* [gentoo-science] [sage-on-gentoo] sci-chemistry/jmol{,-applet}, sci-mathematics/sage-doc fails to compile
[not found] <4E4FA837.3070205@gmail.com>
@ 2011-08-20 13:23 ` P Purkayastha
2011-08-21 7:24 ` Christopher Schwan
0 siblings, 1 reply; 3+ messages in thread
From: P Purkayastha @ 2011-08-20 13:23 UTC (permalink / raw
To: gentoo-science
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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
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* Package: sci-chemistry/jmol-applet-12.0.45-r1
* Repository: sage-on-gentoo
* Maintainer: sci-chemistry@gentoo.org
* USE: amd64 consolekit elibc_glibc kernel_linux multilib policykit userland_GNU
* FEATURES: preserve-libs sandbox
>>> ^[[1m^[[37mcfg-update-1.8.2-r1^[[0m^[[0m: Creating checksum index...
* Using: sun-jdk-1.6
* Applying jmol-nointl.patch ...
[ ok ]
* Applying jmol-manifest.patch ...
[ ok ]
* Applying jmol-applet-Jmol.js-12.0.45-unix.patch ...
[ ok ]
removed `/var/tmp/portage/sci-chemistry/jmol-applet-12.0.45-r1/work/jmol-12.0.45/Jmol.jar'
removed `/var/tmp/portage/sci-chemistry/jmol-applet-12.0.45-r1/work/jmol-12.0.45/JmolApplet.jar'
removed `/var/tmp/portage/sci-chemistry/jmol-applet-12.0.45-r1/work/jmol-12.0.45/JmolApplet0.jar'
removed `/var/tmp/portage/sci-chemistry/jmol-applet-12.0.45-r1/work/jmol-12.0.45/JmolApplet0_Console.jar'
removed `/var/tmp/portage/sci-chemistry/jmol-applet-12.0.45-r1/work/jmol-12.0.45/JmolApplet0_Minimize.jar'
removed `/var/tmp/portage/sci-chemistry/jmol-applet-12.0.45-r1/work/jmol-12.0.45/JmolApplet0_Popup.jar'
removed `/var/tmp/portage/sci-chemistry/jmol-applet-12.0.45-r1/work/jmol-12.0.45/JmolApplet0_ReadersCifPdb.jar'
removed `/var/tmp/portage/sci-chemistry/jmol-applet-12.0.45-r1/work/jmol-12.0.45/JmolApplet0_ReadersMolXyz.jar'
removed `/var/tmp/portage/sci-chemistry/jmol-applet-12.0.45-r1/work/jmol-12.0.45/JmolApplet0_ReadersMore.jar'
removed `/var/tmp/portage/sci-chemistry/jmol-applet-12.0.45-r1/work/jmol-12.0.45/JmolApplet0_ReadersQuantum.jar'
removed `/var/tmp/portage/sci-chemistry/jmol-applet-12.0.45-r1/work/jmol-12.0.45/JmolApplet0_ReadersSimple.jar'
removed `/var/tmp/portage/sci-chemistry/jmol-applet-12.0.45-r1/work/jmol-12.0.45/JmolApplet0_ReadersXml.jar'
removed `/var/tmp/portage/sci-chemistry/jmol-applet-12.0.45-r1/work/jmol-12.0.45/JmolApplet0_ReadersXtal.jar'
removed `/var/tmp/portage/sci-chemistry/jmol-applet-12.0.45-r1/work/jmol-12.0.45/JmolApplet0_ShapeBio.jar'
removed `/var/tmp/portage/sci-chemistry/jmol-applet-12.0.45-r1/work/jmol-12.0.45/JmolApplet0_ShapeSpecial.jar'
removed `/var/tmp/portage/sci-chemistry/jmol-applet-12.0.45-r1/work/jmol-12.0.45/JmolApplet0_ShapeSurface.jar'
removed `/var/tmp/portage/sci-chemistry/jmol-applet-12.0.45-r1/work/jmol-12.0.45/JmolApplet0_Smiles.jar'
removed `/var/tmp/portage/sci-chemistry/jmol-applet-12.0.45-r1/work/jmol-12.0.45/JmolApplet0_Symmetry.jar'
removed `/var/tmp/portage/sci-chemistry/jmol-applet-12.0.45-r1/work/jmol-12.0.45/JmolApplet0_i18n_ar.jar'
removed `/var/tmp/portage/sci-chemistry/jmol-applet-12.0.45-r1/work/jmol-12.0.45/JmolApplet0_i18n_ca.jar'
removed `/var/tmp/portage/sci-chemistry/jmol-applet-12.0.45-r1/work/jmol-12.0.45/JmolApplet0_i18n_cs.jar'
removed `/var/tmp/portage/sci-chemistry/jmol-applet-12.0.45-r1/work/jmol-12.0.45/JmolApplet0_i18n_da.jar'
removed `/var/tmp/portage/sci-chemistry/jmol-applet-12.0.45-r1/work/jmol-12.0.45/JmolApplet0_i18n_de.jar'
removed `/var/tmp/portage/sci-chemistry/jmol-applet-12.0.45-r1/work/jmol-12.0.45/JmolApplet0_i18n_el.jar'
