[gentoo-science] lapack 3.0?

[gentoo-science] lapack 3.0?

[Matthew R. Lee]

I've just installed the science overlay because I want to use rkward
However when I try "emerge -pv rkward" it tells me there are no ebuilds to 
satisfy ">=sci-libs/lapack-3.0"
This is the first time I've used an overlay, so is this a bug in the ebuild of 
rkward or am I missing something?

Matt
-- 
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
Dr. Matthew R. Lee
CASEB & ECIM
Departamento de Ecologia,
P. Universidad Catolica de Chile,
Alameda 340, Santiago.
CP 6513677
CHILE

matt@matthewlee.org
mlee@bio.puc.cl

URL: meiochile.matthewlee.org
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
-- 
gentoo-science@gentoo.org mailing list

Re: [gentoo-science] lapack 3.0?

[Patrice Beaud]

[-- Attachment #1: Type: text/plain, Size: 1636 bytes --]

Matthew R. Lee a écrit :
> I've just installed the science overlay because I want to use rkward
> However when I try "emerge -pv rkward" it tells me there are no ebuilds to 
> satisfy ">=sci-libs/lapack-3.0"
> This is the first time I've used an overlay, so is this a bug in the ebuild of 
> rkward or am I missing something?
>
> Matt
>   
It seems like the ebuild is outdated... (Note: I didn't know however 
RKward existed. Thank you!)

 I make a:
cp -a /usr/portage/local/layman/science/sci-mathematics/rkward/ 
/usr/local/portage/sci-mathematics/

Change the name of the ebuild from rkward-0.3.7_pre1.ebuild to 
rkward-0.4.6.ebuild.


Modify the ebuild:

10c10
< SRC_URI="http://rkward.sourceforge.net/temp/rkward-0.3.7pre1.tar.gz"
---
 > SRC_URI="mirror://sourceforge/${PN}/${P}.tar.gz"
17c17
< DEPEND=">=sci-libs/lapack-3.0
---
 > DEPEND=">=virtual/lapack-3.0
27c27
<       mv rkward-0.3.7pre1 rkward-0.3.7_pre1 || die
---
 > #     mv rkward-0.3.7pre1 rkward-0.3.7_pre1 || die

run
ebuild /usr/local/portage/sci-mathematics/rkward/rkward-0.4.6.ebuild digest


I started emerging and it stops with a sandbox violation:
--------------------------- ACCESS VIOLATION SUMMARY 
---------------------------
LOG FILE = 
"/var/log/sandbox/sandbox-sci-mathematics_-_rkward-0.4.6-14654.log"

open_wr:   /usr/qt/3/etc/settings/.qtrc.lock
open_wr:   /usr/qt/3/etc/settings/.qtrc.lock
--------------------------------------------------------------------------------

I continue without sandbox... :-(
RKward was installed and it works.


Thank you (I can try R) and Good luck !
   Patrice

[-- Attachment #2: patrice.beaud.vcf --]
[-- Type: text/x-vcard, Size: 181 bytes --]

begin:vcard
fn:Patrice Beaud
n:Beaud;Patrice
email;internet:patrice.beaud@a3.epfl.ch
tel;home:+41 26 652 04 09
tel;cell:+41 79 705 96 05
x-mozilla-html:FALSE
version:2.1
end:vcard

Re: [gentoo-science] lapack 3.0?

