'php -v' writes the file /usr/share/snmp/mibs/.index, I suppose it should not: root@inspironM12:/usr/local/portage/sci-libs/gdal(62)# echo "--- before 1st 'll /usr/share/snmp/mibs/.index' ---"; ll /usr/share/snmp/mibs/.index; php -v ; echo "--- before 2nd 'll /usr/share/snmp/mibs/.index' ---"; ll /usr/share/snmp/mibs/.index --- before 1st 'll /usr/share/snmp/mibs/.index' --- /bin/ls: cannot access /usr/share/snmp/mibs/.index: No such file or directory PHP 5.3.6-pl0-gentoo (cli) (built: Mar 22 2011 14:33:00) Copyright (c) 1997-2011 The PHP Group Zend Engine v2.3.0, Copyright (c) 1998-2011 Zend Technologies --- before 2nd 'll /usr/share/snmp/mibs/.index' --- -rw-r--r-- 1 root root 2058 Mar 24 12:48 /usr/share/snmp/mibs/.index This provokes an ACCES VIOLATION during emerging of libvpx, compare http://bugs.gentoo.org/show_bug.cgi?id=360085. root@inspironM12:/usr/local/portage/sci-libs/gdal(63)# emerge -pvD php These are the packages that would be merged, in order: Calculating dependencies... done! [ebuild R ] dev-lang/php-5.3.6 USE="apache2 berkdb bzip2 calendar cgi cli crypt ctype curl doc exif fileinfo filter gd gdbm gmp hash iconv imap ipv6 json kerberos ldap mysql mysqli nls odbc pdo phar posix postgres readline session simplexml snmp soap sockets spell sqlite ssl threads tidy tokenizer truetype unicode xml xmlreader xmlrpc xpm zlib -adabas -bcmath -birdstep -cdb -cjk -curlwrappers -db2 -dbmaker -debug -embed -empress -empress-bcs -enchant -esoob -firebird -flatfile -fpm -frontbase -ftp -gd-external -inifile -interbase -intl -iodbc -kolab -ldap-sasl -libedit -mhash -mssql -mysqlnd -oci8 -oci8-instant-client -pcntl -pic -qdbm -recode -sapdb -sharedext -sharedmem -solid -sqlite3 -sybase-ct -sysvipc -wddx -xmlwriter -xsl -zip" 0 kB Total: 1 package (1 reinstall), Size of downloads: 0 kB Reproducible: Always root@inspironM12:/usr/local/portage/sci-libs/gdal(64)# emerge --info Portage 2.1.9.44 (default/linux/x86/10.0/desktop, gcc-4.5.2, glibc-2.13-r2, 2.6.37-gentoo i686) ================================================================= System uname: Linux-2.6.37-gentoo-i686-Intel-R-_Atom-TM-_CPU_Z520_@_1.33GHz-with-gentoo-2.0.2 Timestamp of tree: Thu, 24 Mar 2011 03:00:01 +0000 app-shells/bash: 4.2_p8 dev-java/java-config: 2.1.11-r3 dev-lang/python: 2.7.1-r1, 3.1.3-r1 dev-util/cmake: 2.8.4 sys-apps/baselayout: 2.0.2 sys-apps/openrc: 0.8.0 sys-apps/sandbox: 2.5 sys-devel/autoconf: 2.13, 2.68 sys-devel/automake: 1.9.6-r3, 1.10.3, 1.11.1 sys-devel/binutils: 2.21 sys-devel/gcc: 4.5.2 sys-devel/gcc-config: 1.4.1 sys-devel/libtool: 2.4-r1 sys-devel/make: 3.82 virtual/os-headers: 2.6.38 (sys-kernel/linux-headers) ACCEPT_KEYWORDS="x86 ~x86" ACCEPT_LICENSE="* -@EULA PUEL dlj-1.1 skype-eula googleearth AdobeFlash-10.1 cadsoft" CBUILD="i686-pc-linux-gnu" CFLAGS="-O2 -march=core2 -mtune=generic -fomit-frame-pointer -pipe" CHOST="i686-pc-linux-gnu" CONFIG_PROTECT="/etc /usr/share/config /var/lib/hsqldb" CONFIG_PROTECT_MASK="/etc/ca-certificates.conf /etc/env.d /etc/env.d/java/ /etc/eselect/postgresql /etc/fonts/fonts.conf /etc/gconf /etc/gentoo-release /etc/php/apache2-php5.3/ext-active/ /etc/php/cgi-php5.3/ext-active/ /etc/php/cli-php5.3/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 -march=core2 -mtune=generic -fomit-frame-pointer -pipe" DISTDIR="/usr/portage/distfiles" FEATURES="assume-digests binpkg-logs distlocks fixlafiles fixpackages news parallel-fetch protect-owned sandbox sfperms strict unknown-features-warn unmerge-logs unmerge-orphans userfetch" FFLAGS="" GENTOO_MIRRORS="http://distfiles.gentoo.org" LANG="en_US.UTF-8" LC_ALL="C" LDFLAGS="-Wl,-O1 -Wl,--as-needed" LINGUAS="de fr" MAKEOPTS="-j1" 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/java-overlay /var/lib/layman/science /var/lib/layman/x11 /usr/local/portage /var/lib/cpan /var/lib/g-octave" SYNC="rsync://rsync.gentoo.org/gentoo-portage" USE="R X Xaw3d a52 aac abiword acl acpi admin afs alsa ao apache2 applet archive arpack