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Bug 353545 - >=dev-lang/R-3.0.1-r1 fails tests
Summary: >=dev-lang/R-3.0.1-r1 fails tests
Alias: None
Product: Gentoo Linux
Classification: Unclassified
Component: Current packages (show other bugs)
Hardware: All Linux
: High normal with 1 vote (vote)
Assignee: Gentoo Science Mathematics related packages
: 376063 460478 466760 (view as bug list)
Depends on: 348843
  Show dependency tree
Reported: 2011-02-02 19:18 UTC by Theo Chatzimichos (RETIRED)
Modified: 2021-08-17 23:43 UTC (History)
10 users (show)

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

build.log (build.log,281.78 KB, text/plain)
2011-02-02 19:19 UTC, Theo Chatzimichos (RETIRED)

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Description Theo Chatzimichos (RETIRED) archtester Gentoo Infrastructure gentoo-dev Security 2011-02-02 19:18:46 UTC
Portage 2.2.0_alpha19 (default/linux/amd64/10.0/desktop/kde, gcc-4.5.2, glibc-2.12.2-r0, 2.6.37-gentoo x86_64)
                        System Settings
System uname: Linux-2.6.37-gentoo-x86_64-Intel-R-_Core-TM-2_Quad_CPU_Q6600_@_2.40GHz-with-gentoo-2.0.1
Timestamp of tree: Unknown
distcc 3.1 x86_64-pc-linux-gnu [disabled]
app-shells/bash:     4.1_p9
dev-java/java-config: 2.1.11-r3
dev-lang/python:     2.7.1, 3.1.3
dev-util/cmake:      2.8.3-r1
sys-apps/baselayout: 2.0.1-r1
sys-apps/openrc:     0.7.0
sys-apps/sandbox:    2.4
sys-devel/autoconf:  2.13, 2.68
sys-devel/automake:  1.9.6-r3, 1.10.3, 1.11.1
sys-devel/binutils:  2.21
sys-devel/gcc:       4.5.2
sys-devel/gcc-config: 1.4.1
sys-devel/libtool:   2.4-r1
sys-devel/make:      3.82
virtual/os-headers: (sys-kernel/linux-headers)
Repositories: gentoo multimedia kde qting-edge linuxteamteilar
ACCEPT_KEYWORDS="amd64 ~amd64"
CFLAGS="-march=core2 -O2 -pipe -ggdb"
CONFIG_PROTECT="/etc /usr/share/config /usr/share/gnupg/qualified.txt /var/lib/hsqldb"
CONFIG_PROTECT_MASK="/etc/ca-certificates.conf /etc/env.d /etc/env.d/java/ /etc/fonts/fonts.conf /etc/gconf /etc/gentoo-release /etc/php/apache2-php5.3/ext-active/ /etc/php/cgi-php5.3/ext-active/ /etc/php/cli-php5.3/ext-active/ /etc/revdep-rebuild /etc/sandbox.d /etc/splash /etc/terminfo /etc/texmf/language.dat.d /etc/texmf/language.def.d /etc/texmf/updmap.d /etc/texmf/web2c"
CXXFLAGS="-march=core2 -O2 -pipe -ggdb"
FEATURES="assume-digests binpkg-logs buildpkg candy distlocks fixlafiles fixpackages news parallel-fetch preserve-libs protect-owned sandbox sfperms splitdebug strict test unknown-features-warn unmerge-logs unmerge-orphans userfetch"
LINGUAS="en el"
PORTAGE_RSYNC_OPTS="--recursive --links --safe-links --perms --times --compress --force --whole-file --delete --stats --timeout=180 --exclude=/distfiles --exclude=/local --exclude=/packages"
PORTDIR_OVERLAY="/var/lib/layman/multimedia /home/tampakrap/Source_Code/gentoo/kde /home/tampakrap/Source_Code/gentoo/qting-edge /home/tampakrap/Source_Code/gentoo/linuxteamteilar"
USE="64bit 7zip X X509 a52 aac aalib acl acpi addressbook akonadi alsa amd64 amr apache2 asf bash-completion berkdb bidi bluetooth branding bzip2 cairo cdda cddb cdio cdparanoia cdr cgi chm cli consolekit cpudetection cracklib crypt cups curl cvs cxx dbus directfb dmx dri dts dv dvb dvd dvdr emboss encode esd exif expat fam fame fbcon ffmpeg firefox flac foomaticdb fortran gdbm gdu gif gimp git glitz gnutls gphoto2 gpm graphviz hal handbook hash hddtemp hpn iconv idn ieee1394 imagemagick ipod ithreads java joystick jpeg jpeg2k kde kdrive kipi kqemu kvm lame lcms ldap libcaca libnotify lirc lm_sensors lzma mad matroska mikmod mjpeg mmx mmxext mng modules mono mp3 mp4 mpeg mplayer mudflap multilib musepack mysql mysqli nas ncurses network networkmanager nfs nls nodrm npp nptl ogg openexr opengl openmp pam pango pcre pdf perl phonon php plasma png policykit ppds pppd python qt qt3support qt4 quicktime radio rar raster rdesktop readline ruby samba sasl scanner sdl semantic-desktop sensord session sftp simplexml smp sndfile snmp speex spell sql sqlite srt sse sse2 sse3 ssl ssse3 startup-notification subtitles subversion svg sysfs syslog tcpd theora threads tiff truetype udev unicode usb v4l v4l2 vcd vdpau vhosts vim-syntax vorbis webkit winbind wma x264 xcb xcomposite xine xinerama xml xmlreader xmlrpc xmlwriter xorg xpm xscreensaver xsl xulrunner xv xvid xvmc yv12 zip zlib" 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" ALSA_PCM_PLUGINS="adpcm alaw asym copy dmix dshare dsnoop empty extplug file hooks iec958 ioplug ladspa lfloat linear meter mmap_emul mulaw multi null plug rate route share shm softvol" APACHE2_MODULES="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" 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 ubx" INPUT_DEVICES="keyboard mouse joystick" KERNEL="linux" LCD_DEVICES="bayrad cfontz cfontz633 glk hd44780 lb216 lcdm001 mtxorb ncurses text" LINGUAS="en el" LIRC_DEVICES="devinput hauppauge" PHP_TARGETS="php5-3" RUBY_TARGETS="ruby18" USERLAND="GNU" VIDEO_CARDS="nv nvidia vesa" 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" 

