Inspired from reading http://pi-ist-genau-3.de/?p=964 ("Computer algebra on Gentoo") I tried emerging sci-mathematics/Macaulay2-1.4. After resolving some annoyances the emerge succeeded; I thought I'd mention them here in case they should be considered as fixable bugs. First, it seems that, for the time being, one has to put something like ">sci-mathematics/pari-2.3.5" in /etc/portage/package.mask since Macaulay2 expects precisely version 2.3.5 of sci-mathematics/pari. Second, I had to add a file /etc/env.d/02locale containing "LC_CTYPE=en_US.utf8". Without this the emerge runs for a long time but fails to install because of filenames with exotic letters in the name. My "emerge --info" is: Portage 2.1.9.24 (default/linux/amd64/10.0/desktop, gcc-4.4.4, glibc-2.11.2-r3, 2.6.34-gentoo-r12 x86_64) ================================================================= System uname: Linux-2.6.34-gentoo-r12-x86_64-Intel-R-_Core-TM-2_Duo_CPU_T7500_@_2.20GHz-with-gentoo-1.12.14 Timestamp of tree: Sat, 04 Dec 2010 08:30:01 +0000 app-shells/bash: 4.1_p7 dev-java/java-config: 2.1.11-r1 dev-lang/python: 2.6.5-r3::sage-on-gentoo, 3.1.2-r4 dev-util/cmake: 2.8.1-r2 sys-apps/baselayout: 1.12.14-r1 sys-apps/sandbox: 2.3-r1 sys-devel/autoconf: 2.13, 2.65-r1 sys-devel/automake: 1.4_p6-r1, 1.7.9-r1, 1.8.5-r3, 1.9.6-r3, 1.10.3, 1.11.1 sys-devel/binutils: 2.20.1-r1 sys-devel/gcc: 4.4.4-r2 sys-devel/gcc-config: 1.4.1 sys-devel/libtool: 2.2.10 sys-devel/make: 3.81-r2 virtual/os-headers: 2.6.36.1 (sys-kernel/linux-headers) ACCEPT_KEYWORDS="amd64" ACCEPT_LICENSE="*" CBUILD="x86_64-pc-linux-gnu" CFLAGS="-march=core2 -O2 -pipe" CHOST="x86_64-pc-linux-gnu" CONFIG_PROTECT="/etc /usr/kde/3.5/env /usr/kde/3.5/share/config /usr/kde/3.5/shutdown /usr/share/X11/xkb /usr/share/config /var/lib/hsqldb" CONFIG_PROTECT_MASK="/etc/ca-certificates.conf /etc/env.d /etc/env.d/java/ /etc/fonts/fonts.conf /etc/gconf /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=core2 -O2 -pipe" DISTDIR="/usr/portage/distfiles" FEATURES="assume-digests binpkg-logs distlocks fixlafiles fixpackages news parallel-fetch protect-owned sandbox sfperms strict unknown-features-warn unmerge-logs unmerge-orphans userfetch" GENTOO_MIRRORS="http://gentoo.tiscali.nl/ http://gentoo.mneisen.org/ http://gentoo.supp.name/ http://de-mirror.org/distro/gentoo/" LDFLAGS="-Wl,-O1 -Wl,--as-needed" MAKEOPTS="-j3" 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="/seven/tmp" PORTDIR="/usr/portage" PORTDIR_OVERLAY="/var/lib/layman/voip /var/lib/layman/kvm /var/lib/layman/kde-sunset /var/lib/layman/sunrise /var/lib/layman/sage-on-gentoo /usr/local/portage" SYNC="rsync://viveka/gentoo-portage" USE="X a52 aac acl acpi alsa amd64 berkdb branding bzip2 cairo canon cdr cli consolekit corefonts cracklib crypt cups cxx dbus dri dts dvd dvdr emacs emboss encode exif fam firefox flac gdbm gif gnome gpm gtk hal iconv java jpeg lcms libmms libnotify mad mikmod mmx mng modules mp3 mp4 mpeg mplayer mudflap multilib ncurses nls nptl nptlonly ogg opengl openmp pam pango pcre pdf perl png ppds pppd python qt3support qt4 readline sdl session spell sse sse2 ssl startup-notification subversion svg sysfs tcpd tiff truetype unicode usb vorbis x264 xcb xft xine xml xorg xulrunner xv xvid xvmc zlib" ALSA_CARDS="ali5451 als4000 atiixp atiixp-modem bt87x ca0106 cmipci emu10k1x ens1370 ens1371 es1938 es1968 fm801 hda-intel intel8x0 intel8x0m maestro3 trident usb-audio via82xx via82xx-modem ymfpci" 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" 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="keyboard mouse evdev" KERNEL="linux" LCD_DEVICES="bayrad cfontz cfontz633 glk hd44780 lb216 lcdm001 mtxorb ncurses text" PHP_TARGETS="php5-2" RUBY_TARGETS="ruby18" USERLAND="GNU" VIDEO_CARDS="nvidia vesa vga" 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, EMERGE_DEFAULT_OPTS, FFLAGS, INSTALL_MASK, LANG, LC_ALL, LINGUAS, PORTAGE_BUNZIP2_COMMAND, PORTAGE_COMPRESS, PORTAGE_COMPRESS_FLAGS, PORTAGE_RSYNC_EXTRA_OPTS
(In reply to comment #0) > Second, I had to add a file /etc/env.d/02locale containing > "LC_CTYPE=en_US.utf8". Without this the emerge runs for a long time but fails > to install because of filenames with exotic letters in the name. Could you attach build.log with that failure?
