Summary: | dev-lang/R-1.9.0-r1: hangs in src_test | ||
---|---|---|---|
Product: | Gentoo Linux | Reporter: | Sascha Silbe <sascha-gentoo-bugzilla> |
Component: | Current packages | Assignee: | Gentoo Science Related Packages <sci> |
Status: | RESOLVED WORKSFORME | ||
Severity: | normal | ||
Priority: | High | ||
Version: | unspecified | ||
Hardware: | All | ||
OS: | All | ||
Whiteboard: | |||
Package list: | Runtime testing required: | --- | |
Attachments: | The output of the failed test |
Description
Sascha Silbe
2004-12-06 12:27:33 UTC
Please give R-2.0.0-r1 a try. I'll try to push that one to stable asap. R-2.0.0-r1 is not in the Portage tree yet and R-2.0.0 fails even earlier than R-1.9.0-r1:
=== cut ===
gcc -shared -L/usr/local/lib -o mgcv.so gcv.o magic.o mat.o matrix.o mgcv.o qp.o tprs.o -llapack -lblas -L/usr/local/lib -L/usr/lib/gcc-lib/i586-pc-linux-gnu/3.3.4 -L/usr/lib/gcc-lib/i586-pc-linux-gnu/3.3.4/../../../../i586-pc-linux-gnu/lib -L/usr/lib/gcc-lib/i586-pc-linux-gnu/3.3.4/../../.. -lfrtbegin -lg2c -lm -lgcc_s -L/var/tmp/portage/portage/R-2.0.0/work/R-2.0.0/lib -lR
make[3]: Leaving directory `/tmp/portage/portage/R-2.0.0/temp/R.INSTALL.18385/mgcv/src'
** R
WARNING: UTF-8 locales are not currently supported
** preparing package for lazy loading
** help
>>> Building/Updating help pages for package 'mgcv'
Formats: text html latex example
Predict.matrix text html latex example
anova.gam text html latex example
exclude.too.far text html latex example
extract.lme.cov text html latex example
formXtViX text html latex
formula.gam text html latex
full.score text html latex
gam text html latex example
gam.check text html latex example
gam.control text html latex
gam.convergence text html latex
gam.fit text html latex
gam.models text html latex example
gam.neg.bin text html latex example
gam.selection text html latex example
gam.setup text html latex
gam.side.conditions text html latex example
gamObject text html latex
gamm text html latex example
gamm.setup text html latex
get.var text html latex example
influence.gam text html latex
interpret.gam text html latex
logLik.gam text html latex
magic text html latex example
magic.post.proc text html latex
mgcv text html latex example
mgcv.control text html latex
mono.con text html latex example
mroot text html latex
new.name text html latex example
notExp text html latex example
null.space.dimension text html latex example
pcls text html latex example
pdIdnot text html latex example
pdTens text html latex example
place.knots text html latex example
plot.gam text html latex example
predict.gam text html latex example
print.gam text html latex
residuals.gam text html latex
s text html latex example
smooth.construct text html latex example
step.gam text html latex example
summary.gam text html latex example
te text html latex example
tensor.prod.model.matrix text html latex example
uniquecombs text html latex example
vis.gam text html latex example
WARNING: UTF-8 locales are not currently supported
WARNING: UTF-8 locales are not currently supported
* DONE (mgcv)
make[2]: Leaving directory `/tmp/portage/portage/R-2.0.0/work/R-2.0.0/src/library/Recommended'
make[1]: Leaving directory `/tmp/portage/portage/R-2.0.0/work/R-2.0.0/src/library/Recommended'
>>> Test phase [check]: dev-lang/R-2.0.0
make[1]: Entering directory `/tmp/portage/portage/R-2.0.0/work/R-2.0.0/tests'
make[2]: Entering directory `/tmp/portage/portage/R-2.0.0/work/R-2.0.0/tests'
make[3]: Entering directory `/tmp/portage/portage/R-2.0.0/work/R-2.0.0/tests/Examples'
make[4]: Entering directory `/tmp/portage/portage/R-2.0.0/work/R-2.0.0/tests/Examples'
make[4]: Leaving directory `/tmp/portage/portage/R-2.0.0/work/R-2.0.0/tests/Examples'
make[4]: Entering directory `/tmp/portage/portage/R-2.0.0/work/R-2.0.0/tests/Examples'
running code in 'base-Ex.R' ...make[4]: *** [base-Ex.Rout] Error 1
make[4]: Leaving directory `/tmp/portage/portage/R-2.0.0/work/R-2.0.0/tests/Examples'
make[3]: *** [test-Examples-Base] Error 2
make[3]: Leaving directory `/tmp/portage/portage/R-2.0.0/work/R-2.0.0/tests/Examples'
make[2]: *** [test-Examples] Error 2
make[2]: Leaving directory `/tmp/portage/portage/R-2.0.0/work/R-2.0.0/tests'
make[1]: *** [test-all-basics] Error 1
make[1]: Leaving directory `/tmp/portage/portage/R-2.0.0/work/R-2.0.0/tests'
make: *** [check] Error 2
!!! ERROR: dev-lang/R-2.0.0 failed.
