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Bug 429374 - dev-java/javatoolkit : please add patch to remove hard coded paths (Gentoo Prefix support)
Summary: dev-java/javatoolkit : please add patch to remove hard coded paths (Gentoo Pr...
Status: RESOLVED FIXED
Alias: None
Product: Gentoo Linux
Classification: Unclassified
Component: Current packages (show other bugs)
Hardware: All Linux
: Normal enhancement (vote)
Assignee: Java team
URL: http://overlays.gentoo.org/proj/alt/b...
Whiteboard:
Keywords:
Depends on:
Blocks: prefix-gx86
  Show dependency tree
 
Reported: 2012-08-01 15:55 UTC by Jeremy Olexa (darkside) (RETIRED)
Modified: 2016-08-19 08:55 UTC (History)
3 users (show)

See Also:
Package list:
Runtime testing required: ---


Attachments
move manpages to EPREFIXEd location (javatoolkit-0.3.0-r9.ebuild.patch,473 bytes, patch)
2016-07-28 11:35 UTC, Martin Mokrejš
Details | Diff
javatoolkit-prefix.patch (javatoolkit-prefix.patch,707 bytes, patch)
2016-07-29 02:07 UTC, Benda Xu
Details | Diff
javatoolkit-0.3.0-r9/temp/environment (environment,135.46 KB, text/plain)
2016-08-01 07:33 UTC, Martin Mokrejš
Details

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Description Jeremy Olexa (darkside) (RETIRED) archtester gentoo-dev Security 2012-08-01 15:55:11 UTC
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.
Comment 1 Martin Mokrejš 2016-06-29 13:23:04 UTC
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'
Comment 2 Martin Mokrejš 2016-07-28 11:35:50 UTC
Created attachment 441802 [details, diff]
move manpages to EPREFIXEd location

This works for me on Gentoo::RAP installation.
Comment 3 Austin English (RETIRED) gentoo-dev 2016-07-28 19:23:19 UTC
(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?
Comment 4 Martin Mokrejš 2016-07-28 19:34:26 UTC
(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.
Comment 5 Benda Xu gentoo-dev 2016-07-29 02:07:09 UTC
Created attachment 441842 [details, diff]
javatoolkit-prefix.patch

The offending path is hard-coded in setup.py

Please review this patch.
Comment 6 Martin Mokrejš 2016-07-31 11:14:09 UTC
(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
Comment 7 Benda Xu gentoo-dev 2016-08-01 01:12:57 UTC
(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.
Comment 8 Martin Mokrejš 2016-08-01 05:38:54 UTC
(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
Comment 9 Benda Xu gentoo-dev 2016-08-01 06:16:37 UTC
(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.
Comment 10 Martin Mokrejš 2016-08-01 07:33:25 UTC
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.
Comment 11 Benda Xu gentoo-dev 2016-08-13 08:01:29 UTC
No objections received.  Landing in tree.  Thanks.

  https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=b890e98ef743513a42ba6

Martin, please test the newest version.
Comment 12 Martin Mokrejš 2016-08-15 09:46:26 UTC
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"
Comment 13 James Le Cuirot gentoo-dev 2016-08-15 19:00:22 UTC
(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.
Comment 14 Martin Mokrejš 2016-08-17 09:39:21 UTC
Benda, any clues what is wrong with my setup then? Thank you.
Comment 15 Benda Xu gentoo-dev 2016-08-19 07:02:24 UTC
(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
Comment 16 Martin Mokrejš 2016-08-19 08:55:37 UTC
> 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 .