build failure for sci-mathematics/sage-4.7-r2 [testsuite] #81
Comments
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Are you trying sage-prefix??? Burcin is blocked with a similar problem. The only thing I can think of is: did you update gmp recently? What is your compiler? Actually add your emerge --info. |
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Don't know what sage-prefix is to have tried it. # genlop gmp
* dev-libs/gmp
Mon Jul 4 14:55:32 2011 >>> dev-libs/gmp-4.3.2
Fri Jul 22 19:48:34 2011 >>> dev-libs/gmp-4.3.2
# emerge --info
Portage 2.1.10.3 (default/linux/amd64/10.0, gcc-4.5.2, glibc-2.13-r4, 2.6.39-gentoo-r3 x86_64)
=================================================================
System uname: Linux-2.6.39-gentoo-r3-x86_64-Intel-R-_Pentium-R-_Dual_CPU_E2180_@_2.00GHz-with-gentoo-2.0.3
Timestamp of tree: Tue, 26 Jul 2011 11:45:01 +0000
app-shells/bash: 4.1_p9
dev-java/java-config: 2.1.11-r3
dev-lang/python: 2.7.1-r1::sage-on-gentoo, 3.1.3-r1
dev-util/cmake: 2.8.4-r1
dev-util/pkgconfig: 0.26
sys-apps/baselayout: 2.0.3
sys-apps/openrc: 0.8.3-r1
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: 2.20.1-r1
sys-devel/gcc: 4.5.2
sys-devel/gcc-config: 1.4.1-r1
sys-devel/libtool: 2.2.10
sys-devel/make: 3.82
sys-kernel/linux-headers: 2.6.36.1 (virtual/os-headers)
sys-libs/glibc: 2.13-r4
Repositories: gentoo science emacs sage-on-gentoo my_local_overlay
ACCEPT_KEYWORDS="amd64"
ACCEPT_LICENSE="* -@EULA"
CBUILD="x86_64-pc-linux-gnu"
CFLAGS="-march=native -O2 -pipe -ggdb"
CHOST="x86_64-pc-linux-gnu"
CONFIG_PROTECT="/etc"
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/terminfo /etc/texmf/language.dat.d /etc/texmf/language.def.d /etc/texmf/updmap.d /etc/texmf/web2c"
CXXFLAGS="-march=native -O2 -pipe -ggdb"
DISTDIR="/usr/portage/distfiles"
FEATURES="assume-digests binpkg-logs distlocks ebuild-locks fixlafiles fixpackages news parallel-fetch protect-owned sandbox sfperms splitdebug strict unknown-features-warn unmerge-logs unmerge-orphans userfetch"
FFLAGS=""
GENTOO_MIRRORS="ftp://mirror.bytemark.co.uk/gentoo/ http://mirror.bytemark.co.uk/gentoo/ rsync://mirror.bytemark.co.uk/gentoo/"
LDFLAGS="-Wl,-O1 -Wl,--as-needed -Wl,-O1 -Wl,--hash-style=gnu -Wl,--sort-common"
LINGUAS="en en_GB"
MAKEOPTS="-j3"
PKGDIR="/usr/portage/packages"
PORTAGE_CONFIGROOT="/"
PORTAGE_RSYNC_OPTS="--recursive --links --safe-links --perms --times --compress --force --whole-file --delete --stats --timeout=180 --exclude=/distfiles --exclude=/local --exclude=/packages"
PORTAGE_TMPDIR="/var/tmp"
PORTDIR="/usr/portage"
PORTDIR_OVERLAY="/var/lib/layman/science /var/lib/layman/emacs /var/lib/layman/sage-on-gentoo /usr/local/portage"
SYNC="rsync://rsync.uk.gentoo.org/gentoo-portage"
USE="X acl alsa amd64 apache2 bash-completion bazaar berkdb bluetooth bzip2 cairo cleartype cli corefonts cracklib crypt cups cvs cxx darcs dbus dri emacs ffmpeg fortran gdbm git glib gpm iconv ipv6 java jpeg jpeg2k latex libnotify libsamplerate mercurial mmx modules mp3 mudflap multilib ncurses nls nptl nptlonly opengl openmp pam pcre pdf perl php png pppd pulseaudio python readline samba session spell sqlite sse sse2 ssl subversion svg sysfs system-sqlite tcpd theora truetype type1 unicode vaapi vdpau webkit xcb xft xml xorg xvg zlib" ALSA_CARDS="hda-intel usb-audio dummy" 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" CALLIGRA_FEATURES="braindump flow karbon kexi kpresenter krita tables words" CAMERAS="ptp2" 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 evdev" KERNEL="linux" LCD_DEVICES="bayrad cfontz cfontz633 glk hd44780 lb216 lcdm001 mtxorb ncurses text" LINGUAS="en en_GB" PHP_TARGETS="php5-3" RUBY_TARGETS="ruby18" USERLAND="GNU" VIDEO_CARDS="dummy fbdev intel nouveau nv vesa nvidia" 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"
Unset: CPPFLAGS, CTARGET, EMERGE_DEFAULT_OPTS, INSTALL_MASK, LANG, LC_ALL, PORTAGE_BUNZIP2_COMMAND, PORTAGE_COMPRESS, PORTAGE_COMPRESS_FLAGS, PORTAGE_RSYNC_EXTRA_OPTS
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This is a problem with the latest Cython release. There were two different tarballs for Cython-0.14.1. See these links for example: https://trac.macports.org/ticket/28682 The first tarball (size 1314345, md5 6341bf3b2c49a39b8046219f6696f5c4) compiles Sage fine, the second (size 1315824, md51ae1947c1218110f0e41fc95b2bc4530) gives these errors. I uploaded the old tarball here if anyone needs it: http://sage.math.washington.edu/home/burcin/Cython-0.14.1.tar.gz |
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I thought you told me something about cython but I couldn't remember what. The good question is why 2 tarballs and which one is in portage's distfiles. I certainly never had problems. cython's manifest: -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA512 DIST Cython-0.14.1.tar.gz 1315824 RMD160 2df38d0fcbd653ef2ae7f56d21004c781029ec16 SHA1 2edc619bea5636fdc265d21112cd4a3654132603 SHA256 8 9e3f64ea0f97cd29b28d0831a7022dc1f8cf4ffb7be52b9f2fc4b5dcf9243c7 So it looks like we get the "bad" one from portage except it is bad only on some computers. I'll file a bug in gentoo bugzilla for this. |
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This is now: |
