Created attachment 412340 [details] build.log (xz compressed) sci-visualization/paraview-4.4.0 fails to build, expecting a /usr/lib64/mysql/libmysqlclient.so file, which is not present: make[2]: *** No rule to make target '/usr/lib64/mysql/libmysqlclient.so', needed by 'lib/libvtkIOMySQL-pv4.4.so.1'. Stop. CMakeFiles/Makefile2:11158: recipe for target 'VTK/IO/MySQL/CMakeFiles/vtkIOMySQL.dir/all' failed make[1]: *** [VTK/IO/MySQL/CMakeFiles/vtkIOMySQL.dir/all] Error 2 # emerge --info sci-visualization/paraview virtual/mysql dev-db/mariadb Portage 2.2.20.1 (python 3.4.3-final-0, default/linux/amd64/13.0/desktop/plasma/systemd, gcc-4.9.3, glibc-2.21-r1, 4.2.0-gentoo-r1 x86_64) ================================================================= System Settings ================================================================= System uname: Linux-4.2.0-gentoo-r1-x86_64-AMD_A10-7800_Radeon_R7,_12_Compute_Cores_4C+8G-with-gentoo-2.2 KiB Mem: 15381476 total, 7440364 free KiB Swap: 0 total, 0 free Timestamp of repository gentoo: Sun, 20 Sep 2015 14:15:01 +0000 sh bash 4.3_p42 ld GNU ld (Gentoo 2.25.1 p1.1) 2.25.1 ccache version 3.2.3 [disabled] app-shells/bash: 4.3_p42::gentoo dev-java/java-config: 2.2.0::gentoo dev-lang/perl: 5.22.0::gentoo dev-lang/python: 2.7.10::gentoo, 3.3.5-r1::gentoo, 3.4.3::gentoo dev-util/ccache: 3.2.3::gentoo dev-util/cmake: 3.3.2::gentoo dev-util/pkgconfig: 0.28-r3::gentoo sys-apps/baselayout: 2.2::gentoo sys-apps/sandbox: 2.8::gentoo sys-devel/autoconf: 2.13::gentoo, 2.69-r1::gentoo sys-devel/automake: 1.11.6-r1::gentoo, 1.12.6::gentoo, 1.13.4::gentoo, 1.14.1::gentoo, 1.15::gentoo sys-devel/binutils: 2.25.1-r1::gentoo sys-devel/gcc: 4.9.3::gentoo sys-devel/gcc-config: 1.8-r1::gentoo sys-devel/libtool: 2.4.6-r1::gentoo sys-devel/make: 4.1-r1::gentoo sys-kernel/linux-headers: 4.2::gentoo (virtual/os-headers) sys-libs/glibc: 2.21-r1::gentoo Repositories: gentoo location: /var/cache/portage/gentoo sync-type: rsync sync-uri: rsync://rsync.de.gentoo.org/gentoo-portage priority: -1000 kde location: /var/lib/layman/kde sync-type: laymansync sync-uri: git://anongit.gentoo.org/proj/kde.git masters: gentoo priority: 50 sage-on-gentoo location: /var/lib/layman/sage-on-gentoo sync-type: laymansync sync-uri: git://github.com/cschwan/sage-on-gentoo.git masters: gentoo priority: 50 local location: /var/cache/portage/local masters: gentoo priority: 100 ACCEPT_KEYWORDS="amd64 ~amd64" ACCEPT_LICENSE="* -@EULA" CBUILD="x86_64-pc-linux-gnu" CFLAGS="-pipe -O2 -march=bdver3" CHOST="x86_64-pc-linux-gnu" CONFIG_PROTECT="/etc /usr/lib64/libreoffice/program/sofficerc /usr/share/config /usr/share/gnupg/qualified.txt /usr/share/themes/oxygen-gtk/gtk-2.0 /usr/share/themes/oxygen-gtk/gtk-3.0" 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/cgi-php5.6/ext-active/ /etc/php/cli-php5.6/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="-pipe -O2 -march=bdver3" DISTDIR="/var/cache/portage/distfiles" EMERGE_DEFAULT_OPTS="--keep-going --nospinner" FCFLAGS="-O2 -pipe" FEATURES="assume-digests binpkg-logs buildsyspkg compressdebug config-protect-if-modified distlocks ebuild-locks fixlafiles merge-sync news parallel-fetch parallel-install 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.spline.inf.fu-berlin.de/mirrors/gentoo/ http://ftp-stud.hs-esslingen.de/pub/Mirrors/gentoo/ http://distfiles.gentoo.org" LANG="en_GB.UTF-8" LDFLAGS="-Wl,-O1 -Wl,--as-needed -Wl,--hash-style=gnu" MAKEOPTS="-j5" PKGDIR="/var/cache/portage/packages" PORTAGE_COMPRESS="xz" 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="X a52 aac aacplus aacs acl acpi alsa amd64 appindicator audit avahi bash-completion bdplus berkdb bluetooth bluray branding bzip2 cairo caps cdda cddb cdio cdr celt cjk cli conntrack cracklib crypt cups cxx dbus declarative dirac dri dts dvb dvd dvdr egl emboss encode exif fam fax ffmpeg firefox flac fontconfig fortran gdbm gif glamor gles gles2 gmp gpm gstreamer gtk ibus iconv ipv6 jpeg jpeg2k kde kipi ladspa