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Bug 630960

Summary: sci-geosciences/grass-7.2.0 - configure: error: MySQL library directory /usr/lib64/mysql does not exist
Product: Gentoo Linux Reporter: Martin Mokrejš <mmokrejs>
Component: Current packagesAssignee: Sci-geo Project <sci-geosciences>
Status: RESOLVED TEST-REQUEST    
Severity: normal CC: dschridde+gentoobugs, kripton
Priority: Normal    
Version: unspecified   
Hardware: All   
OS: Linux   
Whiteboard:
Package list:
Runtime testing required: ---

Description Martin Mokrejš 2017-09-14 08:31:13 UTC 
Seems the configure is passed a wrong path to mysql location. The ebuild shoudl decide whether mysql or mariadb is installed and inject proper path to configure:

>>> Emerging (1 of 1) sci-geosciences/grass-7.2.0::gentoo
 * grass-7.2.0.tar.gz SHA256 SHA512 WHIRLPOOL size ;-) ...                                                                                                                                                                                                                                                              [ ok ]
>>> Unpacking source...
>>> Unpacking grass-7.2.0.tar.gz to /scratch/var/tmp/portage/sci-geosciences/grass-7.2.0/work
>>> Source unpacked in /scratch/var/tmp/portage/sci-geosciences/grass-7.2.0/work
>>> Preparing source in /scratch/var/tmp/portage/sci-geosciences/grass-7.2.0/work/grass-7.2.0 ...
 * Applying grass-7.0.1-declare-inespg.patch ...                                                                                                                                                                                                                                                                        [ ok ]
 * Running autoconf ...                                                                                                                                                                                                                                                                                                 [ ok ]
 * Fixing python shebangs ...                                                                                                                                                                                                                                                                                           [ ok ]
>>> Source prepared.
>>> Configuring source in /scratch/var/tmp/portage/sci-geosciences/grass-7.2.0/work/grass-7.2.0 ...

 * Requested wxWidgets:        3.0
 * Using wxWidgets:            gtk2-unicode-3.0

 * econf: updating grass-7.2.0/config.sub with /usr/share/gnuconfig/config.sub
 * econf: updating grass-7.2.0/config.guess with /usr/share/gnuconfig/config.guess
./configure --prefix=/usr --build=x86_64-pc-linux-gnu --host=x86_64-pc-linux-gnu --mandir=/usr/share/man --infodir=/usr/share/info --datadir=/usr/share --sysconfdir=/etc --localstatedir=/var/lib --libdir=/usr/lib64 --enable-shared --disable-w11 --with-cxx --with-tiff --with-png --without-postgres --with-mysql --with-mysql-includes=/usr/include/mysql --with-mysql-libs=/usr/lib64/mysql --with-sqlite --with-opengl --without-odbc --without-fftw --without-blas --with-lapack --with-cairo --with-freetype --with-freetype-includes=/usr/include/freetype2 --with-nls --with-readline --without-opendwg --with-regex --with-pthread --with-openmp --without-opencl --with-gdal=/usr/bin/gdal-config --without-liblas --with-wxwidgets=/usr/lib64/wx/config/gtk2-unicode-3.0 --without-netcdf --without-geos --with-proj-includes=/usr/include/libprojectM --with-proj-libs=/usr/lib64 --with-proj-share=/usr/share/proj/ --with-x

...

checking whether to use MySQL... yes
checking for location of MySQL includes... /usr/include/mysql
checking for mysql.h... yes
checking for location of MySQL library... /usr/lib64/mysql
configure: error: *** MySQL library directory /usr/lib64/mysql does not exist.