[Matthew R. Lee]

On Saturday 24 February 2007 18:50, Patrice Beaud wrote:
> Matthew R. Lee a écrit :
> > I've just installed the science overlay because I want to use rkward
> > However when I try "emerge -pv rkward" it tells me there are no ebuilds
> > to satisfy ">=sci-libs/lapack-3.0"
> > This is the first time I've used an overlay, so is this a bug in the
> > ebuild of rkward or am I missing something?
> >
> > Matt
>
> It seems like the ebuild is outdated... (Note: I didn't know however
> RKward existed. Thank you!)
>
>  I make a:
> cp -a /usr/portage/local/layman/science/sci-mathematics/rkward/
> /usr/local/portage/sci-mathematics/
>
> Change the name of the ebuild from rkward-0.3.7_pre1.ebuild to
> rkward-0.4.6.ebuild.
>
>
> Modify the ebuild:
>
> 10c10
> < SRC_URI="http://rkward.sourceforge.net/temp/rkward-0.3.7pre1.tar.gz"
> ---
>
>  > SRC_URI="mirror://sourceforge/${PN}/${P}.tar.gz"
>
> 17c17
> < DEPEND=">=sci-libs/lapack-3.0
> ---
>
>  > DEPEND=">=virtual/lapack-3.0
>
> 27c27
> <       mv rkward-0.3.7pre1 rkward-0.3.7_pre1 || die
> ---
>
>  > #     mv rkward-0.3.7pre1 rkward-0.3.7_pre1 || die
>
> run
> ebuild /usr/local/portage/sci-mathematics/rkward/rkward-0.4.6.ebuild digest
>
>
> I started emerging and it stops with a sandbox violation:
> --------------------------- ACCESS VIOLATION SUMMARY
> ---------------------------
> LOG FILE =
> "/var/log/sandbox/sandbox-sci-mathematics_-_rkward-0.4.6-14654.log"
>
> open_wr:   /usr/qt/3/etc/settings/.qtrc.lock
> open_wr:   /usr/qt/3/etc/settings/.qtrc.lock
> ---------------------------------------------------------------------------
>-----
>
> I continue without sandbox... :-(
> RKward was installed and it works.
>
>
> Thank you (I can try R) and Good luck !
>    Patrice

Patrice,
Thanks for the help.  I made some modifications to the ebuild and I too now 
have rkward-0.4.6 running.  I didn't encounter the same problem with the sand 
box, which is just as well as I don't know how to run an ebuild without the 
sandbox :-)
Given that this ebuild is a. out of date, and b. doesn't work.  Is there 
anyone maintaining it?  I would volunteer, but I have zero experience of 
putting ebuilds together.  If someone who knows what they are doing was 
available on the end of the email to answer my (bleedin' obvious questions, 
I'm just a marine ecologist :-)) I'd give it a go.  I'd like to learn how to 
create ebuilds as there are other packages in addition to rkward that I'd 
like to see in the tree, like xtides

Matt 
-- 
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
Dr. Matthew R. Lee
CASEB & ECIM
Departamento de Ecologia,
P. Universidad Catolica de Chile,
Alameda 340, Santiago.
CP 6513677
CHILE

matt@matthewlee.org
mlee@bio.puc.cl

URL: meiochile.matthewlee.org
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
--
gentoo-science@gentoo.org mailing list

Re: [gentoo-science] lapack 3.0?

[M. Edward (Ed) Borasky]