removed `/var/tmp/portage/sci-chemistry/jmol-applet-12.0.45-r1/work/jmol-12.0.45/JmolApplet0_i18n_en_GB.jar'
removed `/var/tmp/portage/sci-chemistry/jmol-applet-12.0.45-r1/work/jmol-12.0.45/JmolApplet0_i18n_es.jar'
removed `/var/tmp/portage/sci-chemistry/jmol-applet-12.0.45-r1/work/jmol-12.0.45/JmolApplet0_i18n_et.jar'
removed `/var/tmp/portage/sci-chemistry/jmol-applet-12.0.45-r1/work/jmol-12.0.45/JmolApplet0_i18n_fi.jar'
removed `/var/tmp/portage/sci-chemistry/jmol-applet-12.0.45-r1/work/jmol-12.0.45/JmolApplet0_i18n_fr.jar'
removed `/var/tmp/portage/sci-chemistry/jmol-applet-12.0.45-r1/work/jmol-12.0.45/JmolApplet0_i18n_hu.jar'
removed `/var/tmp/portage/sci-chemistry/jmol-applet-12.0.45-r1/work/jmol-12.0.45/JmolApplet0_i18n_id.jar'
removed `/var/tmp/portage/sci-chemistry/jmol-applet-12.0.45-r1/work/jmol-12.0.45/JmolApplet0_i18n_it.jar'
removed `/var/tmp/portage/sci-chemistry/jmol-applet-12.0.45-r1/work/jmol-12.0.45/JmolApplet0_i18n_ko.jar'
removed `/var/tmp/portage/sci-chemistry/jmol-applet-12.0.45-r1/work/jmol-12.0.45/JmolApplet0_i18n_nb.jar'
removed `/var/tmp/portage/sci-chemistry/jmol-applet-12.0.45-r1/work/jmol-12.0.45/JmolApplet0_i18n_nl.jar'
removed `/var/tmp/portage/sci-chemistry/jmol-applet-12.0.45-r1/work/jmol-12.0.45/JmolApplet0_i18n_oc.jar'
removed `/var/tmp/portage/sci-chemistry/jmol-applet-12.0.45-r1/work/jmol-12.0.45/JmolApplet0_i18n_pl.jar'
removed `/var/tmp/portage/sci-chemistry/jmol-applet-12.0.45-r1/work/jmol-12.0.45/JmolApplet0_i18n_pt.jar'
removed `/var/tmp/portage/sci-chemistry/jmol-applet-12.0.45-r1/work/jmol-12.0.45/JmolApplet0_i18n_pt_BR.jar'
removed `/var/tmp/portage/sci-chemistry/jmol-applet-12.0.45-r1/work/jmol-12.0.45/JmolApplet0_i18n_ru.jar'
removed `/var/tmp/portage/sci-chemistry/jmol-applet-12.0.45-r1/work/jmol-12.0.45/JmolApplet0_i18n_sl.jar'
removed `/var/tmp/portage/sci-chemistry/jmol-applet-12.0.45-r1/work/jmol-12.0.45/JmolApplet0_i18n_sv.jar'
removed `/var/tmp/portage/sci-chemistry/jmol-applet-12.0.45-r1/work/jmol-12.0.45/JmolApplet0_i18n_ta.jar'
removed `/var/tmp/portage/sci-chemistry/jmol-applet-12.0.45-r1/work/jmol-12.0.45/JmolApplet0_i18n_tr.jar'
removed `/var/tmp/portage/sci-chemistry/jmol-applet-12.0.45-r1/work/jmol-12.0.45/JmolApplet0_i18n_uk.jar'
removed `/var/tmp/portage/sci-chemistry/jmol-applet-12.0.45-r1/work/jmol-12.0.45/JmolApplet0_i18n_zh_CN.jar'
removed `/var/tmp/portage/sci-chemistry/jmol-applet-12.0.45-r1/work/jmol-12.0.45/JmolApplet0_i18n_zh_TW.jar'
removed `/var/tmp/portage/sci-chemistry/jmol-applet-12.0.45-r1/work/jmol-12.0.45/JmolAppletSigned.jar'
removed `/var/tmp/portage/sci-chemistry/jmol-applet-12.0.45-r1/work/jmol-12.0.45/JmolAppletSigned0.jar'
removed `/var/tmp/portage/sci-chemistry/jmol-applet-12.0.45-r1/work/jmol-12.0.45/JmolAppletSigned0_Console.jar'
removed `/var/tmp/portage/sci-chemistry/jmol-applet-12.0.45-r1/work/jmol-12.0.45/JmolAppletSigned0_Minimize.jar'
removed `/var/tmp/portage/sci-chemistry/jmol-applet-12.0.45-r1/work/jmol-12.0.45/JmolAppletSigned0_MultiTouch.jar'
removed `/var/tmp/portage/sci-chemistry/jmol-applet-12.0.45-r1/work/jmol-12.0.45/JmolAppletSigned0_Popup.jar'
removed `/var/tmp/portage/sci-chemistry/jmol-applet-12.0.45-r1/work/jmol-12.0.45/JmolAppletSigned0_ReadersCifPdb.jar'
removed `/var/tmp/portage/sci-chemistry/jmol-applet-12.0.45-r1/work/jmol-12.0.45/JmolAppletSigned0_ReadersMolXyz.jar'
removed `/var/tmp/portage/sci-chemistry/jmol-applet-12.0.45-r1/work/jmol-12.0.45/JmolAppletSigned0_ReadersMore.jar'