!!! Please attach the following file when seeking support:
!!! /scratch/var/tmp/portage/sci-geosciences/grass-7.2.0/work/grass-7.2.0/config.log
 * ERROR: sci-geosciences/grass-7.2.0::gentoo failed (configure phase):
 *   econf failed
 * 
 * Call stack:
 *               ebuild.sh, line  115:  Called src_configure
 *             environment, line 4525:  Called econf '--enable-shared' '--disable-w11' '--with-cxx' '--with-tiff' '--with-png' '--without-postgres' '--with-mysql' '--with-mysql-includes=/usr/include/mysql' '--with-mysql-libs=/usr/lib64/mysql' '--with-sqlite' '--with-opengl' '--without-odbc' '--without-fftw' '--without-blas' '--with-lapack' '--with-cairo' '--with-freetype' '--with-freetype-includes=/usr/include/freetype2' '--with-nls' '--with-readline' '--without-opendwg' '--with-regex' '--with-pthread' '--with-openmp' '--without-opencl' '--with-gdal=/usr/bin/gdal-config' '--without-liblas' '--with-wxwidgets=/usr/lib64/wx/config/gtk2-unicode-3.0' '--without-netcdf' '--without-geos' '--with-proj-includes=/usr/include/libprojectM' '--with-proj-libs=/usr/lib64' '--with-proj-share=/usr/share/proj/' '--with-x'
 *        phase-helpers.sh, line  665:  Called __helpers_die 'econf failed'
 *   isolated-functions.sh, line  117:  Called die
 * The specific snippet of code:
 *              die "$@"
 * 
 * If you need support, post the output of `emerge --info '=sci-geosciences/grass-7.2.0::gentoo'`,
 * the complete build log and the output of `emerge -pqv '=sci-geosciences/grass-7.2.0::gentoo'`.
 * The complete build log is located at '/scratch/var/tmp/portage/sci-geosciences/grass-7.2.0/temp/build.log'.
 * The ebuild environment file is located at '/scratch/var/tmp/portage/sci-geosciences/grass-7.2.0/temp/environment'.
 * Working directory: '/scratch/var/tmp/portage/sci-geosciences/grass-7.2.0/work/grass-7.2.0'
 * S: '/scratch/var/tmp/portage/sci-geosciences/grass-7.2.0/work/grass-7.2.0'

>>> Failed to emerge sci-geosciences/grass-7.2.0, Log file:

>>>  '/scratch/var/tmp/portage/sci-geosciences/grass-7.2.0/temp/build.log'


# equery files mysql           
 * Searching for mysql ...
 * Contents of virtual/mysql-5.6-r9:
#
This is likely wrong dependency check for real mysql/mariadb installation.



# equery files mariadb | grep lib
/usr/include/mysql/server/json_lib.h
/usr/include/mysql/server/private/my_libwrap.h
/usr/include/mysql/server/typelib.h
/usr/lib32
/usr/lib32/libmariadb.so
/usr/lib32/libmariadb.so.3
/usr/lib32/libmysqlclient.so
/usr/lib32/libmysqlclient.so.18
/usr/lib32/libmysqlservices.a
/usr/lib32/mariadb
/usr/lib32/mariadb/plugin
/usr/lib32/mariadb/plugin/auth_gssapi_client.so
/usr/lib32/mariadb/plugin/client_ed25519.so
/usr/lib32/mariadb/plugin/daemon_example.ini
/usr/lib32/mariadb/plugin/dialog.so
/usr/lib32/mariadb/plugin/mysql_clear_password.so
/usr/lib32/mariadb/plugin/sha256_password.so
/usr/lib32/pkgconfig
/usr/lib32/pkgconfig/mariadb.pc
/usr/lib64
/usr/lib64/libmariadb.so
/usr/lib64/libmariadb.so.3
/usr/lib64/libmysqlclient.so
/usr/lib64/libmysqlclient.so.18
/usr/lib64/libmysqlservices.a
/usr/lib64/mariadb
/usr/lib64/mariadb/plugin
/usr/lib64/mariadb/plugin/adt_null.so
/usr/lib64/mariadb/plugin/auth_0x0100.so
/usr/lib64/mariadb/plugin/auth_ed25519.so
/usr/lib64/mariadb/plugin/auth_gssapi_client.so
/usr/lib64/mariadb/plugin/auth_pam.so
/usr/lib64/mariadb/plugin/auth_socket.so
/usr/lib64/mariadb/plugin/auth_test_plugin.so
/usr/lib64/mariadb/plugin/client_ed25519.so
/usr/lib64/mariadb/plugin/cracklib_password_check.so
/usr/lib64/mariadb/plugin/daemon_example.ini
/usr/lib64/mariadb/plugin/debug_key_management.so
/usr/lib64/mariadb/plugin/dialog.so
/usr/lib64/mariadb/plugin/dialog_examples.so
/usr/lib64/mariadb/plugin/example_key_management.so
/usr/lib64/mariadb/plugin/file_key_management.so
/usr/lib64/mariadb/plugin/ha_example.so
/usr/lib64/mariadb/plugin/ha_test_sql_discovery.so
/usr/lib64/mariadb/plugin/handlersocket.so
/usr/lib64/mariadb/plugin/libdaemon_example.so
/usr/lib64/mariadb/plugin/locales.so
/usr/lib64/mariadb/plugin/metadata_lock_info.so
/usr/lib64/mariadb/plugin/mypluglib.so
/usr/lib64/mariadb/plugin/mysql_clear_password.so
/usr/lib64/mariadb/plugin/qa_auth_client.so
/usr/lib64/mariadb/plugin/qa_auth_interface.so
/usr/lib64/mariadb/plugin/qa_auth_server.so
/usr/lib64/mariadb/plugin/query_cache_info.so
/usr/lib64/mariadb/plugin/query_response_time.so
/usr/lib64/mariadb/plugin/semisync_master.so
/usr/lib64/mariadb/plugin/semisync_slave.so
/usr/lib64/mariadb/plugin/server_audit.so
/usr/lib64/mariadb/plugin/sha256_password.so
/usr/lib64/mariadb/plugin/simple_password_check.so
/usr/lib64/mariadb/plugin/sql_errlog.so
/usr/lib64/pkgconfig
/usr/lib64/pkgconfig/mariadb.pc
#