                        Package Settings

dev-lang/R-2.12.0 was built with the following:
USE="X bash-completion cairo java jpeg (multilib) nls perl png readline threads -doc -lapack -minimal -tk"
Comment 1 Theo Chatzimichos (RETIRED) archtester Gentoo Infrastructure gentoo-dev Security 2011-02-02 19:19:29 UTC
Created attachment 261366 [details]
Comment 2 Theo Chatzimichos (RETIRED) archtester Gentoo Infrastructure gentoo-dev Security 2011-06-06 13:05:02 UTC
2.12.2 is fine, I'll let you decide what to do here
Comment 3 Theo Chatzimichos (RETIRED) archtester Gentoo Infrastructure gentoo-dev Security 2011-06-11 19:03:30 UTC
It came back :/
preserved-rebuild tried to rebuild it and now tests fail in the same way, I have no idea what hapenned here
Comment 4 Sébastien Fabbro (RETIRED) gentoo-dev 2011-07-28 20:36:03 UTC
*** Bug 376063 has been marked as a duplicate of this bug. ***
Comment 5 Justin Lecher (RETIRED) gentoo-dev 2011-11-21 16:08:25 UTC
What about 2.1{3,4}.0?
Comment 6 Markus Oehme 2012-02-18 12:45:00 UTC
I see the error

running code in 'reg-BLAS.R' ...make[3]: *** [reg-BLAS.Rout] Error 1
make[3]: Leaving directory `/var/tmp/portage/dev-lang/R-2.14.1/work/R-2.14.1/tests'
make[2]: *** [test-Reg] Error 2
make[2]: Leaving directory `/var/tmp/portage/dev-lang/R-2.14.1/work/R-2.14.1/tests'
make[1]: *** [test-all-basics] Error 1
make[1]: Leaving directory `/var/tmp/portage/dev-lang/R-2.14.1/work/R-2.14.1/tests'
make: *** [check] Error 2

for R-2.14.1.
Comment 7 Patrick Lauer gentoo-dev 2012-04-04 15:07:24 UTC
  comparing 'reg-S4.Rout' to './' ... OK
running code in 'reg-BLAS.R' ...make[3]: *** [reg-BLAS.Rout] Error 1
make[3]: Leaving directory `/var/tmp/portage/dev-lang/R-2.15.0/work/R-2.15.0/tests'
make[2]: *** [test-Reg] Error 2
make[2]: Leaving directory `/var/tmp/portage/dev-lang/R-2.15.0/work/R-2.15.0/tests'
make[1]: *** [test-all-basics] Error 1
make[1]: Leaving directory `/var/tmp/portage/dev-lang/R-2.15.0/work/R-2.15.0/tests'
make: *** [check] Error 2
 * ERROR: dev-lang/R-2.15.0 failed (test phase):
 *   Make check failed. See above for details.

Still same in newer versions
Comment 8 Julian Ospald 2013-03-10 00:13:28 UTC
*** Bug 460478 has been marked as a duplicate of this bug. ***
Comment 9 Michael Palimaka (kensington) gentoo-dev 2013-04-08 10:42:12 UTC
No change in 3.0.0 (please consider restricting them).
Comment 10 Sébastien Fabbro (RETIRED) gentoo-dev 2013-09-24 16:32:49 UTC
*** Bug 466760 has been marked as a duplicate of this bug. ***
Comment 11 Sébastien Fabbro (RETIRED) gentoo-dev 2013-09-24 16:37:39 UTC
bug is valid when using blas-reference as a dependency, as sadly R devs decided to rewrite blas. other blas implementations do pass tests, but they are still in science overlay. so for stable candidate R-3.0.1, i switched to using internal blas.
Comment 12 eroen 2014-03-23 14:49:50 UTC
running code in 'reg-BLAS.R' ...Makefile.common:86: recipe for target 'reg-BLAS.Rout' failed

Still present in dev-lang/R-3.0.3.
Comment 13 Kent Fredric (IRC: kent\n) (RETIRED) gentoo-dev 2017-07-01 11:38:40 UTC
Bug year #6 I guess.
Comment 14 Jonas Stein gentoo-dev 2021-08-17 21:23:06 UTC
Is this bug still present in 2021?
Comment 15 Michael Orlitzky gentoo-dev 2021-08-17 23:43:26 UTC
(In reply to Jonas Stein from comment #14)
> Is this bug still present in 2021?

There are still occasional test failures in newer versions of R, but I think we're past the window of opportunity to fix this from the given report in any case.

So I suggest we close it "sorry we ignored it for a decade and now it's too late" and then try harder when people report failures against dev-lang/R-4.1.x.