Davide Cittaro | 1 Jun 14:29 2007
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ncbi-c++ toolkit

Hi all, I would like to share some info on NCBI C++ toolkit for a possible ebuild.
Actually I'm not practical with writing complex ebuilds (I'm going to explain why later). BTW I succesfully compiled NCBI C++ toolkit in this way:

I modified the configure script:

$ diff -Naur configure configure.orig
--- configure   2006-12-04 11:58:09.000000000 +0100
+++ configure.orig       2006-12-04 11:52:44.000000000 +0100
<at> <at> -20602,20 +20602,16 <at> <at>
## NCBI C Toolkit
if test "$with_ncbi_c" != "no" ; then
-   NCBI_C_PATH=${NCBI_C_PATH:="/usr"}
-   #NCBI_C_PATH=${NCBI_C_PATH:="$NCBI"}
+   NCBI_C_PATH=${NCBI_C_PATH:="$NCBI"}
    if test "$ncbi_compiler" = ICC -a -d "$NCBI_C_PATH/ncbi_icc"; then
       NCBI_C_PATH=$NCBI_C_PATH/ncbi_icc
    fi
-   NCBI_C_INCLUDE="-I$NCBI_C_PATH/include/ncbi"
-   #NCBI_C_INCLUDE="-I$NCBI_C_PATH/include${bit64_sfx}"
+   NCBI_C_INCLUDE="-I$NCBI_C_PATH/include${bit64_sfx}"
    if test "$with_debug" = "no" ; then
-     NCBI_C_LIBPATH="$NCBI_C_PATH/lib"
-     #NCBI_C_LIBPATH="$NCBI_C_PATH/lib${bit64_sfx}"
+     NCBI_C_LIBPATH="$NCBI_C_PATH/lib${bit64_sfx}"
    else
-     NCBI_C_LIBPATH="$NCBI_C_PATH/lib"
-     #NCBI_C_LIBPATH="$NCBI_C_PATH/altlib${bit64_sfx}"
+     NCBI_C_LIBPATH="$NCBI_C_PATH/altlib${bit64_sfx}"
    fi
    if test "$with_mt" = "yes" ; then
      NCBI_C_LIBPATH="$NCBI_C_LIBPATH $NCBI_C_LIBPATH/ncbithr.o"

This modification was necessary because gentoo puts NCBI C libraries and headers in places where the C++ toolkit doesn't expect.
I ran configure with these args:

$ ./configure CXXFLAGS=-fexceptions --prefix=/opt/sci-biology --host=i686-pc-linux-gnu --with-mt --with-algo --with-bin-release --with-lfs --with-autodep --with-python=/usr --with-fltk=/usr --with-sqlite3=/usr --with-ctools --without-debug  --without-xerces --without-xalan --without-gui

I've edited Makefile.mk (located into GCC411-ReleaseMT/build) deleting -fno-exceptions in 

MYSQL_INCLUDE = -I/usr/include/mysql -pipe -ffast-math -DHAVE_ERRNO_AS_DEFINE=1 -fno-exception -fno-strict-aliasing

row, otherwise it doesn't compile (I believe this depends on how one compiled mysql...)

and 

$ make 

This is a complex ebuild to me because blast* commands are provided by this toolkit, and they possibly conflict with the ones provided by ncbi-tools. It would be nice to have both installation in slot and select one or the other with eselect (at least blast* commands).

cheers

d
/*
Davide Cittaro
HPC and Bioinformatics Systems <at> Informatics Core

IFOM - Istituto FIRC di Oncologia Molecolare
via adamello, 16
20139 Milano
Italy

tel.: +39(02)574303007
*/


Yuriy Rusinov | 11 Jun 22:52 2007
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Incorrect size of sci-mathematics/octave

Hello !

