Bug 513420 – sci-biology/rmblast-1.2-r1 fails to install (missing cpio depend)

• Product: Gentoo Linux
• Status: RESOLVED FIXED

[Description Patrick Lauer 2014-06-16 03:32:13 UTC]

>>> Install rmblast-1.2-r1 into /var/tmp/portage/sci-biology/rmblast-1.2-r1/image/ category sci-biology
make -j4 DESTDIR=/var/tmp/portage/sci-biology/rmblast-1.2-r1/image/ install 
if test -f /var/tmp/portage/sci-biology/rmblast-1.2-r1/work/rmblast-1.2-ncbi-blast-2.2.23+-src/c++/GCC482-ReleaseMTDLL64/bin/gbench; then \
    make -j --jobserver-fds=3,4 install-gbench; \
else \
    make -j --jobserver-fds=3,4 install-toolkit; \
fi
make[1]: Entering directory '/var/tmp/portage/sci-biology/rmblast-1.2-r1/work/rmblast-1.2-ncbi-blast-2.2.23+-src/c++'
rm -rf /var/tmp/portage/sci-biology/rmblast-1.2-r1/image//opt/rmblast/include/ncbi-tools++
/usr/bin/install -c -d /var/tmp/portage/sci-biology/rmblast-1.2-r1/image//opt/rmblast/bin /var/tmp/portage/sci-biology/rmblast-1.2-r1/image//opt/rmblast/lib /var/tmp/portage/sci-biology/rmblast-1.2-r1/image//opt/rmblast/include/ncbi-tools++
/usr/bin/install -c /var/tmp/portage/sci-biology/rmblast-1.2-r1/work/rmblast-1.2-ncbi-blast-2.2.23+-src/c++/GCC482-ReleaseMTDLL64/bin/* /var/tmp/portage/sci-biology/rmblast-1.2-r1/image//opt/rmblast/bin
/usr/bin/install -c -m 644 /var/tmp/portage/sci-biology/rmblast-1.2-r1/work/rmblast-1.2-ncbi-blast-2.2.23+-src/c++/GCC482-ReleaseMTDLL64/lib/* /var/tmp/portage/sci-biology/rmblast-1.2-r1/image//opt/rmblast/lib
cd /var/tmp/portage/sci-biology/rmblast-1.2-r1/work/rmblast-1.2-ncbi-blast-2.2.23+-src/c++/include && find * -name CVS -prune -o -print |\
            cpio -pd /var/tmp/portage/sci-biology/rmblast-1.2-r1/image//opt/rmblast/include/ncbi-tools++
/bin/sh: line 1: cpio: command not found
Makefile:38: recipe for target 'install-toolkit' failed
make[1]: *** [install-toolkit] Error 127
make[1]: Leaving directory '/var/tmp/portage/sci-biology/rmblast-1.2-r1/work/rmblast-1.2-ncbi-blast-2.2.23+-src/c++'
Makefile:52: recipe for target 'install' failed
make: *** [install] Error 2
 * ERROR: sci-biology/rmblast-1.2-r1::gentoo failed (install phase):
 *   emake failed
 * 
 * If you need support, post the output of `emerge --info '=sci-biology/rmblast-1.2-r1::gentoo'`,
 * the complete build log and the output of `emerge -pqv '=sci-biology/rmblast-1.2-r1::gentoo'`.
 * The complete build log is located at '/var/log/portage/build/sci-biology/rmblast-1.2-r1:20140615-090200.log'.
 * For convenience, a symlink to the build log is located at '/var/tmp/portage/sci-biology/rmblast-1.2-r1/temp/build.log'.
 * The ebuild environment file is located at '/var/tmp/portage/sci-biology/rmblast-1.2-r1/temp/environment'.
 * Working directory: '/var/tmp/portage/sci-biology/rmblast-1.2-r1/work/rmblast-1.2-ncbi-blast-2.2.23+-src/c++'
 * S: '/var/tmp/portage/sci-biology/rmblast-1.2-r1/work/rmblast-1.2-ncbi-blast-2.2.23+-src/c++'
 * QA Notice: command not found:
 * 
 *      /bin/sh: line 1: cpio: command not found