removed `/var/tmp/portage/sci-chemistry/jmol-applet-12.0.45-r1/work/jmol-12.0.45/JmolAppletSigned0_ReadersQuantum.jar'
removed `/var/tmp/portage/sci-chemistry/jmol-applet-12.0.45-r1/work/jmol-12.0.45/JmolAppletSigned0_ReadersSimple.jar'
removed `/var/tmp/portage/sci-chemistry/jmol-applet-12.0.45-r1/work/jmol-12.0.45/JmolAppletSigned0_ReadersXml.jar'
removed `/var/tmp/portage/sci-chemistry/jmol-applet-12.0.45-r1/work/jmol-12.0.45/JmolAppletSigned0_ReadersXtal.jar'
removed `/var/tmp/portage/sci-chemistry/jmol-applet-12.0.45-r1/work/jmol-12.0.45/JmolAppletSigned0_ShapeBio.jar'
removed `/var/tmp/portage/sci-chemistry/jmol-applet-12.0.45-r1/work/jmol-12.0.45/JmolAppletSigned0_ShapeSpecial.jar'
removed `/var/tmp/portage/sci-chemistry/jmol-applet-12.0.45-r1/work/jmol-12.0.45/JmolAppletSigned0_ShapeSurface.jar'
removed `/var/tmp/portage/sci-chemistry/jmol-applet-12.0.45-r1/work/jmol-12.0.45/JmolAppletSigned0_Smiles.jar'
removed `/var/tmp/portage/sci-chemistry/jmol-applet-12.0.45-r1/work/jmol-12.0.45/JmolAppletSigned0_Symmetry.jar'
removed `/var/tmp/portage/sci-chemistry/jmol-applet-12.0.45-r1/work/jmol-12.0.45/JmolAppletSigned0_i18n_ar.jar'
removed `/var/tmp/portage/sci-chemistry/jmol-applet-12.0.45-r1/work/jmol-12.0.45/JmolAppletSigned0_i18n_ca.jar'
removed `/var/tmp/portage/sci-chemistry/jmol-applet-12.0.45-r1/work/jmol-12.0.45/JmolAppletSigned0_i18n_cs.jar'
removed `/var/tmp/portage/sci-chemistry/jmol-applet-12.0.45-r1/work/jmol-12.0.45/JmolAppletSigned0_i18n_da.jar'
removed `/var/tmp/portage/sci-chemistry/jmol-applet-12.0.45-r1/work/jmol-12.0.45/JmolAppletSigned0_i18n_de.jar'
removed `/var/tmp/portage/sci-chemistry/jmol-applet-12.0.45-r1/work/jmol-12.0.45/JmolAppletSigned0_i18n_el.jar'
removed `/var/tmp/portage/sci-chemistry/jmol-applet-12.0.45-r1/work/jmol-12.0.45/JmolAppletSigned0_i18n_en_GB.jar'
removed `/var/tmp/portage/sci-chemistry/jmol-applet-12.0.45-r1/work/jmol-12.0.45/JmolAppletSigned0_i18n_es.jar'
removed `/var/tmp/portage/sci-chemistry/jmol-applet-12.0.45-r1/work/jmol-12.0.45/JmolAppletSigned0_i18n_et.jar'
removed `/var/tmp/portage/sci-chemistry/jmol-applet-12.0.45-r1/work/jmol-12.0.45/JmolAppletSigned0_i18n_fi.jar'
removed `/var/tmp/portage/sci-chemistry/jmol-applet-12.0.45-r1/work/jmol-12.0.45/JmolAppletSigned0_i18n_fr.jar'
removed `/var/tmp/portage/sci-chemistry/jmol-applet-12.0.45-r1/work/jmol-12.0.45/JmolAppletSigned0_i18n_hu.jar'
removed `/var/tmp/portage/sci-chemistry/jmol-applet-12.0.45-r1/work/jmol-12.0.45/JmolAppletSigned0_i18n_id.jar'
removed `/var/tmp/portage/sci-chemistry/jmol-applet-12.0.45-r1/work/jmol-12.0.45/JmolAppletSigned0_i18n_it.jar'
removed `/var/tmp/portage/sci-chemistry/jmol-applet-12.0.45-r1/work/jmol-12.0.45/JmolAppletSigned0_i18n_ko.jar'
removed `/var/tmp/portage/sci-chemistry/jmol-applet-12.0.45-r1/work/jmol-12.0.45/JmolAppletSigned0_i18n_nb.jar'
removed `/var/tmp/portage/sci-chemistry/jmol-applet-12.0.45-r1/work/jmol-12.0.45/JmolAppletSigned0_i18n_nl.jar'
removed `/var/tmp/portage/sci-chemistry/jmol-applet-12.0.45-r1/work/jmol-12.0.45/JmolAppletSigned0_i18n_oc.jar'
removed `/var/tmp/portage/sci-chemistry/jmol-applet-12.0.45-r1/work/jmol-12.0.45/JmolAppletSigned0_i18n_pl.jar'
removed `/var/tmp/portage/sci-chemistry/jmol-applet-12.0.45-r1/work/jmol-12.0.45/JmolAppletSigned0_i18n_pt.jar'
removed `/var/tmp/portage/sci-chemistry/jmol-applet-12.0.45-r1/work/jmol-12.0.45/JmolAppletSigned0_i18n_pt_BR.jar'
removed `/var/tmp/portage/sci-chemistry/jmol-applet-12.0.45-r1/work/jmol-12.0.45/JmolAppletSigned0_i18n_ru.jar'
