Had a discussion with Ralph (sera) on IRC. He requested that a bug be opened for the patch in the URL for the next time javatoolkit is touched. Please ask if you have any questions. Thanks.
Although I do not know what used to be in the patch, here is a current issue on Gentoo:Prefix: running install_data creating /scratch/mmokrejs/gentoo_rap/var/tmp/portage/dev-java/javatoolkit-0.3.0-r9/image/_python2.7/usr creating /scratch/mmokrejs/gentoo_rap/var/tmp/portage/dev-java/javatoolkit-0.3.0-r9/image/_python2.7/usr/share creating /scratch/mmokrejs/gentoo_rap/var/tmp/portage/dev-java/javatoolkit-0.3.0-r9/image/_python2.7/usr/share/man creating /scratch/mmokrejs/gentoo_rap/var/tmp/portage/dev-java/javatoolkit-0.3.0-r9/image/_python2.7/usr/share/man/man1 copying src/man/findclass.1 -> /scratch/mmokrejs/gentoo_rap/var/tmp/portage/dev-java/javatoolkit-0.3.0-r9/image/_python2.7/usr/share/man/man1 running install_egg_info Writing /scratch/mmokrejs/gentoo_rap/var/tmp/portage/dev-java/javatoolkit-0.3.0-r9/image/_python2.7/scratch/mmokrejs/gentoo_rap/usr/lib64/python2.7/site-packages/javatoolkit-0.3.0-py2.7.egg-info ESC[32;01m*ESC[0m python2_7: running distutils-r1_run_phase distutils-r1_python_install_all >>> Completed installing javatoolkit-0.3.0-r9 into /scratch/mmokrejs/gentoo_rap/var/tmp/portage/dev-java/javatoolkit-0.3.0-r9/image/ ESC[32;01m*ESC[0m Final size of build directory: 91 KiB ESC[32;01m*ESC[0m Final size of installed tree: 125 KiB ESC[33;01m*ESC[0m QA Notice: the following files are outside of the prefix: ESC[33;01m*ESC[0m /usr ESC[33;01m*ESC[0m /usr/share ESC[33;01m*ESC[0m /usr/share/man ESC[33;01m*ESC[0m /usr/share/man/man1 ESC[33;01m*ESC[0m /usr/share/man/man1/findclass.1 ESC[31;01m*ESC[0m ERROR: dev-java/javatoolkit-0.3.0-r9::gentoo failed: ESC[31;01m*ESC[0m Aborting due to QA concerns: there are files installed outside the prefix ESC[31;01m*ESC[0m ESC[31;01m*ESC[0m Call stack: ESC[31;01m*ESC[0m misc-functions.sh, line 603: Called install_qa_check ESC[31;01m*ESC[0m misc-functions.sh, line 217: Called source 'install_symlink_html_docs' ESC[31;01m*ESC[0m 05prefix, line 114: Called install_qa_check_prefix ESC[31;01m*ESC[0m 05prefix, line 27: Called die ESC[31;01m*ESC[0m The specific snippet of code: ESC[31;01m*ESC[0m die "Aborting due to QA concerns: there are files installed outside the prefix" ESC[31;01m*ESC[0m ESC[31;01m*ESC[0m If you need support, post the output of `emerge --info '=dev-java/javatoolkit-0.3.0-r9::gentoo'`, ESC[31;01m*ESC[0m the complete build log and the output of `emerge -pqv '=dev-java/javatoolkit-0.3.0-r9::gentoo'`. ESC[31;01m*ESC[0m The complete build log is located at '/scratch/mmokrejs/gentoo_rap/var/tmp/portage/dev-java/javatoolkit-0.3.0-r9/temp/build.log'. ESC[31;01m*ESC[0m The ebuild environment file is located at '/scratch/mmokrejs/gentoo_rap/var/tmp/portage/dev-java/javatoolkit-0.3.0-r9/temp/environment'. ESC[31;01m*ESC[0m Working directory: '/scratch/mmokrejs/gentoo_rap/var/tmp/portage/dev-java/javatoolkit-0.3.0-r9/image/scratch/mmokrejs/gentoo_rap' ESC[31;01m*ESC[0m S: '/scratch/mmokrejs/gentoo_rap/var/tmp/portage/dev-java/javatoolkit-0.3.0-r9/work/javatoolkit-0.3.0'
Created attachment 441802 [details, diff] move manpages to EPREFIXEd location This works for me on Gentoo::RAP installation.
