Bug 541134

Summary:	sci-biology/samtools-1.2 - make: *** No rule to make target '-L/usr/lib64', needed by 'test/merge/test_bam_translate'. Stop.
Product:	Gentoo Linux	Reporter:	Toralf Förster <toralf>
Component:	Current packages	Assignee:	Gentoo Science Biology related packages <sci-biology>
Status:	RESOLVED FIXED
Severity:	normal	CC:	jlec
Priority:	Normal
Version:	unspecified
Hardware:	All
OS:	Linux
Whiteboard:
Package list:		Runtime testing required:	---
Attachments:	emerge log

Description Toralf Förster gentoo-dev

2015-02-23 13:05:45 UTC

Created attachment 397312 [details]
emerge log

c -o cut_target.o cut_target.c
x86_64-pc-linux-gnu-gcc -march=native -O2 -pipe -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1 -I. -I/usr/include -c -o phase.o phase.c
x86_64-pc-linux-gnu-gcc -march=native -O2 -pipe -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1 -I. -I/usr/include -c -o bam2depth.o bam2depth.c
x86_64-pc-linux-gnu-gcc -march=native -O2 -pipe -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1 -I. -I/usr/include -c -o padding.o padding.c
x86_64-pc-linux-gnu-gcc -march=native -O2 -pipe -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1 -I. -I/usr/include -c -o bedcov.o bedcov.c
x86_64-pc-linux-gnu-gcc -march=native -O2 -pipe -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1 -I. -I/usr/include -c -o bamshuf.o bamshuf.c
x86_64-pc-linux-gnu-gcc -march=native -O2 -pipe -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1 -I. -I/usr/include -c -o faidx.o faidx.c
x86_64-pc-linux-gnu-gcc -march=native -O2 -pipe -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1 -I. -I/usr/include -c -o stats.o stats.c
x86_64-pc-linux-gnu-gcc -march=native -O2 -pipe -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1 -I. -I/usr/include -c -o stats_isize.o stats_isize.c
x86_64-pc-linux-gnu-gcc -march=native -O2 -pipe -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1 -I. -I/usr/include -c -o bam_flags.o bam_flags.c
x86_64-pc-linux-gnu-gcc -march=native -O2 -pipe -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1 -I. -I/usr/include -c -o bam_split.o bam_split.c
x86_64-pc-linux-gnu-gcc -march=native -O2 -pipe -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1 -I. -I/usr/include -c -o bam_tview.o bam_tview.c
x86_64-pc-linux-gnu-gcc -march=native -O2 -pipe -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1 -I. -I/usr/include -c -o bam_tview_curses.o bam_tview_curses.c
x86_64-pc-linux-gnu-gcc -march=native -O2 -pipe -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1 -I. -I/usr/include -c -o bam_tview_html.o bam_tview_html.c
x86_64-pc-linux-gnu-gcc -march=native -O2 -pipe -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1 -I. -I/usr/include -c -o bam_lpileup.o bam_lpileup.c
x86_64-pc-linux-gnu-gcc -march=native -O2 -pipe -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1 -I. -I/usr/include -fPIC -c -o bam_aux.o bam_aux.c
x86_64-pc-linux-gnu-gcc -march=native -O2 -pipe -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1 -I. -I/usr/include -fPIC -c -o bam.o bam.c
x86_64-pc-linux-gnu-gcc -march=native -O2 -pipe -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1 -I. -I/usr/include -fPIC -c -o bam_import.o bam_import.c
x86_64-pc-linux-gnu-gcc -march=native -O2 -pipe -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1 -I. -I/usr/include -fPIC -c -o sam.o sam.c
x86_64-pc-linux-gnu-gcc -march=native -O2 -pipe -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1 -I. -I/usr/include -fPIC -c -o sam_header.o sam_header.c
x86_64-pc-linux-gnu-gcc -march=native -O2 -pipe -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1 -I. -I/usr/include -fPIC -c -o bam_plbuf.o bam_plbuf.c
x86_64-pc-linux-gnu-ar -csru libbam.a bam_aux.o bam.o bam_import.o sam.o sam_header.o bam_plbuf.o