removed `/var/tmp/portage/sci-chemistry/jmol-applet-12.0.45-r1/work/jmol-12.0.45/JmolAppletSigned0_i18n_sl.jar'
removed `/var/tmp/portage/sci-chemistry/jmol-applet-12.0.45-r1/work/jmol-12.0.45/JmolAppletSigned0_i18n_sv.jar'
removed `/var/tmp/portage/sci-chemistry/jmol-applet-12.0.45-r1/work/jmol-12.0.45/JmolAppletSigned0_i18n_ta.jar'
removed `/var/tmp/portage/sci-chemistry/jmol-applet-12.0.45-r1/work/jmol-12.0.45/JmolAppletSigned0_i18n_tr.jar'
removed `/var/tmp/portage/sci-chemistry/jmol-applet-12.0.45-r1/work/jmol-12.0.45/JmolAppletSigned0_i18n_uk.jar'
removed `/var/tmp/portage/sci-chemistry/jmol-applet-12.0.45-r1/work/jmol-12.0.45/JmolAppletSigned0_i18n_zh_CN.jar'
removed `/var/tmp/portage/sci-chemistry/jmol-applet-12.0.45-r1/work/jmol-12.0.45/JmolAppletSigned0_i18n_zh_TW.jar'
removed `/var/tmp/portage/sci-chemistry/jmol-applet-12.0.45-r1/work/jmol-12.0.45/JmolData.jar'
removed `/var/tmp/portage/sci-chemistry/jmol-applet-12.0.45-r1/work/jmol-12.0.45/plugin-jars/dadmlbrowser.jar'
removed `/var/tmp/portage/sci-chemistry/jmol-applet-12.0.45-r1/work/jmol-12.0.45/plugin-jars/dirbrowser.jar'
`netscape.jar' -> `netscape.tempjar'
removed `Acme.jar'
removed `commons-cli-1.0.jar'
removed `gnujaxp-onlysax.jar'
removed `gnujaxp.jar'
removed `itext-1.4.5.jar'
removed `junit.jar'
removed `saxon.jar'
removed `vecmath1.2-1.14.jar'
removed `vecmath1.2-1.14.tar.gz'
`netscape.tempjar' -> `netscape.jar'
* Disabling all optional ANT_TASKS
[echo] XSLT class 'com.icl.saxon.StyleSheet' not found.
[echo] Note that the documentation is NOT generated now.
[echo] Generating user's guide
[java] Java Result: 1
[echo] Generating history of changes
[java] Java Result: 1
[echo] Generating developer's guide
[java] Java Result: 1
BUILD FAILED
/var/tmp/portage/sci-chemistry/jmol-applet-12.0.45-r1/work/jmol-12.0.45/build.xml:304: jarsigner returned: 1
Total time: 15 seconds
* ERROR: sci-chemistry/jmol-applet-12.0.45-r1 failed (compile phase):
* eant failed
*
* Call stack:
* ebuild.sh, line 56: Called src_compile
* environment, line 4331: Called eant '-Dlibjars.uptodate=true' 'main'
* environment, line 898: Called die
* The specific snippet of code:
* ant ${antflags} "${@}" || die "eant failed"
*
* If you need support, post the output of 'emerge --info =sci-chemistry/jmol-applet-12.0.45-r1',
* the complete build log and the output of 'emerge -pqv =sci-chemistry/jmol-applet-12.0.45-r1'.
* This ebuild is from an overlay named 'sage-on-gentoo': '/var/lib/layman/sage-on-gentoo/'
!!! When you file a bug report, please include the following information:
GENTOO_VM=sun-jdk-1.6 CLASSPATH="" JAVA_HOME="/opt/sun-jdk-1.6.0.26"
JAVACFLAGS="-source 1.4 -target 1.4" COMPILER="javac"
and of course, the output of emerge --info
* The complete build log is located at '/var/tmp/portage/sci-chemistry/jmol-applet-12.0.45-r1/temp/build.log'.
* The ebuild environment file is located at '/var/tmp/portage/sci-chemistry/jmol-applet-12.0.45-r1/temp/environment'.
* S: '/var/tmp/portage/sci-chemistry/jmol-applet-12.0.45-r1/work/jmol-12.0.45'
[-- Attachment #3: build-jmol.log.txt --]
[-- Type: text/plain, Size: 12053 bytes --]
* Package: sci-chemistry/jmol-12.0.45
* Repository: sage-on-gentoo
* Maintainer: je_fro@gentoo.org sci-chemistry@gentoo.org
* USE: amd64 client-only consolekit elibc_glibc kernel_linux multilib policykit userland_GNU
* FEATURES: preserve-libs sandbox
>>> ^[[1m^[[37mcfg-update-1.8.2-r1^[[0m^[[0m: Checksum index is up-to-date ...
* Using: sun-jdk-1.6
* Applying jmol-nointl.patch ...
[ ok ]
* Applying jmol-manifest.patch ...