I try to emerge sci-mathematics/octave package and emerge -pv sci-mathematics/octave gives this message
Calculating dependencies \!!! Digest verification failed:
!!! /usr/local/sci/sci-mathematics/octave/octave- 2.9.12.ebuild
!!! Reason: Filesize does not match recorded size
!!! Got: 4067
!!! Expected: 4065
... done!
my emerge --info is
Portage 2.1.2.7 (default-linux/amd64/2006.1, gcc-4.1.2 , glibc-2.5-r3, 2.6.20-gentoo-r8 x86_64)
=================================================================
System uname: 2.6.20-gentoo-r8 x86_64 AMD Athlon(tm) 64 Processor 3000+
Gentoo Base System release 1.12.9
Timestamp of tree: Mon, 11 Jun 2007 18:20:02 +0000
ccache version 2.4 [disabled]
dev-java/java-config: 1.3.7, 2.0.32
dev-lang/python:     2.4.4-r4
dev-python/pycrypto: 2.0.1-r5
dev-util/ccache:     2.4-r7
sys-apps/sandbox:    1.2.17
sys-devel/autoconf:  2.13, 2.61
sys-devel/automake:  1.4_p6, 1.5, 1.6.3, 1.7.9-r1, 1.8.5-r3, 1.9.6-r2, 1.10
sys-devel/binutils:  2.16.1-r3
sys-devel/gcc-config: 1.3.16
sys-devel/libtool:   1.5.22
virtual/os-headers:  2.6.17-r2
ACCEPT_KEYWORDS="amd64"
AUTOCLEAN="yes"
CBUILD="x86_64-pc-linux-gnu"
CFLAGS="-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"
CONFIG_PROTECT_MASK="/etc/env.d /etc/env.d/java/ /etc/gconf /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"
CXXFLAGS="-O2 -pipe"
DISTDIR="/usr/portage/distfiles"
FEATURES="distlocks metadata-transfer sandbox sfperms strict"
GENTOO_MIRRORS="http://adelie.polymtl.ca/ ftp://gentoo.arcticnetwork.ca/pub/gentoo/ http://gentoo.arcticnetwork.ca/ ftp://mirrors.tera-byte.com/pub/gentoo http://gentoo.mirrors.tera-byte.com/ http://gentoo.osuosl.org/ ftp://distro.ibiblio.org/pub/linux/distributions/gentoo/ http://distro.ibiblio.org/pub/linux/distributions/gentoo/ ftp://ftp.gtlib.gatech.edu/pub/gentoo http://www.gtlib.gatech.edu/pub/gentoo "
LANG="ru_RU.UTF-8"
LC_ALL=""
LINGUAS="en ru"
PKGDIR="/usr/portage/packages"
PORTAGE_RSYNC_OPTS="--recursive --links --safe-links --perms --times --compress --force --whole-file --delete --delete-after --stats --timeout=180 --exclude=/distfiles --exclude=/local --exclude=/packages --filter=H_**/files/digest-*"
PORTAGE_TMPDIR="/var/tmp"
PORTDIR="/usr/portage"
PORTDIR_OVERLAY="/usr/local/portage /usr/local/sci"
SYNC="rsync://rsync.europe.gentoo.org/gentoo-portage"
USE="amd64 berkdb bitmap-fonts cli cracklib crypt cups dri firefox fortran gdbm gnome gpm gtk iconv ipv6 isdnlog libg++ midi mudflap ncurses nls nptl nptlonly openmp pam pcre perl ppds pppd python qt readline reflection session spl ssl tcpd truetype-fonts type1-fonts unicode xorg 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 mulaw multi null plug rate route share shm softvol" ELIBC="glibc" INPUT_DEVICES="keyboard mouse evdev" KERNEL="linux" LCD_DEVICES="bayrad cfontz cfontz633 glk hd44780 lb216 lcdm001 mtxorb ncurses text" LINGUAS="en ru" USERLAND="GNU" VIDEO_CARDS="nv"
Unset:  CTARGET, EMERGE_DEFAULT_OPTS, INSTALL_MASK, LDFLAGS, MAKEOPTS, PORTAGE_COMPRESS, PORTAGE_COMPRESS_FLAGS, PORTAGE_RSYNC_EXTRA_OPTS

Is it my error or not ?

--
Best regards,
Sincerely yours,
Yuriy Rusinov

Philip Webb | 12 Jun 01:38 2007
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Re: Incorrect size of sci-mathematics/octave

070612 Yuriy Rusinov wrote:
> emerge -pv sci-mathematics/octave gives this message
>  Calculating dependencies \!!! Digest verification failed:
>  !!! /usr/local/sci/sci-mathematics/octave/octave-2.9.12.ebuild
>  !!! Reason: Filesize does not match recorded size
>  !!! Got: 4067
>  !!! Expected: 4065

Try resyncing: that seems to be the usual cure.

-- 
========================,,============================================
SUPPORT     ___________//___,  Philip Webb : purslow <at> chass.utoronto.ca
ELECTRIC   /] [] [] [] [] []|  Centre for Urban & Community Studies
TRANSIT    `-O----------O---'  University of Toronto
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Alden Huang | 12 Jun 04:03 2007
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Re: Incorrect size of sci-mathematics/octave

If rsync doesn't work immediately you might have to give it a few days 
to update...
You could also try deleting the tarball from /usr/portage/distfiles and 
refetching....maybe the download was corrupted.