Portage 2.2.10 (default/linux/amd64/13.0, gcc-4.8.2, glibc-2.19, 3.15.0-gentoo x86_64)
=================================================================
System uname: Linux-3.15.0-gentoo-x86_64-AMD_Phenom-tm-_II_X4_965_Processor-with-gentoo-2.2
KiB Mem:     7919000 total,    700168 free
KiB Swap:   25165812 total,  24791124 free
Timestamp of tree: Unknown
ld GNU ld (Gentoo 2.24 p1.4) 2.24
app-shells/bash:          4.2_p47
dev-lang/python:          2.7.6-r1, 3.2.5-r4, 3.3.5, 3.4.0
dev-util/cmake:           2.8.12.2-r1
dev-util/pkgconfig:       0.28-r1
sys-apps/baselayout:      2.2
sys-apps/openrc:          0.12.4
sys-apps/sandbox:         2.6-r1
sys-devel/autoconf:       2.69
sys-devel/automake:       1.9.6-r3, 1.14.1
sys-devel/binutils:       2.24-r3
sys-devel/gcc:            4.8.2
sys-devel/gcc-config:     1.8
sys-devel/libtool:        2.4.2-r1
sys-devel/make:           4.0-r1
sys-kernel/linux-headers: 3.14 (virtual/os-headers)
sys-libs/glibc:           2.19
Repositories: gentoo
ACCEPT_KEYWORDS="amd64 ~amd64"
ACCEPT_LICENSE="* -@EULA"
CBUILD="x86_64-pc-linux-gnu"
CFLAGS="-O2 -pipe"
CHOST="x86_64-pc-linux-gnu"
CONFIG_PROTECT="/etc /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/php/apache2-php5.5/ext-active/ /etc/php/cgi-php5.5/ext-active/ /etc/php/cli-php5.5/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="-O2 -pipe"
DISTDIR="/usr/portage/distfiles"
FCFLAGS="-O2 -pipe"
FEATURES="assume-digests binpkg-logs buildpkg config-protect-if-modified distlocks ebuild-locks fixlafiles merge-sync news parallel-fetch preserve-libs protect-owned sandbox sfperms split-log strict unknown-features-warn unmerge-logs unmerge-orphans userfetch userpriv usersandbox usersync"
FFLAGS="-O2 -pipe"
GENTOO_MIRRORS="http://mirrors.163.com/gentoo/ ftp://ftp.kaist.ac.kr/gentoo/ http://ftp.kaist.ac.kr/pub/gentoo/ http://gentoo.mirrors.hoobly.com/ http://gentoo.mirrors.easynews.com/linux/gentoo/"
LANG="en_US.utf8"
LDFLAGS="-Wl,-O1 -Wl,--as-needed"
MAKEOPTS="-j4"
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"
PORTDIR="/usr/portage"
PORTDIR_OVERLAY=""
USE="acl amd64 berkdb bindist bzip2 cli cracklib crypt cxx dri fortran gdbm iconv ipv6 mmx modules multilib ncurses nls nptl openmp pam pcre readline session sse sse2 ssl tcpd unicode 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" 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" OFFICE_IMPLEMENTATION="libreoffice" PHP_TARGETS="php5-5" PYTHON_SINGLE_TARGET="python2_7" PYTHON_TARGETS="python2_7 python3_2 pypy python3_3 python3_4" RUBY_TARGETS="ruby19 ruby20" 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:  CPPFLAGS, CTARGET, EMERGE_DEFAULT_OPTS, INSTALL_MASK, LC_ALL, PORTAGE_BUNZIP2_COMMAND, PORTAGE_COMPRESS, PORTAGE_COMPRESS_FLAGS, PORTAGE_RSYNC_EXTRA_OPTS, SYNC, USE_PYTHON

[Comment 1 Justin Lecher (RETIRED) 2015-06-16 08:38:48 UTC]

+  16 Jun 2015; Justin Lecher <[e-mail]> -rmblast-1.2.ebuild,
+  rmblast-1.2-r1.ebuild:
+  Add missing dependency on cpio, bug #513420
+