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List Archive: gentoo-science
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To: gentoo-science@g.o
From: P Purkayastha <ppurka@...>
Subject: Re: [sage-on-gentoo] sci-chemistry/jmol{,-applet}, sci-mathematics/sage-doc fails to compile
Date: Sun, 21 Aug 2011 23:43:23 +0800
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:
>> 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=""
>> 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_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://"
>> 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"
> 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.

[sage-on-gentoo] sci-chemistry/jmol{,-applet}, sci-mathematics/sage-doc fails to compile
-- P Purkayastha
Re: [sage-on-gentoo] sci-chemistry/jmol{,-applet}, sci-mathematics/sage-doc fails to compile
-- Christopher Schwan
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Updated Jul 05, 2012

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