Не знаю что произошло но, система перестала запоминает какие пакеты уже установлены. Например если набрать
emerge php -vp
These are the packages that would be merged, in order:
Calculating dependencies... done!
[ebuild N ] sys-process/procps-3.2.8_p11 USE="unicode" 0 kB
[ebuild N ] sys-process/psmisc-22.14 USE="ipv6 nls -X (-selinux)" 0 kB
[ebuild N ] x11-proto/xproto-7.0.22 USE="-doc" 0 kB
[ebuild N ] dev-libs/libpcre-8.12 USE="bzip2 cxx recursion-limit static-libs (unicode) zlib" 0 kB
[ebuild N ] x11-proto/xextproto-7.2.0 USE="-doc" 0 kB
[ebuild N ] x11-libs/xtrans-1.2.6 USE="-doc" 0 kB
[ebuild N ] dev-libs/apr-1.4.5 USE="static-libs urandom uuid -doc -older-kernels-compatibility" 0 kB
[ebuild N ] dev-db/unixODBC-2.3.1 USE="minimal static-libs -odbcmanual" 0 kB
[ebuild N ] x11-proto/kbproto-1.0.5 0 kB
[ebuild N ] media-fonts/font-util-1.2.0 0 kB
[ebuild N ] x11-misc/util-macros-1.15.0 0 kB
[ebuild N ] dev-libs/libmcrypt-2.5.8-r2 0 kB
[ebuild N ] app-admin/eselect-php-0.6.2 0 kB
[ebuild N ] x11-proto/xf86bigfontproto-1.2.0 0 kB
[ebuild N ] x11-proto/inputproto-2.0.2 0 kB
[ebuild N ] x11-proto/xcb-proto-1.6-r2 0 kB
[ebuild N ] dev-libs/libpthread-stubs-0.3 USE="static-libs" 0 kB
[ebuild N ] dev-perl/TermReadKey-2.300.0 0 kB
[ebuild N ] dev-perl/Net-Daemon-0.480.0 0 kB
[ebuild N ] perl-core/Storable-2.20 0 kB
[ebuild N ] perl-core/File-Spec-3.31 0 kB
[ebuild N ] perl-core/Sys-Syslog-0.290.0 0 kB
[ebuild N ] sys-apps/sysvinit-2.88-r3 USE="(-ibm) (-selinux) -static" 0 kB
[ebuild N ] x11-libs/libICE-1.0.7 USE="ipv6 static-libs -doc" 0 kB
[ebuild N ] net-analyzer/net-snmp-5.4.2.1-r4 USE="bzip2 ipv6 perl ssl tcpd zlib -X -diskio -doc -elf -extensible -lm_sensors -mfd-rewrites -minimal -python -rpm (-selinux) -sendmail -smux" 0 kB
[ebuild N F ] dev-db/oracle-instantclient-basic-10.2.0.3-r1 36,190 kB
[ebuild N ] x11-libs/libXdmcp-1.1.0 USE="static-libs -doc" 0 kB
[ebuild N ] x11-libs/libXau-1.0.6 USE="static-libs" 0 kB
[ebuild N ] virtual/perl-Storable-2.20 0 kB
[ebuild N ] virtual/perl-File-Spec-3.31 0 kB
[ebuild N ] virtual/perl-Sys-Syslog-0.290.0 0 kB
[ebuild N ] net-mail/mailbase-1 USE="pam" 0 kB
[ebuild N ] virtual/init-0 0 kB
[ebuild N ] x11-libs/libSM-1.2.0 USE="ipv6 static-libs uuid -doc" 0 kB
[ebuild N ] x11-libs/libxcb-1.7 USE="static-libs -doc (-selinux)" 0 kB
[ebuild N ] dev-perl/PlRPC-0.202.0 0 kB
[ebuild N ] mail-mta/ssmtp-2.64-r2 USE="ipv6 mta ssl -gnutls" 0 kB
[ebuild N ] x11-libs/libX11-1.4.4 USE="ipv6 static-libs -doc -test" 0 kB
[ebuild N ] dev-perl/DBI-1.615 USE="-test" 0 kB
[ebuild N ] virtual/mta-0 0 kB
[ebuild N ] x11-libs/libXt-1.1.1 USE="static-libs" 0 kB
[ebuild N ] x11-libs/libXext-1.3.0 USE="static-libs -doc" 0 kB
[ebuild N ] x11-libs/libXpm-3.5.9 USE="static-libs" 0 kB
[ebuild N ] sys-apps/baselayout-2.0.3 USE="-build" 0 kB
[ebuild N ] sys-apps/openrc-0.9.8.4 USE="ncurses pam static-libs unicode -debug (-selinux)" 0 kB
[ebuild N ] dev-db/mysql-init-scripts-2.0_pre1-r2 0 kB
[ebuild N ] dev-db/mysql-5.1.61 USE="berkdb community perl ssl -big-tables -cluster -debug -embedded -extraengine -latin1 -max-idx-128 -minimal -pbxt -profiling (-selinux) -static -test -xtradb" 0 kB
[ebuild N ] virtual/mysql-5.1 USE="-embedded -minimal -static" 0 kB
[ebuild N ] dev-perl/DBD-mysql-4.01.7 0 kB
[ebuild N ] dev-libs/apr-util-1.3.12 USE="berkdb gdbm mysql odbc static-libs -doc -freetds -ldap -postgres -sqlite" 0 kB
[ebuild N ] app-admin/apache-tools-2.2.22 USE="ssl" 0 kB
[ebuild N ] www-servers/apache-2.2.22 USE="ssl -debug -doc -ldap (-selinux) -static -suexec -threads" APACHE2_MODULES="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 -asis -auth_digest -authn_dbd -cern_meta -charset_lite -dbd -dumpio -ident -imagemap -log_forensic -proxy -proxy_ajp -proxy_balancer -proxy_connect -proxy_ftp -proxy_http -proxy_scgi -reqtimeout -substitute -version" APACHE2_MPMS="-event -itk -peruser -prefork -worker" 0 kB
[ebuild N ] dev-lang/php-5.3.10 USE="apache2 berkdb bzip2 cgi cli crypt ctype curl curlwrappers fileinfo filter gd gdbm hash iconv ipv6 json mysql mysqli mysqlnd nls oci8-instant-client odbc phar posix readline session simplexml snmp sockets ssl tokenizer truetype unicode xml xmlrpc xmlwriter xpm zip zlib -bcmath -calendar -cdb -cjk -debug -doc -embed -enchant -exif -firebird -flatfile -fpm (-frontbase) -ftp -gmp -imap -inifile -intl -iodbc -kerberos -kolab -ldap -ldap-sasl -libedit -mhash -mssql -pcntl -pdo -pic -postgres -qdbm -recode -sharedmem -soap -spell -sqlite -sqlite3 -suhosin (-sybase-ct) -sysvipc -threads -tidy -wddx -xmlreader -xsl" 0 kB
Total: 53 packages (53 new), Size of downloads: 36,190 kB
Fetch Restriction: 1 package (1 unsatisfied)
При чём если установить все эти 53 пакета при следующей сборке php будет тоже самое.
При этом и php и apach2 и mysql уже около полу года крутятся на сервере и прекрасно себя чувствуют.
Обновления периодически делаю.
С чем это может быть связано?