Checking GLSA 201408-11 >>> No upgrade path exists for these packages: dev-lang/php-5.4.39 The given GLSA is for PHP 5.4 versions below 5.4.32, so this is a false alarm.
Reported and closed as invalid: https://bugs.gentoo.org/show_bug.cgi?id=545286
I have nearly the same issue with php 5.4.41 for the 5.4 slot. All my php packages are up2date but the following GLSA are listed as affected. # equery l php * Searching for php ... [IP-] [ ] dev-lang/php-5.4.41:5.4 [IP-] [ ] dev-lang/php-5.5.26:5.5 [IP-] [ ] dev-lang/php-5.6.10:5.6 # glsa-check -l affected [A] means this GLSA was marked as applied (injected), [U] means the system is not affected and [N] indicates that the system might be affected. 201408-11 [N] PHP: Multiple vulnerabilities ( dev-lang/php ) 201411-04 [N] PHP: Multiple vulnerabilities ( dev-lang/php ) 201503-03 [N] PHP: Multiple vulnerabilities ( dev-lang/php ) # emerge --info Portage 2.2.20 (python 2.7.9-final-0, default/linux/amd64/13.0, gcc-4.7.3, glibc-2.20-r2, 3.18.11-gentoo_20150422-1 x86_64) ================================================================= System uname: Linux-3.18.11-gentoo_20150422-1-x86_64-Intel-R-_Xeon-R-_CPU_E3-1246_v3_@_3.50GHz-with-gentoo-2.2 KiB Mem: 16495068 total, 1759624 free KiB Swap: 8388604 total, 7768288 free Timestamp of repository gentoo: Sat, 11 Jul 2015 11:45:01 +0000 sh bash 4.3_p33-r2 ld GNU ld (Gentoo 2.24 p1.4) 2.24 app-shells/bash: 4.3_p33-r2::gentoo dev-java/java-config: 2.2.0::gentoo dev-lang/perl: 5.20.2::gentoo dev-lang/python: 2.7.9-r1::gentoo, 3.3.5-r1::gentoo, 3.4.1::gentoo dev-util/cmake: 3.2.2::gentoo dev-util/pkgconfig: 0.28-r2::gentoo sys-apps/baselayout: 2.2::gentoo sys-apps/openrc: 0.17::gentoo sys-apps/sandbox: 2.6-r1::gentoo sys-devel/autoconf: 2.13::gentoo, 2.69::gentoo sys-devel/automake: 1.11.6-r1::gentoo, 1.12.6::gentoo, 1.13.4::gentoo, 1.14.1::gentoo sys-devel/binutils: 2.24-r3::gentoo sys-devel/gcc: 4.5.4::gentoo, 4.6.3::gentoo, 4.7.3-r1::gentoo, 4.8.4::gentoo sys-devel/gcc-config: 1.7.3::gentoo sys-devel/libtool: 2.4.6::gentoo sys-devel/make: 4.1-r1::gentoo sys-kernel/linux-headers: 3.18::gentoo (virtual/os-headers) sys-libs/glibc: 2.20-r2::gentoo Repositories: gentoo location: /usr/portage sync-type: rsync sync-uri: rsync://rsync.de.gentoo.org/gentoo-portage priority: -1000 morlix-gentoo-overlay location: /usr/local/portage sync-type: git sync-uri: ssh://teissler@morlixsrv1.dyndns.org/srv/git/gentoo-overlay.git masters: gentoo ACCEPT_KEYWORDS="amd64" ACCEPT_LICENSE="* -@EULA" CBUILD="x86_64-pc-linux-gnu" CFLAGS="-march=native -O2 -pipe" CHOST="x86_64-pc-linux-gnu" CONFIG_PROTECT="/etc /usr/lib64/fax /usr/share/gnupg/qualified.txt /var/spool/fax/etc" CONFIG_PROTECT_MASK="/etc/ca-certificates.conf /etc/env.d /etc/fonts/fonts.conf /etc/gconf /etc/gentoo-release /etc/php/apache2-php5.4/ext-active/ /etc/php/apache2-php5.5/ext-active/ /etc/php/apache2-php5.6/ext-active/ /etc/php/cgi-php5.4/ext-active/ /etc/php/cgi-php5.5/ext-active/ /etc/php/cgi-php5.6/ext-active/ /etc/php/cli-php5.4/ext-active/ /etc/php/cli-php5.5/ext-active/ /etc/php/cli-php5.6/ext-active/ /etc/revdep-rebuild /etc/sandbox.d /etc/terminfo" CXXFLAGS="-march=native -O2 -pipe" DISTDIR="/usr/portage/distfiles" FCFLAGS="-march=native -O2 -pipe" FEATURES="assume-digests binpkg-logs ccache config-protect-if-modified distlocks ebuild-locks fixlafiles merge-sync news parallel-fetch preserve-libs protect-owned sandbox sfperms strict unknown-features-warn unmerge-logs unmerge-orphans userfetch userpriv usersandbox usersync" FFLAGS="-march=native -O2 -pipe" GENTOO_MIRRORS="ftp://de-mirror.org/distro/gentoo/ rsync://de-mirror.org/gentoo/ http://mirror.netcologne.de/gentoo/ ftp://linux.rz.ruhr-uni-bochum.de/gentoo-mirror/ rsync://ftp.halifax.rwth-aachen.de/gentoo/ ftp://ftp.tu-clausthal.de/pub/linux/gentoo/ rsync://ftp-stud.hs-esslingen.de/gentoo/" LANG="de_DE.utf8" LDFLAGS="-Wl,-O1 -Wl,--as-needed" MAKEOPTS="-j5" 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" PORTAGE_TMPDIR="/var/tmp" USE="acl amd64 apache2 berkdb bzip2 caps clamav cli cracklib crypt cryptsetup cxx device-mapper dri fam fortran gdbm gnutls gzip iconv ipv6 ldap lm_sensors lzma maildir mmx mmxext modules multilib mysql ncurses nls nptl openmp pam pcre posix quota readline session sse sse2 ssl ssse3 syslog tcpd udev unicode vim-syntax zlib" ABI_X86="64" 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="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 auth_digest version" CALLIGRA_FEATURES="kexi words flow plan sheets stage tables krita karbon braindump author" CAMERAS="ptp2" COLLECTD_PLUGINS="df interface irq load memory rrdtool swap syslog" CPU_FLAGS_X86="aes avx avx2 fma3 mmx mmxext popcnt sse sse2 sse3 sse4_1 sse4_2 ssse3" 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 ublox ubx" INPUT_DEVICES="keyboard mouse evdev" KERNEL="linux" LCD_DEVICES="bayrad cfontz cfontz633 glk hd44780 lb216 lcdm001 mtxorb ncurses text" LIBREOFFICE_EXTENSIONS="presenter-console presenter-minimizer" OFFICE_IMPLEMENTATION="libreoffice" PHP_TARGETS="php5-5" PYTHON_SINGLE_TARGET="python2_7" PYTHON_TARGETS="python2_7 python3_3" RUBY_TARGETS="ruby19 ruby20" USERLAND="GNU" VIDEO_CARDS="radeon" 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, LC_ALL, PORTAGE_BUNZIP2_COMMAND, PORTAGE_COMPRESS, PORTAGE_COMPRESS_FLAGS, PORTAGE_RSYNC_EXTRA_OPTS, USE_PYTHON
The PHP 5.4 branch is gone from the tree, which would alleviate this. Please reopen if there are additional false positives.