Matthew R. Lee wrote:
> On Saturday 24 February 2007 18:50, Patrice Beaud wrote:
>   
>> Matthew R. Lee a écrit :
>>     
>>> I've just installed the science overlay because I want to use rkward
>>> However when I try "emerge -pv rkward" it tells me there are no ebuilds
>>> to satisfy ">=sci-libs/lapack-3.0"
>>> This is the first time I've used an overlay, so is this a bug in the
>>> ebuild of rkward or am I missing something?
>>>
>>> Matt
>>>       
>> It seems like the ebuild is outdated... (Note: I didn't know however
>> RKward existed. Thank you!)
>>
>>  I make a:
>> cp -a /usr/portage/local/layman/science/sci-mathematics/rkward/
>> /usr/local/portage/sci-mathematics/
>>
>> Change the name of the ebuild from rkward-0.3.7_pre1.ebuild to
>> rkward-0.4.6.ebuild.
>>
>>
>> Modify the ebuild:
>>
>> 10c10
>> < SRC_URI="http://rkward.sourceforge.net/temp/rkward-0.3.7pre1.tar.gz"
>> ---
>>
>>  > SRC_URI="mirror://sourceforge/${PN}/${P}.tar.gz"
>>
>> 17c17
>> < DEPEND=">=sci-libs/lapack-3.0
>> ---
>>
>>  > DEPEND=">=virtual/lapack-3.0
>>
>> 27c27
>> <       mv rkward-0.3.7pre1 rkward-0.3.7_pre1 || die
>> ---
>>
>>  > #     mv rkward-0.3.7pre1 rkward-0.3.7_pre1 || die
>>
>> run
>> ebuild /usr/local/portage/sci-mathematics/rkward/rkward-0.4.6.ebuild digest
>>
>>
>> I started emerging and it stops with a sandbox violation:
>> --------------------------- ACCESS VIOLATION SUMMARY
>> ---------------------------
>> LOG FILE =
>> "/var/log/sandbox/sandbox-sci-mathematics_-_rkward-0.4.6-14654.log"
>>
>> open_wr:   /usr/qt/3/etc/settings/.qtrc.lock
>> open_wr:   /usr/qt/3/etc/settings/.qtrc.lock
>> ---------------------------------------------------------------------------
>> -----
>>
>> I continue without sandbox... :-(
>> RKward was installed and it works.
>>
>>
>> Thank you (I can try R) and Good luck !
>>    Patrice
>>     
>
> Patrice,
> Thanks for the help.  I made some modifications to the ebuild and I too now 
> have rkward-0.4.6 running.  I didn't encounter the same problem with the sand 
> box, which is just as well as I don't know how to run an ebuild without the 
> sandbox :-)
> Given that this ebuild is a. out of date, and b. doesn't work.  Is there 
> anyone maintaining it?  I would volunteer, but I have zero experience of 
> putting ebuilds together.  If someone who knows what they are doing was 
> available on the end of the email to answer my (bleedin' obvious questions, 
> I'm just a marine ecologist :-)) I'd give it a go.  I'd like to learn how to 
> create ebuilds as there are other packages in addition to rkward that I'd 
> like to see in the tree, like xtides
>
> Matt 
>   
I'm a little curious about something ... does "rkward" actually require 
an external Lapack, or is this optional? The reason I ask is that R 
itself *contains* a copy of Lapack, and the R developers have deprecated 
linking against external Lapack libraries!

-- 
M. Edward (Ed) Borasky, FBG, AB, PTA, PGS, MS, MNLP, NST, ACMC(P)
http://borasky-research.blogspot.com/

If God had meant for carrots to be eaten cooked, He would have given rabbits fire.

-- 
gentoo-science@gentoo.org mailing list

Re: [gentoo-science] lapack 3.0?

[Matthew R. Lee]