[ ok ]
removed `/var/tmp/portage/sci-chemistry/jmol-12.0.45/work/jmol-12.0.45/Jmol.jar'
removed `/var/tmp/portage/sci-chemistry/jmol-12.0.45/work/jmol-12.0.45/JmolApplet.jar'
removed `/var/tmp/portage/sci-chemistry/jmol-12.0.45/work/jmol-12.0.45/JmolApplet0.jar'
removed `/var/tmp/portage/sci-chemistry/jmol-12.0.45/work/jmol-12.0.45/JmolApplet0_Console.jar'
removed `/var/tmp/portage/sci-chemistry/jmol-12.0.45/work/jmol-12.0.45/JmolApplet0_Minimize.jar'
removed `/var/tmp/portage/sci-chemistry/jmol-12.0.45/work/jmol-12.0.45/JmolApplet0_Popup.jar'
removed `/var/tmp/portage/sci-chemistry/jmol-12.0.45/work/jmol-12.0.45/JmolApplet0_ReadersCifPdb.jar'
removed `/var/tmp/portage/sci-chemistry/jmol-12.0.45/work/jmol-12.0.45/JmolApplet0_ReadersMolXyz.jar'
removed `/var/tmp/portage/sci-chemistry/jmol-12.0.45/work/jmol-12.0.45/JmolApplet0_ReadersMore.jar'
removed `/var/tmp/portage/sci-chemistry/jmol-12.0.45/work/jmol-12.0.45/JmolApplet0_ReadersQuantum.jar'
removed `/var/tmp/portage/sci-chemistry/jmol-12.0.45/work/jmol-12.0.45/JmolApplet0_ReadersSimple.jar'
removed `/var/tmp/portage/sci-chemistry/jmol-12.0.45/work/jmol-12.0.45/JmolApplet0_ReadersXml.jar'
removed `/var/tmp/portage/sci-chemistry/jmol-12.0.45/work/jmol-12.0.45/JmolApplet0_ReadersXtal.jar'
removed `/var/tmp/portage/sci-chemistry/jmol-12.0.45/work/jmol-12.0.45/JmolApplet0_ShapeBio.jar'
removed `/var/tmp/portage/sci-chemistry/jmol-12.0.45/work/jmol-12.0.45/JmolApplet0_ShapeSpecial.jar'
removed `/var/tmp/portage/sci-chemistry/jmol-12.0.45/work/jmol-12.0.45/JmolApplet0_ShapeSurface.jar'
removed `/var/tmp/portage/sci-chemistry/jmol-12.0.45/work/jmol-12.0.45/JmolApplet0_Smiles.jar'
removed `/var/tmp/portage/sci-chemistry/jmol-12.0.45/work/jmol-12.0.45/JmolApplet0_Symmetry.jar'
removed `/var/tmp/portage/sci-chemistry/jmol-12.0.45/work/jmol-12.0.45/JmolApplet0_i18n_ar.jar'
removed `/var/tmp/portage/sci-chemistry/jmol-12.0.45/work/jmol-12.0.45/JmolApplet0_i18n_ca.jar'
removed `/var/tmp/portage/sci-chemistry/jmol-12.0.45/work/jmol-12.0.45/JmolApplet0_i18n_cs.jar'
removed `/var/tmp/portage/sci-chemistry/jmol-12.0.45/work/jmol-12.0.45/JmolApplet0_i18n_da.jar'
removed `/var/tmp/portage/sci-chemistry/jmol-12.0.45/work/jmol-12.0.45/JmolApplet0_i18n_de.jar'
removed `/var/tmp/portage/sci-chemistry/jmol-12.0.45/work/jmol-12.0.45/JmolApplet0_i18n_el.jar'
removed `/var/tmp/portage/sci-chemistry/jmol-12.0.45/work/jmol-12.0.45/JmolApplet0_i18n_en_GB.jar'
removed `/var/tmp/portage/sci-chemistry/jmol-12.0.45/work/jmol-12.0.45/JmolApplet0_i18n_es.jar'
removed `/var/tmp/portage/sci-chemistry/jmol-12.0.45/work/jmol-12.0.45/JmolApplet0_i18n_et.jar'
removed `/var/tmp/portage/sci-chemistry/jmol-12.0.45/work/jmol-12.0.45/JmolApplet0_i18n_fi.jar'
removed `/var/tmp/portage/sci-chemistry/jmol-12.0.45/work/jmol-12.0.45/JmolApplet0_i18n_fr.jar'
removed `/var/tmp/portage/sci-chemistry/jmol-12.0.45/work/jmol-12.0.45/JmolApplet0_i18n_hu.jar'
removed `/var/tmp/portage/sci-chemistry/jmol-12.0.45/work/jmol-12.0.45/JmolApplet0_i18n_id.jar'
removed `/var/tmp/portage/sci-chemistry/jmol-12.0.45/work/jmol-12.0.45/JmolApplet0_i18n_it.jar'
removed `/var/tmp/portage/sci-chemistry/jmol-12.0.45/work/jmol-12.0.45/JmolApplet0_i18n_ko.jar'
removed `/var/tmp/portage/sci-chemistry/jmol-12.0.45/work/jmol-12.0.45/JmolApplet0_i18n_nb.jar'
removed `/var/tmp/portage/sci-chemistry/jmol-12.0.45/work/jmol-12.0.45/JmolApplet0_i18n_nl.jar'
removed `/var/tmp/portage/sci-chemistry/jmol-12.0.45/work/jmol-12.0.45/JmolApplet0_i18n_oc.jar'
removed `/var/tmp/portage/sci-chemistry/jmol-12.0.45/work/jmol-12.0.45/JmolApplet0_i18n_pl.jar'
removed `/var/tmp/portage/sci-chemistry/jmol-12.0.45/work/jmol-12.0.45/JmolApplet0_i18n_pt.jar'
removed `/var/tmp/portage/sci-chemistry/jmol-12.0.45/work/jmol-12.0.45/JmolApplet0_i18n_pt_BR.jar'
