[gentoo-science] failures while trying to build sage

[gentoo-science] failures while trying to build sage

[P Purkayastha]

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Hi,

   I am trying to build sage-4.7_rc0. I encountered two failures:

1. Checksum failure on trying to merge pari. I could work around this by 
copying pari-2.4.3-r1 to a local overlay and re-digesting the ebuild. 
The package which failed the digest was elldata.tgz.

2. I have not been able to build sage. Apparently it can not find 
Python.h. The build log is attached.
Here is some more pertinent information:

~ [1] > emerge --info "=sci-mathematics/sage-4.7_rc0"
Portage 2.2.0_alpha30 (default/linux/amd64/10.0/desktop/kde, gcc-4.4.5, 
libc-0-r0, 2.6.38-gentoo-r3 x86_64)
=================================================================
                         System Settings
=================================================================
System uname: 
Linux-2.6.38-gentoo-r3-x86_64-Intel-R-_Core-TM-_i5_CPU_M_460_@_2.53GHz-with-gentoo-2.0.2
Timestamp of tree: Sun, 24 Apr 2011 03:30:01 +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
sys-apps/baselayout: 2.0.2
sys-apps/openrc:     0.8.2
sys-apps/sandbox:    2.4
sys-devel/autoconf:  2.13, 2.65-r1
sys-devel/automake:  1.9.6-r3, 1.10.3, 1.11.1
sys-devel/binutils:  2.20.1-r1
sys-devel/gcc:       4.4.5
sys-devel/gcc-config: 1.4.1
sys-devel/libtool:   2.2.10
sys-devel/make:      3.81-r2
sys-kernel/linux-headers: 2.6.36.1
virtual/os-headers:  0
Repositories: gentoo enlightenment sage-on-gentoo myself
Installed sets:
ACCEPT_KEYWORDS="amd64"
ACCEPT_LICENSE="*"
CBUILD="x86_64-pc-linux-gnu"
CFLAGS="-march=native -O2 -pipe"
CHOST="x86_64-pc-linux-gnu"
CONFIG_PROTECT="/etc /usr/share/config /usr/share/gnupg/qualified.txt 
/usr/share/xsessions"
CONFIG_PROTECT_MASK="/etc/ca-certificates.conf /etc/env.d 
/etc/env.d/java/ /etc/fonts/fonts.conf /etc/gconf /etc/gentoo-release 
/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"
DISTDIR="/usr/portage/distfiles"
EMERGE_DEFAULT_OPTS="--with-bdeps=y"
FEATURES="assume-digests binpkg-logs distlocks fixlafiles fixpackages 
news parallel-fetch preserve-libs protect-owned sandbox sfperms strict 
unknown-features-warn unmerge-logs unmerge-orphans userfetch"
FFLAGS=""
GENTOO_MIRRORS="http://distfiles.gentoo.org"
LDFLAGS="-Wl,-O1 -Wl,--as-needed"
LINGUAS="en en_US"
MAKEOPTS="-j4"
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/enlightenment 
/var/lib/layman/sage-on-gentoo /usr/local/portage"
SYNC="rsync://rsync.gentoo.org/gentoo-portage"
USE="X a52 aac accessibility acl acpi akonadi alsa amd64 bash-completion 
berkdb branding bzip2 cairo cdda cddb cdr cli consolekit cracklib crypt 
cups curl curlwrappers cxx dbus djvu dri dts dvd dvdr encode exif fam 
fbcon ffmpeg flac fontconfig ftp fuse gdbm gdu gif gnutls gphoto2 gpm 
gstreamer gtk iconv ieee1394 imagemagick jpeg lame latex lcms ldap 
libsamplerate lzma mad mmap mmx mmx2 mng modules mp3 mp4 mpeg mudflap 
multilib musepack musicbrainz ncurses networkmanager nls nptl nptlonly 
ogg opengl openmp oss pam pango pch pcmcia pcre pdf perl plasma png 
policykit ppds pppd python qt3support qt4 readline savedconfig sdl 
session smp speex spell sqlite srt sse sse2 ssl ssse3 
startup-notification svg sysfs taglib tcpd theora threads tiff truetype 
udev unicode usb v4l v4l2 vdpau vim-syntax vorbis wicd wifi wmf x264 
xattr xcf xcomposite xft xinerama xml xorg xosd xpm xulrunner xv xvid 
xvmc yv12 zeroconf zlib zsh-completion" ALSA_CARDS="hda-intel" 
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" 
CAMERAS="*" 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="evdev keyboard mouse synaptics" 
KERNEL="linux" LCD_DEVICES="bayrad cfontz cfontz633 glk hd44780 lb216 
lcdm001 mtxorb ncurses text" LINGUAS="en en_US" PHP_TARGETS="php5-3" 
RUBY_TARGETS="ruby18" USERLAND="GNU" VIDEO_CARDS="nvidia vesa" 
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, INSTALL_MASK, LANG, LC_ALL, 
PORTAGE_BUNZIP2_COMMAND, PORTAGE_COMPRESS, PORTAGE_COMPRESS_FLAGS, 
PORTAGE_RSYNC_EXTRA_OPTS