latex lcms ldap libnotify libsecret lua_target_lua5-2 lv2 lz4 lzma lzo mad mmx mmxext mng modemmanager modplug modules mp3 mp4 mpeg mplayer mtp multilib multitarget mysql ncurses netlink networkmanager nls nptl ogg openal opencl openexr opengl openmax openmp opus pam pango pch pcre pdf phonon plasma png policykit ppds pulseaudio qml qt3support qt4 qt5 readline rtmp samba scanner schroedinger sctp sdl seccomp semantic-desktop session speex spell sse sse2 ssl startup-notification subversion svg systemd tcpd theora threads tiff truetype udev udisks unicode upnp upnp-av upower usb v4l vaapi vdpau vorbis vpx wavpack wayland webp widgets x264 x265 xattr xcb xcomposite xinerama xml xrandr xscreensaver xv xvid xz zeroconf zlib" ABI_X86="64" ALSA_CARDS="hda-intel" 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="stage words flow sheets gemini" CAMERAS="ptp2" COLLECTD_PLUGINS="df interface irq load memory rrdtool swap syslog" CPU_FLAGS_X86="3dnow 3dnowext mmx mmxext sse sse2 sse3" DRACUT_MODULES="btrfs caps systemd" ELIBC="glibc" ENLIGHTENMENT_MODULES="*" 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" GRUB_PLATFORMS="coreboot efi-64 pc" INPUT_DEVICES="evdev joystick" KERNEL="linux" LCD_DEVICES="bayrad cfontz cfontz633 glk hd44780 lb216 lcdm001 mtxorb ncurses text" LIBREOFFICE_EXTENSIONS="presenter-console presenter-minimizer" LINGUAS="de en en_GB ar fa" LIRC_DEVICES="devinput" 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="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, INSTALL_MASK, LC_ALL, PORTAGE_BUNZIP2_COMMAND, PORTAGE_COMPRESS_FLAGS, PORTAGE_RSYNC_EXTRA_OPTS, USE_PYTHON ================================================================= Package Settings ================================================================= virtual/mysql-5.6-r6::gentoo was built with the following: USE="-embedded -static -static-libs" ABI_X86="32 64 -x32" CHOST="" dev-db/mariadb-10.1.7_rc::gentoo was built with the following: USE="community cracklib pam perl server ssl tools -bindist -client-libs (-cluster) -debug -embedded -extraengine -galera -innodb-lz4 -innodb-lzo -innodb-snappy -jemalloc -latin1 -mroonga -odbc -oqgraph -profiling (-selinux) -sphinx -sst-rsync -sst-xtrabackup -static -static-libs -systemtap -tcmalloc -test -tokudb -xml" ABI_X86="32 64 -x32" CFLAGS="-pipe -O2 -march=bdver3 -fno-strict-aliasing" CXXFLAGS="-pipe -O2 -march=bdver3 -fno-strict-aliasing -felide-constructors -fno-strict-aliasing"
Possibly related: bug #475492, bug #474952.
I have the same issue. 'MAKEOPTS=-j1 emerge -v1 paraview' fails with: cd /var/tmp/portage/sci-visualization/paraview-4.4.0/work/paraview-4.4.0_build/VTK/IO/MySQL && /usr/bin/x86_64-pc-linux-gnu-g++ -DMPICH_IGNORE_CXX_SEEK -DVTK_IN_VTK -DvtkIOMySQL_EXPORTS ... -o CMakeFiles/vtkIOMySQL.dir/vtkIOMySQL_AutoInit.cxx.o -c /var/tmp/portage/sci-visualization/paraview-4.4.0/work/ParaView-v4.4.0-source/VTK/IO/MySQL/vtkIOMySQL_AutoInit.cxxmake[2]: *** No rule to make target '/usr/lib64/mysql/libmysqlclient.so', needed by 'lib/libvtkIOMySQL-pv4.4.so.1'. Stop. make[2]: Leaving directory '/var/tmp/portage/sci-visualization/paraview-4.4.0/work/paraview-4.4.0_build' CMakeFiles/Makefile2:13557: recipe for target 'VTK/IO/MySQL/CMakeFiles/vtkIOMySQL.dir/all' failed make[1]: *** [VTK/IO/MySQL/CMakeFiles/vtkIOMySQL.dir/all] Error 2 And I really do not have /usr/lib64/mysql/libmysqlclient.so.
Given the ebuild, what do 'mysql_config --version', 'mysql_config --variable=pkglibdir' and 'mysql_config --libs' return ?
(In reply to Rafał Mużyło from comment #3) > Given the ebuild, what do 'mysql_config --version', 'mysql_config > --variable=pkglibdir' and 'mysql_config --libs' return ? # mysql_config --version 6.1.6 # mysql_config --variable=pkglibdir /usr/lib64 # mysql_config --libs -L/usr/lib64 -lmysqlclient -lpthread -lz -lm -lrt -lssl -lcrypto -ldl
I also tried to remove the standard portage vtk (sci-libs/vtk-6.1.0-r1). But it did not help either to emrge paraview-4.4.0 .
