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The latest R-2.5.0 fails to emerge. make[5]: Entering directory `/var/tmp/portage/dev-lang/R-2.5.0/work/R-2.5.0/src/library/grDevices/src' make[5]: `Makedeps' is up to date. make[5]: Leaving directory `/var/tmp/portage/dev-lang/R-2.5.0/work/R-2.5.0/src/library/grDevices/src' make[5]: Entering directory `/var/tmp/portage/dev-lang/R-2.5.0/work/R-2.5.0/src/library/grDevices/src' i686-pc-linux-gnu-gcc -I../../../../include -I../../../../include -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I/usr/local/include -fpic -march=pentium4 -O2 -pipe -std=gnu99 -c chull.c -o chull.o i686-pc-linux-gnu-gcc -I../../../../include -I../../../../include -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I/usr/local/include -fpic -march=pentium4 -O2 -pipe -std=gnu99 -c devNull.c -o devNull.o i686-pc-linux-gnu-gcc -I../../../../include -I../../../../include -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I/usr/local/include -fpic -march=pentium4 -O2 -pipe -std=gnu99 -c devPicTeX.c -o devPicTeX.o i686-pc-linux-gnu-gcc -I../../../../include -I../../../../include -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I/usr/local/include -fpic -march=pentium4 -O2 -pipe -std=gnu99 -c devPS.c -o devPS.o i686-pc-linux-gnu-gcc -I../../../../include -I../../../../include -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I/usr/local/include -fpic -march=pentium4 -O2 -pipe -std=gnu99 -c devQuartz.c -o devQuartz.o i686-pc-linux-gnu-gcc -I../../../../include -I../../../../include -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I/usr/local/include -fpic -march=pentium4 -O2 -pipe -std=gnu99 -c init.c -o init.o i686-pc-linux-gnu-gcc -shared -Wl,-O1 -Wl,--as-needed -o grDevices.so chull.o devNull.o devPicTeX.o devPS.o devQuartz.o init.o -L../../../../lib -lR mkdir -p -- ../../../../library/grDevices/libs make[5]: Leaving directory `/var/tmp/portage/dev-lang/R-2.5.0/work/R-2.5.0/src/library/grDevices/src' make[4]: Leaving directory `/var/tmp/portage/dev-lang/R-2.5.0/work/R-2.5.0/src/library/grDevices/src' Warning: unable to load shared library '/var/tmp/portage/dev-lang/R-2.5.0/work/R-2.5.0/modules//lapack.so': /var/tmp/portage/dev-lang/R-2.5.0/work/R-2.5.0/lib/libRlapack.so: undefined symbol: _gfortran_st_write Error in solve.default(rgb) : lapack routines cannot be loaded Error: unable to load R code in package 'grDevices' Execution halted make[3]: *** [all] Error 1 make[3]: Leaving directory `/var/tmp/portage/dev-lang/R-2.5.0/work/R-2.5.0/src/library/grDevices' make[2]: *** [R] Error 1 make[2]: Leaving directory `/var/tmp/portage/dev-lang/R-2.5.0/work/R-2.5.0/src/library' make[1]: *** [R] Error 1 make[1]: Leaving directory `/var/tmp/portage/dev-lang/R-2.5.0/work/R-2.5.0/src' make: *** [R] Error 1 !!! ERROR: dev-lang/R-2.5.0 failed. Call stack: ebuild.sh, line 1614: Called dyn_compile ebuild.sh, line 971: Called qa_call 'src_compile' ebuild.sh, line 44: Called src_compile R-2.5.0.ebuild, line 83: Called die !!! emake failed Reproducible: Always Steps to Reproduce: 1.#emerge -av =dev-lang/R-2.5.0 [ebuild U ] dev-lang/R-2.5.0 [2.4.1] USE="X jpeg nls png readline tk -blas -debug -lapack" 0 kB Portage 2.1.2.5 (default-linux/x86/2007.0, gcc-4.1.2, glibc-2.5-r1, 2.6.21-gentoo i686) ================================================================= System uname: 2.6.21-gentoo i686 Mobile Intel(R) Pentium(R) 4 - M CPU 1.80GHz Gentoo Base System release 1.12.10 Timestamp of tree: Mon, 30 Apr 2007 21:00:10 +0000 dev-java/java-config: 1.3.7, 2.0.31-r7 dev-lang/python: 2.4.4 dev-python/pycrypto: 2.0.1-r5 sys-apps/sandbox: 1.2.18.1 sys-devel/autoconf: 2.13, 2.61 sys-devel/automake: 1.4_p6, 1.5, 1.6.3, 1.7.9-r1, 1.8.5-r3, 1.9.6-r2, 1.10 sys-devel/binutils: 2.17 sys-devel/gcc-config: 1.3.16 sys-devel/libtool: 1.5.23b virtual/os-headers: 2.6.20-r2 ACCEPT_KEYWORDS="x86 ~x86" AUTOCLEAN="yes" CBUILD="i686-pc-linux-gnu" CFLAGS="-march=pentium4 -O2 -pipe" CHOST="i686-pc-linux-gnu" CONFIG_PROTECT="/etc /usr/share/X11/xkb" CONFIG_PROTECT_MASK="/etc/env.d /etc/env.d/java/ /etc/gconf /etc/java-config/vms/ /etc/php/apache1-php5/ext-active/ /etc/php/apache2-php5/ext-active/ /etc/php/cgi-php5/ext-active/ /etc/php/cli-php5/ext-active/ /etc/revdep-rebuild /etc/terminfo /etc/texmf/web2c" CXXFLAGS="-march=pentium4 -O2 -pipe" DISTDIR="/usr/portage/distfiles" FEATURES="distlocks metadata-transfer parallel-fetch sandbox sfperms strict" GENTOO_MIRRORS="http://gentoo.osuosl.org" LANG="zh_CN.UTF-8" LDFLAGS="-Wl,-O1 -Wl,--as-needed" LINGUAS="zh_CN" MAKEOPTS="-j2" PKGDIR="/usr/portage/packages" PORTAGE_RSYNC_OPTS="--recursive --links --safe-links --perms --times --compress --force --whole-file --delete --delete-after --stats --timeout=180 --exclude=/distfiles --exclude=/local --exclude=/packages --filter=H_**/files/digest-*" PORTAGE_TMPDIR="/var/tmp" PORTDIR="/usr/portage" PORTDIR_OVERLAY="/usr/local/portage" SYNC="rsync://ftp3.tsinghua.edu.cn/gentoo/gentoo-portage" USE="X acpi alsa apache2 bash-completion bitmap-fonts cjk cracklib crypt cups dbus dri dvd emacs fortran gdbm gif gtk iconv jpeg mmx mmxext mp3 mysql ncurses nls nptl nptlonly pam pcre pdf png readline reflection sse sse2 ssl tcpd tetex truetype truetype-fonts type1-fonts ucs2 unicode x86 xft xml xorg zlib" ALSA_CARDS="intel8x0" ALSA_PCM_PLUGINS="ioplug dmix iec958" ELIBC="glibc" INPUT_DEVICES="keyboard mouse" KERNEL="linux" LCD_DEVICES="bayrad cfontz cfontz633 glk hd44780 lb216 lcdm001 mtxorb ncurses text" LINGUAS="zh_CN" USERLAND="GNU" VIDEO_CARDS="ati radeon" Unset: CTARGET, EMERGE_DEFAULT_OPTS, INSTALL_MASK, LC_ALL, PORTAGE_COMPRESS, PORTAGE_COMPRESS_FLAGS, PORTAGE_RSYNC_EXTRA_OPTS
Hi Wei-Wei Guo, Thanks for your bug report. I think this is caused by your --as-needed LDFLAG. Could you please try without and see if it emerges? Thanks, Markus
It emerges without the LDFLAG. Thanks, Wei-Wei (In reply to comment #1) > Hi Wei-Wei Guo, > > Thanks for your bug report. I think this is caused by your > --as-needed LDFLAG. Could you please try without and > see if it emerges? > > Thanks, > Markus
*** Bug 191287 has been marked as a duplicate of this bug. ***
*R-2.5.0 (27 Apr 2007) 27 Apr 2007; Danny van Dyk <kugelfang@gentoo.org> +R-2.5.0.ebuild: New version. As-needed patches have been applied upstream. This version can't be build in parallel anymore. Hmmm, dunno what was applied upstream but it clearly didn't fix it.
Is there a patch/fix documented anywhere? If so, I can test and validate the fix.
R-2.5.* builds just fine for me using --as-needed. Does emerging R with USE='lapack' link properly? In this case I'd be fine punting the lapack useflag alltogether and forcing R to use a decent external lapack lib rather than one of these (potentially buggy) internal implementations that often are a maintenance nightmare anyway. Thanks, Markus
I still got the same undefined symbol problem even with USE=lapack.
Emerge with USE=blas atlas succeeded :)
Hi Markus, with blas flag it works correctly here too. can you make it mandatory?
I will do so as soon as ia64 keywords lapack-reference on their arch (keep an eye on #189738). Markus
ok, can you put "depends on 189738" in this bug so?
*** Bug 195775 has been marked as a duplicate of this bug. ***
fixed in >=dev-lang/R-2.6.1
(In reply to comment #13) > fixed in >=dev-lang/R-2.6.1 this is not true for =dev-lang/R-2.7.[12] with USE=-lapack it compiles fine without --as-needed LDFLAGS but breaks the same way 2.5.0 did. maybe a good way is to use USE=lapack and USE=blas atlas as suggested, but i didnt try it myself. please reopen
(In reply to comment #14) > (In reply to comment #13) > > fixed in >=dev-lang/R-2.6.1 > > this is not true for =dev-lang/R-2.7.[12] with USE=-lapack works fine here on 2.8.1, which is being stabilized. please open a new bug with your info and build log if it is not the case.
