Re: [gentoo-science] [sage-on-gentoo] sci-chemistry/jmol{,-applet}, sci-mathematics/sage-doc fails to compile

[Christopher Schwan]

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