On Sunday 25 February 2007 21:38, M. Edward (Ed) Borasky wrote:
> Matthew R. Lee wrote:
> > On Saturday 24 February 2007 18:50, Patrice Beaud wrote:
> >> Matthew R. Lee a écrit :
> >>> I've just installed the science overlay because I want to use rkward
> >>> However when I try "emerge -pv rkward" it tells me there are no ebuilds
> >>> to satisfy ">=sci-libs/lapack-3.0"
> >>> This is the first time I've used an overlay, so is this a bug in the
> >>> ebuild of rkward or am I missing something?
> >>>
> >>> Matt
> >>
> >> It seems like the ebuild is outdated... (Note: I didn't know however
> >> RKward existed. Thank you!)
> >>
> >>  I make a:
> >> cp -a /usr/portage/local/layman/science/sci-mathematics/rkward/
> >> /usr/local/portage/sci-mathematics/
> >>
> >> Change the name of the ebuild from rkward-0.3.7_pre1.ebuild to
> >> rkward-0.4.6.ebuild.
> >>
> >>
> >> Modify the ebuild:
> >>
> >> 10c10
> >> < SRC_URI="http://rkward.sourceforge.net/temp/rkward-0.3.7pre1.tar.gz"
> >> ---
> >>
> >>  > SRC_URI="mirror://sourceforge/${PN}/${P}.tar.gz"
> >>
> >> 17c17
> >> < DEPEND=">=sci-libs/lapack-3.0
> >> ---
> >>
> >>  > DEPEND=">=virtual/lapack-3.0
> >>
> >> 27c27
> >> <       mv rkward-0.3.7pre1 rkward-0.3.7_pre1 || die
> >> ---
> >>
> >>  > #     mv rkward-0.3.7pre1 rkward-0.3.7_pre1 || die
> >>
> >> run
> >> ebuild /usr/local/portage/sci-mathematics/rkward/rkward-0.4.6.ebuild
> >> digest
> >>
> >>
> >> I started emerging and it stops with a sandbox violation:
> >> --------------------------- ACCESS VIOLATION SUMMARY
> >> ---------------------------
> >> LOG FILE =
> >> "/var/log/sandbox/sandbox-sci-mathematics_-_rkward-0.4.6-14654.log"
> >>
> >> open_wr:   /usr/qt/3/etc/settings/.qtrc.lock
> >> open_wr:   /usr/qt/3/etc/settings/.qtrc.lock
> >> ------------------------------------------------------------------------
> >>--- -----
> >>
> >> I continue without sandbox... :-(
> >> RKward was installed and it works.
> >>
> >>
> >> Thank you (I can try R) and Good luck !
> >>    Patrice
> >
> > Patrice,
> > Thanks for the help.  I made some modifications to the ebuild and I too
> > now have rkward-0.4.6 running.  I didn't encounter the same problem with
> > the sand box, which is just as well as I don't know how to run an ebuild
> > without the sandbox :-)
> > Given that this ebuild is a. out of date, and b. doesn't work.  Is there
> > anyone maintaining it?  I would volunteer, but I have zero experience of
> > putting ebuilds together.  If someone who knows what they are doing was
> > available on the end of the email to answer my (bleedin' obvious
> > questions, I'm just a marine ecologist :-)) I'd give it a go.  I'd like
> > to learn how to create ebuilds as there are other packages in addition to
> > rkward that I'd like to see in the tree, like xtides
> >
> > Matt
>
> I'm a little curious about something ... does "rkward" actually require
> an external Lapack, or is this optional? The reason I ask is that R
> itself *contains* a copy of Lapack, and the R developers have deprecated
> linking against external Lapack libraries!
>
I don't know.  But the ebuild was for version 0.3.7.  Back then maybe it did 
need lapack and now it doesn't for the reasons you've given.

Matt
-- 
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
Dr. Matthew R. Lee
CASEB & ECIM
Departamento de Ecologia,
P. Universidad Catolica de Chile,
Alameda 340, Santiago.
CP 6513677
CHILE

matt@matthewlee.org
mlee@bio.puc.cl

URL: meiochile.matthewlee.org
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
--
gentoo-science@gentoo.org mailing list

Re: [gentoo-science] lapack 3.0? (rkward)

[Honza Macháček]

On 26.02.2007 01:38, M. Edward (Ed) Borasky wrote:
> I'm a little curious about something ... does "rkward" actually require
> an external Lapack, or is this optional? The reason I ask is that R
> itself *contains* a copy of Lapack, and the R developers have deprecated
> linking against external Lapack libraries!

  I think I recall some discussion at the bugzilla to the point that all
multimedia packages that compile their own libraries instead of linking
to external ones should be hardmasked, allegedly for the sake of
maintainability. Moreover in my mailbox I've found an old discussion
(28. 8. 2006) of Freemat 2.0 and problems with its dependency on matio,
when accidentally I myself called to attention that Freemat sources
contained their own copy of the matio library, and Andrey G. Grozin
dismissed the option of using them rather fiercely, reasoning:

> This goes against modularity, *the* fundamental principle of any good 
> Linux distribution.

