Bug 402331 – dev-lang/R-2.10.1, dev-lang/R-2.14.1 file locations violate Gentoo standards

• Product: Gentoo Linux
• Status: RESOLVED UPSTREAM

[Description Martin Walch 2012-02-06 01:37:55 UTC]

This does not seem right: wrong or unusual locations, some duplicates

$ equery f R | grep LC_MESSAGES
/usr/lib64/R/library/KernSmooth/po/de/LC_MESSAGES
... long list ...
/usr/lib64/R/share/locale/de/LC_MESSAGES/R.mo

$ equery f R | grep include
/usr/include
/usr/include/Rmath.h
/usr/lib64/R/include
/usr/lib64/R/include/R.h
... long list ...
/usr/lib64/R/library/Matrix/include/cholmod.h

$ equery f R | grep R/bin
/usr/lib/debug/usr/lib64/R/bin
... long list ...
/usr/lib64/R/bin/rtags

$ equery f R | grep [^e]/doc
/usr/lib64/R/library/Matrix/doc
... long list ...
/usr/lib64/R/library/utils/doc/index.html

$ equery f R | grep licenses
/usr/lib64/R/share/licenses
/usr/lib64/R/share/licenses/AGPL-3
/usr/lib64/R/share/licenses/Artistic-1.0
/usr/lib64/R/share/licenses/Artistic-2.0
/usr/lib64/R/share/licenses/GPL-2
/usr/lib64/R/share/licenses/GPL-3
/usr/lib64/R/share/licenses/LGPL-2
/usr/lib64/R/share/licenses/LGPL-2.1
/usr/lib64/R/share/licenses/LGPL-3
/usr/lib64/R/share/licenses/license.db

