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suprafluid
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PostPosted: Fri Jan 10, 2020 9:11 am    Post subject: make Error 13 when installing webapp-config-1.55-r1 Reply with quote

Hi all,

I am unable to install or update webapp-config on a server.

emerge app-admin/webapp-config ends up with

Code:
.....
running build_scripts
creating /tmp/portage/portage/app-admin/webapp-config-1.55-r1/work/webapp-config-1.55-python3_6/scripts
copying and adjusting sbin/webapp-config -> /tmp/portage/portage/app-admin/webapp-config-1.55-r1/work/webapp-config-1.55-python3_6/scripts
copying sbin/webapp-cleaner -> /tmp/portage/portage/app-admin/webapp-config-1.55-r1/work/webapp-config-1.55-python3_6/scripts
changing mode of /tmp/portage/portage/app-admin/webapp-config-1.55-r1/work/webapp-config-1.55-python3_6/scripts/webapp-config from 644 to 755
 * python3_6: running distutils-r1_run_phase python_compile_all
make -j2 -C doc/
make: Entering directory '/tmp/portage/portage/app-admin/webapp-config-1.55-r1/work/webapp-config-1.55/doc'
MAN webapp-config.8
MAN webapp-config.5
make: *** [Makefile:36: webapp-config.8] Error 13
make: *** Waiting for unfinished jobs....
make: *** [Makefile:36: webapp-config.5] Error 13
make: Leaving directory '/tmp/portage/portage/app-admin/webapp-config-1.55-r1/work/webapp-config-1.55/doc'
 * ERROR: app-admin/webapp-config-1.55-r1::gentoo failed (compile phase):
 *   emake failed
 *
 * If you need support, post the output of `emerge --info '=app-admin/webapp-config-1.55-r1::gentoo'`,
 * the complete build log and the output of `emerge -pqv '=app-admin/webapp-config-1.55-r1::gentoo'`.
 * The complete build log is located at '/tmp/portage/portage/app-admin/webapp-config-1.55-r1/temp/build.log'.
 * The ebuild environment file is located at '/tmp/portage/portage/app-admin/webapp-config-1.55-r1/temp/environment'.
 * Working directory: '/tmp/portage/portage/app-admin/webapp-config-1.55-r1/work/webapp-config-1.55'
 * S: '/tmp/portage/portage/app-admin/webapp-config-1.55-r1/work/webapp-config-1.55'



I found out that make error 13 could be some file system denial, but was unable to find out which file access could cause this.

When I change manually to work/webapp-config-1.55/ and execute 'make -j2 -C doc/' on the command line it completes without any error...

Any idea how to get this solved?
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fedeliallalinea
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PostPosted: Fri Jan 10, 2020 9:28 am    Post subject: Reply with quote

You can post full build.log with wgetpaste?
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PostPosted: Fri Jan 10, 2020 9:34 am    Post subject: Reply with quote

sure:

http://dpaste.com/268DQ86

http://dpaste.com/3G0Q0WT
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PostPosted: Fri Jan 10, 2020 9:57 am    Post subject: Reply with quote

Hrmm.. my guess would be that xmlto is failing, but there's no error because of this bothersome 2>/dev/null
Code:
%: %.xml
        @echo MAN $@
        @xmlto man $< 2>/dev/null
I tried to build it and it's working fine for me.
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PostPosted: Fri Jan 10, 2020 10:18 am    Post subject: Reply with quote

I have the identical setup on another server and there I got no problemls at all with installing or upgrading webapp-config.

I strongy assume that this has something todo with some file permissions, but as long as I don't get any details, I don't know what to fix.
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PostPosted: Sat Jan 11, 2020 5:35 pm    Post subject: Reply with quote

If you patch the Makefile to remove the redirect to /dev/null, do you get anything useful? On the affected system, does running xmlto --help produce reasonable output? (This tests whether xmlto is functional at all.)
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PostPosted: Mon Jan 13, 2020 10:56 am    Post subject: Reply with quote

The idea is good, but how can I acheive this? If I edit the Makefine manually in the "work" directory, it is overwritten (newly generated?) each time I emerge the package again.
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fedeliallalinea
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PostPosted: Mon Jan 13, 2020 12:09 pm    Post subject: Reply with quote

suprafluid wrote:
The idea is good, but how can I acheive this? If I edit the Makefine manually in the "work" directory, it is overwritten (newly generated?) each time I emerge the package again.

