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Bug 530670 - sci-biology/plink-1.90_pre140514 USE=blas should DEPEND on virtual/cblas virtual/lapack
Summary: sci-biology/plink-1.90_pre140514 USE=blas should DEPEND on virtual/cblas virt...
Status: RESOLVED FIXED
Alias: None
Product: Gentoo Linux
Classification: Unclassified
Component: Current packages (show other bugs)
Hardware: All Linux
: Normal normal (vote)
Assignee: Gentoo Science Biology related packages
URL:
Whiteboard:
Keywords:
Depends on:
Blocks:
 
Reported: 2014-11-25 16:58 UTC by Toralf Förster
Modified: 2015-06-16 08:29 UTC (History)
2 users (show)

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


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Description Toralf Förster gentoo-dev 2014-11-25 16:58:20 UTC
uintptr_t, uint32_t, Chrom_info*, uint32_t)’:
plink_common.h:731:51: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 3 has type ‘long long unsigned int’ [-Wformat=]
 #define LOGPRINTF(...) sprintf(logbuf, __VA_ARGS__); logprintb();
                                                   ^
plink_data.c:3476:5: note: in expansion of macro ‘LOGPRINTF’
     LOGPRINTF("--set-me-missing: %" PRIu64 " error%s addressed.\n", mendel_erro
     ^
plink_data.c: In function ‘int32_t generate_dummy(char*, char*, uint32_t, uintptr_t, uintptr_t, double, double)’:
plink_data.c:9636:69: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 2 has type ‘long long unsigned int’ [-Wformat=]
     printf("Writing dummy .bed (%" PRIu64 " MB)... 0%%", ullii >> 20);
                                                                     ^
plink_data.c: In function ‘int32_t merge_datasets(char*, char*, char*, char*, char*, char*, char*, char*, char*, long long unsigned int, uint32_t, uint32_t, long long unsigned int, Chrom_info*)’:
plink_data.c:15194:138: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 2 has type ‘long long unsigned int’ [-Wformat=]
 e log file.\n", position_warning_ct - 3, (position_warning_ct == 4)? "" : "s");
                                                                              ^
In file included from plink_data.c:1:0:
plink_common.h:731:51: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 3 has type ‘long long unsigned int’ [-Wformat=]
 #define LOGPRINTF(...) sprintf(logbuf, __VA_ARGS__); logprintb();
                                                   ^
plink_data.c:15469:5: note: in expansion of macro ‘LOGPRINTF’
     LOGPRINTF("%" PRIu64 " overlapping variants, %" PRIu64 " genotyped in both 
     ^
plink_common.h:731:51: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 4 has type ‘long long unsigned int’ [-Wformat=]
 #define LOGPRINTF(...) sprintf(logbuf, __VA_ARGS__); logprintb();
                                                   ^
plink_data.c:15469:5: note: in expansion of macro ‘LOGPRINTF’
     LOGPRINTF("%" PRIu64 " overlapping variants, %" PRIu64 " genotyped in both 
     ^
plink_common.h:731:51: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 5 has type ‘long long unsigned int’ [-Wformat=]
 #define LOGPRINTF(...) sprintf(logbuf, __VA_ARGS__); logprintb();
                                                   ^
plink_data.c:15469:5: note: in expansion of macro ‘LOGPRINTF’
     LOGPRINTF("%" PRIu64 " overlapping variants, %" PRIu64 " genotyped in both 
     ^
In file included from plink_stats.h:4:0,
                 from plink_family.c:5:
plink_matrix.h:52:19: fatal error: cblas.h: No such file or directory
 #include <cblas.h>
                   ^
compilation terminated.
In file included from plink_stats.h:4:0,
                 from plink_filter.c:4:
plink_matrix.h:52:19: fatal error: cblas.h: No such file or directory
 #include <cblas.h>
                   ^
compilation terminated.
In file included from plink_glm.c:5:0:
plink_matrix.h:52:19: fatal error: cblas.h: No such file or directory
 #include <cblas.h>
                   ^
compilation terminated.
In file included from plink_lasso.c:4:0:
plink_matrix.h:52:19: fatal error: cblas.h: No such file or directory
 #include <cblas.h>
                   ^
compilation terminated.
In file included from plink_stats.h:4:0,
                 from plink_ld.c:5:
plink_matrix.h:52:19: fatal error: cblas.h: No such file or directory
 #include <cblas.h>
                   ^
compilation terminated.
In file included from plink_matrix.c:3:0:
plink_matrix.h:52:19: fatal error: cblas.h: No such file or directory
 #include <cblas.h>
                   ^
compilation terminated.
In file included from plink_stats.h:4:0,
                 from plink_stats.c:3:
plink_matrix.h:52:19: fatal error: cblas.h: No such file or directory
 #include <cblas.h>
                   ^
compilation terminated.
Makefile:54: recipe for target 'plink' failed
make: *** [plink] Error 1
 * ERROR: sci-biology/plink-1.90_pre140514::gentoo failed (compile phase):
 *   emake failed