asf aspell assistant audacious audiofile automap automount bash-completion beagle berkdb blas blast bluetooth boo boost branding bzip2 cairo cardbus cdda cddb cdf cdio cdparanoia cdr cg cgi chm cli consolekit corba cracklib crypt css cups curl cxx daap db dbase dbi dbm dbus dell designer devhelp device-mapper dga dia djvu doc dri ds2490 ds9097 ds9097u dts dv dvb dvd dvdr dvi dynamicplugin eds elf emacs emboss emf empathy encode epiphany evo examples exif expat extensions extra extras fam fame ffmpeg fftw firefox fits flac fltk fontconfig foomaticdb fortran fpx fts3 fuse galago garmin gd gdal gdbm gdu gedit geoip geolocation geos gfortran gif gimp ginac git glade glib gml gmp gmtsuppl gnokii gnome gnome-keyring gnome-print gnuplot gnutls gphoto2 gpm grammar graphics graphtft graphviz grass gs gsl gsm gstreamer gtk guile hal harness hddtemp hdf hdf5 hdri http httpd hvm iconv icq icu id3 ide imagemagick imap innodb inotify ipod ipv6 irda ithreads jabber jadetex java java6 jbig john jpeg jpeg2k kdrive kerberos kpathsea kvm ladspa lame lapack laptop latex latex3 lcms ldap lensfun libffi libgda libnotify libsamplerate lirc lm_sensors lua lzo mad mail maildir mailwrapper mapnik math matroska mikmod mmx mmxext mng modules mono moonlight motif mozilla mp3 mp4 mpeg mpi mplayer mtp mudflap musicbrainz mysql mysqli nautilus ncurses neXt netcdf netpbm network networking networkmanager nfs nls nntp nptl nptlonly nsplugin ntfs ntp numpy nvidia obex objc ocaml octave odbc ogdi ogg ole openexr opengl openmp overview pae pam pango pcre pda pdf perl plotutils plugins png podcast policykit posix postgres postscript ppds pppd preview-latex proj projectx pstricks pulseaudio pymol python python-bindings q16 q32 qemu qhull qt3support qt4 quicktime readline reiserfs reports rle romio rpc rrdcgi rrdtool samba sasl science sdk sdl secure-delete semantic-desktop server session sip slang slp smbclient smp sms sndfile snmp soup sox speex spell sql sqlite sse sse2 ssl startup-notification stlport subtitles subversion suexec svg swig sysfs szip t1lib tcl tcpd tex tex4ht texmacs theora threads thunderbird tidy tiff tk tntc tools truetype udev unicode usb userlocales utempter v4l2 virtualbox vorbis wav webdav webdav-serf webkit wifi wmf wxwidgets x264 x86 xattr xcb xemacs xext xine xml xmlreader xmlrpc xorg xpm xulrunner xv xvid xvmc zlib zvbi" ALSA_CARDS="intel8x0" 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" APACHE2_MODULES="actions alias auth_basic auth_digest authn_anon authn_dbd authn_dbm authn_default authn_file authz_dbm authz_default authz_groupfile authz_host authz_owner authz_user autoindex cache cgid dav dav_fs dav_lock dbd deflate dir disk_cache env expires ext_filter file_cache filter headers ident imagemap include info log_config logio mem_cache mime mime_magic negotiation proxy proxy_ajp proxy_balancer proxy_connect proxy_http rewrite setenvif so speling status unique_id userdir usertrack vhost_alias" CAMERAS="canon" COLLECTD_PLUGINS="df interface irq load memory rrdtool swap syslog" 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 ubx" INPUT_DEVICES="keyboard mouse evdev synaptics" KERNEL="linux" LCD_DEVICES="bayrad cfontz cfontz633 glk hd44780 lb216 lcdm001 mtxorb ncurses text" LINGUAS="de fr" NETBEANS_MODULES="apisupport cnd dlight enterprise ergonomics groovy gsf harness ide identity j2ee java mobility nb php profiler ruby websvccommon xml" PHP_TARGETS="php5-3" QEMU_SOFTMMU_TARGETS="i386 ppc ppc64 x86_64" QEMU_USER_TARGETS="arm i386 x86_64" RUBY_TARGETS="ruby18 jruby" USERLAND="GNU" VIDEO_CARDS="psb intel vesa" 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, PORTAGE_BUNZIP2_COMMAND, PORTAGE_COMPRESS, PORTAGE_COMPRESS_FLAGS, PORTAGE_RSYNC_EXTRA_OPTS
This is a known "issue" with the snmp library. It causes all sorts of weird issues, but it is the way it works. The only way around it is to addpredict the file if PHP is run during install. You can find more info in bug 324739.
