Gentoo Archives: gentoo-science

From: P Purkayastha <ppurka@×××××.com>
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 15:43:54
In Reply to: Re: [gentoo-science] [sage-on-gentoo] sci-chemistry/jmol{,-applet}, sci-mathematics/sage-doc fails to compile by Christopher Schwan
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="" >> 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 >
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.