removed `/var/tmp/portage/sci-chemistry/jmol-12.0.45/work/jmol-12.0.45/JmolApplet0_i18n_ru.jar'
removed `/var/tmp/portage/sci-chemistry/jmol-12.0.45/work/jmol-12.0.45/JmolApplet0_i18n_sl.jar'
removed `/var/tmp/portage/sci-chemistry/jmol-12.0.45/work/jmol-12.0.45/JmolApplet0_i18n_sv.jar'
removed `/var/tmp/portage/sci-chemistry/jmol-12.0.45/work/jmol-12.0.45/JmolApplet0_i18n_ta.jar'
removed `/var/tmp/portage/sci-chemistry/jmol-12.0.45/work/jmol-12.0.45/JmolApplet0_i18n_tr.jar'
removed `/var/tmp/portage/sci-chemistry/jmol-12.0.45/work/jmol-12.0.45/JmolApplet0_i18n_uk.jar'
removed `/var/tmp/portage/sci-chemistry/jmol-12.0.45/work/jmol-12.0.45/JmolApplet0_i18n_zh_CN.jar'
removed `/var/tmp/portage/sci-chemistry/jmol-12.0.45/work/jmol-12.0.45/JmolApplet0_i18n_zh_TW.jar'
removed `/var/tmp/portage/sci-chemistry/jmol-12.0.45/work/jmol-12.0.45/JmolAppletSigned.jar'
removed `/var/tmp/portage/sci-chemistry/jmol-12.0.45/work/jmol-12.0.45/JmolAppletSigned0.jar'
removed `/var/tmp/portage/sci-chemistry/jmol-12.0.45/work/jmol-12.0.45/JmolAppletSigned0_Console.jar'
removed `/var/tmp/portage/sci-chemistry/jmol-12.0.45/work/jmol-12.0.45/JmolAppletSigned0_Minimize.jar'
removed `/var/tmp/portage/sci-chemistry/jmol-12.0.45/work/jmol-12.0.45/JmolAppletSigned0_MultiTouch.jar'
removed `/var/tmp/portage/sci-chemistry/jmol-12.0.45/work/jmol-12.0.45/JmolAppletSigned0_Popup.jar'
removed `/var/tmp/portage/sci-chemistry/jmol-12.0.45/work/jmol-12.0.45/JmolAppletSigned0_ReadersCifPdb.jar'
removed `/var/tmp/portage/sci-chemistry/jmol-12.0.45/work/jmol-12.0.45/JmolAppletSigned0_ReadersMolXyz.jar'
removed `/var/tmp/portage/sci-chemistry/jmol-12.0.45/work/jmol-12.0.45/JmolAppletSigned0_ReadersMore.jar'
removed `/var/tmp/portage/sci-chemistry/jmol-12.0.45/work/jmol-12.0.45/JmolAppletSigned0_ReadersQuantum.jar'
removed `/var/tmp/portage/sci-chemistry/jmol-12.0.45/work/jmol-12.0.45/JmolAppletSigned0_ReadersSimple.jar'
removed `/var/tmp/portage/sci-chemistry/jmol-12.0.45/work/jmol-12.0.45/JmolAppletSigned0_ReadersXml.jar'
removed `/var/tmp/portage/sci-chemistry/jmol-12.0.45/work/jmol-12.0.45/JmolAppletSigned0_ReadersXtal.jar'
removed `/var/tmp/portage/sci-chemistry/jmol-12.0.45/work/jmol-12.0.45/JmolAppletSigned0_ShapeBio.jar'
removed `/var/tmp/portage/sci-chemistry/jmol-12.0.45/work/jmol-12.0.45/JmolAppletSigned0_ShapeSpecial.jar'
removed `/var/tmp/portage/sci-chemistry/jmol-12.0.45/work/jmol-12.0.45/JmolAppletSigned0_ShapeSurface.jar'
removed `/var/tmp/portage/sci-chemistry/jmol-12.0.45/work/jmol-12.0.45/JmolAppletSigned0_Smiles.jar'
removed `/var/tmp/portage/sci-chemistry/jmol-12.0.45/work/jmol-12.0.45/JmolAppletSigned0_Symmetry.jar'
removed `/var/tmp/portage/sci-chemistry/jmol-12.0.45/work/jmol-12.0.45/JmolAppletSigned0_i18n_ar.jar'
removed `/var/tmp/portage/sci-chemistry/jmol-12.0.45/work/jmol-12.0.45/JmolAppletSigned0_i18n_ca.jar'
removed `/var/tmp/portage/sci-chemistry/jmol-12.0.45/work/jmol-12.0.45/JmolAppletSigned0_i18n_cs.jar'
removed `/var/tmp/portage/sci-chemistry/jmol-12.0.45/work/jmol-12.0.45/JmolAppletSigned0_i18n_da.jar'
removed `/var/tmp/portage/sci-chemistry/jmol-12.0.45/work/jmol-12.0.45/JmolAppletSigned0_i18n_de.jar'
removed `/var/tmp/portage/sci-chemistry/jmol-12.0.45/work/jmol-12.0.45/JmolAppletSigned0_i18n_el.jar'
removed `/var/tmp/portage/sci-chemistry/jmol-12.0.45/work/jmol-12.0.45/JmolAppletSigned0_i18n_en_GB.jar'
removed `/var/tmp/portage/sci-chemistry/jmol-12.0.45/work/jmol-12.0.45/JmolAppletSigned0_i18n_es.jar'
removed `/var/tmp/portage/sci-chemistry/jmol-12.0.45/work/jmol-12.0.45/JmolAppletSigned0_i18n_et.jar'
removed `/var/tmp/portage/sci-chemistry/jmol-12.0.45/work/jmol-12.0.45/JmolAppletSigned0_i18n_fi.jar'
removed `/var/tmp/portage/sci-chemistry/jmol-12.0.45/work/jmol-12.0.45/JmolAppletSigned0_i18n_fr.jar'
removed `/var/tmp/portage/sci-chemistry/jmol-12.0.45/work/jmol-12.0.45/JmolAppletSigned0_i18n_hu.jar'