~> emerge -pqv "=sci-mathematics/sage-4.7_rc0"
[ebuild  N    ] sci-mathematics/sage-4.7_rc0  USE="latex mpc -examples 
-maximalib -testsuite"
~>

Other packages from sage-on-gentoo that are in package.use. I didn't 
realize that there is USE file that could be symlinked or copied. So, I 
just tried emerge several times and added the USEs necessary. All the 
packages below have successfully merged, except for sage.
# From /etc/portage/package.use
sci-mathematics/pari sage data  gmp
dev-lang/python sage
sci-libs/linbox sage ntl
sci-mathematics/polybori sage
sci-mathematics/eclib pari24
sci-mathematics/lcalc pari24
sci-mathematics/sympow pari24
sci-mathematics/glpk gmp
dev-python/pycrypto gmp
dev-python/mpmath gmp matplotlib
dev-lisp/ecls -unicode
sci-mathematics/maxima -unicode ecls
sci-libs/flint ntl
dev-python/cvxopt glpk
dev-python/sympy ipython  imaging
sci-mathematics/sage mpc
dev-lang/R lapack

[-- Attachment #2: sage.build.log.txt --]
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 * Package:    sci-mathematics/sage-4.7_rc0
 * Repository: sage-on-gentoo
 * Maintainer: sci@gentoo.org
 * USE:        amd64 consolekit elibc_glibc kernel_linux latex mpc multilib policykit userland_GNU
 * FEATURES:   preserve-libs sandbox
>>> ^[[1m^[[37mcfg-update-1.8.2-r1^[[0m^[[0m: Creating checksum index...
 * Applying sage-4.6.1-exp-site-packages.patch ...
 [ ok ]
 * Applying trac_11236-test_eq_for_python_2_7-nt.patch ...
 [ ok ]
 * Applying trac_11244_reenable_deprecationwarnings_in_python27.patch ...
 [ ok ]
 * Applying trac_11244_fix_combinatpartition_warnings.patch ...
 [ ok ]
 * Applying trac_11244_fixmoredeprecationswarnings.patch ...
 [ ok ]
 * Applying sage-4.4.2-flint.patch ...
 [ ok ]
 * Applying sage-4.5.1-fix-qepcad-path.patch ...
 [ ok ]
 * Applying sage-4.6-fix-SAGE_LOCAL.patch ...
 [ ok ]
python2.7 setup.py build
Building interpreters for fast_callable
Updating Cython code....
Traceback (most recent call last):
  File "setup.py", line 879, in <module>
    queue = compile_command_list(ext_modules, deps)
  File "setup.py", line 839, in compile_command_list
    dep_file, dep_time = deps.newest_dep(f,m)
  File "setup.py", line 746, in newest_dep
    for f in self.all_deps(filename, ext_module):
  File "setup.py", line 729, in all_deps
    deps.update(self.all_deps(f, ext_module, path))
  File "setup.py", line 729, in all_deps
    deps.update(self.all_deps(f, ext_module, path))
  File "setup.py", line 729, in all_deps
    deps.update(self.all_deps(f, ext_module, path))
  File "setup.py", line 729, in all_deps
    deps.update(self.all_deps(f, ext_module, path))
  File "setup.py", line 729, in all_deps
    deps.update(self.all_deps(f, ext_module, path))
  File "setup.py", line 729, in all_deps
    deps.update(self.all_deps(f, ext_module, path))
  File "setup.py", line 727, in all_deps
    for f in self.immediate_deps(filename, ext_module):
  File "setup.py", line 709, in immediate_deps
    self._deps[filename] = self.parse_deps(filename, ext_module)
  File "setup.py", line 697, in parse_deps
    raise IOError, msg
IOError: could not find dependency Python.h included in sage/ext/python_object.pxi.
 * ERROR: sci-mathematics/sage-4.7_rc0 failed (compile phase):
 *   Building failed
 * 
 * Call stack:
 *     ebuild.sh, line   56:  Called src_compile
 *   environment, line 5618:  Called distutils_src_compile
 *   environment, line 1624:  Called die
 * The specific snippet of code:
 *               "$(PYTHON)" "${setup_file#*|}" "${_DISTUTILS_GLOBAL_OPTIONS[@]}" build "$@" || die "Building failed";
 * 
 * If you need support, post the output of 'emerge --info =sci-mathematics/sage-4.7_rc0',
 * the complete build log and the output of 'emerge -pqv =sci-mathematics/sage-4.7_rc0'.
 * This ebuild is from an overlay named 'sage-on-gentoo': '/var/lib/layman/sage-on-gentoo/'
 * The complete build log is located at '/var/tmp/portage/sci-mathematics/sage-4.7_rc0/temp/build.log'.
 * The ebuild environment file is located at '/var/tmp/portage/sci-mathematics/sage-4.7_rc0/temp/environment'.
 * S: '/var/tmp/portage/sci-mathematics/sage-4.7_rc0/work/sage-4.7.rc0'