You can run each emerge phases manually with ebuild command.
Code:
# ebuild /var/db/repos/gentoo/app-admin/webapp-config/webapp-config-1.55-r1.ebuild unpack

then you can make change to makefile and after that run
Code:
# ebuild /var/db/repos/gentoo/app-admin/webapp-config/webapp-config-1.55-r1.ebuild install

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PostPosted: Tue Jan 14, 2020 2:10 am    Post subject: Reply with quote

fedeliallalinea's suggestion works for a single pass. I wrote patch instead of edit because the persistent way to do this is to use a user patch, or a modified ebuild which applies a patch, to automatically make the necessary change as part of the src_prepare phase.
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PostPosted: Tue Jan 14, 2020 1:11 pm    Post subject: Reply with quote

Yes done. Got this now with the >/dev/null removed:

Code:

 ebuild /usr/portage/app-admin/webapp-config/webapp-config-1.55-r1.ebuild install
>>> Existing ${T}/environment for 'webapp-config-1.55-r1' will be sourced.
>>> Run 'clean' to start with a fresh environment.
>>> Checking webapp-config-1.55.tar.bz2's mtime...
>>> WORKDIR is up-to-date, keeping...
 * checking ebuild checksums ;-) ...                                                                                         [ ok ]
 * checking auxfile checksums ;-) ...                                                                                        [ ok ]
 * checking miscfile checksums ;-) ...                                                                                       [ ok ]
>>> It appears that 'pretend' has already executed for 'webapp-config-1.55-r1'; skipping.
>>> Remove '/tmp/portage/app-admin/webapp-config-1.55-r1/.pretended' to force pretend.
>>> It appears that 'setup' has already executed for 'webapp-config-1.55-r1'; skipping.
>>> Remove '/tmp/portage/app-admin/webapp-config-1.55-r1/.setuped' to force setup.
>>> It appears that 'unpack' has already executed for 'webapp-config-1.55-r1'; skipping.
>>> Remove '/tmp/portage/app-admin/webapp-config-1.55-r1/.unpacked' to force unpack.
>>> It appears that 'prepare' has already executed for 'webapp-config-1.55-r1'; skipping.
>>> Remove '/tmp/portage/app-admin/webapp-config-1.55-r1/.prepared' to force prepare.
>>> It appears that 'configure' has already executed for 'webapp-config-1.55-r1'; skipping.
>>> Remove '/tmp/portage/app-admin/webapp-config-1.55-r1/.configured' to force configure.
>>> Compiling source in /tmp/portage/app-admin/webapp-config-1.55-r1/work/webapp-config-1.55 ...
 * python2_7: running distutils-r1_run_phase distutils-r1_python_compile
 * DISTUTILS_USE_SETUPTOOLS value is probably incorrect
 *   value:    DISTUTILS_USE_SETUPTOOLS=bdepend (default?)
 *   expected: DISTUTILS_USE_SETUPTOOLS=no
python2.7 setup.py build
running build
running build_py
warning: build_py: byte-compiling is disabled, skipping.

running build_scripts
 * python3_6: running distutils-r1_run_phase distutils-r1_python_compile
python3.6 setup.py build
running build
running build_py
warning: build_py: byte-compiling is disabled, skipping.