removed `/var/tmp/portage/sci-chemistry/jmol-12.0.45/work/jmol-12.0.45/JmolAppletSigned0_i18n_id.jar'
removed `/var/tmp/portage/sci-chemistry/jmol-12.0.45/work/jmol-12.0.45/JmolAppletSigned0_i18n_it.jar'
removed `/var/tmp/portage/sci-chemistry/jmol-12.0.45/work/jmol-12.0.45/JmolAppletSigned0_i18n_ko.jar'
removed `/var/tmp/portage/sci-chemistry/jmol-12.0.45/work/jmol-12.0.45/JmolAppletSigned0_i18n_nb.jar'
removed `/var/tmp/portage/sci-chemistry/jmol-12.0.45/work/jmol-12.0.45/JmolAppletSigned0_i18n_nl.jar'
removed `/var/tmp/portage/sci-chemistry/jmol-12.0.45/work/jmol-12.0.45/JmolAppletSigned0_i18n_oc.jar'
removed `/var/tmp/portage/sci-chemistry/jmol-12.0.45/work/jmol-12.0.45/JmolAppletSigned0_i18n_pl.jar'
removed `/var/tmp/portage/sci-chemistry/jmol-12.0.45/work/jmol-12.0.45/JmolAppletSigned0_i18n_pt.jar'
removed `/var/tmp/portage/sci-chemistry/jmol-12.0.45/work/jmol-12.0.45/JmolAppletSigned0_i18n_pt_BR.jar'
removed `/var/tmp/portage/sci-chemistry/jmol-12.0.45/work/jmol-12.0.45/JmolAppletSigned0_i18n_ru.jar'
removed `/var/tmp/portage/sci-chemistry/jmol-12.0.45/work/jmol-12.0.45/JmolAppletSigned0_i18n_sl.jar'
removed `/var/tmp/portage/sci-chemistry/jmol-12.0.45/work/jmol-12.0.45/JmolAppletSigned0_i18n_sv.jar'
removed `/var/tmp/portage/sci-chemistry/jmol-12.0.45/work/jmol-12.0.45/JmolAppletSigned0_i18n_ta.jar'
removed `/var/tmp/portage/sci-chemistry/jmol-12.0.45/work/jmol-12.0.45/JmolAppletSigned0_i18n_tr.jar'
removed `/var/tmp/portage/sci-chemistry/jmol-12.0.45/work/jmol-12.0.45/JmolAppletSigned0_i18n_uk.jar'
removed `/var/tmp/portage/sci-chemistry/jmol-12.0.45/work/jmol-12.0.45/JmolAppletSigned0_i18n_zh_CN.jar'
removed `/var/tmp/portage/sci-chemistry/jmol-12.0.45/work/jmol-12.0.45/JmolAppletSigned0_i18n_zh_TW.jar'
removed `/var/tmp/portage/sci-chemistry/jmol-12.0.45/work/jmol-12.0.45/JmolData.jar'
removed `/var/tmp/portage/sci-chemistry/jmol-12.0.45/work/jmol-12.0.45/plugin-jars/dadmlbrowser.jar'
removed `/var/tmp/portage/sci-chemistry/jmol-12.0.45/work/jmol-12.0.45/plugin-jars/dirbrowser.jar'
`netscape.jar' -> `netscape.tempjar'
removed `Acme.jar'
removed `commons-cli-1.0.jar'
removed `gnujaxp-onlysax.jar'
removed `gnujaxp.jar'
removed `itext-1.4.5.jar'
removed `junit.jar'
removed `saxon.jar'
removed `vecmath1.2-1.14.jar'
removed `vecmath1.2-1.14.tar.gz'
`netscape.tempjar' -> `netscape.jar'
* Disabling all optional ANT_TASKS
[echo] XSLT class 'com.icl.saxon.StyleSheet' not found.
[echo] Note that the documentation is NOT generated now.
[echo] Generating user's guide
[java] Java Result: 1
[echo] Generating history of changes
[java] Java Result: 1
[echo] Generating developer's guide
[java] Java Result: 1
BUILD FAILED
/var/tmp/portage/sci-chemistry/jmol-12.0.45/work/jmol-12.0.45/build.xml:304: jarsigner returned: 1
Total time: 17 seconds
* ERROR: sci-chemistry/jmol-12.0.45 failed (compile phase):
* eant failed
*
* Call stack:
* ebuild.sh, line 56: Called src_compile
* environment, line 4371: Called eant '-Dlibjars.uptodate=true' 'main'
* environment, line 918: Called die
* The specific snippet of code:
* ant ${antflags} "${@}" || die "eant failed"
*
* If you need support, post the output of 'emerge --info =sci-chemistry/jmol-12.0.45',
* the complete build log and the output of 'emerge -pqv =sci-chemistry/jmol-12.0.45'.
* This ebuild is from an overlay named 'sage-on-gentoo': '/var/lib/layman/sage-on-gentoo/'
!!! When you file a bug report, please include the following information:
GENTOO_VM=sun-jdk-1.6 CLASSPATH="" JAVA_HOME="/opt/sun-jdk-1.6.0.26"
JAVACFLAGS="-source 1.4 -target 1.4" COMPILER="javac"
and of course, the output of emerge --info
* The complete build log is located at '/var/tmp/portage/sci-chemistry/jmol-12.0.45/temp/build.log'.
* The ebuild environment file is located at '/var/tmp/portage/sci-chemistry/jmol-12.0.45/temp/environment'.
