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Bug 246095 - [science overlay] sci-mathematics/Macaulay2
Summary: [science overlay] sci-mathematics/Macaulay2
Status: RESOLVED FIXED
Alias: None
Product: Gentoo Linux
Classification: Unclassified
Component: Current packages (show other bugs)
Hardware: All Linux
: High normal (vote)
Assignee: Default Assignee for New Packages
URL:
Whiteboard:
Keywords: InOverlay
Depends on: 293383
Blocks: gcc-4.3 248365
  Show dependency tree
 
Reported: 2008-11-08 21:16 UTC by Thomas Kahle (RETIRED)
Modified: 2010-11-12 19:07 UTC (History)
2 users (show)

See Also:
Package list:
Runtime testing required: ---


Attachments
New ebuild for Macaulay2-1.2 (Macaulay2-1.2.ebuild,3.59 KB, text/plain)
2009-02-15 12:20 UTC, Thomas Kahle (RETIRED)
Details
Patch for an internal library (patch-3.1.0b,399 bytes, patch)
2009-02-15 12:21 UTC, Thomas Kahle (RETIRED)
Details | Diff
New ebuild for Macaulay2-1.2 (Macaulay2-1.2.ebuild,3.78 KB, text/plain)
2009-02-16 14:29 UTC, Thomas Kahle (RETIRED)
Details

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Description Thomas Kahle (RETIRED) gentoo-dev 2008-11-08 21:16:32 UTC
The error is
c++ -c cf_gcd_charp.cc -w -fno-implicit-templates -I. -I. -I/var/tmp/portage/sci-mathematics/Macaulay2-1.0/work/include -DHAVE_CONFIG_H  -march=core2 -O2 -pipe -fomit-frame-pointer -o cf_gcd_charp.o                                                                
cf_gcd_charp.cc:4:22: error: iostream.h: No such file or directory                                                                 
[...]                                                 
make: *** [cf_gcd_charp.o] Error 1                                                                                                 
make: *** Waiting for unfinished jobs....
----
The program uses deprecated headers.
Details: http://gcc.gnu.org/gcc-4.3/porting_to.html

Reproducible: Always




There is a new version 1.1 available upstream.
This possibly solves the problem.

