Bug 567630 – sci-biology/embassy-emnu-1.05.650 : /.../environment: line 3143: emboss_src_configure: command not found

• Product: Gentoo Linux
• Status: RESOLVED FIXED

[Description Toralf Förster 2015-12-06 09:56:12 UTC]

 *   Applying portage/1.2.0 patch ...
 *   Applying sed/1.5.6 patch ...
 *   Applying as-needed/2.4.3 patch ...
>>> Source prepared.
>>> Configuring source in /var/tmp/portage/sci-biology/embassy-emnu-1.05.650/work/EMNU-1.05.650 ...
/var/tmp/portage/sci-biology/embassy-emnu-1.05.650/temp/environment: line 3143: emboss_src_configure: command not found
>>> Source configured.
>>> Compiling source in /var/tmp/portage/sci-biology/embassy-emnu-1.05.650/work/EMNU-1.05.650 ...
>>> Working in BUILD_DIR: "/var/tmp/portage/sci-biology/embassy-emnu-1.05.650/work/embassy-emnu-1.05.650_build"
/var/tmp/portage/sci-biology/embassy-emnu-1.05.650/temp/environment: line 713: pushd: /var/tmp/portage/sci-biology/embassy-emnu-1.05.650/work/embassy-emnu-1.05.650_build: No such file or directory
 * ERROR: sci-biology/embassy-emnu-1.05.650::gentoo failed (compile phase):


$ cat ./info.txt
  -----------------------------------------------------------------

  This is an stable amd64 chroot image (named amd64-desktop-stable_20151204-104956) at a hardened host acting as a tinderbox.

  -----------------------------------------------------------------

  Portage 2.2.20.1 (python 3.4.3-final-0, default/linux/amd64/13.0/desktop, gcc-4.9.3, glibc-2.21-r1, 4.1.7-hardened-r1 x86_64)
=================================================================
System uname: Linux-4.1.7-hardened-r1-x86_64-Intel-R-_Core-TM-_i7-3770_CPU_@_3.40GHz-with-gentoo-2.2
KiB Mem:    16164644 total,   1034464 free
KiB Swap:          0 total,         0 free
Timestamp of repository gentoo: Sat, 05 Dec 2015 22:37:12 +0000
sh bash 4.3_p39
ld GNU ld (Gentoo 2.25.1 p1.1) 2.25.1
app-shells/bash:          4.3_p39::gentoo
dev-java/java-config:     2.2.0::gentoo
dev-lang/perl:            5.20.2::gentoo
dev-lang/python:          2.7.10-r1::gentoo, 3.4.3::gentoo
dev-util/cmake:           3.3.1-r1::gentoo
dev-util/pkgconfig:       0.28-r2::gentoo
sys-apps/baselayout:      2.2::gentoo
sys-apps/openrc:          0.18.4::gentoo
sys-apps/sandbox:         2.6-r1::gentoo
sys-devel/autoconf:       2.13::gentoo, 2.69::gentoo
sys-devel/automake:       1.9.6-r4::gentoo, 1.10.3-r1::gentoo, 1.11.6-r1::gentoo, 1.13.4::gentoo, 1.14.1::gentoo, 1.15::gentoo
sys-devel/binutils:       2.25.1-r1::gentoo
sys-devel/gcc:            4.9.3::gentoo
sys-devel/gcc-config:     1.7.3::gentoo
sys-devel/libtool:        2.4.6::gentoo
sys-devel/make:           4.1-r1::gentoo
sys-kernel/linux-headers: 3.18::gentoo (virtual/os-headers)
sys-libs/glibc:           2.21-r1::gentoo
Repositories:

gentoo
    location: /usr/portage
    sync-type: rsync
    sync-uri: rsync://rsync.de.gentoo.org/gentoo-portage/
    priority: 1