(In reply to Martin Mokrejš from comment #2) > Created attachment 441802 [details, diff] [details, diff] > move manpages to EPREFIXEd location > > This works for me on Gentoo::RAP installation. Why mkdir -p instead of dodir? Similarly, why not doins instead of mv?
(In reply to Austin English from comment #3) > > Why mkdir -p instead of dodir? Similarly, why not doins instead of mv? Well, a proof of concept. The mv is needed because it undoes wrong 'make install' step and just moves the file installed in $IMAGEDIR to the EPREFIXed place. Ideally somebody should figure out where the EPREFIX should be placed directly without this ebuild change.
Created attachment 441842 [details, diff] javatoolkit-prefix.patch The offending path is hard-coded in setup.py Please review this patch.
(In reply to Benda Xu from comment #5) > Created attachment 441842 [details, diff] [details, diff] > javatoolkit-prefix.patch > > The offending path is hard-coded in setup.py > > Please review this patch. >>> Unpacking source... >>> Unpacking javatoolkit-0.3.0.tar.bz2 to /scratch/mmokrejs/gentoo_rap/var/tmp/portage/dev-java/javatoolkit-0.3.0-r9/work >>> Source unpacked in /scratch/mmokrejs/gentoo_rap/var/tmp/portage/dev-java/javatoolkit-0.3.0-r9/work >>> Preparing source in /scratch/mmokrejs/gentoo_rap/var/tmp/portage/dev-java/javatoolkit-0.3.0-r9/work/javatoolkit-0.3.0 ... /scratch/mmokrejs/gentoo_rap/var/tmp/portage/dev-java/javatoolkit-0.3.0-r9/temp/environment: line 3519: hprefixify: command not found
(In reply to Martin Mokrejš from comment #6) > >>> Unpacking source... > >>> Unpacking javatoolkit-0.3.0.tar.bz2 to /scratch/mmokrejs/gentoo_rap/var/tmp/portage/dev-java/javatoolkit-0.3.0-r9/work > >>> Source unpacked in /scratch/mmokrejs/gentoo_rap/var/tmp/portage/dev-java/javatoolkit-0.3.0-r9/work > >>> Preparing source in /scratch/mmokrejs/gentoo_rap/var/tmp/portage/dev-java/javatoolkit-0.3.0-r9/work/javatoolkit-0.3.0 ... > /scratch/mmokrejs/gentoo_rap/var/tmp/portage/dev-java/javatoolkit-0.3.0-r9/ > temp/environment: line 3519: hprefixify: command not found When was the last time you synchronized your repo? `emaint sync -a` will fix that.
(In reply to Benda Xu from comment #7) > `emaint sync -a` will fix that. Thanks, hprefixify seem to be known now but the original issue persists: * QA Notice: the following files are outside of the prefix: * /usr * /usr/share * /usr/share/man * /usr/share/man/man1 * /usr/share/man/man1/findclass.1 * ERROR: dev-java/javatoolkit-0.3.0-r9::gentoo failed: * Aborting due to QA concerns: there are files installed outside the prefix * * Call stack: * misc-functions.sh, line 603: Called install_qa_check * misc-functions.sh, line 217: Called source 'install_symlink_html_docs' * 05prefix, line 114: Called install_qa_check_prefix * 05prefix, line 27: Called die
(In reply to Martin Mokrejš from comment #8) > (In reply to Benda Xu from comment #7) > > > `emaint sync -a` will fix that. > > Thanks, hprefixify seem to be known now but the original issue persists: > > > * QA Notice: the following files are outside of the prefix: > * /usr > * /usr/share > * /usr/share/man > * /usr/share/man/man1 > * /usr/share/man/man1/findclass.1 > * ERROR: dev-java/javatoolkit-0.3.0-r9::gentoo failed: > * Aborting due to QA concerns: there are files installed outside the > prefix > * > * Call stack: > * misc-functions.sh, line 603: Called install_qa_check > * misc-functions.sh, line 217: Called source 'install_symlink_html_docs' > * 05prefix, line 114: Called install_qa_check_prefix > * 05prefix, line 27: Called die You'll need to apply the patch again.