http://www.math.uiuc.edu/Macaulay2/Downloads/index.html


denkmatte tom # emerge --info
Portage 2.2_rc13 (default-linux/x86/2007.0/desktop, gcc-4.3.2, glibc-2.6.1-r0, 2.6.26.5 i686)
=================================================================                            
System uname: Linux-2.6.26.5-i686-Intel-R-_Core-TM-2_Duo_CPU_L7500_@_1.60GHz-with-glibc2.0   
Timestamp of tree: Thu, 06 Nov 2008 12:45:01 +0000                                           
distcc 2.18.3 i686-pc-linux-gnu (protocols 1 and 2) (default port 3632) [disabled]           
ccache version 2.4 [enabled]                                                                 
app-shells/bash:     3.2_p33                                                                 
dev-java/java-config: 1.3.7, 2.1.6                                                           
dev-lang/python:     2.5.2-r7                                                                
dev-python/pycrypto: 2.0.1-r6                                                                
dev-util/ccache:     2.4-r7                                                                  
dev-util/cmake:      2.6.1                                                                   
sys-apps/baselayout: 2.0.0                                                                   
sys-apps/openrc:     0.3.0-r1                                                                
sys-apps/sandbox:    1.2.18.1-r2                                                             
sys-devel/autoconf:  2.13, 2.61-r2                                                           
sys-devel/automake:  1.5, 1.7.9-r1, 1.8.5-r3, 1.9.6-r2, 1.10.1-r1                            
sys-devel/binutils:  2.18-r3                                                                 
sys-devel/gcc-config: 1.4.0-r4                                                               
sys-devel/libtool:   1.5.26                                                                  
virtual/os-headers:  2.6.23-r3                                                               
ACCEPT_KEYWORDS="x86"                                                                        
CBUILD="i686-pc-linux-gnu"                                                                   
CFLAGS="-march=core2 -O2 -pipe -fomit-frame-pointer"                                         
CHOST="i686-pc-linux-gnu"                                                                    
CONFIG_PROTECT="/etc /usr/kde/3.5/env /usr/kde/3.5/share/config /usr/kde/3.5/shutdown /usr/kde/4.1/env /usr/kde/4.1/share/config /usr/kde/4.1/shutdown /usr/share/config"                                                                                             
CONFIG_PROTECT_MASK="/etc/ca-certificates.conf /etc/env.d /etc/env.d/java/ /etc/fonts/fonts.conf /etc/gconf /etc/gentoo-release /etc/php/apache2-php5/ext-active/ /etc/php/cgi-php5/ext-active/ /etc/php/cli-php5/ext-active/ /etc/revdep-rebuild /etc/terminfo /etc/texmf/web2c /etc/udev/rules.d"                                                                                                      
CXXFLAGS="-march=core2 -O2 -pipe -fomit-frame-pointer"                                                                             
DISTDIR="/usr/portage/distfiles"                                                                                                   
FEATURES="ccache distlocks parallel-fetch preserve-libs protect-owned sandbox sfperms strict unmerge-orphans userfetch"            
GENTOO_MIRRORS="http://gentoo.tiscali.nl/"                                                                                         
LANG="en_US.UTF-8"                                                                                                                 
LDFLAGS="-Wl,-O1 -Wl,--as-needed"                                                                                                  
LINGUAS="en en_US de ja es fr it"                                                                                                  
MAKEOPTS="-j3"                                                                                                                     
PKGDIR="/usr/portage/packages"                                                                                                     
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="/usr/local/portage/layman/science /usr/local/portage/layman/sunrise /usr/local/portage/tom-overlay"
SYNC="rsync://rsync.de.gentoo.org/gentoo-portage"
USE="X a52 aac acl acpi alsa anthy apache2 avahi bash-completion berkdb bluetooth bzip2 cairo canna cddb cdparanoia cdr cjk cli cracklib crypt ctype cups curl daap dbus dri dvd dvdr dvdread eds emacs encode esd evo expat fam fbcon ffmpeg firefox flac fortran freewnn ftp gd gdbm gif glut gmp gnome gnome-keyring gphoto2 gpm graphviz gstreamer gtk guile hal hdaps iconv ieee1394 imagemagick imap imlib ipod ipv6 isdnlog java javascript jpeg kde kdeprefix kerberos latex ldap leim libnotify lm_sensors m17n-lib mad midi migemo mikmod mime mmx mp3 mp4 mpeg mplayer mudflap mule musicbrainz mysql mysqli ncurses nepomuk networkmanager nls nptl nptlonly nsplugin obex ocaml ogg oggvorbis openal opengl openmp oss pam pcmcia pcre pdf perl php plasma plotutils png pppd python qt3 qt3support qt4 quicktime readline reflection samba sasl sdl session slang spell spl sqlite3 sse ssl svg tcpd texlive theora tiff tk truetype unicode usb v4l v4l2 vhosts vim vim-syntax visualization vorbis wifi win32codecs wxwindows x86 xcomposite xine xinerama xml xorg xulrunner xv xvid zeroconf zlib" ALSA_CARDS="ali5451 als4000 atiixp atiixp-modem bt87x ca0106 cmipci emu10k1        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 auth_digest authn_anon authn_dbd authn_dbm authn_default authn_file authz_dbm authz_default authz_groupfile authz_host authz_owner authz_user autoindex cache dav dav_fs dav_lock dbd deflate dir disk_cache env expires ext_filter file_cache filter headers ident imagemap include info log_config logio mem_cache mimemime_magic negotiation proxy proxy_ajp proxy_balancer proxy_connect proxy_http rewrite setenvif so speling status unique_id userdir usertrack vhost_alias" ELIBC="glibc" FRITZCAPI_CARDS="fcpcmcia" INPUT_DEVICES="keyboard mouse evdev" KERNEL="linux" LCD_DEVICES="bayrad cfontz cfontz633 glk hd44780 lb216 lcdm001 mtxorb ncurses text" LINGUAS="en en_US de ja es fr it" USERLAND="GNU" VIDEO_CARDS="intel"
Unset:  CPPFLAGS, CTARGET, EMERGE_DEFAULT_OPTS, FFLAGS, INSTALL_MASK, LC_ALL, PORTAGE_COMPRESS, PORTAGE_COMPRESS_FLAGS, PORTAGE_RSYNC_EXTRA_OPTS
Comment 1 Wormo (RETIRED) gentoo-dev 2008-11-10 00:17:40 UTC
Would you be interested in trying out the version bump yourself, and see if it fixes gcc 4.3 compatibility problems?
Comment 2 Thomas Kahle (RETIRED) gentoo-dev 2008-11-10 09:17:13 UTC
(In reply to comment #1)
> Would you be interested in trying out the version bump yourself, and see if it
> fixes gcc 4.3 compatibility problems?

Ok, I will have a look.
Comment 3 Markus Dittrich (RETIRED) gentoo-dev 2008-11-10 13:36:29 UTC
Hi Thomas,

Thanks a lot and please let us know how things go. 
Macaulay2 builds have been tricky at times in the past.
I'll try to look at it myself.

cheers,
Markus
Comment 4 Thomas Kahle (RETIRED) gentoo-dev 2008-11-15 14:09:32 UTC
(In reply to comment #2)
> (In reply to comment #1)
> > Would you be interested in trying out the version bump yourself, and see if it
> > fixes gcc 4.3 compatibility problems?
> 
> Ok, I will have a look.
> 

The new version 1.1 still has the old header style and does not build without patching. 

