Issue installing Matrix Package

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Issue installing Matrix Package

shivali-2
Hi,

I installed R-3.1.1 on AIX-5.3 and my installation hanged up while
installing Matrix Package.
so i killed the gmake ; gmake install the software nad tired installing
Matrix package manually -

[ncmr0202][/gpfs1/home/shivali/gang/R-3.1.1/bin/package]>
/gpfs1/home/shivali/gang/R-3.1.1/bin/R CMD INSTALL Matrix

the package compiled successfully but while loading Matrix package the
installation hanged up -
in method for 'coerce' with signature '"sparseMatrix","graphNEL"': no
definition for class "graphNEL"
in method for 'coerce' with signature '"TsparseMatrix","graphNEL"': no
definition for class "graphNEL"
Creating a generic function for 'format' from package 'base' in package
'Matrix'
Creating a generic function for 'qr.R' from package 'base' in package
'Matrix'
Creating a generic function for 'qr.Q' from package 'base' in package
'Matrix'
Creating a generic function for 'qr.qy' from package 'base' in package
'Matrix'
Creating a generic function for 'qr.qty' from package 'base' in package
'Matrix'
Creating a generic function for 'qr.coef' from package 'base' in package
'Matrix'
Creating a generic function for 'qr.resid' from package 'base' in package
'Matrix'
Creating a generic function for 'qr.fitted' from package 'base' in package
'Matrix'
** help
*** installing help indices
** building package indices
Loading required package: Matrix


On checking more i come accross the CPU utilization for thread using ps
-ef command (CPU priority penalty ) is inreasing upto 120 max limit.


[ncmr0202][/gpfs1/home/shivali/gang/R-3.1.1]> ps -ef | grep R-3.1.1
 shivali 323978 459010   0 14:36:14 pts/14  0:00 grep R-3.1.1
    root 492034 336504   0 14:34:36 pts/11  0:00 sh
/gpfs1/home/shivali/gang/R-3.1.1/lib/R/bin/Rcmd INSTALL Matrix
    root 525188 492034 120 14:34:37 pts/11  0:30
/gpfs1/home/shivali/gang/R-3.1.1/lib/R/bin/exec/R --args --args --args
nextArgMatrix
[ncmr0202][/gpfs1/home/shivali/gang/R-3.1.1]>


Please help

Regards,
Shivali Gangwar



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AIX-5.3 Issue installing Matrix Package

Martin Maechler
I've changed the subject to draw attention to this issue.

For more, see inline below

> Hi,
> I installed R-3.1.1 on AIX-5.3 and my installation hanged up while
> installing Matrix Package.
> so i killed the gmake ; gmake install the software nad tired installing
> Matrix package manually -

> [ncmr0202][/gpfs1/home/shivali/gang/R-3.1.1/bin/package]>
> /gpfs1/home/shivali/gang/R-3.1.1/bin/R CMD INSTALL Matrix

> the package compiled successfully but while loading Matrix package the
> installation hanged up -
> in method for 'coerce' with signature '"sparseMatrix","graphNEL"': no
> definition for class "graphNEL"
> in method for 'coerce' with signature '"TsparseMatrix","graphNEL"': no
> definition for class "graphNEL"
> Creating a generic function for 'format' from package 'base' in package 'Matrix'
> Creating a generic function for 'qr.R' from package 'base' in package 'Matrix'
> Creating a generic function for 'qr.Q' from package 'base' in package 'Matrix'
> Creating a generic function for 'qr.qy' from package 'base' in package 'Matrix'
> Creating a generic function for 'qr.qty' from package 'base' in package 'Matrix'
> Creating a generic function for 'qr.coef' from package 'base' in package 'Matrix'
> Creating a generic function for 'qr.resid' from package 'base' in package 'Matrix'
> Creating a generic function for 'qr.fitted' from package 'base' in package 'Matrix'
> ** help
> *** installing help indices
> ** building package indices
> Loading required package: Matrix

> On checking more i come accross the CPU utilization for thread using
> ps -ef command (CPU priority penalty ) is inreasing upto 120 max limit.