Created attachment 442176 [details] javatoolkit-0.3.0-r9/temp/environment Sorry, I forgot to re-apply. So now, hprefixify is not recognized again and QA issue still present.
No objections received. Landing in tree. Thanks. https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=b890e98ef743513a42ba6 Martin, please test the newest version.
Hi Benda, I cannot help myself but I did : 'emerge --sync', also did 'emaint sync -a' but I still get: >>> Completed installing javatoolkit-0.3.0-r9 into /scratch/mmokrejs/gentoo_rap/var/tmp/portage/dev-java/javatoolkit-0.3.0-r9/image/ * Final size of build directory: 91 KiB * Final size of installed tree: 125 KiB * QA Notice: command not found: * * /scratch/mmokrejs/gentoo_rap/var/tmp/portage/dev-java/javatoolkit-0.3.0-r9/temp/environment: line 3517: hprefixify: command not found * QA Notice: the following files are outside of the prefix: * /usr * /usr/share * /usr/share/man * /usr/share/man/man1 * /usr/share/man/man1/findclass.1 * ERROR: dev-java/javatoolkit-0.3.0-r9::gentoo failed: * Aborting due to QA concerns: there are files installed outside the prefix * * Call stack: * misc-functions.sh, line 603: Called install_qa_check * misc-functions.sh, line 217: Called source 'install_symlink_html_docs' * 05prefix, line 114: Called install_qa_check_prefix * 05prefix, line 27: Called die * The specific snippet of code: * die "Aborting due to QA concerns: there are files installed outside the prefix" * * If you need support, post the output of `emerge --info '=dev-java/javatoolkit-0.3.0-r9::gentoo'`, Please version bump the ebuild and also, introduce some checks. Currently I have: $ emerge --info '=dev-java/javatoolkit-0.3.0-r9::gentoo' Portage 2.3.0 (python 2.7.12-final-0, prefix/linux-standalone/amd64, gcc-5.4.0, unavailable, 2.6.32-573.12.1.el6.Bull.88.x86_64 x86_64) ================================================================= System Settings ================================================================= System uname: Linux-2.6.32-573.12.1.el6.Bull.88.x86_64-x86_64-Intel-R-_Xeon-R-_CPU_E5-2670_0_@_2.60GHz-with-redhat-6.4-Santiago KiB Mem: 131942764 total, 110169024 free KiB Swap: 65536128 total, 65477508 free Timestamp of repository gentoo: Mon, 15 Aug 2016 09:30:01 +0000 sh bash 4.3_p46 ld GNU ld (Gentoo 2.26) 2.26.20160125 app-shells/bash: 4.3_p46::rap dev-java/java-config: 2.2.0-r3::gentoo dev-lang/perl: 5.24.0-r1::gentoo dev-lang/python: 2.7.12::gentoo, 3.4.4::gentoo dev-util/cmake: 3.5.2-r1::gentoo dev-util/pkgconfig: 0.29.1::gentoo sys-apps/baselayout: 2.2-r1::gentoo sys-apps/sandbox: 2.10-r2::gentoo sys-devel/autoconf: 2.69-r2::gentoo sys-devel/automake: 1.13.4-r1::gentoo, 1.14.1-r1::gentoo, 1.15-r2::gentoo sys-devel/binutils: 2.26::rap, 2.26.1::gentoo sys-devel/gcc: 4.2.4-r1::gentoo, 5.4.0::gentoo sys-devel/gcc-config: 1.8_p20160608::rap 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::rap