This chroot image is located at a hardened amd64 system.

Portage 2.2.14 (python 2.7.8-final-0, default/linux/amd64/13.0, gcc-4.8.3, glibc-2.20, 3.17.4-hardened x86_64)
=================================================================
System uname: Linux-3.17.4-hardened-x86_64-Intel-R-_Core-TM-_i7-3770_CPU_@_3.40GHz-with-gentoo-2.2
KiB Mem:    16166892 total,   5978892 free
KiB Swap:   16777212 total,  16777212 free
Timestamp of tree: Mon, 24 Nov 2014 19:15:01 +0000
ld GNU ld (Gentoo 2.24 p1.4) 2.24
app-shells/bash:          4.3_p30-r1
dev-lang/perl:            5.20.1-r2
dev-lang/python:          2.7.8, 3.3.5-r1
dev-util/pkgconfig:       0.28-r2
sys-apps/baselayout:      2.2
sys-apps/openrc:          0.13.5
sys-apps/sandbox:         2.6-r1
sys-devel/autoconf:       2.69
sys-devel/automake:       1.14.1
sys-devel/binutils:       2.24-r3
sys-devel/gcc:            4.8.3
sys-devel/gcc-config:     1.8
sys-devel/libtool:        2.4.3-r2
sys-devel/make:           4.1-r1
sys-kernel/linux-headers: 3.17-r1 (virtual/os-headers)
sys-libs/glibc:           2.20
Repositories: gentoo
ACCEPT_KEYWORDS="amd64 ~amd64"
ACCEPT_LICENSE="*"
CBUILD="x86_64-pc-linux-gnu"
CFLAGS="-O2 -pipe"
CHOST="x86_64-pc-linux-gnu"
CONFIG_PROTECT="/etc"
CONFIG_PROTECT_MASK="/etc/ca-certificates.conf /etc/env.d /etc/gconf /etc/gentoo-release /etc/sandbox.d /etc/terminfo"
CXXFLAGS="-O2 -pipe"
DISTDIR="/usr/portage/distfiles"
EMERGE_DEFAULT_OPTS="--nospinner --tree --quiet-build --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"
FFLAGS="-O2 -pipe"
GENTOO_MIRRORS="http://mirror.leaseweb.com/gentoo/ http://ftp.uni-erlangen.de/pub/mirrors/gentoo http://ftp-stud.hs-esslingen.de/pub/Mirrors/gentoo/ http://gd.tuwien.ac.at/opsys/linux/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=""
SYNC="rsync://rsync.de.gentoo.org/gentoo-portage"
USE="acl amd64 berkdb bindist bzip2 cli cracklib crypt cxx dri fortran gdbm iconv ipv6 mbox mmx modules multilib ncurses nls nptl openmp pam pax_kernel 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_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, USE_PYTHON
Comment 1 Justin Lecher (RETIRED) gentoo-dev 2015-06-16 08:29:28 UTC
  09 Jun 2015; Justin Lecher <jlec@gentoo.org> metadata.xml,
  plink-1.90_pre140514.ebuild:
  Fix build problems related to missing blas, bug #530670; bug #550142