Gentoo Archives: gentoo-science

From: Christopher Schwan <cschwan@××××××××××××××××××.de>
To: gentoo-science@l.g.o
Subject: Re: [gentoo-science] [sage-on-gentoo] sci-chemistry/jmol{,-applet}, sci-mathematics/sage-doc fails to compile
Date: Sun, 21 Aug 2011 07:25:03
Message-Id: 20532226.xhhlZSpIRx@cschwan-laptop
In Reply to: [gentoo-science] [sage-on-gentoo] sci-chemistry/jmol{,-applet}, sci-mathematics/sage-doc fails to compile by P Purkayastha
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="" > 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://" > 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