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Gentoo used to have the old version. I got the old tarball from my distfiles directory. They must have changed to the new tarball at some point. I get fetch errors if I try to install cython again. This is not a Gentoo bug, they have the latest release tarball on their mirrors. We should report the error with compiling Sage to the Cython list and try the newly released Cython-0.15rc0.tar.gz with Sage. Can anybody make an ebuild for that? I'd be happy to try the prefix with that. For the record, sage-prefix is an effort to replace the Sage build system with portage: https://bitbucket.org/burcin/sage-prefix |
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OK, did you mix up the tarball sizes in your previous message because the Manifest for cython in my freshly synced tree indicate a tarball of size 1315824 which you said is the bad one. |
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No, I didn't mix them up. The recent tarball, which is larger, won't work with Sage. |
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OK the fact that this cython doesn't compile sage is a cython problem. But Gentoo should get the proper tarball for 0.14.1 the manifest on my computer (synced 20mn) says the larger tarball is in distfiles, it has to be corrected. |
ls -l /usr/portage/distfiles/Cython-0.14.1.tar.gz -rw-rw-r-- 1 portage portage 1314345 Feb 4 23:30 /usr/portage/distfiles/Cython-0.14.1.tar.gz So actually we had the right one to start with in Gentoo before switching to the wrong one :( |
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Oh dear. I didn't understand fully - so the wrong tarball is now distributed upstream. How did Robert Bradshaw allow that. GENTOO_MIRRORS="" ebuild /usr/portage/dev-python/cython/cython-0.14.1.ebuild fetch >>> Downloading 'http://www.cython.org/release/Cython-0.14.1.tar.gz' --2011-07-31 11:52:40-- http://www.cython.org/release/Cython-0.14.1.tar.gz Resolving www.cython.org (www.cython.org)... 128.208.160.197 Connecting to www.cython.org (www.cython.org)|128.208.160.197|:80... connected. HTTP request sent, awaiting response... 200 OK Length: 1315824 (1.3M) [application/x-gzip] Saving to: `/usr/portage/distfiles/Cython-0.14.1.tar.gz' 100%[==========================================================================================>] 1,315,824 337K/s in 4.8s 2011-07-31 11:52:45 (269 KB/s) - `/usr/portage/distfiles/Cython-0.14.1.tar.gz' saved [1315824/1315824] * Cython-0.14.1.tar.gz RMD160 SHA1 SHA256 size ;-) ... [ ok ] * checking ebuild checksums ;-) ... [ ok ] * checking auxfile checksums ;-) ... [ ok ] * checking miscfile checksums ;-) ... I can prepare a 0.15rc0 but someone should ping Robert about this. |
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I will prepare a cython-0.14.1 ebuild based on the sage spkg to mask the current broken portage one. That will fix the current issue. |
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There is an extra patch in the sage spkg for cython so I added an ebuild with that in. Hopefully that will work. |
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I guess the sage ebuild dependencies should be adjusted so that an "emerge sage" doesn't pull in the "bad" cython. |
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Yes. But I want to be sure it works before adjusting the dependency. |
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Darn I changed it because it didn't work here but the build failed because I was using m4ri-9999.... So -r1 may have worked. I'll see if I can revert to an earlier version. |
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OK 0.14.1-r1 is back in the overlay and it works here. Dependencies in sage have been adjusted. Re-open if it doesn't work for you. |
Hi,
Sage builds here now without failure, so thanks!
Unfortunately I get "incompatible types" errors when building with the testsuite useflag.
I get one error in
and 14 errors in sage/crypto/boolean_function.c. All the errors are:
and the all occur in functions
pyx_pf_4sage_6crypto_16boolean_function_15BooleanFunction___cinit
pyx_pf_4sage_6crypto_16boolean_function_15BooleanFunction_12__call
pyx_pf_4sage_6crypto_16boolean_function_15BooleanFunction_15walsh_hadamard_transform
__pyx_pf_4sage_6crypto_16boolean_function_15BooleanFunction_18is_symmetric
__pyx_pf_4sage_6crypto_16boolean_function_15BooleanFunction_27annihilator
__pyx_pf_4sage_6crypto_16boolean_function_15BooleanFunction_29__setitem
boolean_function.c contains line 377
typedef struct __pyx_t_4sage_6crypto_16boolean_function_bitset_s __pyx_t_4sage_6crypto_16boolean_function_bitset_t[1];and combinat_cython.c contains lines
struct __pyx_obj_4sage_5rings_7integer_Integer { /* 742 */ struct __pyx_obj_4sage_9structure_7element_EuclideanDomainElement __pyx_base; mpz_t value; }; ... struct __pyx_obj_4sage_5rings_7integer_Integer *__pyx_v_s; /* 2353 */ ... mpz_t __pyx_t_3; /* 2356 */ ... __pyx_t_3 = __pyx_v_s->value; /* 2427 */Any thoughts?
(sorry, attempt at using github flavored markdown is not quite working out...)
ta,
Jez.
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