running build_scripts
 * python3_6: running distutils-r1_run_phase python_compile_all
make -j2 -C doc/
make: Entering directory '/tmp/portage/app-admin/webapp-config-1.55-r1/work/webapp-config-1.55/doc'
MAN webapp-config.8
MAN webapp-config.5
xmlto: /tmp/portage/app-admin/webapp-config-1.55-r1/work/webapp-config-1.55/doc/webapp-config.5.xml does not validate (status 3)
xmlto: Fix document syntax or use --skip-validation option
I/O error : Attempt to load network entity http://www.oasis-open.org/docbook/xml/4.2/docbookx.dtd
/tmp/portage/app-admin/webapp-config-1.55-r1/work/webapp-config-1.55/doc/webapp-config.5.xml:3: warning: failed to load external entity "http://www.oasis-open.org/docbook/xml/4.2/docbookx.dtd"
 "http://www.oasis-open.org/docbook/xml/4.2/docbookx.dtd">
                                                          ^
I/O error : Attempt to load network entity http://www.oasis-open.org/docbook/xml/4.2/docbookx.dtd
warning: failed to load external entity "http://www.oasis-open.org/docbook/xml/4.2/docbookx.dtd"
validity error : Could not load the external subset "http://www.oasis-open.org/docbook/xml/4.2/docbookx.dtd"
Document /tmp/portage/app-admin/webapp-config-1.55-r1/work/webapp-config-1.55/doc/webapp-config.5.xml does not validate
xmlto: /tmp/portage/app-admin/webapp-config-1.55-r1/work/webapp-config-1.55/doc/webapp-config.8.xml does not validate (status 3)
xmlto: Fix document syntax or use --skip-validation option
I/O error : Attempt to load network entity http://www.oasis-open.org/docbook/xml/4.2/docbookx.dtd
/tmp/portage/app-admin/webapp-config-1.55-r1/work/webapp-config-1.55/doc/webapp-config.8.xml:3: warning: failed to load external entity "http://www.oasis-open.org/docbook/xml/4.2/docbookx.dtd"
 "http://www.oasis-open.org/docbook/xml/4.2/docbookx.dtd">
                                                          ^
I/O error : Attempt to load network entity http://www.oasis-open.org/docbook/xml/4.2/docbookx.dtd
warning: failed to load external entity "http://www.oasis-open.org/docbook/xml/4.2/docbookx.dtd"
validity error : Could not load the external subset "http://www.oasis-open.org/docbook/xml/4.2/docbookx.dtd"
Document /tmp/portage/app-admin/webapp-config-1.55-r1/work/webapp-config-1.55/doc/webapp-config.8.xml does not validate
make: *** [Makefile:36: webapp-config.5] Error 13
make: *** Waiting for unfinished jobs....
make: *** [Makefile:36: webapp-config.8] Error 13
make: Leaving directory '/tmp/portage/app-admin/webapp-config-1.55-r1/work/webapp-config-1.55/doc'
 * ERROR: app-admin/webapp-config-1.55-r1::gentoo failed (compile phase):
 *   emake failed
 *
 * If you need support, post the output of `emerge --info '=app-admin/webapp-config-1.55-r1::gentoo'`,
 * the complete build log and the output of `emerge -pqv '=app-admin/webapp-config-1.55-r1::gentoo'`.
 * The complete build log is located at '/tmp/portage/app-admin/webapp-config-1.55-r1/temp/build.log'.
 * The ebuild environment file is located at '/tmp/portage/app-admin/webapp-config-1.55-r1/temp/environment'.
 * Working directory: '/tmp/portage/app-admin/webapp-config-1.55-r1/work/webapp-config-1.55'
 * S: '/tmp/portage/app-admin/webapp-config-1.55-r1/work/webapp-config-1.55'

Getting http://www.oasis-open.org/docbook/xml/4.2/docbookx.dtd manually with wget succeeds...
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PostPosted: Tue Jan 14, 2020 1:32 pm    Post subject: Reply with quote

You installed app-text/docbook-xml-dtd:4.2?
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PostPosted: Tue Jan 14, 2020 1:37 pm    Post subject: Reply with quote

yes, app-text/docbook-xml-dtd-4.2-r3:4.2::gentoo is installed.
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PostPosted: Wed Jan 15, 2020 2:25 am    Post subject: Reply with quote

suprafluid wrote:
Getting http://www.oasis-open.org/docbook/xml/4.2/docbookx.dtd manually with wget succeeds...
Downloading from the Internet is not allowed inside the network sandbox. The invocation must run correctly without network access.
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PostPosted: Thu Jan 16, 2020 9:45 am    Post subject: Reply with quote

Sorry guys, I do not know what do check now, emerging app-admin/webapp-config sitll does not complete and I do not know how to kame this thing validate the xml "xmlto: /tmp/portage/app-admin/webapp-config-1.55-r1/work/webapp-config-1.55/doc/webapp-config.8.xml does not validate (status 3)"
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PostPosted: Fri Jan 17, 2020 2:26 am    Post subject: Reply with quote

You might be able to work around this if you instruct xmlto not to validate the file. However, it would be better to understand why your locally installed Docbook files are not sufficient for xmlto to validate offline. What is the output of equery check app-text/docbook-xml-dtd ; emerge --info app-text/xmlto?
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PostPosted: Fri Jan 17, 2020 8:02 am    Post subject: Reply with quote

equery check app-text/docbook-xml-dtd
Code:

* Checking app-text/docbook-xml-dtd-4.1.2-r7 ...
   45 out of 45 files passed

* Checking app-text/docbook-xml-dtd-4.2-r3 ...
   43 out of 43 files passed

* Checking app-text/docbook-xml-dtd-4.3-r2 ...
   44 out of 44 files passed

* Checking app-text/docbook-xml-dtd-4.4-r3 ...
   46 out of 46 files passed

* Checking app-text/docbook-xml-dtd-4.5-r2 ...
   46 out of 46 files passed

emerge --info app-text/xmlto
Code:

Portage 2.3.79 (python 3.6.9-final-0, default/linux/amd64/17.0/no-multilib/hardened, gcc-9.2.0, glibc-2.29-r7, 4.17.6 x86_64)
=================================================================
                         System Settings
=================================================================
System uname: Linux-4.17.6-x86_64-Intel-R-_Xeon-R-_CPU_E5-2630_v4_@_2.20GHz-with-gentoo-2.6
KiB Mem:     4025048 total,   2166924 free
KiB Swap:    8388604 total,   8386300 free
Timestamp of repository gentoo: Thu, 16 Jan 2020 09:30:01 +0000
Head commit of repository gentoo: 5d71472b29d9afd3e65ad6a0fa4f9b6f44866a56
sh bash 4.4_p23-r1
ld GNU ld (Gentoo 2.32 p2) 2.32.0
distcc 3.3.3 x86_64-pc-linux-gnu [disabled]
ccache version 3.7.6 [disabled]
app-shells/bash:          4.4_p23-r1::gentoo
dev-lang/perl:            5.30.1::gentoo
dev-lang/python:          2.7.17::gentoo, 3.6.9::gentoo, 3.7.5-r1::gentoo
dev-util/ccache:          3.7.6::gentoo
dev-util/cmake:           3.14.6::gentoo
dev-util/pkgconfig:       0.29.2::gentoo
sys-apps/baselayout:      2.6-r1::gentoo
sys-apps/openrc:          0.42.1::gentoo
sys-apps/sandbox:         2.13::gentoo
sys-devel/autoconf:       2.69-r4::gentoo
sys-devel/automake:       1.16.1-r1::gentoo
sys-devel/binutils:       2.32-r1::gentoo
sys-devel/gcc:            9.2.0-r2::gentoo
sys-devel/gcc-config:     2.1::gentoo
sys-devel/libtool:        2.4.6-r6::gentoo
sys-devel/make:           4.2.1-r4::gentoo
sys-kernel/linux-headers: 4.19::gentoo (virtual/os-headers)
sys-libs/glibc:           2.29-r7::gentoo
Repositories:

gentoo
    location: /usr/portage
    sync-type: rsync
    sync-uri: rsync://rsync.gentoo.org/gentoo-portage
    priority: -1000
    sync-rsync-extra-opts:
    sync-rsync-verify-jobs: 2
    sync-rsync-verify-metamanifest: yes
    sync-rsync-verify-max-age: 24

