc240 dc25 dell1600n_net dmc epjitsu epson epson2 fujitsu genesys gt68xx hp hp3500 hp3900 hp4200 hp5400 hp5590 hpljm1005 hpsj5s hs2p ibm kodak kvs1025 leo lexmark ma1509 matsushita microtek microtek2 mustek mustek_pp mustek_usb nec net niash p5 pie pixma plustek plustek_pp qcam ricoh rts8891 s9036 sceptre sharp sm3600 sm3840 snapscan sp15c st400 stv680 tamarack teco1 teco2 teco3 test u12 umax umax1220u umax_pp xerox_mfp" USERLAND="GNU" VIDEO_CARDS="intel" 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, FFLAGS, INSTALL_MASK, PORTAGE_COMPRESS, PORTAGE_COMPRESS_FLAGS, PORTAGE_RSYNC_EXTRA_OPTS
Created attachment 245721 [details] pykde4-4.4.5 build
Created attachment 245722 [details] avogadro-1.0.1 build
Created attachment 245723 [details] avogadro-1.0.1 environment
Created attachment 245725 [details] pykde4-4.4.5 environment
emerge -pv =sci-chemistry/avogadro-1.0.1 These are the packages that would be merged, in order: Calculating dependencies... done! [ebuild R ] sci-chemistry/avogadro-1.0.1 USE="glsl python" 0 kB Total: 1 package (1 reinstall), Size of downloads: 0 kB emerge -pv kde-base/pykde4 These are the packages that would be merged, in order: Calculating dependencies... done! [ebuild R ] kde-base/pykde4-4.4.5 USE="examples (-aqua) -debug -doc (-kdeenablefinal) (-kdeprefix) -semantic-desktop" 0 kB Total: 1 package (1 reinstall), Size of downloads: 0 kB
confirmed, with a weird dependency cycle on my box, i can't use some plasmoids for this..
Created attachment 245773 [details] English build.log for kde-base/pykde4-4.4.5
there is bug 332503 for pykde4
(Hi, I'm the Fedora package maintainer for avogadro and we're also seeing this.) This is the offending construct: // return the C++ pointer return wrapper->u.cppPtr; That member 'u' doesn't exist anymore: http://www.riverbankcomputing.com/pipermail/pyqt/2010-August/027580.html and as the reply there evidences, this wasn't ever public API.
This is the relevant SIP change: http://www.riverbankcomputing.com/hg/sip/rev/956c80d8e9fa A quick hack would probably be to just return wrapper->data; instead of wrapper->u.cppPtr, but I think we should be using: return sip_API->api_get_address(wrapper); which is a new API function introduced in SIP 4.11 for this purpose. Of course this needs to be wrapped with a check for the SIP version to be acceptable for upstream avogadro.
Created attachment 247308 [details, diff] Proposed upstreamable patch
FYI: http://koji.fedoraproject.org/koji/taskinfo?taskID=2467400 2467400 build (dist-rawhide, /avogadro:6476c1a6de44b40f540b303cc36e0520aae6b3c9) completed successfully In other words, the patch I attached fixes the build for me in Fedora's build system. Can it please be applied upstream (and in the Gentoo ebuild as well)?
(In reply to comment #12) > Can it please be applied upstream (and in the Gentoo ebuild as well)? > this patch seems working. please apply it in portage.
it is happily segf'ing here.
When does it segfault? During build? While doing something (what?) at runtime? GDB backtrace? Valgrind log?
Starting program: /usr/bin/avogadro Traceback (most recent call last): File "/usr/share/gdb/auto-load/usr/lib64/gcc/x86_64-pc-linux-gnu/4.5.1/libstdc++.so.6.0.14-gdb.py", line 59, in <module> from libstdcxx.v6.printers import register_libstdcxx_printers ImportError: No module named libstdcxx.v6.printers [Thread debugging using libthread_db enabled] Gtk-Message: Failed to load module "gnomebreakpad": libgnomebreakpad.so: cannot open shared object file: No such file or directory "Avogadro version: 1.0.1 Git: LibAvogadro version: 1.0.1 Git: " Locale: "en_GB" Translation successfully loaded. "System has OpenGL support." "About to test OpenGL capabilities." "OpenGL capabilities found: " "Double Buffering." "Direct Rendering." "Antialiasing." Loading plugins: "/usr/bin/../lib64/avogadro/1_0" Searching for plugins in "/usr/bin/../lib64/avogadro/1_0/colors" Searching for plugins in "/usr/bin/../lib64/avogadro/1_0/engines" Searching for plugins in "/usr/bin/../lib64/avogadro/1_0/extensions" Searching for plugins in "/usr/bin/../lib64/avogadro/1_0/tools" Searching for plugins in "/usr/bin/../lib64/avogadro/1_0/contrib" Loading plugins: "/home/justin/.avogadro/1_0/plugins" Searching for plugins in "/home/justin/.avogadro/1_0/plugins/colors" Searching for plugins in "/home/justin/.avogadro/1_0/plugins/engines" Searching for plugins in "/home/justin/.avogadro/1_0/plugins/extensions" Searching for plugins in "/home/justin/.avogadro/1_0/plugins/tools" Searching for plugins in "/home/justin/.avogadro/1_0/plugins/contrib" QStackedLayout::setCurrentWidget: Widget 0x1439990 not contained in stack [New Thread 0x2aaad6b3c710 (LWP 28829)] [New Thread 0x2aaadf4fe710 (LWP 28839)] Program received signal SIGSEGV, Segmentation fault. 