When calling 'phpdoc' from the command line, I got this: $ phpdoc : bad interpreter: No such file or directory Sure enough, first line is: #!/usr/lib/php5/bin/php^M The whole file has a CR at the end of every line (was it editted under windows?), and so it won't run. Of course, removing all of them, or at least the one in the first line solves the problem. Anyway, this should be fixed. Reproducible: Always Steps to Reproduce: 1. 2. 3. Portage 2.0.53_rc7 (default-linux/x86/2005.0, gcc-3.3.6, glibc-2.3.5-r3, 2.6.13-gentoo-r4 i686) ================================================================= System uname: 2.6.13-gentoo-r4 i686 AMD Sempron(tm) 2400+ Gentoo Base System version 1.12.0_pre11 distcc 2.18.3 i686-pc-linux-gnu (protocols 1 and 2) (default port 3632) [disabled] ccache version 2.4 [enabled] dev-lang/python: 2.3.5, 2.4.2 sys-apps/sandbox: 1.2.13 sys-devel/autoconf: 2.13, 2.59-r7 sys-devel/automake: 1.4_p6, 1.5, 1.6.3, 1.7.9-r1, 1.8.5-r3, 1.9.6-r1 sys-devel/binutils: 2.16.1 sys-devel/libtool: 1.5.20-r1 virtual/os-headers: 2.6.11-r3 ACCEPT_KEYWORDS="x86 ~x86" AUTOCLEAN="yes" CBUILD="i686-pc-linux-gnu" CFLAGS="-O2 -march=athlon-xp -pipe -fomit-frame-pointer" CHOST="i686-pc-linux-gnu" CONFIG_PROTECT="/etc /usr/kde/2/share/config /usr/kde/3.3/env /usr/kde/3.3/share/config /usr/kde/3.3/shutdown /usr/kde/3.4/env /usr/kde/3.4/share/config /usr/kde/3.4/shutdown /usr/kde/3/share/config /usr/lib/X11/xkb /usr/lib/mozilla/defaults/pref /usr/share/config /var/qmail/control"CONFIG_PROTECT_MASK="/etc/gconf /etc/terminfo /etc/texmf/web2c /etc/env.d" CXXFLAGS="-O2 -march=athlon-xp -pipe -fomit-frame-pointer" DISTDIR="/usr/portage/distfiles" FEATURES="autoconfig ccache distlocks sandbox sfperms strict" GENTOO_MIRRORS="http://distfiles.gentoo.org http://distro.ibiblio.org/pub/linux/distributions/gentoo" LANG="en_US.UTF-8" LINGUAS="pt_BR" PKGDIR="/usr/portage/packages" PORTAGE_TMPDIR="/var/tmp" PORTDIR="/usr/portage" PORTDIR_OVERLAY="/usr/local/portage" SYNC="rsync://rsync.gentoo.org/gentoo-portage" USE="x86 16bit 3dnow 3dnowext X aalib acl acpi aim alsa apache2 apm arts audiofile avi bash-completion berkdb bitmap-fonts bonobo bzip2 bzlib cdb cddb cjk crypt cups curl eds emboss encode esd ethereal exif expat fam foomaticdb fortran gd gdbm gif glut gnome gpm gstreamer gtk gtk2 gtkhtml guile hal icq idn imagemagick imap imlib ipv6 irc java jpeg lcms libg++ libwww mad mbox mhash mikmod mime mmx mmxext mng mozilla moznocompose moznoirc moznomail mp3 mpeg msn mysql ncurses nis nls offensive ogg oggvorbis opengl oss pam pcre pdflib perl php png postgres procmail python quicktime readline recode samba sdl snmp spell sse sse2 ssl svg svga tcltk tcpd tetex tiff truetype truetype-fonts type1-fonts udev unicode usb vorbis xml xml2 xmms xv yahoo zlib linguas_pt_BR userland_GNU kernel_linux elibc_glibc" Unset: ASFLAGS, CTARGET, LC_ALL, LDFLAGS, MAKEOPTS
Will be fixed in dev-php/PEAR-PhpDocumentor-1.3.0_rc5.
dev-php/PEAR-PhpDocumentor-1.3.0_rc5 is in the tree now.