Philip Webb wrote:
> 070612 Yuriy Rusinov wrote:
>   
>> emerge -pv sci-mathematics/octave gives this message
>>  Calculating dependencies \!!! Digest verification failed:
>>  !!! /usr/local/sci/sci-mathematics/octave/octave-2.9.12.ebuild
>>  !!! Reason: Filesize does not match recorded size
>>  !!! Got: 4067
>>  !!! Expected: 4065
>>     
>
> Try resyncing: that seems to be the usual cure.
>
>   

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Jeffrey Gardner | 12 Jun 06:44 2007
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Re: Incorrect size of sci-mathematics/octave


Alden Huang wrote:
> Philip Webb wrote:
>> 070612 Yuriy Rusinov wrote:
>>  
>>> emerge -pv sci-mathematics/octave gives this message
>>>  Calculating dependencies \!!! Digest verification failed:

Sorry about that...I forgot to fix the manifest. It's fixed now, but
you'll note that I've removed all KEYWORDS for this ebuild as it's only
had the most rudimentary testing, and it's not quite ready for prime time.

You'll have to add your arch to the KEYWORDS variable if you want to
upgrade to octave-2.9.12.

In the future you can fix this with:

ebuild /usr/local/science/sci-mathematics/octave-2.9.12.ebuild digest

je_fro

--
Jeffrey Gardner
Gentoo Developer
Public PGP Key ID: 4A5D8F23
hkp://pgpkeys.mit.edu
Justin Findlay | 12 Jun 07:48 2007
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Re: Incorrect size of sci-mathematics/octave

On AD 2007 June 11 Monday 11:44:46 PM -0500, Jeffrey Gardner wrote:
> Sorry about that...I forgot to fix the manifest. It's fixed now, but
> you'll note that I've removed all KEYWORDS for this ebuild as it's only
> had the most rudimentary testing, and it's not quite ready for prime time.

Or maybe you can find a relevant dev on irc and let them know. :-)

> ebuild /usr/local/science/sci-mathematics/octave-2.9.12.ebuild digest

Or
# ebuild $(equery which =octave-2.9.12) digest

Justin
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George Shapovalov | 12 Jun 11:26 2007
X-Face
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Re: Incorrect size of sci-mathematics/octave

Tuesday, 12. June 2007, Alden Huang Ви написали:
> If rsync doesn't work immediately you might have to give it a few days
> to update...
Um, no, not that long. Standard interval between pushes frm the cvs to the 
master sync is 30 min, give it another ~30 to propagate to the mirrors and 
you should be fine. Well, even using webrsync is fater - it is pulled 
together every day, not couple :).

> You could also try deleting the tarball from /usr/portage/distfiles and
> refetching....maybe the download was corrupted.
That would eb the first thing to try. Resync and try (some mirrors are faulty, 
so if you don't believe a particular one you might want to resync again to 
get another one, but I mostly saw few just outright deleting all digests, no 
screwing them). If that does not change much, fetch the source from the 
upstream and compare size/md5/sha1 manually with what's in the digest. If 
this differs, then please file a bug report. (that may mean that upstream 
silently changed their source. Bad upstream :)).

George
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de Almeida, Valmor F. | 21 Jun 15:56 2007
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mpi python recommendation


Hello list,

I would appreciate recommendations on what to use for developing mpi
python codes. I've seen several packages on public domain: mympi, pypar,
mpi python, mpi4py and it would be helpful to start in the right
direction.

Thanks,

--
Valmor de Almeida
ORNL

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Jeffrey Gardner | 21 Jun 21:23 2007
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Autodock released under GPL!

Nice addition ribosome!
-- 
Jeffrey Gardner
Gentoo Developer
Public PGP Key ID: 4A5D8F23
hkp://pgpkeys.mit.edu
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Olivier Fisette | 22 Jun 00:17 2007
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Re: Autodock released under GPL!

On Thursday, 21 June 2007 15:23, Jeffrey Gardner wrote:
> Nice addition ribosome!

The AutoDock ebuild was mainly written by a colleague, so thanks Luc! Whilst 
on the topic, if you use AutoDock, please do take the time to register as a 
user on their Web site. It is nice to see AutoDock 4 released as open source 
software that we can redistribute freely, but registering will help its 
development team with grant proposals.

Cheers,

--

-- 
Olivier Fisette (ribosome)
Gentoo Linux Developer
Scientific applications

Gmane