# emerge --info '=sci-geosciences/grass-7.2.0::gentoo'
Portage 2.3.8 (python 2.7.13-final-0, default/linux/amd64/13.0, gcc-4.9.4, glibc-2.25-r5, 4.4.82-default-pciehp x86_64)
=================================================================
                         System Settings
=================================================================
System uname: Linux-4.4.82-default-pciehp-x86_64-Intel-R-_Core-TM-_i7-2640M_CPU_@_2.80GHz-with-gentoo-2.4.1
KiB Mem:    16375288 total,   8141596 free
KiB Swap:          0 total,         0 free
Timestamp of repository gentoo: Wed, 13 Sep 2017 22:00:01 +0000
Head commit of repository gentoo: 336598d94d73ca9f82a6021ea1269a883049d68c
sh bash 4.4_p12
ld GNU ld (Gentoo 2.28.1 p1.0) 2.28.1
app-shells/bash:          4.4_p12::gentoo
dev-java/java-config:     2.2.0-r3::gentoo
dev-lang/perl:            5.24.2::gentoo
dev-lang/python:          2.7.13::gentoo, 3.4.6::gentoo, 3.5.3::gentoo, 3.6.1-r1::gentoo
dev-util/cmake:           3.9.2::gentoo
dev-util/pkgconfig:       0.29.2::gentoo
sys-apps/baselayout:      2.4.1-r2::gentoo
sys-apps/openrc:          0.30::gentoo
sys-apps/sandbox:         2.10-r4::gentoo
sys-devel/autoconf:       2.13::gentoo, 2.69-r4::gentoo
sys-devel/automake:       1.11.6-r2::gentoo, 1.12.6-r1::gentoo, 1.13.4-r1::gentoo, 1.14.1-r1::gentoo, 1.15.1-r1::gentoo
sys-devel/binutils:       2.25.1-r1::gentoo, 2.26.1::gentoo, 2.27-r1::gentoo, 2.28-r2::gentoo, 2.28.1::gentoo
sys-devel/gcc:            4.3.6-r1::gentoo, 4.4.7::gentoo, 4.6.4::gentoo, 4.7.4::gentoo, 4.8.5::gentoo, 4.9.4::gentoo, 5.3.0::gentoo, 5.4.0-r3::gentoo, 6.2.0-r1::gentoo, 6.3.0::gentoo, 7.1.0-r1::gentoo
sys-devel/gcc-config:     1.8-r1::gentoo
sys-devel/libtool:        2.4.6-r4::gentoo
sys-devel/make:           4.2.1-r1::gentoo
sys-kernel/linux-headers: 4.13::gentoo (virtual/os-headers)
sys-libs/glibc:           2.25-r5::gentoo
Repositories:

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

science
    location: /scratch/mmokrejs/proj/sci
    masters: gentoo
    priority: 0

layman
    location: /var/lib/layman
    masters: gentoo
    priority: 1

haskell
    location: /var/lib/layman/haskell
    masters: gentoo
    priority: 50