* S: '/var/tmp/portage/sci-chemistry/jmol-12.0.45/work/jmol-12.0.45'
[-- Attachment #4: build-sage-doc.log.txt --]
[-- Type: text/plain, Size: 4940 bytes --]
--2011-08-20 20:21:53-- http://www.sagemath.org/doc-bz2/sage-4.7.1-doc-html.tar.bz2
Resolving www.sagemath.org... 128.208.160.197
Connecting to www.sagemath.org|128.208.160.197|:80... connected.
HTTP request sent, awaiting response... 200 OK
Length: 2651527 (2.5M) [application/x-bzip2]
Saving to: “/opt/distfiles/sage-doc-html-4.7.1.tar.bz2”
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1950K .......... .......... .......... .......... .......... 77% 442K 2s
2000K .......... .......... .......... .......... .......... 79% 369K 2s
2050K .......... .......... .......... .......... .......... 81% 500K 2s
2100K .......... .......... .......... .......... .......... 83% 460K 2s
2150K .......... .......... .......... .......... .......... 84% 444K 1s
2200K .......... .......... .......... .......... .......... 86% 426K 1s
2250K .......... .......... .......... .......... .......... 88% 160K 1s
2300K .......... .......... .......... .......... .......... 90% 426K 1s
2350K .......... .......... .......... .......... .......... 92% 412K 1s
2400K .......... .......... .......... .......... .......... 94% 495K 1s
2450K .......... .......... .......... .......... .......... 96% 449K 0s
2500K .......... .......... .......... .......... .......... 98% 383K 0s
2550K .......... .......... .......... ......... 100% 506K=9.1s
2011-08-20 20:22:02 (283 KB/s) - “/opt/distfiles/sage-doc-html-4.7.1.tar.bz2” saved [2651527/2651527]
!!! Fetched file: sage-doc-html-4.7.1.tar.bz2 VERIFY FAILED!
!!! Reason: Filesize does not match recorded size
!!! Got: 2651527
!!! Expected: 10015277
('Filesize does not match recorded size', 2651527, 10015277)
Refetching... File renamed to '/opt/distfiles/sage-doc-html-4.7.1.tar.bz2._checksum_failure_.CR2nnB'
!!! Couldn't download 'sage-doc-html-4.7.1.tar.bz2'. Aborting.
* Fetch failed for 'sci-mathematics/sage-doc-4.7.1', Log file:
* '/var/tmp/portage/sci-mathematics/sage-doc-4.7.1/temp/build.log'
^ permalink raw reply [flat|nested] 3+ messages in thread
* Re: [gentoo-science] [sage-on-gentoo] sci-chemistry/jmol{,-applet}, sci-mathematics/sage-doc fails to compile
2011-08-20 13:23 ` [gentoo-science] [sage-on-gentoo] sci-chemistry/jmol{,-applet}, sci-mathematics/sage-doc fails to compile P Purkayastha
@ 2011-08-21 7:24 ` Christopher Schwan
2011-08-21 15:43 ` P Purkayastha
0 siblings, 1 reply; 3+ messages in thread
From: Christopher Schwan @ 2011-08-21 7:24 UTC (permalink / raw
To: gentoo-science
On Saturday 20 August 2011 21:23:01 P Purkayastha wrote:
> 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
Hi,
Francois fixed the problem with sage-doc's Manifest. I wasnt able to produce
the problems with jmol. I first tried icedtea6-bin until I saw you are using
sun-jdk. However, that did not produce the (un)desired result. Do you have any
ideas, Francois?
To circumvent the problems with jmol, compile sage-notebook without java
(USE=-java). You wont be able to plot in 3d though.
Cheers,
Christopher
^ permalink raw reply [flat|nested] 3+ messages in thread
* Re: [gentoo-science] [sage-on-gentoo] sci-chemistry/jmol{,-applet}, sci-mathematics/sage-doc fails to compile
2011-08-21 7:24 ` Christopher Schwan
@ 2011-08-21 15:43 ` P Purkayastha
0 siblings, 0 replies; 3+ messages in thread
From: P Purkayastha @ 2011-08-21 15:43 UTC (permalink / raw
To: gentoo-science
On 08/21/2011 03:24 PM, Christopher Schwan wrote:
> On Saturday 20 August 2011 21:23:01 P Purkayastha wrote:
>> 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
>
> Hi,
>
> Francois fixed the problem with sage-doc's Manifest. I wasnt able to produce
> the problems with jmol. I first tried icedtea6-bin until I saw you are using
> sun-jdk. However, that did not produce the (un)desired result. Do you have any
> ideas, Francois?
>
> To circumvent the problems with jmol, compile sage-notebook without java
> (USE=-java). You wont be able to plot in 3d though.
>
> Cheers,
> Christopher
>
It seems Francois is unable to post to the ML. So, here's my reply that
I sent to him earlier this day, in order to document my problem in the ML.
Hi Francois,
I didn't have ant-nodeps installed. Perhaps no package pulled it in?
Also, I had changed my jdk from icedtea to sun-jdk a few weeks ago and
it seems ant-core was merged before the switch of jdk's.
All of them have merged successfully now. Thanks for your help.
punarbasu.
^ permalink raw reply [flat|nested] 3+ messages in thread
end of thread, other threads:[~2011-08-21 15:43 UTC | newest]
Thread overview: 3+ messages (download: mbox.gz follow: Atom feed
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2011-08-20 13:23 ` [gentoo-science] [sage-on-gentoo] sci-chemistry/jmol{,-applet}, sci-mathematics/sage-doc fails to compile P Purkayastha
2011-08-21 7:24 ` Christopher Schwan
2011-08-21 15:43 ` P Purkayastha
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