I can't think of any reason my setup should trigger a build failure. The build still fails if I unset CFLAGS/CXXFLAGS. Thanks! # emerge Macaulay2 [SNIP] make[3]: Entering directory `/var/tmp/portage/Macaulay2-0.9.2/work/Macaulay2-0.9.2/Macaulay2/m2/cache/doc' running example 0001 loaddata: map has disappeared or changed its location: 0xb7dfb000-0xb7f2f000 r-x 327029609 command line argument 3 :1:2: failed to load data from '../../../libexec/Macaulay2-i686-data' contents of 0001.example: R = QQ[x..z]; C = res coker vars R length C make[3]: *** [0001.out] Error 1 make[3]: Leaving directory `/var/tmp/portage/Macaulay2-0.9.2/work/Macaulay2-0.9.2/Macaulay2/m2/cache/doc' make[2]: *** [phase3] Error 2 make[2]: Leaving directory `/var/tmp/portage/Macaulay2-0.9.2/work/Macaulay2-0.9.2/Macaulay2/m2' make[1]: *** [all] Error 2 make[1]: Leaving directory `/var/tmp/portage/Macaulay2-0.9.2/work/Macaulay2-0.9.2/Macaulay2' make: *** [all] Error 2 make: Leaving directory `/var/tmp/portage/Macaulay2-0.9.2/work/Macaulay2-0.9.2' !!! ERROR: sci-mathematics/Macaulay2-0.9.2 failed. Call stack: ebuild.sh, line 1526: Called dyn_compile ebuild.sh, line 923: Called src_compile Macaulay2-0.9.2.ebuild, line 54: Called die !!! (no error message) !!! If you need support, post the topmost build error, and the call stack if relevant. # emerge --info Portage 2.1_pre7-r2 (default-linux/x86/2006.0, gcc-3.4.6, glibc-2.4-r1, 2.6.15-suspend2-r6 i686) ================================================================= System uname: 2.6.15-suspend2-r6 i686 Intel(R) Pentium(R) III Mobile CPU 850MHz Gentoo Base System version 1.12.0_pre16 dev-lang/python: 2.4.2-r1 sys-apps/sandbox: 1.2.17 sys-devel/autoconf: 2.13, 2.59-r7 sys-devel/automake: 1.4_p6, 1.5, 1.6.3, 1.7.9-r1, 1.8.5-r3, 1.9.6-r2 sys-devel/binutils: 2.16.1-r2 sys-devel/libtool: 1.5.22 virtual/os-headers: 2.6.11-r3 ACCEPT_KEYWORDS="x86 ~x86" AUTOCLEAN="yes" CBUILD="i686-pc-linux-gnu" CFLAGS="-march=pentium3 -O3 -pipe" CHOST="i686-pc-linux-gnu" CONFIG_PROTECT="/etc /usr/kde/2/share/config /usr/kde/3/share/config /usr/lib/mozilla/defaults/pref /usr/share/X11/xkb /usr/share/config /var/qmail/control" CONFIG_PROTECT_MASK="/etc/gconf /etc/init.d /etc/pam.d /etc/revdep-rebuild /etc/terminfo /etc/texmf/web2c /etc/udev /etc/env.d" CXXFLAGS="-march=pentium3 -O3 -pipe" DISTDIR="/usr/portage/distfiles" FEATURES="autoconfig ccache distlocks metadata-transfer parallel-fetch sandbox sfperms strict userpriv usersandbox" GENTOO_MIRRORS="http://toughguy.caltech.edu/pub/linux/gentoo/ http://ftp-mirror.internap.com/pub/gentoo/ " MAKEOPTS="-j1" PKGDIR="/usr/portage/packages" PORTAGE_TMPDIR="/var/tmp" PORTDIR="/usr/portage" PORTDIR_OVERLAY="/usr/local/portage" SYNC="rsync://rsync.gentoo.org/gentoo-portage" USE="x86 X a52 aac aalib acl acpi alsa avi bash-completion berkdb bitmap-fonts blas bonobo bzip2 cairo cdparanoia cdr cli cmucl crypt cscope ctype cups dba dbus djvu dri dv dvd dvi eds emboss encode esd exif expat fastbuild firefox flac fontconfig foomaticdb force-cgi-redirect fortran fpx ftp gd gdbm gif glibc-omitfp glitz gnome gpm gstreamer gtk gtk2 gtkhtml hal howl i8x0 imlib ipv6 javascript jbig joystick jpeg lcms ldap libg++ libwww lzo mad memlimit mikmod mmx mono motif moznocompose moznoirc moznomail mozsvg mp3 mpeg nautilus ncurses new-login nls nptl nptlonly nsplugin offensive ogg ole opengl oss pam pcmcia pcre perl pic png posix python quicktime readline real rtc samba sdl session simplexml slang slp soap sockets speex spell spl sse ssl svg t1lib tcpd tetex theora tiff tokenizer truetype truetype-fonts type1-fonts udev unicode usb vidix vorbis win32codecs wmf xml xml2 xmms xsl xv xvid zlib elibc_glibc input_devices_keyboard input_devices_mouse kernel_linux userland_GNU video_cards_i810" Unset: ASFLAGS, CTARGET, EMERGE_DEFAULT_OPTS, LANG, LC_ALL, LDFLAGS, LINGUAS
