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
Message-Id: 4E51279B.9090702@gmail.com
In Reply to: Re: [gentoo-science] [sage-on-gentoo] sci-chemistry/jmol{,-applet}, sci-mathematics/sage-doc fails to compile by Christopher Schwan
1 On 08/21/2011 03:24 PM, Christopher Schwan wrote:
2 > On Saturday 20 August 2011 21:23:01 P Purkayastha wrote:
3 >> Hi,
4 >> I was updating world today and the following packages failed:
5 >>
6 >> 1. sci-chemistry/jmol-applet-12.0.45-r1 and sci-chemistry/jmol-12.0.45
7 >> failed to compile.The errors are almost the same for both the packages.
8 >>
9 >> 2. sci-mathematics/sage-doc-4.7.1 failed with a digest failure.
10 >>
11 >>
12 >> The build logs are attached with this email.
13 >>
14 >> My emerge --info is given below. Please let me know if you need any further
15 >> information.
16 >>
17 >> Portage 2.2.0_alpha51 (default/linux/amd64/10.0/desktop/kde, gcc-4.4.5,
18 >> glibc-2.12.2-r0, 2.6.38-gentoo-r6 x86_64)
19 >> =================================================================
20 >> System uname: Linux-2.6.38-gentoo-r6-x86_64-Intel-R-_Core-TM-_i5_CPU_M_460_@
21 >> _2.53GHz-with-gentoo-2.0.3
22 >> Timestamp of tree: Sat, 20 Aug 2011 11:30:02 +0000
23 >> app-shells/bash: 4.1_p9
24 >> dev-java/java-config: 2.1.11-r3
25 >> dev-lang/python: 2.7.1-r1::sage-on-gentoo, 3.1.3-r1
26 >> dev-util/cmake: 2.8.4-r1
27 >> dev-util/pkgconfig: 0.26
28 >> sys-apps/baselayout: 2.0.3
29 >> sys-apps/openrc: 0.8.3-r1
30 >> sys-apps/sandbox: 2.4
31 >> sys-devel/autoconf: 2.13, 2.68
32 >> sys-devel/automake: 1.9.6-r3, 1.10.3, 1.11.1
33 >> sys-devel/binutils: 2.20.1-r1
34 >> sys-devel/gcc: 4.4.5
35 >> sys-devel/gcc-config: 1.4.1-r1
36 >> sys-devel/libtool: 2.4-r1
37 >> sys-devel/make: 3.82
38 >> sys-kernel/linux-headers: 2.6.38 (virtual/os-headers)
39 >> sys-libs/glibc: 2.12.2
40 >> Repositories: gentoo enlightenment sage-on-gentoo myself
41 >> Installed sets:
42 >> ACCEPT_KEYWORDS="amd64"
43 >> ACCEPT_LICENSE="*"
44 >> CBUILD="x86_64-pc-linux-gnu"
45 >> CFLAGS="-march=native -O2 -pipe"
46 >> CHOST="x86_64-pc-linux-gnu"
47 >> CONFIG_PROTECT="/etc /usr/share/config /usr/share/gnupg/qualified.txt
48 >> /usr/share/xsessions"
49 >> CONFIG_PROTECT_MASK="/etc/ca-certificates.conf /etc/env.d /etc/env.d/java/
50 >> /etc/fonts/fonts.conf /etc/gconf /etc/gentoo-release /etc/revdep-rebuild
51 >> /etc/sandbox.d /etc/terminfo /etc/texmf/language.dat.d
52 >> /etc/texmf/language.def.d /etc/texmf/updmap.d /etc/texmf/web2c"
53 >> CXXFLAGS="-march=native -O2 -pipe"
54 >> DISTDIR="/usr/portage/distfiles"
55 >> EMERGE_DEFAULT_OPTS="--with-bdeps=y"
56 >> FEATURES="assume-digests binpkg-logs distlocks ebuild-locks fixlafiles
57 >> fixpackages news parallel-fetch preserve-libs protect-owned sandbox sfperms
58 >> strict unknown-features-warn unmerge-logs unmerge-orphans userfetch"
59 >> FFLAGS=""
60 >> GENTOO_MIRRORS="http://distfiles.gentoo.org"
61 >> LANG="en_US.UTF8"
62 >> LC_ALL="en_US.UTF-8"
63 >> LDFLAGS="-Wl,-O1 -Wl,--as-needed"
64 >> LINGUAS="en en_US"
65 >> MAKEOPTS="-j2"
66 >> PKGDIR="/usr/portage/packages"
67 >> PORTAGE_CONFIGROOT="/"
68 >> PORTAGE_RSYNC_OPTS="--recursive --links --safe-links --perms --times
69 >> --compress --force --whole-file --delete --stats --timeout=180
70 >> --exclude=/distfiles --exclude=/local --exclude=/packages"
71 >> PORTAGE_TMPDIR="/var/tmp"
72 >> PORTDIR="/usr/portage"
73 >> PORTDIR_OVERLAY="/var/lib/layman/enlightenment
74 >> /var/lib/layman/sage-on-gentoo /usr/local/portage"
75 >> SYNC="rsync://rsync.gentoo.org/gentoo-portage"
76 >> USE="X a52 aac accessibility acl acpi akonadi alsa amd64 bash-completion