(In reply to comment #0) > I thought I'd mention them here in case they > should be considered as fixable bugs. That is always a good choice. Thanks. > First, it seems that, for the time being, one has to put something like > ">sci-mathematics/pari-2.3.5" in /etc/portage/package.mask since Macaulay2 > expects precisely version 2.3.5 of sci-mathematics/pari. Is there a newer version of pari somewhere? The last stable release is 2.3.5, everything beyond that is in alpha and afaiks not in the tree? Also it does not expect exactly 2.3.5, I'm running M2 with sci-mathematics/pari-2.3.4-r1 and everything is fine. > Second, I had to add a file /etc/env.d/02locale containing > "LC_CTYPE=en_US.utf8". Without this the emerge runs for a long time but fails > to install because of filenames with exotic letters in the name. Indeed, I did not test this. I will have a look but to be future proof you shoud probably migrate to utf8 at some point. Please attach a build.log.
I think I'll have to redo the emerge, it may have been confused by the fact that I had the science overlay enabled for a while. Stay tuned,
Good news, this time I had much less problems! Preparations were: Unmerge Macaulay2 and a number of math packages that it pulls in, cleaning out related entries in /etc/portage/package.keywords and /etc/portage/package.use. Remove the /etc/env.d/02profile file. Reboot. Verified after reboot that LC_CTYPE is unset. Checked that revdep-rebuild does not want to rebuild anything. I do have the following deviation from a "vanilla" system: dev-libs/mpfr in package.keywords, since downgrading appears to be tricky. This means I have version 3.0.0_p3. When typing `emerge Macaulay2' I successively need to put cddlib, lrslib, normaliz, gfan, mpir, nauty, frobby, cdd+ in package.keywords, and also declare lrslib to use gmp in package.use. The emerge gets launched and completes. This time Macaulay2 actually gets emerged; maybe this was in fact so the first time as well and I just misunderstood. There is a message in the console that goes >>> Recording sci-mathematics/Macaulay2 in "world" favorites file... * Messages for package sci-mathematics/Macaulay2-1.4: * This package installs one or more file names containing characters that * do not match your current locale settings. The current setting for * filesystem encoding is 'ANSI_X3.4-1968'. * * usr/share/doc/Macaulay2/Macaulay2Doc/html/___Gr\ufffd\ufffdbner_spbases.html * * For best results, UTF-8 encoding is recommended. See the Gentoo Linux * Localization Guide for instructions about how to configure your locale * for UTF-8 encoding: * * http://www.gentoo.org/doc/en/guide-localization.xml *
(In reply to comment #4) > Good news, this time I had much less problems! All right. > I do have the following deviation from a "vanilla" system: dev-libs/mpfr in > package.keywords, since downgrading appears to be tricky. This means I have > version 3.0.0_p3. That is fine. > When typing `emerge Macaulay2' I successively need to put cddlib, lrslib, > normaliz, gfan, mpir, nauty, frobby, cdd+ in package.keywords, and also declare > lrslib to use gmp in package.use. Of course, Macaulay2 and its dependencies are mostly in ~arch. > * This package installs one or more file names containing characters that > * do not match your current locale settings. The current setting for > * filesystem encoding is 'ANSI_X3.4-1968'. > * > * > usr/share/doc/Macaulay2/Macaulay2Doc/html/___Gr\ufffd\ufffdbner_spbases.html > * > * For best results, UTF-8 encoding is recommended. See the Gentoo Linux > * Localization Guide for instructions about how to configure your locale > * for UTF-8 encoding: > * > * http://www.gentoo.org/doc/en/guide-localization.xml > * This message is expected. The developers of Macaulay2 use a UTF-8 computers and the auto-generated documentation uses file names derived from names of functions. In this case "Gröbner" appears and leads to the garbage file name. If I see this correctly your M2 should work fine! (The worst that can happen is that this one help file is not available on your machine.) I will ask upstream about this when I see them next time, but as far as I can see there is no issue with the ebuild. I'm closing this bug, please reopen (or open a new one) if you encounter any (other) problems. Thanks!