Hi Justin, Thanks for you report. I can confirm your error on my box but will have to take a closer look to figure out what is going on. Thanks, Markus
I hit a different compilation error, maybe do a revision bump (newer versions are available)
(In reply to comment #2) > I hit a different compilation error, maybe do a revision bump (newer versions > are available) > Yeah, I am way behind with this one - I'll try to bump it soon. Best, Markus
I've just bumped Macaulay2 to v 0.9.95. Please test and let me know how that goes - it seems to work fine for me. If all is well we should probably move this version into stable soon. Thanks, Markus
(In reply to comment #4) > I've just bumped Macaulay2 to v 0.9.95. Please test and > let me know how that goes - it seems to work fine for me. > If all is well we should probably move this version into stable > soon. It hangs endlessly (three hours now) at the following point: making subset make[1]: Entering directory `/var/tmp/portage/ntl-5.3/work/ntl-5.3/src' g++ -I../include -I. -O2 -Wno-deprecated -o subset subset.c ntl.a -lgmp -lm make[1]: Leaving directory `/var/tmp/portage/ntl-5.3/work/ntl-5.3/src' subset 40 40 20 10 999999 f n: b: size: prune: seed: alg [fqQxr]: Portage 2.1.1-r1 (default-linux/x86/2006.1/desktop, gcc-4.1.1, glibc-2.4-r4, 2.6.18-gentoo-r2 i686) ================================================================= System uname: 2.6.18-gentoo-r2 i686 AMD Athlon(tm) XP 2500+ Gentoo Base System version 1.12.6 Last Sync: Mon, 13 Nov 2006 06:20:01 +0000 app-admin/eselect-compiler: [Not Present] dev-java/java-config: 1.3.7, 2.0.30 dev-lang/python: 2.4.3-r4 dev-python/pycrypto: 2.0.1-r5 dev-util/ccache: [Not Present] dev-util/confcache: [Not Present] sys-apps/sandbox: 1.2.17 sys-devel/autoconf: 2.13, 2.60 sys-devel/automake: 1.4_p6, 1.5, 1.6.3, 1.7.9-r1, 1.8.5-r3, 1.9.6-r2 sys-devel/binutils: 2.16.1-r3 sys-devel/gcc-config: 1.3.13-r4 sys-devel/libtool: 1.5.22 virtual/os-headers: 2.6.17-r1 ACCEPT_KEYWORDS="x86" AUTOCLEAN="yes" CBUILD="i686-pc-linux-gnu" CFLAGS="-O2" CHOST="i686-pc-linux-gnu" CONFIG_PROTECT="/etc /usr/kde/3.5/env /usr/kde/3.5/share/config /usr/kde/3.5/shutdown /usr/share/X11/xkb /usr/share/config" CONFIG_PROTECT_MASK="/etc/env.d /etc/env.d/java/ /etc/gconf /etc/java-config/vms/ /etc/revdep-rebuild /etc/terminfo /etc/texmf/web2c" CXXFLAGS="-O2" DISTDIR="/usr/portage/distfiles" FEATURES="autoconfig ccache collision-protect distlocks metadata-transfer parallel-fetch sandbox sfperms strict test" GENTOO_MIRRORS="ftp://sunsite.informatik.rwth-aachen.de/pub/Linux/gentoo/" LANG="de_DE@euro" LC_ALL="de_DE.utf8" LINGUAS="de" 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'" PORTAGE_TMPDIR="/var/tmp" PORTDIR="/usr/portage" PORTDIR_OVERLAY="/usr/local/portage" SYNC="rsync://rsync.informatik.rwth-aachen.de/gentoo-portage" USE="x86 3dnow 3dnowext X Xaw3d a52 aiglx alsa artworkextra asf audiofile bash-completion beagle berkdb bidi bitmap-fonts bootsplash branding bzip2 cairo cdda cddb cdparanoia cdr cli cracklib crypt css cups curl custom-cflags dbus dga directfb divx4linux dlloader dri dts dvd dvdr dvdread dvi eds elibc_glibc emacs emboss encode esd evo exif expat fam fat fbcon ffmpeg firefox fortran ftp gb gcj gdbm gif gnome gpm gstreamer gtk gtk2 gtkhtml hal iconv icq idn imagemagick imap input_devices_keyboard input_devices_mouse ipv6 isdnlog java javascript jikes jpeg jpeg2k kde kernel_linux ldap leim libg++ linguas_de lm_sensors mad maildir matroska mbox mhash mikmod mime mmx mmxext mng mono mp3 mpeg mpeg2 mule mysql nautilus ncurses nforce2 nls nocardbus nptl nptlonly nsplugin nvidia objc ogg opengl pam pcre pdf perl plotutils pmu png ppds pppd preview-latex print python qt3 qt4 quicktime readline reflection reiserfs samba sdk session slang spell spl sse ssl svg svga t1lib tcltk tcpd tetex theora thunderbird tiff truetype truetype-fonts type1-fonts udev unicode usb userland_GNU vcd video_cards_fbdev video_cards_radeon video_cards_vesa videos vorbis win32codecs wmf wxwindows xine xml xorg xosd xv xvid zlib" Unset: CTARGET, EMERGE_DEFAULT_OPTS, INSTALL_MASK, LDFLAGS, PORTAGE_RSYNC_EXTRA_OPTS
