Gentoo Archives: gentoo-science

From: P Purkayastha <ppurka@×××××.com>
To: gentoo-science <gentoo-science@l.g.o>
Subject: [gentoo-science] [sage-on-gentoo] sci-chemistry/jmol{,-applet}, sci-mathematics/sage-doc fails to compile
Date: Sat, 20 Aug 2011 13:23:40
Message-Id: CADZU3NZrLaHXhWWUH4Jje=P5ssYNUUmMAuggWNd_sftRTyri-A@mail.gmail.com
Hi,
  I was updating world today and the following packages failed:

1.  sci-chemistry/jmol-applet-12.0.45-r1 and sci-chemistry/jmol-12.0.45
failed to compile.The errors are almost the same for both the packages.

2. sci-mathematics/sage-doc-4.7.1 failed with a digest failure.


The build logs are attached with this email.

My emerge --info is given below. Please let me know if you need any further
information.

Portage 2.2.0_alpha51 (default/linux/amd64/10.0/desktop/kde, gcc-4.4.5,
glibc-2.12.2-r0, 2.6.38-gentoo-r6 x86_64)
=================================================================
System uname: Linux-2.6.38-gentoo-r6-x86_64-Intel-R-_Core-TM-_i5_CPU_M_460_@
_2.53GHz-with-gentoo-2.0.3
Timestamp of tree: Sat, 20 Aug 2011 11:30:02 +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:            4.4.5
sys-devel/gcc-config:     1.4.1-r1
sys-devel/libtool:        2.4-r1
sys-devel/make:           3.82
sys-kernel/linux-headers: 2.6.38 (virtual/os-headers)
sys-libs/glibc:           2.12.2
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 ebuild-locks 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"
LANG="en_US.UTF8"
LC_ALL="en_US.UTF-8"
LDFLAGS="-Wl,-O1 -Wl,--as-needed"
LINGUAS="en en_US"
MAKEOPTS="-j2"
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 declarative 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 kipi lame latex lcms ldap
libsamplerate lzma mad mmap mmx mmx2 mng modules mp3 mp4 mpeg mudflap
multilib musepack ncurses networkmanager nls nptl nptlonly ogg opengl openmp
oss pam pango pch pcmcia pcre pdf perl phonon plasma png policykit ppds pppd
python qt3support qt4 readline savedconfig sdl session smp speex spell
sqlite srt sse sse2 ssl ssse3 svg sysfs system-sqlite 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" CALLIGRA_FEATURES="kexi words flow plan stage
tables krita karbon braindump active" 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, PORTAGE_BUNZIP2_COMMAND,
PORTAGE_COMPRESS, PORTAGE_COMPRESS_FLAGS, PORTAGE_RSYNC_EXTRA_OPTS

Attachments

File name MIME type
build-jmol-applet.log.txt text/plain
build-jmol.log.txt text/plain
build-sage-doc.log.txt text/plain

Replies

Subject Author
Re: [gentoo-science] [sage-on-gentoo] sci-chemistry/jmol{,-applet}, sci-mathematics/sage-doc fails to compile Christopher Schwan <cschwan@××××××××××××××××××.de>