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Bug 665760

Summary: dev-lang/R-3.5.1 - Error: segfault from C stack overflow
Product: Gentoo Linux Reporter: Martin Mokrejš <mmokrejs>
Component: Current packagesAssignee: Gentoo Science Mathematics related packages <sci-mathematics>
Status: UNCONFIRMED ---    
Severity: normal CC: jstein
Priority: Normal    
Version: unspecified   
Hardware: All   
OS: Linux   
Whiteboard:
Package list:
Runtime testing required: ---
Attachments: build.log

Description Martin Mokrejš 2018-09-12 08:32:16 UTC
Hi,
 on a Gentoo-Prefix host I cannot upgrade from 3.4.1 to 3.5.1.


x86_64-pc-linux-gnu-gcc -shared -L/apps/gentoo/var/tmp/portage/dev-lang/R-3.5.1/work/R-3.5.1/lib -Wl,--as-needed -Wl,-rpath=/apps/gentoo/usr/lib64/R/lib -o survival.so agexact.o agfit4.o agfit5.o agmart.o agmart2.o agmart3.o agscore.o agsurv3.o agsurv4.o agsurv5.o chinv2.o chinv3.o cholesky2.o cholesky3.o cholesky5.o chsolve2.o chsolve3.o chsolve5.o concordance1.o cox_Rcallback.o coxcount1.o coxdetail.o coxexact.o coxfit5.o coxfit6.o coxmart.o coxmart2.o coxph_wtest.o coxsafe.o coxscho.o coxscore.o dmatrix.o doloop.o finegray.o gchol.o init.o pyears1.o pyears2.o pyears3b.o pystep.o survConcordance.o survdiff2.o survfit4.o survfitci.o survpenal.o survreg6.o survreg7.o survregc1.o survregc2.o survsplit.o tmerge.o -L/apps/gentoo/var/tmp/portage/dev-lang/R-3.5.1/work/R-3.5.1/lib -lR
make[3]: Leaving directory '/apps/gentoo/var/tmp/portage/dev-lang/R-3.5.1/temp/RtmpiHkbj3/R.INSTALL16c1bac8ba1/survival/src'
installing to /apps/gentoo/var/tmp/portage/dev-lang/R-3.5.1/work/R-3.5.1/library/survival/libs
** R
** data
*** moving datasets to lazyload DB
** inst
** byte-compile and prepare package for lazy loading
Error: segfault from C stack overflow
* removing '/apps/gentoo/var/tmp/portage/dev-lang/R-3.5.1/work/R-3.5.1/library/survival'
make[2]: *** [Makefile:53: survival.ts] Error 1
make[2]: Leaving directory '/apps/gentoo/var/tmp/portage/dev-lang/R-3.5.1/work/R-3.5.1/src/library/Recommended'
make[1]: *** [Makefile:39: recommended-packages] Error 2
make[1]: Leaving directory '/apps/gentoo/var/tmp/portage/dev-lang/R-3.5.1/work/R-3.5.1/src/library/Recommended'
make: *** [Makefile:77: stamp-recommended] Error 2
 * ERROR: dev-lang/R-3.5.1::gentoo failed (compile phase):
 *   emake failed
 * 
 * If you need support, post the output of `emerge --info '=dev-lang/R-3.5.1::gentoo'`,
 * the complete build log and the output of `emerge -pqv '=dev-lang/R-3.5.1::gentoo'`.
 * The complete build log is located at '/apps/gentoo/var/tmp/portage/dev-lang/R-3.5.1/temp/build.log'.
 * The ebuild environment file is located at '/apps/gentoo/var/tmp/portage/dev-lang/R-3.5.1/temp/environment'.
 * Working directory: '/apps/gentoo/var/tmp/portage/dev-lang/R-3.5.1/work/R-3.5.1'
 * S: '/apps/gentoo/var/tmp/portage/dev-lang/R-3.5.1/work/R-3.5.1'

 

$ emerge --info '=dev-lang/R-3.5.1::gentoo'
Portage 2.3.49 (python 2.7.15-final-0, default/linux/amd64/17.0/no-multilib/prefix/kernel-3.2+, gcc-8.2.0, glibc-2.25-r11, 2.6.32-696.20.1.el6.x86_64 x86_64)
=================================================================
                         System Settings
=================================================================
System uname: Linux-2.6.32-696.20.1.el6.x86_64-x86_64-Intel-R-_Xeon-R-_CPU_E5-2695_v3_@_2.30GHz-with-centos-6.9-Final
KiB Mem:   132048928 total,  24715232 free
KiB Swap:    2097148 total,   1857348 free
Timestamp of repository gentoo: Mon, 10 Sep 2018 16:30:01 +0000
Head commit of repository gentoo: 1742ee0f7f6457446116f4d60677e6d3ff2b2fd6
sh bash 4.4_p23
ld GNU ld (Gentoo 2.30 p2) 2.30.0
app-shells/bash:          4.4_p23::gentoo
dev-java/java-config:     2.2.0-r4::gentoo
dev-lang/perl:            5.26.2::gentoo
dev-lang/python:          2.7.15::gentoo, 3.4.8-r1::gentoo, 3.5.5-r1::gentoo, 3.6.6::gentoo, 3.7.0::gentoo
dev-util/cmake:           3.12.2::gentoo
dev-util/pkgconfig:       0.29.2::gentoo
sys-apps/baselayout:      2.6-r1::gentoo
sys-apps/sandbox:         2.13::gentoo
sys-devel/autoconf:       2.13::gentoo, 2.69-r4::gentoo
sys-devel/automake:       1.14.1-r1::gentoo, 1.15.1-r2::gentoo, 1.16.1-r1::gentoo
sys-devel/binutils:       2.29.1-r1::gentoo, 2.30-r2::gentoo, 2.31.1::gentoo
sys-devel/gcc:            3.4.6-r2::gentoo, 4.1.2::gentoo, 4.2.4-r1::gentoo, 4.4.7::gentoo, 4.9.4::gentoo, 5.4.0-r4::gentoo, 7.3.0-r3::gentoo, 8.2.0-r2::gentoo
sys-devel/gcc-config:     2.0::gentoo
sys-devel/libtool:        2.4.6-r5::gentoo
sys-devel/make:           4.2.1-r4::gentoo
sys-kernel/linux-headers: 4.17::gentoo (virtual/os-headers)
sys-libs/glibc:           2.25-r11::gentoo
Repositories:

gentoo
    location: /apps/gentoo/usr/portage
    sync-type: rsync
    sync-uri: rsync://rsync.gentoo.org/gentoo-portage
    priority: -1000
    sync-rsync-verify-jobs: 1
    sync-rsync-verify-metamanifest: yes
    sync-rsync-extra-opts: 
    sync-rsync-verify-max-age: 24

local
    location: /apps/gentoo/usr/local/portage
    masters: gentoo
    priority: 0

haskell
    location: /apps/gentoo/var/lib/layman/haskell
    masters: gentoo
    priority: 50

science
    location: /apps/gentoo/var/lib/layman/science
    masters: gentoo
    priority: 50

ACCEPT_KEYWORDS="amd64 ~amd64"
ACCEPT_LICENSE="* -@EULA dlj-1.1 sun-bcla-java-vm Oracle-BCLA-JavaSE IBM-J1.6 skype-eula Nero-EULA-US AdobeFlash-10.3 skype-4.0.0.7-copyright AdobeFlash-11.x Intel-SDP OPERA-2014"
CBUILD="x86_64-pc-linux-gnu"
CFLAGS="-O2 -pipe -O2 -pipe -march=native -ftree-vectorize"
CHOST="x86_64-pc-linux-gnu"
CONFIG_PROTECT="/etc /usr/share/gnupg/qualified.txt /usr/share/maven-bin-3.3/conf"
CONFIG_PROTECT_MASK="/apps/gentoo/etc/gentoo-release /etc/ca-certificates.conf /etc/dconf /etc/env.d /etc/fonts/fonts.conf /etc/gconf /etc/revdep-rebuild /etc/sandbox.d /etc/terminfo"
CXXFLAGS="-O2 -pipe -O2 -pipe -march=native -ftree-vectorize"
DISTDIR="/apps/gentoo/usr/portage/distfiles"
ENV_UNSET="DBUS_SESSION_BUS_ADDRESS DISPLAY 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-logs config-protect-if-modified distlocks ebuild-locks fixlafiles force-prefix merge-sync multilib-strict news nostrip parallel-fetch preserve-libs protect-owned sfperms splitdebug strict unknown-features-warn unmerge-logs unmerge-orphans unprivileged"
FFLAGS="-O2 -pipe"
GENTOO_MIRRORS="http://ftp.fi.muni.cz/pub/linux/gentoo/ http://gentoo.mirror.web4u.cz/ rsync://gentoo.mirror.dkm.cz/gentoo/ ftp://gentoo.mirror.web4u.cz/"
LDFLAGS="-Wl,--as-needed"
LINGUAS="en_US en_GB en cs"
MAKEOPTS="-j4"
PKGDIR="/apps/gentoo/usr/portage/packages"
PORTAGE_CONFIGROOT="/apps/gentoo/"
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="/apps/gentoo/var/tmp"
USE="X alsa amd64 apache apache2 avx avx2 berkdb boost bzip2 cairo cgi cli coin cracklib crypt cryptlib cxx dbus device-mapper dhcp dri emboss encode fax fbcon ffmpeg fontconfig fortran gbm gd gdbm gimp glpk gnutls gtk hal hwdb iconv imaging innodb ithreads java javafx javascript jce jpeg jpg js jscript keymap ladspa lapack lcms libnotify libtirpc lm_sensors mad mmx modules mpi mpich2 mysql ncurses nfs nls nptl nptlonly nscd objc openmp openssl pcre pdf perl php png polkit postscript ppds pppd prefix python qt3support readline resolvconf seccomp server session slideshow sndfile sparsehash sqlite sse sse2 sse3 sse4_1 sse4_2 ssl ssse3 static-libs suexec svg syslog tcl tcpd threads tiff tk truetype unicode usb v4l v4l2 vim-syntax vnc wavpack wifi x11 xcb xml xorg xrandr xv xvid xvmc 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="karbon plan sheets stage words" COLLECTD_PLUGINS="df interface irq load memory rrdtool swap syslog" CPU_FLAGS_X86="avx avx2 fma3 mmx mmxext popcnt sse sse2 sse3 sse4_1 sse4_2 ssse3" ELIBC="glibc" GPSD_PROTOCOLS="ashtech aivdm earthmate evermore fv18 garmin garmintxt gpsclock 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" OFFICE_IMPLEMENTATION="libreoffice" PHP_TARGETS="php5-6 php7-0" POSTGRES_TARGETS="postgres9_5 postgres10" PYTHON_SINGLE_TARGET="python2_7" PYTHON_TARGETS="python2_7 python3_5 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, LANG, LC_ALL, PORTAGE_BINHOST, PORTAGE_BUNZIP2_COMMAND, PORTAGE_COMPRESS, PORTAGE_COMPRESS_FLAGS, PORTAGE_RSYNC_EXTRA_OPTS
Comment 1 Martin Mokrejš 2018-09-12 08:33:20 UTC
Created attachment 546692 [details]
build.log