Repositories: gentoo location: /scratch/mmokrejs/gentoo_rap/usr/portage sync-type: rsync sync-uri: rsync://rsync.gentoo.org/gentoo-portage priority: -1000 eclass-overrides: rap layman location: /scratch/mmokrejs/gentoo_rap/var/lib/layman masters: gentoo priority: 0 eclass-overrides: rap rap location: /scratch/mmokrejs/gentoo_rap/usr/portage-stage sync-type: git sync-uri: https://anongit.gentoo.org/git/proj/android.git masters: gentoo eclass-overrides: rap haskell location: /scratch/mmokrejs/gentoo_rap/var/lib/layman/haskell masters: gentoo priority: 50 eclass-overrides: rap science location: /scratch/mmokrejs/gentoo_rap/var/lib/layman/science masters: gentoo priority: 50 eclass-overrides: rap ACCEPT_KEYWORDS="amd64 ~amd64 ~amd64-linux" ACCEPT_LICENSE="* -@EULA dlj-1.1 sun-bcla-java-vm Oracle-BCLA-JavaSE IBM-J1.6 skype-eula Nero-EULA-US AdobeFlash-10.3 skype-4.0.0.7-copyright AdobeFlash-11.x" CBUILD="x86_64-pc-linux-gnu" CFLAGS="-O2 -pipe -O2 -pipe -march=native" CHOST="x86_64-pc-linux-gnu" CONFIG_PROTECT="/etc /usr/share/gnupg/qualified.txt" 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 /etc/texmf/language.dat.d /etc/texmf/language.def.d /etc/texmf/updmap.d /etc/texmf/web2c" CXXFLAGS="-O2 -pipe -O2 -pipe -march=native" DISTDIR="/scratch/mmokrejs/gentoo_rap/usr/portage/distfiles" FCFLAGS="-O2 -pipe" FEATURES="assume-digests binpkg-logs config-protect-if-modified distlocks ebuild-locks fixlafiles force-prefix merge-sync news noclean nostrip parallel-fetch preserve-libs protect-owned sfperms splitdebug strict unknown-features-warn unmerge-logs unmerge-orphans unprivileged userfetch userpriv usersync" FFLAGS="-O2 -pipe" GENTOO_MIRRORS="http://gentoo.wheel.sk/ http://ftp.fi.muni.cz/pub/linux/gentoo/ http://gentoo.mirror.web4u.cz/ rsync://gentoo.mirror.dkm.cz/gentoo/ ftp://gentoo.mirror.web4u.cz/" LDFLAGS="-Wl,-O1 -Wl,--as-needed" MAKEOPTS="-j8" PKGDIR="/scratch/mmokrejs/gentoo_rap/usr/portage/packages" PORTAGE_CONFIGROOT="/scratch/mmokrejs/gentoo_rap/" 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="/scratch/mmokrejs/gentoo_rap/var/tmp" USE="X amd64 apache apache2 avx avx2 berkdb bindist boost bzip2 cairo cgi cli coin consolekit cracklib crypt cryptlib cxx dbus device-mapper dhcp dri emboss encode fax fbcon ffmpeg fontconfig fortran gbm gd gdbm gimp glpk gnutls gtk hal hwdb iconv imaging innodb java javascript jce jpeg jpg js jscript keymap ladspa lapack lcms libnotify lm_sensors mad mmx mmxext modules mpi mpich2 mysql ncurses nfs nls nptl nptlonly nscd openmp pcre pdf perl php png policykit polkit ppds pppd prefix python qt3support readline resolvconf seccomp server session slideshow sndfile sqlite sse sse2 sse3 sse4_1 sse4_2 ssl ssse3 suexec svg syslog tcl tcpd threads tiff tk truetype unicode usb v4l v4l2 vim-syntax vnc wavpack wifi x11 xcb xml xorg xrandr xv xvid xvmc 