(In reply to Rafał Mużyło from comment #3) > Given the ebuild, what do 'mysql_config --version', 'mysql_config > --variable=pkglibdir' and 'mysql_config --libs' return ? rose@caiman:/home/rose(30)$ mysql_config --version 10.1.7 rose@caiman:/home/rose(31)$ mysql_config --variable=pkglibdir /usr/lib64 rose@caiman:/home/rose(32)$ mysql_config --libs -L/usr/lib64 -lmysqlclient -lpthread -lz -lm -ldl -lbfd -lssl -lcrypto
BTW., I have the following libmysqlclient: rose@caiman:/home/rose(51)$ ll /usr/lib64/libmysqlclient.so* lrwxrwxrwx 1 root root 20 15. Sep 08:57 /usr/lib64/libmysqlclient.so -> libmysqlclient.so.18* lrwxrwxrwx 1 root root 24 15. Sep 08:57 /usr/lib64/libmysqlclient.so.18 -> libmysqlclient.so.18.0.0* -rwxr-xr-x 1 root root 3537560 15. Sep 08:57 /usr/lib64/libmysqlclient.so.18.0.0* rose@caiman:/home/rose(52)$ ll /usr/lib32/libmysqlclient.so* lrwxrwxrwx 1 root root 20 15. Sep 08:57 /usr/lib32/libmysqlclient.so -> libmysqlclient.so.18* lrwxrwxrwx 1 root root 24 15. Sep 08:57 /usr/lib32/libmysqlclient.so.18 -> libmysqlclient.so.18.0.0* -rwxr-xr-x 1 root root 3432236 15. Sep 08:57 /usr/lib32/libmysqlclient.so.18.0.0*
@comment 4 and comment 6: Interesting... It would seem the snippet in the ebuild for both of you should go into the proper branch, yet doesn't. Time for wild guesses then: is there a chance both of you have a shell other than bash set as your default one ?
(In reply to Rafał Mużyło from comment #8) > Time for wild guesses then: is there a chance both of you have a shell other > than bash set as your default one ? Nope. $ readlink /bin/sh /bin/bash
rose@caiman:/home/rose(55)$ ll /bin/sh lrwxrwxrwx 1 root root 4 20. Aug 07:33 /bin/sh -> bash*
rose@caiman:/home/rose(56)$ ll /bin/bash -rwxr-xr-x 1 root root 795576 20. Aug 07:33 /bin/bash* rose@caiman:/home/rose(57)$ echo $SHELL /bin/bash
And the version is 4.3_p42: rose@caiman:/home/rose(58)$ genlop -t bash | tail Wed Jun 17 11:34:02 2015 >>> app-shells/bash-4.3_p39 merge time: 49 seconds. Thu Aug 13 13:15:32 2015 >>> app-shells/bash-4.3_p39 merge time: 1 minute and 28 seconds. Thu Aug 20 07:33:55 2015 >>> app-shells/bash-4.3_p42 merge time: 1 minute and 33 seconds.
Very likely paraview's build system is a bit broken. # mysql_config --libs -L/usr/lib64 -lmysqlclient -lpthread -lz -lm -lrt -lssl -lcrypto -ldl This implies that libmysqlclient.so is located directly under /usr/lib64 paraview insists on '/usr/lib64/mysql/libmysqlclient.so'. I will try to reproduce and fix that (I haven't compiled with +mysql while doing the bump as I found out right now...).
Got it, the version comparison in the ebuild is faulty: [[ $(mysql_config --version | sed 's/\.//g') -lt 5529 ]] it assumes a version number "6.1.06" instead of "6.1.6", or similar. In short, this comparison cannot work.
(In reply to Matthias Maier from comment #14) > Got it, the version comparison in the ebuild is faulty: > > [[ $(mysql_config --version | sed 's/\.//g') -lt 5529 ]] > > > it assumes a version number "6.1.06" instead of "6.1.6", or similar. In > short, this comparison cannot work. ...OK, my mistake, I've read it as if that would work.
This is now fixed in version 4.3.1 and 4.4.0 commit 42b0f9c7e6dbd0b751f6728f226cd4c5ed946cc6 Author: Matthias Maier <tamiko@gentoo.org> Date: Mon Sep 21 16:29:51 2015 -0500 sci-visualization/paraview: Fix configuration issue with dev-db/mysql-6.1.6, bug #560916 dev-db/mysql-5.5.29 and older have left the tree two years ago. Remove buggy compatibility code that identified version 6.1.6 being less than 5.5.29... Gentoo-Bug: 560916 Package-Manager: portage-2.2.20.1
Thanks! On a sidenote: There is the versionator.eclass with `version_is_at_least` or `sort -V` from sys-apps/coreutils.
> On a sidenote: There is the versionator.eclass with `version_is_at_least` Yes, I know that. And this is exactly how I would have refactored it. The point is that this workaround is obsolete. ;-)
