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Bug 587932

Summary: sys-apps/baselayout-2.2-r1: emerge fails with "non-empty dir found where we needed a symlink: /usr/local/lib"
Product: Gentoo Linux Reporter: Markus Wernig <public>
Component: Current packagesAssignee: Gentoo Linux bug wranglers <bug-wranglers>
Status: RESOLVED WORKSFORME    
Severity: major    
Priority: Normal    
Version: unspecified   
Hardware: All   
OS: Linux   
Whiteboard:
Package list:
Runtime testing required: ---

Description Markus Wernig 2016-07-03 23:52:45 UTC 
Emerging sys-apps/baselayout-2.2-r1 results in an error if /usr/local/lib is a directory.

Since many applications (probably not the ones installed via emerge) install stuff there, this directory is more than likely to exist (it does here, with files from about 10 programs compiled separately).

Since I don't know how to split the files there into a multilib layout, this blocks all further updates.

Reproducible: Always

Steps to Reproduce:
1. Have an application compiled from source that installs files into /usr/local/lib
2. run emerge -DuNav world
3.



# emerge --info
Portage 2.3.0 (python 3.4.4-final-0, default/linux/amd64/13.0/desktop/plasma, gcc-5.3.0, glibc-2.23-r2, 4.6.3-gentoo x86_64)
=================================================================
System uname: Linux-4.6.3-gentoo-x86_64-Intel-R-_Core-TM-_i7-6820HQ_CPU_@_2.70GHz-with-gentoo-2.2
KiB Mem:    16230372 total,   5954020 free
KiB Swap:    8388604 total,   8388604 free
Timestamp of repository gentoo: Sun, 03 Jul 2016 23:30:02 +0000
sh bash 4.3_p46
ld GNU ld (Gentoo 2.25.1 p1.1) 2.25.1
app-shells/bash:          4.3_p46::gentoo
dev-java/java-config:     2.2.0-r3::gentoo
dev-lang/perl:            5.24.0-r1::gentoo
dev-lang/python:          2.7.11-r2::gentoo, 3.4.4::gentoo, 3.5.1-r2::gentoo
dev-util/cmake:           3.5.2-r1::gentoo
dev-util/pkgconfig:       0.29.1::gentoo
sys-apps/baselayout:      2.2::gentoo
sys-apps/openrc:          0.21::gentoo
sys-apps/sandbox:         2.10-r2::gentoo
sys-devel/autoconf:       2.13::gentoo, 2.69-r2::gentoo
sys-devel/automake:       1.11.6-r2::gentoo, 1.12.6-r1::gentoo, 1.13.4-r1::gentoo, 1.14.1-r1::gentoo, 1.15-r2::gentoo
sys-devel/binutils:       2.25.1-r1::gentoo
sys-devel/gcc:            4.9.3::gentoo, 5.3.0::gentoo, 5.4.0::gentoo
sys-devel/gcc-config:     1.8-r1::gentoo
sys-devel/libtool:        2.4.6-r2::gentoo
sys-devel/make:           4.2.1::gentoo
sys-kernel/linux-headers: 4.6::gentoo (virtual/os-headers)
sys-libs/glibc:           2.23-r2::gentoo
Repositories:

gentoo
    location: /usr/portage
    sync-type: rsync
    sync-uri: rsync://rsync.gentoo.org/gentoo-portage
    priority: -1000