Comment 5 Thomas Kahle (RETIRED) gentoo-dev 2008-11-15 16:02:02 UTC
Hi, 
upstream quickly responded, the reason are the old version of libfac and factory that we use. 

Here's the full answer from  Daniel Grayson (dan@math.uiuc.edu)
---
You are using an old version of "factory", a third party library that we
download.  That particular issue was fixed by its authors in version 3.0.4, so
you must be using 3.0.3, which is what we specified in Macaulay2 1.1.  Now we
are using 3.1.0.  This would be easy for you to update in our makefiles.  Let
me know if a problem arises.  You should keep the libfac library version number
in sync, too.
---

By the way, the package Singular also provides libfac, so we have two copies of this as soon as we install both packages. If someone is bored it would be useful to make an ebuild for it and strip it from these packages.
Comment 6 Markus Dittrich (RETIRED) gentoo-dev 2008-11-16 12:52:41 UTC
(In reply to comment #5)
> Hi, 
> upstream quickly responded, the reason are the old version of libfac and
> factory that we use. 
> 
> Here's the full answer from  Daniel Grayson (dan@math.uiuc.edu)
> ---
> You are using an old version of "factory", a third party library that we
> download.  That particular issue was fixed by its authors in version 3.0.4, so
> you must be using 3.0.3, which is what we specified in Macaulay2 1.1.  Now we
> are using 3.1.0.  This would be easy for you to update in our makefiles.  Let
> me know if a problem arises.  You should keep the libfac library version number
> in sync, too.
> ---

Sounds like a plan :)

> 
> By the way, the package Singular also provides libfac, so we have two copies of
> this as soon as we install both packages. If someone is bored it would be
> useful to make an ebuild for it and strip it from these packages.
> 

Unfortunately, I am not too bored these days ;)

I'll have a look at everything soon.

Best,
Markus
Comment 7 Thomas Kahle (RETIRED) gentoo-dev 2009-01-28 16:43:21 UTC
Hi, let me announce that there will be version 1.2 of Macaulay2 really soon !
Despite from that, as the developers are very active between version it would be extremely cool to have an ebuild which installs the svn version. 
This should be pretty similar to just grabbing a tarball and installing from it.
Comment 8 Thomas Kahle (RETIRED) gentoo-dev 2009-02-15 12:20:20 UTC
Created attachment 182118 [details]
New ebuild for Macaulay2-1.2

I have modified the ebuild to build the current version. Please test and comment.
Comment 9 Thomas Kahle (RETIRED) gentoo-dev 2009-02-15 12:21:04 UTC
Created attachment 182119 [details, diff]
Patch for an internal library
Comment 10 Thomas Kahle (RETIRED) gentoo-dev 2009-02-15 12:45:08 UTC
One more remark on dependencies:
Pari (and probably ntl) must be built with the "gmp" useflag. 
I don't know how to realize this. Can EAPI-2 features like 
DEPEND app-misc/foo[bar] already be used ?
Comment 11 Thomas Kahle (RETIRED) gentoo-dev 2009-02-16 14:29:11 UTC
Created attachment 182239 [details]
New ebuild for Macaulay2-1.2

Sorry for spamming your inbox. This is an updated version which checks for pari being built with gmp useflag and: Tests now work ! (on my machine)
Comment 12 Thomas Kahle (RETIRED) gentoo-dev 2009-05-11 15:16:10 UTC
sci-mathematics/Macaulay2-1.2-r2 is in the science overlay.
Please test.
Comment 13 Thomas Kahle (RETIRED) gentoo-dev 2009-08-10 08:21:11 UTC
I don't know anything of Gentoo policies, but is Pmasking the way here ??
It scares users away from testing the new version in the science overlay.
The overlay version has all these issues resolved. 

@sci-mathematics: Could somebody look at this version??
Comment 14 Tomáš Chvátal (RETIRED) gentoo-dev 2009-11-14 16:56:21 UTC
removed from main tree.
Comment 15 Thomas Kahle (RETIRED) gentoo-dev 2009-11-14 19:08:52 UTC
New versions are being published in the science-overlay.
Comment 16 François Bissey 2010-02-19 06:52:23 UTC
I took on myself to adjust the dependencies as I have moved mpir
from dev-libs to sci-libs as discussed in bug #293383
May be it should be made a blocker to this bug.
Comment 17 Thomas Kahle (RETIRED) gentoo-dev 2010-02-19 11:59:00 UTC
Thanks for updating. Macaulay2 now works with mpir-1.3.1
Added blocker. 
Comment 18 Thomas Kahle (RETIRED) gentoo-dev 2010-11-12 19:07:24 UTC
Version 1.4 of Macaulay2 is now back in the tree.
Thanks everyone contributing!