(In reply to comment #5) > making subset > make[1]: Entering directory `/var/tmp/portage/ntl-5.3/work/ntl-5.3/src' > g++ -I../include -I. -O2 -Wno-deprecated -o subset subset.c ntl.a -lgmp -lm > make[1]: Leaving directory `/var/tmp/portage/ntl-5.3/work/ntl-5.3/src' > subset 40 40 20 10 999999 f > n: b: size: prune: seed: alg [fqQxr]: > Looks like it hangs in dev-libs/ntl (one of the dependencies) not in Macaulay2 proper ;) Seems like you've hit bug #143484. Thanks a lot for testing, Markus
(In reply to comment #6) > Looks like it hangs in dev-libs/ntl (one of the dependencies) not > in Macaulay2 proper ;) Seems like you've hit bug #143484. Argh. Yes, of course....
*** Bug 155235 has been marked as a duplicate of this bug. ***
../../../../image/usr/share/doc/Macaulay2-0.9.95/LLLBases/examples/_kernel__L__L__L.errors:0: (output file) error return code: (1,0) ../../../../image/usr/share/doc/Macaulay2-0.9.95/LLLBases/examples/_kernel__L__L__L.m2:0: (input file) ../m2/debugging.m2:4:17:(0):[9]: 4 error(s) occurred running example files ../m2/html.m2:703:40:(0):[8]: --back trace-- ../m2/methods.m2:93:80:(0):[7]: --back trace-- ../m2/option.m2:9:8:(0):[6]: --back trace-- ../m2/html.m2:502:6:(0):[5]: --back trace-- ../m2/methods.m2:93:80:(0):[4]: --back trace-- ../m2/option.m2:9:8:(0):[3]: --back trace-- a string:1:1:(1):[2]: --back trace-- ../m2/methods.m2:286:22:(0):[2]: --back trace-- startup.m2:442:28:(0):[0]: --back trace-- startup.m2:525:1:(0):[0]: --back trace-- make[2]: *** [install-others] Error 1 make[2]: Leaving directory `/var/tmp/portage/Macaulay2-0.9.95/work/Macaulay2-0.9.95/Macaulay2/packages' make[1]: *** [install] Error 2 make[1]: Leaving directory `/var/tmp/portage/Macaulay2-0.9.95/work/Macaulay2-0.9.95/Macaulay2' make: *** [install] Error 2 make: Leaving directory `/var/tmp/portage/Macaulay2-0.9.95/work/Macaulay2-0.9.95' Version 0.9.95 fails with this error.
Hi Christian, Thanks for the heads up :) I just checked and Macaulay2-0.9.95 compiles fine on both of my x86 dev boxes. Unfortunately, from your output I can't really tell what the problem might be. Would you be able to post the complete emerge log up to the failure somewhere? Thanks, Markus
Created attachment 110064 [details] build.log Here you are...
Thanks, could you please also post the output of one of the error files that Macaulay claims to create (such as _is__L__L__L.errors). I had a peak at the source, but I don't know M. well enough to make sense of the return code. Thanks, Markus
Created attachment 110173 [details] output
Created attachment 110174 [details] input
Thanks Christian! Like I suspected, the last line in the error output says it all: *** out of memory, exiting *** This has happened to me several times during Macaulay's testing routines, but never during the actual compile. How much memory does your box have? It compiles fine here on my laptop with 512M of ram. cheers, Markus
(In reply to comment #15) > Like I suspected, the last line in the error output says it all: > *** out of memory, exiting *** > This has happened to me several times during Macaulay's > testing routines, but never during the actual compile. How > much memory does your box have? It compiles fine here > on my laptop with 512M of ram. 1GB, although it happens in a chroot, plenty of memory is free and there are 512 MB of swap space.