ACCEPT_KEYWORDS="amd64"
ACCEPT_LICENSE="*"
CBUILD="x86_64-pc-linux-gnu"
CFLAGS="-march=ivybridge -O2 -pipe"
CHOST="x86_64-pc-linux-gnu"
CONFIG_PROTECT="/etc /usr/share/gnupg/qualified.txt"
CONFIG_PROTECT_MASK="/etc/ca-certificates.conf /etc/env.d /etc/gconf /etc/gentoo-release /etc/php/apache2-php7.2/ext-active/ /etc/php/apache2-php7.3/ext-active/ /etc/php/cgi-php7.2/ext-active/ /etc/php/cgi-php7.3/ext-active/ /etc/php/cli-php7.2/ext-active/ /etc/php/cli-php7.3/ext-active/ /etc/revdep-rebuild /etc/sandbox.d /etc/terminfo"
CXXFLAGS="-march=ivybridge -O2 -pipe -std=c++11"
DISTDIR="/usr/portage/distfiles"
ENV_UNSET="DBUS_SESSION_BUS_ADDRESS DISPLAY GOBIN PERL5LIB PERL5OPT PERLPREFIX PERL_CORE PERL_MB_OPT PERL_MM_OPT XAUTHORITY XDG_CACHE_HOME XDG_CONFIG_HOME XDG_DATA_HOME XDG_RUNTIME_DIR"
FCFLAGS="-O2 -pipe"
FEATURES="assume-digests binpkg-docompress binpkg-dostrip binpkg-logs config-protect-if-modified distlocks ebuild-locks fixlafiles ipc-sandbox merge-sync multilib-strict network-sandbox news parallel-fetch pid-sandbox preserve-libs protect-owned sandbox sfperms strict unknown-features-warn unmerge-logs unmerge-orphans userfetch userpriv usersandbox usersync xattr"
FFLAGS="-O2 -pipe"
GENTOO_MIRRORS="http://distfiles.gentoo.org"
LANG="de_DE.utf8"
LDFLAGS="-Wl,-O1 -Wl,--as-needed"
MAKEOPTS="-j1"
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="/tmp/"
USE="(-frontbase) (-selinux) (-sybase-ct) acl amd64 apache2 authdaemond berkdb btree bzip2 calendar cdb cgi clamdtop cli compat crypt ctype curl cxx dovecot eai exif fileinfo filter ftp gd gdbm geoip hardened hash iconv imap intl ipv6 jpeg json libmysqlclient libtirpc maildir mysql mysqli ncurses nls nptl opcache openmp pam pcre pdo phar php pie png posix readline sasl seccomp session simplexml soap spell split-usr ssl ssp tokenizer tokyocabinet truetype unicode urandom vhosts xattr xml xmlreader xmlwriter xtpax zip zlib" ABI_X86="64" ADA_TARGET="gnat_2018" 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="karbon sheets words" COLLECTD_PLUGINS="df interface irq load memory rrdtool swap syslog" CPU_FLAGS_X86="mmx sse sse2" ELIBC="glibc" GPSD_PROTOCOLS="ashtech aivdm earthmate evermore fv18 garmin garmintxt gpsclock greis isync itrax mtk3301 nmea ntrip navcom oceanserver oldstyle oncore rtcm104v2 rtcm104v3 sirf skytraq superstar2 timing tsip tripmate tnt ublox ubx" INPUT_DEVICES="libinput keyboard mouse" KERNEL="linux" LCD_DEVICES="bayrad cfontz cfontz633 glk hd44780 lb216 lcdm001 mtxorb ncurses text" LIBREOFFICE_EXTENSIONS="presenter-console presenter-minimizer" NETBEANS_MODULES="apisupport cnd groovy gsf harness ide identity j2ee java mobility nb php profiler soa visualweb webcommon websvccommon xml" OFFICE_IMPLEMENTATION="libreoffice" PHP_TARGETS="php7-2" POSTGRES_TARGETS="postgres10 postgres11" PYTHON_SINGLE_TARGET="python3_6" PYTHON_TARGETS="python2_7 python3_6" RUBY_TARGETS="ruby24 ruby25" 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"
Unset:  CC, CPPFLAGS, CTARGET, CXX, EMERGE_DEFAULT_OPTS, INSTALL_MASK, LC_ALL, LINGUAS, PORTAGE_BINHOST, PORTAGE_BUNZIP2_COMMAND, PORTAGE_COMPRESS, PORTAGE_COMPRESS_FLAGS, PORTAGE_RSYNC_EXTRA_OPTS

=================================================================
                        Package Settings
=================================================================

app-text/xmlto-0.0.28-r1::gentoo was built with the following:
USE="-latex -text"



Neither emerge @world nor emerge @system changed anything...
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PostPosted: Mon Jan 20, 2020 9:29 am    Post subject: Reply with quote

i have encountered the similar error……
when i emerge @world will met this error, emerge wpa_supplicant get this error, [/code]too
[code]
Error: dev-lang/spideonkey-60.5.2_p0-r2
emake failed

if you need support, post the output of `emerge --info ` = dev-lang/spidermonkey-60.5.2_p0-r2::gentoo
the complete build log and the output of `emerge --info` = dev-lang/spidermonkey-60.5.2_p0-r2::gentoo
the complete build log is located at '/vat/tmp/portage/dev-lang/spidermonkey-60.5.2_p0-r2/temp/build.log'
The ebuild environment file is located at '/vat/tmp/portage/dev-lang/spidermonkey-60.5.2_p0-r2/temp/environment'
Working directory: '/vat/tmp/portage/dev-lang/spidermonkey-60.5.2_p0-r2/work/mozjs-60.5.2_p0-r2/jsobj'
S: '/var/tmp/portage/dev-lang/spidermonkey-60.5.2_p0-r2/work/mozjs-60.5.2_p0-r2'[/post]
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suprafluid
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PostPosted: Mon Jan 20, 2020 9:57 am    Post subject: Reply with quote

You get the same "xml does not validate " error?
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fedeliallalinea
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PostPosted: Mon Jan 20, 2020 12:01 pm    Post subject: Reply with quote

Freed you can post full build.log?
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Freed
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PostPosted: Mon Jan 20, 2020 2:18 pm    Post subject: Reply with quote

i doubt that i encouter the trouble not mentioned in install instruction probably because i use stage 4 not stage3 the install instruction used. when i update world or emerge some softwares such as wpa_supplicant the error about dev-lang/spidermonkey will appear. i determine to reinstall my gentoo with stage3 not stage4 to see if the error appear again.
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