77 >> berkdb branding bzip2 cairo cdda cddb cdr cli consolekit cracklib crypt cups
78 >> curl curlwrappers cxx dbus declarative djvu dri dts dvd dvdr encode exif
79 >> fam fbcon ffmpeg flac fontconfig ftp fuse gdbm gdu gif gnutls gphoto2 gpm
80 >> gstreamer gtk iconv ieee1394 imagemagick jpeg kipi lame latex lcms ldap
81 >> libsamplerate lzma mad mmap mmx mmx2 mng modules mp3 mp4 mpeg mudflap
82 >> multilib musepack ncurses networkmanager nls nptl nptlonly ogg opengl
83 >> openmp oss pam pango pch pcmcia pcre pdf perl phonon plasma png policykit
84 >> ppds pppd python qt3support qt4 readline savedconfig sdl session smp speex
85 >> spell sqlite srt sse sse2 ssl ssse3 svg sysfs system-sqlite taglib tcpd
86 >> theora threads tiff truetype udev unicode usb v4l v4l2 vdpau vim-syntax
87 >> vorbis wicd wifi wmf x264 xattr xcf xcomposite xft xinerama xml xorg xosd
88 >> xpm xulrunner xv xvid xvmc yv12 zeroconf zlib zsh-completion"
89 >> ALSA_CARDS="hda-intel" ALSA_PCM_PLUGINS="adpcm alaw asym copy dmix dshare
90 >> dsnoop empty extplug file hooks iec958 ioplug ladspa lfloat linear meter
91 >> mmap_emul mulaw multi null plug rate route share shm softvol"
92 >> APACHE2_MODULES="actions alias auth_basic authn_alias authn_anon authn_dbm
93 >> authn_default authn_file authz_dbm authz_default authz_groupfile authz_host
94 >> authz_owner authz_user autoindex cache cgi cgid dav dav_fs dav_lock deflate
95 >> dir disk_cache env expires ext_filter file_cache filter headers include
96 >> info log_config logio mem_cache mime mime_magic negotiation rewrite
97 >> setenvif speling status unique_id userdir usertrack vhost_alias"
98 >> CALLIGRA_FEATURES="kexi words flow plan stage tables krita karbon braindump
99 >> active" CAMERAS="*" COLLECTD_PLUGINS="df interface irq load memory rrdtool
100 >> swap syslog" ELIBC="glibc"
101 >> GPSD_PROTOCOLS="ashtech aivdm earthmate evermore fv18 garmin garmintxt
102 >> gpsclock itrax mtk3301 nmea ntrip navcom oceanserver oldstyle oncore
103 >> rtcm104v2 rtcm104v3 sirf superstar2 timing tsip tripmate tnt ubx"
104 >> INPUT_DEVICES="evdev keyboard mouse synaptics" KERNEL="linux"
105 >> LCD_DEVICES="bayrad cfontz cfontz633 glk hd44780 lb216 lcdm001 mtxorb
106 >> ncurses text" LINGUAS="en en_US" PHP_TARGETS="php5-3" RUBY_TARGETS="ruby18"
107 >> USERLAND="GNU" VIDEO_CARDS="nvidia vesa" XTABLES_ADDONS="quota2 psd pknock
108 >> lscan length2 ipv4options ipset ipp2p iface geoip fuzzy condition tee tarpit
109 >> sysrq steal rawnat logmark ipmark dhcpmac delude chaos account"
110 >> Unset: CPPFLAGS, CTARGET, INSTALL_MASK, PORTAGE_BUNZIP2_COMMAND,
111 >> PORTAGE_COMPRESS, PORTAGE_COMPRESS_FLAGS, PORTAGE_RSYNC_EXTRA_OPTS
112 >
113 > Hi,
114 >
115 > Francois fixed the problem with sage-doc's Manifest. I wasnt able to produce
116 > the problems with jmol. I first tried icedtea6-bin until I saw you are using
117 > sun-jdk. However, that did not produce the (un)desired result. Do you have any
118 > ideas, Francois?
119 >
120 > To circumvent the problems with jmol, compile sage-notebook without java
121 > (USE=-java). You wont be able to plot in 3d though.
122 >
123 > Cheers,
124 > Christopher
125 >
126
127 It seems Francois is unable to post to the ML. So, here's my reply that
128 I sent to him earlier this day, in order to document my problem in the ML.
129
130
131 Hi Francois,
132
133 I didn't have ant-nodeps installed. Perhaps no package pulled it in?
134 Also, I had changed my jdk from icedtea to sun-jdk a few weeks ago and
135 it seems ant-core was merged before the switch of jdk's.
136
137 All of them have merged successfully now. Thanks for your help.
138 punarbasu.