dev-lang/R-1.9.0-r1 does not complete the test "internet.R" within several hours, fully loading the CPU in the meantime: make[2]: Entering directory `/tmp/portage/portage/R-1.9.0-r1/work/R-1.9.0/tests' running tests of Internet and socket functions expect some differences make[3]: Entering directory `/tmp/portage/portage/R-1.9.0-r1/work/R-1.9.0/tests' running code in 'internet.R' ... It seems to be stuck in a loop trying to read from a socket: root@cube:~# ps auxww|grep '[^]]R.bin' portage 11087 86.3 3.1 20888 16392 pts/47 RN+ 20:44 34:34 /var/tmp/portage/portage/R-1.9.0-r1/work/R-1.9.0/bin/R.bin --vanilla root@cube:~# strace -p 11087 recv(3, "", 179, 0) = 0 recv(3, "", 179, 0) = 0 recv(3, "", 179, 0) = 0 recv(3, "", 179, 0) = 0 recv(3, "", 179, 0) = 0 recv(3, "", 179, 0) = 0 recv(3, "", 179, 0) = 0 recv(3, "", 179, 0) = 0 recv(3, "", 179, 0) = 0 recv(3, "", 179, 0) = 0 recv(3, "", 179, 0) = 0 recv(3, "", 179, 0) = 0 recv(3, "", 179, 0) = 0 [...] root@cube:~# ls -l /proc/11087/fd/ total 4 lr-x------ 1 portage portage 64 Dec 6 21:24 0 -> /tmp/portage/portage/R-1.9.0-r1/work/R-1.9.0/tests/internet.R l-wx------ 1 portage portage 64 Dec 6 21:24 1 -> /tmp/portage/portage/R-1.9.0-r1/work/R-1.9.0/tests/internet.Rout l-wx------ 1 portage portage 64 Dec 6 21:22 2 -> /tmp/portage/portage/R-1.9.0-r1/work/R-1.9.0/tests/internet.Rout lrwx------ 1 portage portage 64 Dec 6 21:24 3 -> socket:[911924]
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.