Maybe the calls to ulimit -v 200000 et al. that Macaulay uses during compiling the docs cause trouble. I'll see that I can come up with a patch to get rid of those. Thanks for your help, Markus
Hi Christian, Macaulay is a real memory hog and some of the tests require in excess of 1G. I've spent the last week removing some of the worst offenders including the one you posted. Could you please give it another shot sometime and report all files (of the type *.error) that still fail if any. Thanks, Markus
(In reply to comment #18) > Macaulay is a real memory hog and some of the tests require > in excess of 1G. I've spent the last week removing some > of the worst offenders including the one you posted. Could you please > give it another shot sometime and report all files (of the type *.error) > that still fail if any. So, why aren't tests only executed with FEATURES/USE=test? The current version emerges just fine. * QA Notice: Pre-stripped files found: * /var/tmp/portage/sci-mathematics/Macaulay2-0.9.95/image/usr/bin/personality /var/tmp/portage/sci-mathematics/Macaulay2-0.9.95/image/usr/bin/M2 * QA Notice: Package has poor programming practices which may compile * fine but exhibit random runtime failures. * LLL.cpp:129: warning: dereferencing type-punned pointer will break strict-aliasing rules ntl_interface.cpp:48: warning: dereferencing type-punned pointer will break strict-aliasing rules gbring.cpp:1163: warning: dereferencing type-punned pointer will break strict-aliasing rules gbring.cpp:1164: warning: dereferencing type-punned pointer will break strict-aliasing rules gbring.cpp:1168: warning: dereferencing type-punned pointer will break strict-aliasing rules gbring.cpp:1169: warning: dereferencing type-punned pointer will break strict-aliasing rules gbring.cpp:1179: warning: dereferencing type-punned pointer will break strict-aliasing rules gbring.cpp:1180: warning: dereferencing type-punned pointer will break strict-aliasing rules gbring.cpp:1181: warning: dereferencing type-punned pointer will break strict-aliasing rules gbring.cpp:1182: warning: dereferencing type-punned pointer will break strict-aliasing rules gbring.cpp:1222: warning: dereferencing type-punned pointer will break strict-aliasing rules gbring.cpp:1223: warning: dereferencing type-punned pointer will break strict-aliasing rules gbring.cpp:1380: warning: dereferencing type-punned pointer will break strict-aliasing rules
(In reply to comment #19) > So, why aren't tests only executed with FEATURES/USE=test? The current > version emerges just fine. > They are, I was just sloppy in my formulation! When Macaulay2 builds its docs it "runs" through all its examples files, several of which are memory intense as well. The failures you reported before occurred during running these doc building routines. I've fixed those as well. Thank you very much for testing by the way. I appreciate it. I am aware of the QA issues and I'll report them upstream. I guess its save to close this bug then. Best, Markus > * QA Notice: Pre-stripped files found: > * /var/tmp/portage/sci-mathematics/Macaulay2-0.9.95/image/usr/bin/personality > /var/tmp/portage/sci-mathematics/Macaulay2-0.9.95/image/usr/bin/M2 > > * QA Notice: Package has poor programming practices which may compile > * fine but exhibit random runtime failures. > * LLL.cpp:129: warning: dereferencing type-punned pointer will break > strict-aliasing rules > ntl_interface.cpp:48: warning: dereferencing type-punned pointer will break > strict-aliasing rules > gbring.cpp:1163: warning: dereferencing type-punned pointer will break > strict-aliasing rules > gbring.cpp:1164: warning: dereferencing type-punned pointer will break > strict-aliasing rules > gbring.cpp:1168: warning: dereferencing type-punned pointer will break > strict-aliasing rules > gbring.cpp:1169: warning: dereferencing type-punned pointer will break > strict-aliasing rules > gbring.cpp:1179: warning: dereferencing type-punned pointer will break > strict-aliasing rules > gbring.cpp:1180: warning: dereferencing type-punned pointer will break > strict-aliasing rules > gbring.cpp:1181: warning: dereferencing type-punned pointer will break > strict-aliasing rules > gbring.cpp:1182: warning: dereferencing type-punned pointer will break > strict-aliasing rules > gbring.cpp:1222: warning: dereferencing type-punned pointer will break > strict-aliasing rules > gbring.cpp:1223: warning: dereferencing type-punned pointer will break > strict-aliasing rules > gbring.cpp:1380: warning: dereferencing type-punned pointer will break > strict-aliasing rules >