!!! Function src_test, Line 520, Exitcode 0
!!! Make check failed. See above for details.
!!! If you need support, post the topmost build error, NOT this status message.
=== cut ===
About R-2.0.0: Would be nice to know your "emerge info" and the output of the failed test (look for it in /tmp/portage/portage/R-2.0.0/work/R-2.0.0/tests/Examples, the filename is quite obvious if you "ls", don't remember it at the moment) Gentoo Base System version 1.4.16 Portage 2.0.51-r3 (default-linux/x86/2004.0, gcc-3.3.4, glibc-2.3.4.20040808-r1, 2.6.9-infra-skas3-v7-cube-1 i686) ================================================================= System uname: 2.6.9-infra-skas3-v7-cube-1 i686 AMD Athlon(tm) XP 1700+ distcc 2.16 i586-pc-linux-gnu (protocols 1 and 2) (default port 3632) [disabled] ccache version 2.3 [enabled] Autoconf: sys-devel/autoconf-2.59-r5 Automake: sys-devel/automake-1.8.5-r1 Binutils: sys-devel/binutils-2.15.90.0.1.1-r3 Headers: sys-kernel/linux26-headers-2.6.8.1-r2 Libtools: sys-devel/libtool-1.5.2-r5 ACCEPT_KEYWORDS="x86" AUTOCLEAN="yes" CFLAGS="-march=pentium -mcpu=athlon-tbird -O3 -pipe" CHOST="i586-pc-linux-gnu" COMPILER="" CONFIG_PROTECT="/etc /usr/X11R6/lib/X11/xkb /usr/kde/2/share/config /usr/kde/3.3/env /usr/kde/3.3/share/config /usr/kde/3.3/shutdown /usr/kde/3/share/config /usr/lib/mozilla/defaults/pref /usr/share/config /usr/share/texmf/dvipdfm/config/ /usr/share/texmf/dvips/config/ /usr/share/texmf/tex/generic/config/ /usr/share/texmf/tex/platex/config/ /usr/share/texmf/xdvi/ /usr/vice/etc /var/qmail/alias /var/qmail/control" CONFIG_PROTECT_MASK="/etc/afs/C /etc/afs/afsws /etc/afs/modload /etc/gconf /etc/make.globals /etc/terminfo /etc/env.d" CXXFLAGS="-march=pentium -mcpu=athlon-tbird -O3 -pipe" DISTDIR="/usr/portage/distfiles" FEATURES="autoaddcvs autoconfig ccache distlocks maketest sandbox sfperms strict userpriv usersandbox" GENTOO_MIRRORS="ftp://ftp.easynet.nl/mirror/gentoo/ http://gentoo.inode.at/ ftp://gentoo.inode.at/source/" MAKEOPTS="-j2" PKGDIR="/usr/portage/packages" PORTAGE_TMPDIR="/var/tmp/portage" PORTDIR="/usr/portage" PORTDIR_OVERLAY="/usr/local/portage-local--main--1.0" SYNC="rsync://hybrid.sascha.silbe.org/gentoo-portage" USE="x86 3dnow X acl afs alsa apm avi berkdb bitmap-fonts blas bzlib cdr crypt doc dvd dvdr encode fam flac foomaticdb fortran gdbm gif gimpprint gtk gtk2 gtkhtml guile hbci imagemagick imap imlib ipv6 j-noaim j-nomsn j-noyahoo jabber jpeg krb4 lapack lcms libwww lvm1 mad maildir makecheck mbox mikmod mmx monitor mpeg mysql nas ncurses nls oggvorbis opengl oss pam pdflib plotutils png postgres python qt qtmt quicktime readline samba scanner sdl skey spell sqlite sse ssl tetex tiff truetype unicode xml xml2 xv xvid zlib linguas_en,de" Created attachment 48104 [details]
The output of the failed test
Since the test fails when calling an lapack function, here's version information about that as well: [ Searching for package 'lapack' in all categories among: ] * installed packages [I--] [ ] sci-libs/lapack-config-1.0.1 (0) [I--] [ ] sci-libs/lapack-atlas-3.6.0 (0) Could you perhaps try if it builds on your machine when using ordinary lapack? After hitting lapack-atlas Bug #77484 (related to Portage Bug #73580), I've now installed lapack-reference (not lapack which I first supposed to be the right one). Still the same result. (Sorry about that R-2.0.0-r1 :-) ) Please try again w/o "lapack" in your use. Further try R-2.0.1 please. Neither 2.0.0 nor 2.0.1 fail "make check" for me. Closing due to lack of feedback and the fact it works here. Please reopen with details if 2.0.1 and/or 2.1.0-r1 fail src_test(), they pass here. |