ACCEPT_KEYWORDS="amd64 ~amd64"
ACCEPT_LICENSE="*"
CBUILD="x86_64-pc-linux-gnu"
CFLAGS="-O2 -march=native -pipe -fomit-frame-pointer"
CHOST="x86_64-pc-linux-gnu"
CONFIG_PROTECT="/etc /usr/lib64/libreoffice/program/sofficerc /usr/share/config /usr/share/gnupg/qualified.txt /usr/share/themes/oxygen-gtk/gtk-2.0 /var/lib/hsqldb"
CONFIG_PROTECT_MASK="/etc/ca-certificates.conf /etc/dconf /etc/env.d /etc/fonts/fonts.conf /etc/gconf /etc/gentoo-release /etc/revdep-rebuild /etc/sandbox.d /etc/terminfo"
CXXFLAGS="-O2 -march=native -pipe -fomit-frame-pointer"
DISTDIR="/usr/portage/distfiles"
EMERGE_DEFAULT_OPTS="--autounmask-write=y"
FCFLAGS="-O2 -pipe"
FEATURES="assume-digests binpkg-logs config-protect-if-modified distlocks ebuild-locks fixlafiles merge-sync news parallel-fetch preserve-libs protect-owned sfperms strict unknown-features-warn unmerge-logs unmerge-orphans userfetch userpriv usersandbox usersync xattr"
FFLAGS="-O2 -pipe"
GENTOO_MIRRORS="http://sunsite.cnlab-switch.ch/ftp/mirror/gentoo/ ftp://sunsite.cnlab-switch.ch/mirror/gentoo/ http://de-mirror.org/gentoo/"
LANG="en_US.utf8"
LDFLAGS="-Wl,-O1 -Wl,--as-needed"
MAKEOPTS="-j9"
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 --exclude=/.git"
PORTAGE_TMPDIR="/var/tmp"
USE="X a52 aac acl acpi alsa amd64 bash-completion berkdb bluetooth branding bzip2 cairo caps cdda cdr cli consolekit cracklib crypt cups cxx dbus declarative dri dts dvd dvdr emboss encode exif fam firefox flac fortran gdbm gif glamor gpm gstreamer gtk http iconv imap ipv6 jce jpeg kde kipi lcms ldap libav libnotify mad mmx mmxext mng modules mp3 mp4 mpeg multilib multitarget ncurses networkmanager nls nptl nss ogg opengl openmp otr pam pango pcre pcsc pcsc-lite pdf phonon plasma png policykit ppds pulseaudio qml qt3support qt4 qt5 readline sdl seccomp session spell sse sse2 sse3 sse4_1 sse4_2 ssl ssse3 startup-notification subversion svg synaptics tcpd tiff tools truetype udev udisks unicode upower usb utils vorbis widgets wxwidgets x264 xattr xcb xcomposite xinerama xml xscreensaver xv xvid zlib" ABI_X86="64 32" ALSA_CARDS="hda-intel usb-audio" APACHE2_MODULES="authn_core authz_core socache_shmcb unixd 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" CALLIGRA_FEATURES="kexi words flow plan sheets stage tables krita karbon braindump author" CAMERAS="all" 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" GRUB_PLATFORMS="pc efi-64" INPUT_DEVICES="keyboard mouse evdev synaptics void alps" KERNEL="linux" LCD_DEVICES="bayrad cfontz cfontz633 glk hd44780 lb216 lcdm001 mtxorb ncurses text" LIBREOFFICE_EXTENSIONS="presenter-console presenter-minimizer" LINGUAS="en de" NETBEANS_MODULES="apisupport java javafx profiler websvccommon enterprise" OFFICE_IMPLEMENTATION="libreoffice" PHP_TARGETS="php5-5" PYTHON_SINGLE_TARGET="python3_4" PYTHON_TARGETS="python2_7 python3_4" RUBY_TARGETS="ruby20 ruby21" USERLAND="GNU" VIDEO_CARDS="fbdev intel nouveau" 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:  CC, CPPFLAGS, CTARGET, CXX, INSTALL_MASK, LC_ALL, PORTAGE_BUNZIP2_COMMAND, PORTAGE_COMPRESS, PORTAGE_COMPRESS_FLAGS, PORTAGE_RSYNC_EXTRA_OPTS, USE_PYTHON
Comment 1 William Hubbs gentoo-dev 2016-07-07 16:51:35 UTC 
The easiest way to do this conversion is the following, as root:

# cd /usr/local
# mv lib lib64
# ln -snf lib64 lib

This is set up like this by default with baselayout-2.2, so I'm not sure
why your system isn't set up this way.
Comment 2 Markus Wernig 2016-07-08 13:17:08 UTC 
(In reply to William Hubbs from comment #1)
> The easiest way to do this conversion is the following, as root:
> 
> # cd /usr/local
> # mv lib lib64
> # ln -snf lib64 lib
> 
> This is set up like this by default with baselayout-2.2, so I'm not sure
> why your system isn't set up this way.

Thanks for the update!

Both lib and lib64 existed as directories under /usr/local:

# ls -l /usr/local
total 20
drwxr-xr-x 2 root root 4096 Sep 25  2015 bin
drwxr-xr-x 3 root root 4096 Sep 25  2015 lib
drwxr-xr-x 2 root root 4096 Jan  7  2016 lib64
drwxr-xr-x 2 root root 4096 Mar 18 13:31 sbin
drwxr-xr-x 6 root root 4096 Sep 25  2015 share

/usr/local/lib64 was empty, though.

I removed it and set up the symlink manually.

There were some libs from locally installed programs in /usr/local/lib. Fortunately, all of them were 64bit libs.

So this is now WORKSFORME.