0x00002aaaab96f7e8 in QX11Info::screen (this=0x162a3a0) at kernel/qx11info_x11.cpp:476 476 kernel/qx11info_x11.cpp: No such file or directory. in kernel/qx11info_x11.cpp (gdb) bt #0 0x00002aaaab96f7e8 in QX11Info::screen (this=0x162a3a0) at kernel/qx11info_x11.cpp:476 #1 0x00002aaaab48f88b in QGLWidget::event (this=0x162a170, e=0x7fffffffb470) at qgl.cpp:3835 #2 0x00002aaaab8d5ab4 in QApplicationPrivate::notify_helper (this=0x6bac60, receiver=0x162a170, e=0x7fffffffb470) at kernel/qapplication.cpp:4300 #3 0x00002aaaab8d9b3a in QApplication::notify (this=<value optimized out>, receiver=0x162a170, e=0x7fffffffb470) at kernel/qapplication.cpp:4183 #4 0x00002aaaac4c7c5b in QCoreApplication::notifyInternal (this=0x7fffffffc1e0, receiver=0x162a170, event=0x7fffffffb470) at kernel/qcoreapplication.cpp:704 #5 0x00002aaaab927e20 in sendEvent (this=0x162a170, parent=<value optimized out>, f=<value optimized out>) at ../../include/QtCore/../../src/corelib/kernel/qcoreapplication.h:215 #6 QWidget::setParent (this=0x162a170, parent=<value optimized out>, f=<value optimized out>) at kernel/qwidget.cpp:9867 #7 0x00002aaaab928312 in QWidget::setParent (this=<value optimized out>, parent=<value optimized out>) at kernel/qwidget.cpp:9734 #8 0x00002aaaab8fea9c in QLayout::addChildWidget (this=<value optimized out>, w=0x162a170) at kernel/qlayout.cpp:1016 #9 0x00002aaaab8e34b8 in QBoxLayout::insertWidget (this=0x1629f90, index=-1, widget=0x162a170, stretch=0, alignment=...) at kernel/qboxlayout.cpp:1032 #10 0x00002aaaab8e36cb in QBoxLayout::addWidget (this=<value optimized out>, widget=<value optimized out>, stretch=<value optimized out>, alignment=<value optimized out>) at kernel/qboxlayout.cpp:1112 #11 0x0000000000454988 in Avogadro::MainWindow::readSettings (this=0x84bea0) at /var/tmp/portage/sci-chemistry/avogadro-1.0.1/work/avogadro-1.0.1/avogadro/src/mainwindow.cpp:2817 #12 0x0000000000455375 in Avogadro::MainWindow::event (this=0x84bea0, event=0x7fffffffc040) at /var/tmp/portage/sci-chemistry/avogadro-1.0.1/work/avogadro-1.0.1/avogadro/src/mainwindow.cpp:460 #13 0x00002aaaab8d5ab4 in QApplicationPrivate::notify_helper (this=0x6bac60, receiver=0x84bea0, e=0x7fffffffc040) at kernel/qapplication.cpp:4300 #14 0x00002aaaab8d9b3a in QApplication::notify (this=<value optimized out>, receiver=0x84bea0, e=0x7fffffffc040) at kernel/qapplication.cpp:4183 #15 0x00002aaaac4c7c5b in QCoreApplication::notifyInternal (this=0x7fffffffc1e0, receiver=0x84bea0, event=0x7fffffffc040) at kernel/qcoreapplication.cpp:704 #16 0x00002aaaab91d33f in sendEvent (this=0x84bea0) at ../../include/QtCore/../../src/corelib/kernel/qcoreapplication.h:215 #17 QWidget::ensurePolished (this=0x84bea0) at kernel/qwidget.cpp:9329 #18 0x00002aaaab9246fb in QWidget::setVisible (this=0x84bea0, visible=<value optimized out>) at kernel/qwidget.cpp:7368 #19 0x000000000042c012 in main (argc=1, argv=<value optimized out>) at /var/tmp/portage/sci-chemistry/avogadro-1.0.1/work/avogadro-1.0.1/avogadro/src/main.cpp:239
I am preparing a new Avogadro 1.0.2 release, I will be making sure the SIP fixes get into it.
(In reply to comment #17) > I am preparing a new Avogadro 1.0.2 release, I will be making sure the SIP > fixes get into it. > Welcome back! :)
Thanks life has been truly hectic. I am preparing a new release and it contains a superset of these fixes for new versions of SIP. I am hoping to tag and release next week. Sorry for the lack of communication, I have been a little swamped.
FYI, you'll also want this one, it fixes a crash when using SIP >= 4.10.4 together with Python >= 2.7. (SIP now uses PyCapsule and Avogadro didn't expect that.) http://pkgs.fedoraproject.org/gitweb/?p=avogadro.git;a=blob;f=avogadro-1.0.1-pycapsule.patch;h=de4e2ca75b7da0bacda5d5ffc6eccde2286325ba;hb=HEAD
I think I have that one too - I went hunting for patches. I reformulated a little. If you get chance to try out Avogadro 1.0.2_rc1 it contains those fixes (available from SourceForge).
*** Bug 345423 has been marked as a duplicate of this bug. ***
+ 26 Mar 2011; Justin Lecher <jlec@gentoo.org> avogadro-1.0.1.ebuild, + +files/avogadro-1.0.1-sip-backport.patch: + Backported sip patch from 1.0.2_rc1, #335644 +