> [ncmr0202][/gpfs1/home/shivali/gang/R-3.1.1]> ps -ef | grep R-3.1.1
>  shivali 323978 459010   0 14:36:14 pts/14  0:00 grep R-3.1.1
>     root 492034 336504   0 14:34:36 pts/11  0:00 sh /gpfs1/home/shivali/gang/R-3.1.1/lib/R/bin/Rcmd INSTALL Matrix
>     root 525188 492034 120 14:34:37 pts/11  0:30 /gpfs1/home/shivali/gang/R-3.1.1/lib/R/bin/exec/R --args --args --args nextArgMatrix
> [ncmr0202][/gpfs1/home/shivali/gang/R-3.1.1]>

As maintainer of the Matrix package I'm currently claiming that
this is more an issue of AIX configuration when installing R
(and hence the Matrix package) than an issue of the Matrix
package per se.

> Please help

I'm trying,  asking a few questions:

- Have made use of the many hints and consideration about AIX
  installation in the official "R Administration and Installation"
  Manual, notably section 'C.5 AIX', see, e.g.,
         http://cran.rstudio.org/doc/manuals/r-release/R-admin.html#AIX

- What was the exact output when running  ..../configure ?

- Have you set environment variables / PATH for compilers,
  libraries, etc?  If yes, which one?

Hoping this will lead further,
Martin Maechler

> Regards,
> Shivali Gangwar

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Re: AIX-5.3 Issue installing Matrix Package

Ei-ji Nakama
hi,

>>     root 492034 336504   0 14:34:36 pts/11  0:00 sh /gpfs1/home/shivali/gang/R-3.1.1/lib/R/bin/Rcmd INSTALL Matrix

maybe sh running is not good.
please install bash.
CONFIG_SHELL=/boo/foo/bash before running `configure && make'.

--
Best Regards,
--
Eiji NAKAMA <nakama (a) ki.rim.or.jp>
"\u4e2d\u9593\u6804\u6cbb"  <nakama (a) ki.rim.or.jp>

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Re: AIX-5.3 Issue installing Matrix Package

shivali-2
Hi ,

Thanks, but i tried with bash also result is same -
Package Matrix facing issue while Loading  -
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~`
Creating a generic function for 'qr.qty' from package 'base' in package
'Matrix'
Creating a generic function for 'qr.coef' from package 'base' in package
'Matrix'
Creating a generic function for 'qr.resid' from package 'base' in package
'Matrix'
Creating a generic function for 'qr.fitted' from package 'base' in package
'Matrix'
** help
*** installing help indices
** building package indices
Loading required package: Matrix              ==> Hanged up here
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~``



[ncmr0202][/gpfs1/home/shivali]> ps -ef | grep R-3.1.1
 shivali 413756 480210   0 12:49:03 pts/31  0:00 bash
/gpfs1/home/shivali/gang/R-3.1.1/lib/R/bin/Rcmd INSTALL
Matrix_1.1-4.tar.gz
 shivali 291478 413756 120 12:49:03 pts/31 146:54
/gpfs1/home/shivali/gang/R-3.1.1/lib/R/bin/exec/R --args --args --args
nextArgMatrix_1.1-4.tar.gz
 shivali 356902 254484   0 15:17:37 pts/24  0:00 grep R-3.1.1
[ncmr0202][/gpfs1/home/shivali]>

Regards,
Shivali Gangwar

> hi,
>
>>>     root 492034 336504   0 14:34:36 pts/11  0:00 sh
>>> /gpfs1/home/shivali/gang/R-3.1.1/lib/R/bin/Rcmd INSTALL Matrix
>
> maybe sh running is not good.
> please install bash.
> CONFIG_SHELL=/boo/foo/bash before running `configure && make'.
>
> --
> Best Regards,
> --
> Eiji NAKAMA <nakama (a) ki.rim.or.jp>
> "\u4e2d\u9593\u6804\u6cbb"  <nakama (a) ki.rim.or.jp>
>
> Email secured by Check Point
>



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