x86_64-pc-linux-gnu-gcc -Wl,-O1 -Wl,--as-needed  -shared -Wl,--soname,libbam.so.1.0 -o libbam.so.1.0 bam_aux.o bam.o bam_import.o sam.o sam_header.o bam_plbuf.o -L/usr/lib64 -lhts -lz
ln -sf libbam.so.1.0 libbam.so.0
ln -sf libbam.so.1.0 libbam.so
x86_64-pc-linux-gnu-gcc -pthread -Wl,-O1 -Wl,--as-needed  -o samtools bam_index.o bam_plcmd.o sam_view.o bam_cat.o bam_md.o bam_reheader.o bam_sort.o bedidx.o kprobaln.o bam_rmdup.o bam_rmdupse.o bam_mate.o bam_stat.o bam_color.o bamtk.o bam2bcf.o bam2bcf_indel.o errmod.o sample.o cut_target.o phase.o bam2depth.o padding.o bedcov.o bamshuf.o faidx.o stats.o stats_isize.o bam_flags.o bam_split.o bam_tview.o bam_tview_curses.o bam_tview_html.o bam_lpileup.o libbam.so -L/usr/lib64 -lhts  -L/usr/lib64 -lncurses -lm -lz
x86_64-pc-linux-gnu-gcc -march=native -O2 -pipe -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1 -I. -I/usr/include -c -o misc/ace2sam.o misc/ace2sam.c
x86_64-pc-linux-gnu-gcc -Wl,-O1 -Wl,--as-needed  -o misc/ace2sam misc/ace2sam.o  -lz
x86_64-pc-linux-gnu-gcc -march=native -O2 -pipe -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1 -I. -I/usr/include -DMAQ_LONGREADS -c -o misc/maq2sam-long.o misc/maq2sam.c
x86_64-pc-linux-gnu-gcc -Wl,-O1 -Wl,--as-needed  -o misc/maq2sam-long misc/maq2sam-long.o  -lz
x86_64-pc-linux-gnu-gcc -march=native -O2 -pipe -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1 -I. -I/usr/include -c -o misc/maq2sam-short.o misc/maq2sam.c
x86_64-pc-linux-gnu-gcc -Wl,-O1 -Wl,--as-needed  -o misc/maq2sam-short misc/maq2sam-short.o  -lz
x86_64-pc-linux-gnu-gcc -march=native -O2 -pipe -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1 -I. -I/usr/include -c -o misc/md5fa.o misc/md5fa.c
x86_64-pc-linux-gnu-gcc -march=native -O2 -pipe -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1 -I. -I/usr/include -c -o misc/md5.o misc/md5.c
x86_64-pc-linux-gnu-gcc -Wl,-O1 -Wl,--as-needed  -o misc/md5fa misc/md5fa.o misc/md5.o  -lz
x86_64-pc-linux-gnu-gcc -march=native -O2 -pipe -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1 -I. -I/usr/include -DMD5SUM_MAIN -c -o misc/md5sum-lite.o misc/md5.c
x86_64-pc-linux-gnu-gcc -Wl,-O1 -Wl,--as-needed  -o misc/md5sum-lite misc/md5sum-lite.o 
x86_64-pc-linux-gnu-gcc -march=native -O2 -pipe -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1 -I. -I/usr/include -c -o misc/wgsim.o misc/wgsim.c
x86_64-pc-linux-gnu-gcc -Wl,-O1 -Wl,--as-needed  -o misc/wgsim misc/wgsim.o  -lm -lz
x86_64-pc-linux-gnu-gcc -march=native -O2 -pipe -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1 -I. -I/usr/include -c -o test/merge/test_bam_translate.o test/merge/test_bam_translate.c
x86_64-pc-linux-gnu-gcc -march=native -O2 -pipe -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1 -I. -I/usr/include -c -o test/test.o test/test.c
make: *** No rule to make target '-L/usr/lib64', needed by 'test/merge/test_bam_translate'.  Stop.
 * ERROR: sci-biology/samtools-1.2::gentoo failed (compile phase):
 *   emake failed
 * 
 * If you need support, post the output of `emerge --info '=sci-biology/samtools-1.2::gentoo'`,
 * the complete build log and the output of `emerge -pqv '=sci-biology/samtools-1.2::gentoo'`.
 * The complete build log is located at '/var/log/portage/sci-biology:samtools-1.2:20150223-065420.log'.
 * For convenience, a symlink to the build log is located at '/var/tmp/portage/sci-biology/samtools-1.2/temp/build.log'.
 * The ebuild environment file is located at '/var/tmp/portage/sci-biology/samtools-1.2/temp/environment'.
 * Working directory: '/var/tmp/portage/sci-biology/samtools-1.2/work/samtools-1.2'
 * S: '/var/tmp/portage/sci-biology/samtools-1.2/work/samtools-1.2'


        This is a built bot  hardened-unstable  chroot named amd64-hardened-unstable at a hardened stable host.