vmware
    location: /var/lib/layman/vmware
    masters: gentoo
    priority: 50

ACCEPT_KEYWORDS="amd64 ~amd64"
ACCEPT_LICENSE="* -@EULA dlj-1.1 sun-bcla-java-vm Oracle-BCLA-JavaSE IBM-J1.6 skype-eula Nero-EULA-US AdobeFlash-10.3 skype-4.0.0.7-copyright AdobeFlash-11.x OPERA-2014 RAR Intel-SDP"
CBUILD="x86_64-pc-linux-gnu"
CFLAGS="-O2 -pipe -mpclmul -mpopcnt -march=native -ftree-vectorize"
CHOST="x86_64-pc-linux-gnu"
CONFIG_PROTECT="/etc /etc/stunnel/stunnel.conf /usr/lib64/libreoffice/program/sofficerc /usr/share/easy-rsa /usr/share/gnupg/qualified.txt /usr/share/maven-bin-3.2/conf /usr/share/maven-bin-3.3/conf /var/bind /var/lib/hsqldb /var/spool/torque"
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/apache2-php7.1/ext-active/ /etc/php/cgi-php5.6/ext-active/ /etc/php/cgi-php7.1/ext-active/ /etc/php/cli-php5.6/ext-active/ /etc/php/cli-php7.1/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="-O2 -pipe -mpclmul -mpopcnt -march=native -ftree-vectorize"
DISTDIR="/scratch/usr/portage/distfiles"
FCFLAGS="-O2 -pipe"
FEATURES="assume-digests binpkg-logs config-protect-if-modified distlocks ebuild-locks fixlafiles merge-sync multilib-strict news nostrip parallel-fetch preserve-libs protect-owned sandbox sfperms splitdebug strict unknown-features-warn unmerge-logs unmerge-orphans userfetch userpriv usersandbox usersync xattr"
FFLAGS="-O2 -pipe"
GENTOO_MIRRORS="http://gentoo.wheel.sk/ http://ftp.fi.muni.cz/pub/linux/gentoo/ http://gentoo.mirror.web4u.cz/ rsync://gentoo.mirror.dkm.cz/gentoo/ ftp://gentoo.mirror.web4u.cz/"
LDFLAGS="-Wl,-O1 -Wl,--as-needed"
MAKEOPTS="-j2"
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="/scratch/var/tmp"
USE="R X acpi alsa amd64 amr apache apache2 asm avx berkdb bindist bluetooth boost bzip2 cairo cgi cli coin consolekit cracklib crypt cryptlib cryptsetup cups cxx dbus device-mapper dhcp directfb dri drm dvd emboss encode fax fbcon ffmpeg flac fontconfig fortran fuse gbm gcrypt gd gdbm geoip geolocation gimp glpk gmp gnutls gpm gtk hal hpijs hwdb iconv id3tag imaging innodb inotify java javafx javascript jce jpeg jpg js jscript keymap ladspa lame lapack laptop lcms libnotify lm_sensors mad matroska mmx modemmanager modules mp3 multicore multilib multimedia mysql ncurses networkmanager nfs nls nptl nptlonly nscd ntfs ntfsdecrypt ntfsprogs objc ocr ogg opengl openmp pam parport pcre pdf pdfimport pdl perl php pkcs11 plplot png policykit polkit postproc postscript ppds ppp pppd pptx pulseaudio python qt3support qt4 qt5 readline rendering resolvconf samba scanner sctp seccomp server session sha512 slideshow sna sndfile sqlite sse sse2 sse3 sse4_1 sse4_2 ssh ssh-agent ssl sslv2 sslv3 ssse3 startup-notification suexec svg syslog tcl tcpd threads tiff tk truetype twolame udev unicode upower usb v4l v4l2 vim-syntax vnc wavpack wifi x11 xattr xcb xml xorg xrandr xv xvid xvmc zlib" ABI_X86="64 32" 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="alias authz_host auth_basic auth_digest cgi cgid deflate dir env filter include info mem_cache mime mime_magic negotiation remoteip setenvif status userdir vhost_alias rewrite usertrack cache file_cache disk_cache charset_lite log_config log_forensic" CALLIGRA_FEATURES="kexi words flow plan sheets stage tables krita karbon braindump author" 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 isync itrax mtk3301 nmea ntrip navcom oceanserver oldstyle oncore rtcm104v2 rtcm104v3 sirf skytraq superstar2 timing tsip tripmate tnt ublox ubx" GRUB_PLATFORMS="pc" INPUT_DEVICES="libinput keyboard mouse" KERNEL="linux" L10N="en-US en en-GB cs" LCD_DEVICES="bayrad cfontz cfontz633 glk hd44780 lb216 lcdm001 mtxorb ncurses text" LIBREOFFICE_EXTENSIONS="presenter-console presenter-minimizer" LINGUAS="en_US en_GB en cs" OFFICE_IMPLEMENTATION="libreoffice" POSTGRES_TARGETS="postgres9_5" PYTHON_SINGLE_TARGET="python2_7" PYTHON_TARGETS="python2_7 python3_5" RUBY_TARGETS="ruby20 ruby21 ruby23 ruby24" USERLAND="GNU" VIDEO_CARDS="vesa vmware fbdev intel i915 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, EMERGE_DEFAULT_OPTS, INSTALL_MASK, LANG, LC_ALL, PORTAGE_BUNZIP2_COMMAND, PORTAGE_COMPRESS, PORTAGE_COMPRESS_FLAGS, PORTAGE_RSYNC_EXTRA_OPTS
Comment 1 Amy Liffey gentoo-dev 2018-05-24 11:26:27 UTC 
Seems to work fine for 7.4.0. Feel free to reopen if the problem remains.