emerge --info
Portage 2.1.10.44 (default/linux/amd64/10.0/desktop/kde, gcc-4.4.6, glibc-2.13-r4, 3.2.1-gentoo-r2-libre x86_64)
=================================================================
System uname: Linux-3.2.1-gentoo-r2-libre-x86_64-Intel-R-_Core-TM-2_Quad_CPU_Q8400_@_2.66GHz-with-gentoo-2.0.3
Timestamp of tree: Sun, 05 Feb 2012 12:45:01 +0000
distcc 3.1 x86_64-pc-linux-gnu [disabled]
ccache version 3.1.6 [enabled]
app-shells/bash:          4.1_p9
dev-java/java-config:     2.1.11-r3
dev-lang/python:          2.7.2-r3, 3.1.4-r3
dev-util/ccache:          3.1.6
dev-util/cmake:           2.8.6-r4
dev-util/pkgconfig:       0.26
sys-apps/baselayout:      2.0.3
sys-apps/openrc:          0.9.8.4
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:       2.21.1-r1
sys-devel/gcc:            4.4.6-r1
sys-devel/gcc-config:     1.4.1-r1
sys-devel/libtool:        2.4-r1
sys-devel/make:           3.82-r1
sys-kernel/linux-headers: 3.1 (virtual/os-headers)
sys-libs/glibc:           2.13-r4
Repositories: gentoo java-overlay x11 x-portage worldforge-overlay
ACCEPT_KEYWORDS="amd64"
ACCEPT_LICENSE="@FREE bea.ri.jsr173 dom4j GPL-2-with-MySQL-FLOSS-exception icu JasPer2.0 jaxen JDOM NCSA-HDF Radiance saxpath wxWinFDL-3 GPL freedist MOTIF Allegro unRAR MSttfEULA UCAR-Unidata GDLS ISOC-rfc intel-ucode atheros-hal Apple AdobeFlash-10.3 GMGPL"
CBUILD="x86_64-pc-linux-gnu"
CFLAGS="-march=native -O2 -fgcse-after-reload -pipe"
CHOST="x86_64-pc-linux-gnu"
CONFIG_PROTECT="/etc /usr/share/config /usr/share/gnupg/qualified.txt /usr/share/openvpn/easy-rsa /var/lib/hsqldb"
CONFIG_PROTECT_MASK="/etc/ca-certificates.conf /etc/env.d /etc/env.d/java/ /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="-march=native -O2 -fgcse-after-reload -pipe"
DISTDIR="/usr/portage/distfiles"
FEATURES="assume-digests binpkg-logs ccache collision-protect distlocks ebuild-locks fixlafiles metadata-transfer multilib-strict news parallel-fetch protect-owned sandbox sfperms splitdebug strict unknown-features-warn unmerge-logs unmerge-orphans userfetch"
FFLAGS="-march=native -O2 -fgcse-after-reload -pipe"
GENTOO_MIRRORS="ftp://ftp.snt.utwente.nl/pub/os/linux/gentoo ftp://mirror.switch.ch/mirror/gentoo/"
LANG="de_DE.utf8"
LC_ALL="de_DE.utf8"
LDFLAGS="-Wl,-O1 -Wl,--as-needed"
LINGUAS="de"
MAKEOPTS="-j5"
PKGDIR="/usr/portage/packages"
PORTAGE_COMPRESS="xz"
PORTAGE_COMPRESS_FLAGS="-6"
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/x11 /usr/local/portage /usr/local/portage/worldforge"
SYNC="rsync://rsync3.de.gentoo.org/gentoo-portage"
USE="64bit X Xaw3d a52 aac aalib accessibility acl acpi agg akode allegro alsa amarok amd64 amr apache2 autoipd bash-completion bazaar berkdb bittorrent blender blender-game branding bzip2 cairo captury ccache cdaudio cdda cdr cdrom cegui cjk cli clucene consolekit cracklib crypt cups curl cviewer cvs cxx daap dbus deblob declarative default-font designer-plugin desktopglobe devil dga dirac djvu doc dri dts dvd dvdnav dvdr emacs embedded emboss encode exif fam fbcon ffmpeg fftw firefox fits flac fltk fortran gallium gcj gdbm gdu ggi git gles glitz gmm gmp gopher gpg gpm gpu grub gstreamer guile gzip htmlhandbook i18n iceweasel icons iconv icq icu idn imagemagick insecure-savers intel ipv6 jabber jack java java6 javascript jingle jpeg kde kde4 kdebuild kdecards kdehiddenvisibility kdepim kdm kipi kontact ktts lastfm latex lcms ldap libcaca libnotify libssh2 libwww llvm lm_sensors logitech-mouse lua lzma lzo matroska mdnsresponder-compat mercurial mmx mng modules mp3tunes mpeg mpeg2 mpfr mpi mtp mudflap mule multilib musepack mysql ncurses nepomuk networkmanager nio2 nls noamazon nova nowin nptl nptlonly nsplugin offensive ogg ogg123 ogre openal opencl openexr opengl openmp openssl opensslcrypt openstreetmap openxml oscar otr oxygen pae pam pango pcre pdf phonon pkcs11 plasma player png policykit posix povray ppds pppd private-headers python qt3support qt4 ramfs readline redland reiser4 reiserfs romio rss schroedinger sdl sdl-image semantic-desktop sensord session shm shmvideo sna sndfile solver songs sound speex spell sse sse2 sse3 ssl ssse3 startup-notification subversion svg sysfs systemtap tcpd telepathy tetex theora threads tidy tiff tk tools truetype type1 udev unicode usb v4l2 vaapi vhook video videos visualization vorbis vpx wav wavpack wifi wikipedia wmf wxwindows x264 xcb xcomposite xemacs xerces-c xft xhtml xine xml xorg xosd xprint xrandr xscreensaver xulrunner xv xvid xvmc zeroconf zfs zip zlib" 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" 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 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" CALLIGRA_FEATURES="kexi words flow plan stage tables krita karbon braindump" CAMERAS="ptp2" 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="evdev" KERNEL="linux" LCD_DEVICES="bayrad cfontz cfontz633 glk hd44780 lb216 lcdm001 mtxorb ncurses text" LINGUAS="de" PHP_TARGETS="php5-3" QEMU_SOFTMMU_TARGETS="i386 x86_64" QEMU_USER_TARGETS="i386 x86_64" RUBY_TARGETS="ruby18" USERLAND="GNU" VIDEO_CARDS="fbdev i965 intel" 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_RSYNC_EXTRA_OPTS

[Comment 1 Sébastien Fabbro (RETIRED) 2012-02-06 21:09:12 UTC]

these locations might not be up to gentoo standards, but respect upstream. some programs and documentation within R hardcode these locations, so it will be much of a pain to maintain to have R really respect pure fhs standards and pointing to licenses.

other distros do the same as us.

so if you are really annoyed with it, i would suggest to report upstream.