local
    location: /usr/local/portage
    masters: gentoo
    priority: 2

ACCEPT_KEYWORDS="amd64"
ACCEPT_LICENSE="*"
CBUILD="x86_64-pc-linux-gnu"
CFLAGS="-march=native -O2 -pipe"
CHOST="x86_64-pc-linux-gnu"
CONFIG_PROTECT="/etc /etc/stunnel/stunnel.conf /usr/share/gnupg/qualified.txt /var/lib/hsqldb /var/yp/Makefile"
CONFIG_PROTECT_MASK="/etc/ca-certificates.conf /etc/dconf /etc/env.d /etc/fonts/fonts.conf /etc/gconf /etc/gentoo-release /etc/php/apache2-php5.5/ext-active/ /etc/php/apache2-php5.6/ext-active/ /etc/php/cgi-php5.5/ext-active/ /etc/php/cgi-php5.6/ext-active/ /etc/php/cli-php5.5/ext-active/ /etc/php/cli-php5.6/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 -pipe"
DISTDIR="/var/tmp/distfiles"
EMERGE_DEFAULT_OPTS="--deep --color=n --nospinner --tree --quiet-build --accept-properties=-interactive --accept-restrict=-fetch"
FCFLAGS="-O2 -pipe"
FEATURES="assume-digests binpkg-logs config-protect-if-modified distlocks ebuild-locks fixlafiles ipc-sandbox merge-sync network-sandbox news parallel-fetch 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://ftp.uni-erlangen.de/pub/mirrors/gentoo rsync://mirror.netcologne.de/gentoo/ ftp://sunsite.informatik.rwth-aachen.de/pub/Linux/gor.bytemark.co.uk/gentoo/ rsync://ftp.snt.utwente.nl/gentoo"
LANG="en_US.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"
PORTAGE_TMPDIR="/var/tmp"
USE="X a52 aac acl acpi alsa amd64 avx berkdb bluetooth branding btrfs bzip2 cairo cdda cdr cli consolekit cracklib crypt cups custom-cflags cxx dbus dri drmkms dts dvd dvdr eglfs emboss encode exif fam firefox flac fortran fpm gd gdbm gif glamor gnome-keyring gnutls gpm gtk gui hdf5 help iconv icu imap ipv6 javascript javaxml kerberos lapack lcms ldap libnotify mad mmx mmxext mng mod modules mp3 mp4 mpeg multilib multimedia mysql ncurses nls nptl nscd nss ogg opengl openmp pam pango pax_kernel pcre pcre16 pdf plasma png ppds qt3support qt4 readline scripts sdl seccomp session smartcard sockets spell sql sse sse2 sse4_1 ssl ssse3 startup-notification svg system-icu system-libvpx system-sqlite tcpd theora thinkpad tiff udev udisks ufed uml unicode upower usb video vorbis widgets wxwidgets x264 xattr xcb xml xmlreader xmp xslt xv xvid 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_GB" OFFICE_IMPLEMENTATION="libreoffice" PHP_TARGETS="php5-5" PYTHON_SINGLE_TARGET="python2_7" PYTHON_TARGETS="python2_7 python3_4" RUBY_TARGETS="ruby20 ruby21" USERLAND="GNU" VIDEO_CARDS="fbdev glint intel mach64 mga nouveau nv r128 radeon savage sis tdfx trident vesa via vmware 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, INSTALL_MASK, LC_ALL, PORTAGE_BUNZIP2_COMMAND, PORTAGE_COMPRESS, PORTAGE_COMPRESS_FLAGS, PORTAGE_RSYNC_EXTRA_OPTS, USE_PYTHON

[Comment 1 Toralf Förster 2015-12-06 09:56:14 UTC]

Created attachment 418646 [details]
emerge-history.txt

[Comment 2 Toralf Förster 2015-12-06 09:56:17 UTC]

Created attachment 418648 [details]
environment

[Comment 3 Toralf Förster 2015-12-06 09:56:19 UTC]

Created attachment 418650 [details]
sci-biology:embassy-emnu-1.05.650:20151206-012634.log

[Comment 4 Justin Lecher (RETIRED) 2015-12-07 08:23:03 UTC]

commit a386eb79419ed1b5aa18ad8fc15f676357d26b5d
Author: Justin Lecher <[e-mail]>
Date:   Mon Dec 7 09:18:37 2015 +0100

    sci-biology/embassy-emnu: Fix call to eclass function

    Gentoo-Bug: https://bugs.gentoo.org/show_bug.cgi?id=567630

    Package-Manager: portage-2.2.26
    Signed-off-by: Justin Lecher <[e-mail]>

    https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=a386eb79419ed1b5aa18ad8fc15f676357d26b5d

commit 71bd83d299c3ba0eb3947f3931ab20868fcb0291
Author: Justin Lecher <[e-mail]>
Date:   Mon Dec 7 09:12:04 2015 +0100

    eclass: Ignore generated manpages

    Signed-off-by: Justin Lecher <[e-mail]>

    https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=71bd83d299c3ba0eb3947f3931ab20868fcb0291

commit ca640bd52f96271d48643af641085ff1fc79aad1
Author: Justin Lecher <[e-mail]>
Date:   Mon Dec 7 09:10:52 2015 +0100

    emboss-r1.eclass: fix DOC strings

    Signed-off-by: Justin Lecher <[e-mail]>

    https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=ca640bd52f96271d48643af641085ff1fc79aad1