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="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="ptp2" COLLECTD_PLUGINS="df interface irq load memory rrdtool swap syslog" CPU_FLAGS_X86="aes avx 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" LINGUAS="en en_US cs cz" OFFICE_IMPLEMENTATION="libreoffice" PHP_TARGETS="php5-5" PYTHON_SINGLE_TARGET="python2_7" PYTHON_TARGETS="python2_7" RUBY_TARGETS="ruby20 ruby21" USERLAND="GNU" VIDEO_CARDS="amdgpu fbdev intel nouveau radeon radeonsi vesa dummy v4l" 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" USE_PYTHON="2.7" Unset: CC, CPPFLAGS, CTARGET, CXX, EMERGE_DEFAULT_OPTS, INSTALL_MASK, LANG, LC_ALL, PORTAGE_BUNZIP2_COMMAND, PORTAGE_COMPRESS, PORTAGE_COMPRESS_FLAGS, PORTAGE_RSYNC_EXTRA_OPTS ================================================================= Package Settings ================================================================= dev-java/javatoolkit-0.3.0-r9::gentoo was built with the following: USE="(prefix)" PYTHON_TARGETS="python2_7"
(In reply to Martin Mokrejš from comment #12) > /scratch/mmokrejs/gentoo_rap/var/tmp/portage/dev-java/javatoolkit-0.3.0-r9/ > temp/environment: line 3517: hprefixify: command not found It's working fine here. Either this problem is specific to prefix or you're overriding the prefix eclass in an overlay.
Benda, any clues what is wrong with my setup then? Thank you.
(In reply to James Le Cuirot from comment #13) > (In reply to Martin Mokrejš from comment #12) > > /scratch/mmokrejs/gentoo_rap/var/tmp/portage/dev-java/javatoolkit-0.3.0-r9/ > > temp/environment: line 3517: hprefixify: command not found > > It's working fine here. Either this problem is specific to prefix or you're > overriding the prefix eclass in an overlay. (In reply to Martin Mokrejš from comment #14) > Benda, any clues what is wrong with my setup then? Thank you. Thanks to James' hint. It must be due to prefix.eclass in the rap overlay. Please update it according to: https://wiki.gentoo.org/wiki/Prefix/libc#Synchronize_with_the_RAP_repository
> https://wiki.gentoo.org/wiki/Prefix/libc#Synchronize_with_the_RAP_repository Something is wrong with the test. $ EPREFIX=/scratch/mmokrejs/gentoo_rap $ [ -d ${EPREFIX}/usr/portage-stage/.git ] || rm -rf ${EPREFIX}/usr/portage-stage $ ls -latr /scratch/mmokrejs/gentoo_rap/usr/portage-stage/ total 176 drwxrwxr-x 13 mmokrejs mmokrejs 4096 Jun 30 11:59 .. drwxr-xr-x 3 mmokrejs mmokrejs 4096 Jun 30 11:59 sys-kernel drwxr-xr-x 4 mmokrejs mmokrejs 4096 Jun 30 11:59 sys-fs drwxr-xr-x 6 mmokrejs mmokrejs 4096 Jun 30 11:59 sys-devel drwxr-xr-x 9 mmokrejs mmokrejs 4096 Jun 30 11:59 sys-apps drwxr-xr-x 2 mmokrejs mmokrejs 4096 Jun 30 11:59 scripts drwxr-xr-x 3 mmokrejs mmokrejs 4096 Jun 30 11:59 sci-visualization drwxr-xr-x 4 mmokrejs mmokrejs 4096 Jun 30 11:59 sci-physics drwxr-xr-x 3 mmokrejs mmokrejs 4096 Jun 30 11:59 sci-mathematics drwxr-xr-x 3 