        
Portage 2.2.14 (python 2.7.9-final-0, hardened/linux/amd64, gcc-4.9.2, glibc-2.19-r1, 3.18.7-hardened x86_64)
=================================================================
                         System Settings
=================================================================
System uname: Linux-3.18.7-hardened-x86_64-Intel-R-_Core-TM-_i7-3770_CPU_@_3.40GHz-with-gentoo-2.2
KiB Mem:    16164808 total,    687092 free
KiB Swap:   16777212 total,  16753724 free
Timestamp of tree: Mon, 23 Feb 2015 04:00:01 +0000
ld GNU ld (Gentoo 2.24 p1.4) 2.24
app-shells/bash:          4.3_p33-r1
dev-lang/perl:            5.20.2
dev-lang/python:          2.7.9-r2, 3.3.5-r1
sys-apps/baselayout:      2.2
sys-apps/openrc:          0.12.4
sys-apps/sandbox:         2.6-r1
sys-devel/autoconf:       2.13, 2.69
sys-devel/automake:       1.9.6-r4, 1.10.3-r1, 1.11.6-r1, 1.13.4
sys-devel/binutils:       2.24-r3
sys-devel/gcc:            4.8.3, 4.9.2
sys-devel/gcc-config:     1.7.3
sys-devel/libtool:        2.4.2-r1
sys-devel/make:           4.0-r1
sys-kernel/linux-headers: 3.16 (virtual/os-headers)
sys-libs/glibc:           2.19-r1
Repositories: gentoo
ACCEPT_KEYWORDS="amd64 ~amd64"
ACCEPT_LICENSE="*"
CBUILD="x86_64-pc-linux-gnu"
CFLAGS="-march=native -O2 -pipe"
CHOST="x86_64-pc-linux-gnu"
CONFIG_PROTECT="/etc /usr/share/config /var/spool/torque"
CONFIG_PROTECT_MASK="/etc/ca-certificates.conf /etc/env.d /etc/fonts/fonts.conf /etc/gconf /etc/gentoo-release /etc/sandbox.d /etc/terminfo"
CXXFLAGS="-march=native -O2 -pipe"
DISTDIR="/usr/portage/distfiles"
EMERGE_DEFAULT_OPTS="--nospinner --tree --quiet-build --quiet  --deep --jobs 1"
FCFLAGS="-O2 -pipe"
FEATURES="assume-digests binpkg-logs config-protect-if-modified distlocks ebuild-locks fixlafiles merge-sync 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"
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"
PORTDIR="/usr/portage"
PORTDIR_OVERLAY=""
USE="X acl aes-ni alsa amd64 apache2 avx avx2 berkdb bzip2 cli corefonts cracklib crypt cups cxx dbus dnssec dri drmkms dvd ecc extraengine ffmpeg fontconfig fortran fpm gdbm gtk gudev gui hardened iconv isag jpeg justify libav libvirtd logrotate macvtap mbox minizip mmx modules multilib mysql ncurses nls nptl ogg opengl openmp pam pax_kernel pcre plasma png policykit qemu qt3support qt4 readline session spice sse sse2 sse4 sse4_1 sse4_2 ssh-askpass ssl ssse3 tcpd theora thinkpad threads tk tls truetype uml unicode urandom usb usbredir uxa v4l v4l2 video vorbis xa xattr xmp xscreensaver xtpax xvfb xvmc zenmap 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" OFFICE_IMPLEMENTATION="libreoffice" PHP_TARGETS="php5-5" PYTHON_ SINGLE_TARGET="python2_7" PYTHON_TARGETS="python2_7 python3_3" 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, INSTALL_MASK, LC_ALL, PORTAGE_BUNZIP2_COMMAND, PORTAGE_COMPRESS, PORTAGE_COMPRESS_FLAGS, PORTAGE_RSYNC_EXTRA_OPTS, SYNC, USE_PYTHON

Comment 1 Justin Lecher (RETIRED) gentoo-dev

2015-02-28 10:52:50 UTC

+  28 Feb 2015; Justin Lecher <jlec@gentoo.org>
+  files/samtools-1.2-buildsystem.patch, samtools-1.2.ebuild:
+  Fix depend rules in make which break due to unbundling of htslib, #541134; use
+  LD_LIBRARY_PATH druing tests
+