  Anyway, lapack dependence in a frontend to an actual computation
package looks rather suspiciously. Having tried to remove the lapack
dependence from the rkward ebuild did not reveal anything, of course,
when I have lapack-atlas installed. So I grepped the rkward sources case
insensitively for lapack -- since it appears only as R_LAPACK_FLAG,
libRlapack.* and -lRlapack, I think the package really uses algebra
libraries only through R.
  I checked the rkward dependencies in its INSTALL file -- looks like
those in the ebuild (>=x11-libs/qt-3.3.4, >=kde-base/kdelibs-3.4.1) are
too restrictive, the INSTALL file says only ``KDE-libraries and headers
(>= 3.x)'' and ``Qt-libraries and headers (>= 3.x)''. On the other hand,
the rkward INSTALL file claims dependency on R shared library and PHP
comand line interface, so the ebuild probably should test whether PHP
has CLI installed (the R shared library is always installed by the R
ebuild). Unfortunately this is the point where my knowledge of Gentoo
portage reaches its limits, so I cannot try such modification to the ebuild.

  Experimenting, I tried to dispose of all the src_*() functions, but
then the ebuild failed to actually install any files to my system;
nevertheless src_unpack() probably is excessive. At least on my computer
the ebuild installed without it.

  With best regards
						Honza Macháček

-- 
gentoo-science@gentoo.org mailing list

Re: [gentoo-science] lapack 3.0? (rkward)

[M. Edward (Ed) Borasky]

Honza Macháček wrote:
> On 26.02.2007 01:38, M. Edward (Ed) Borasky wrote:
>   
>> I'm a little curious about something ... does "rkward" actually require
>> an external Lapack, or is this optional? The reason I ask is that R
>> itself *contains* a copy of Lapack, and the R developers have deprecated
>> linking against external Lapack libraries!
>>     
>
>   I think I recall some discussion at the bugzilla to the point that all
> multimedia packages that compile their own libraries instead of linking
> to external ones should be hardmasked, allegedly for the sake of
> maintainability. Moreover in my mailbox I've found an old discussion
> (28. 8. 2006) of Freemat 2.0 and problems with its dependency on matio,
> when accidentally I myself called to attention that Freemat sources
> contained their own copy of the matio library, and Andrey G. Grozin
> dismissed the option of using them rather fiercely, reasoning:
>
>   
>> This goes against modularity, *the* fundamental principle of any good 
>> Linux distribution.
>>     
Well, here's the logic of the R developers (from 
http://cran.fhcrc.org/doc/manuals/R-admin.html):


        "A.3.2 LAPACK

Provision is made for using an external LAPACK library, principally to 
cope with BLAS libraries which contain a copy of LAPACK (such as 
|libsunperf| on Solaris, |vecLib| on Mac OS X and ACML on 
`ix86'/`x86_64' Linux). However, the likely performance gains are 
thought to be small (and may be negative), and the default is not to 
search for a suitable LAPACK library, and this is definitely *not* 
recommended.

[snip]

"For problems compiling LAPACK using recent versions of |gcc| on `ix86' 
Linux, see New platforms 
<http://cran.fhcrc.org/doc/manuals/R-admin.html#New-platforms>: these 
problems have surfaced in Fedora Core 3's distribution, for example.

"Please *do* bear in mind that using --with-lapack is `definitely *not* 
recommended': it is provided *only* because it is necessary on some 
platforms."

In any event, when I have beta-tested R releases on my Athlon Thunderbird, when I use the "with-lapack" option and link R with the external Atlas LAPACK I get many failures in the "make check-all" pass. These don't happen when I just use the Atlas BLAS, so I don't use the external LAPACK with R.
-- 
M. Edward (Ed) Borasky, FBG, AB, PTA, PGS, MS, MNLP, NST, ACMC(P)
http://borasky-research.blogspot.com/

If God had meant for carrots to be eaten cooked, He would have given rabbits fire.

-- 
gentoo-science@gentoo.org mailing list