mmokrejs mmokrejs 4096 Jun 30 11:59 sci-libs drwxr-xr-x 3 mmokrejs mmokrejs 4096 Jun 30 11:59 sci-electronics drwxr-xr-x 5 mmokrejs mmokrejs 4096 Jun 30 11:59 profiles drwxr-xr-x 4 mmokrejs mmokrejs 4096 Jun 30 11:59 net-proxy drwxr-xr-x 6 mmokrejs mmokrejs 4096 Jun 30 11:59 net-misc drwxr-xr-x 3 mmokrejs mmokrejs 4096 Jun 30 11:59 net-mail drwxr-xr-x 4 mmokrejs mmokrejs 4096 Jun 30 11:59 net-libs drwxr-xr-x 3 mmokrejs mmokrejs 4096 Jun 30 11:59 net-dialup drwxr-xr-x 4 mmokrejs mmokrejs 4096 Jun 30 11:59 net-analyzer drwxr-xr-x 2 mmokrejs mmokrejs 4096 Jun 30 11:59 metadata drwxr-xr-x 3 mmokrejs mmokrejs 4096 Jun 30 11:59 media-video drwxr-xr-x 4 mmokrejs mmokrejs 4096 Jun 30 11:59 media-libs drwxr-xr-x 4 mmokrejs mmokrejs 4096 Jun 30 11:59 media-gfx drwxr-xr-x 3 mmokrejs mmokrejs 4096 Jun 30 11:59 kde-base drwxr-xr-x 2 mmokrejs mmokrejs 4096 Jun 30 11:59 eclass drwxr-xr-x 4 mmokrejs mmokrejs 4096 Jun 30 11:59 dev-util drwxr-xr-x 3 mmokrejs mmokrejs 4096 Jun 30 11:59 dev-qt drwxr-xr-x 4 mmokrejs mmokrejs 4096 Jun 30 11:59 dev-python drwxr-xr-x 3 mmokrejs mmokrejs 4096 Jun 30 11:59 dev-libs drwxr-xr-x 4 mmokrejs mmokrejs 4096 Jun 30 11:59 dev-lang drwxr-xr-x 3 mmokrejs mmokrejs 4096 Jun 30 11:59 dev-java drwxr-xr-x 3 mmokrejs mmokrejs 4096 Jun 30 11:59 dev-embedded drwxr-xr-x 3 mmokrejs mmokrejs 4096 Jun 30 11:59 app-text drwxr-xr-x 3 mmokrejs mmokrejs 4096 Jun 30 11:59 app-shells drwxr-xr-x 3 mmokrejs mmokrejs 4096 Jun 30 11:59 app-portage drwxr-xr-x 3 mmokrejs mmokrejs 4096 Jun 30 11:59 app-misc drwxr-xr-x 3 mmokrejs mmokrejs 4096 Jun 30 11:59 app-benchmarks -rw-r--r-- 1 mmokrejs mmokrejs 12 Jun 30 11:59 .gitignore drwxr-xr-x 3 mmokrejs mmokrejs 4096 Jun 30 11:59 x11-proto drwxr-xr-x 3 mmokrejs mmokrejs 4096 Jun 30 11:59 x11-misc drwxr-xr-x 3 mmokrejs mmokrejs 4096 Jun 30 11:59 x11-base drwxr-xr-x 3 mmokrejs mmokrejs 4096 Jun 30 11:59 sys-process drwxr-xr-x 4 mmokrejs mmokrejs 4096 Jun 30 11:59 sys-libs drwxr-xr-x 7 mmokrejs mmokrejs 4096 Jun 30 11:59 .git drwxr-xr-x 43 mmokrejs mmokrejs 4096 Jun 30 11:59 . $ if [ -d /scratch/mmokrejs/gentoo_rap/usr/portage-stage/.git ]; then echo yes; fi yes $ $ rm -rf ${EPREFIX}/usr/portage-stage $ ls -latr /scratch/mmokrejs/gentoo_rap/usr/portage-stage/ ls: cannot access '/scratch/mmokrejs/gentoo_rap/usr/portage-stage/': No such file or directory $ $ emaint sync -r rap $ emerge --sync $ layman -S $ emerge javatoolkit And now it also went through for me, confirming FIXED status. Thank you! Note: I would have appreciated a fat note that neither "emerge" nor "layman" will keep me updated against RAP. Especially because Benda told me elsewhere that RAP uses gentoo-x86 tree (unlike Prefix which has its own). That I mistakenly interpreted that the usual "emerge --sync" is enough. I highly recommend expanding the section in https://wiki.gentoo.org/wiki/Prefix/libc#Synchronize_with_the_RAP_repository .