R devel - Jul 2012 - installing spam package is failing (spam_0.29-1)

The primary error seems to be:

 "Creating a new generic function for "diff" in "spam"
   Error in setGeneric(f, where = where) :
     must supply a function skeleton, explicitly or via an existing
function"

And the full output follows. Any thoughts on what may be happening
and/or how to work around the problem?

Thanks!
> install.packages('fields')
Installing package(s) into ?/usr/local/lib/R/site-library?
(as ?lib? is unspecified)
--- Please select a CRAN mirror for use in this session ---
CRAN mirror

 1: Argentina (La Plata)      2: Argentina (Mendoza)
[...]

Selection: 1
also installing the dependency ?spam?

trying URL
'http://mirror.fcaglp.unlp.edu.ar/CRAN/src/contrib/spam_0.29-1.tar.gz'
Content type 'application/x-gzip' length 396179 bytes (386 Kb)
opened URL
=================================================downloaded 386 Kb

trying URL
'http://mirror.fcaglp.unlp.edu.ar/CRAN/src/contrib/fields_6.6.3.tar.gz'
Content type 'application/x-gzip' length 2488570 bytes (2.4 Mb)
opened URL
=================================================downloaded 2.4 Mb

* installing *source* package ?spam? ...
** libs
gfortran   -fpic  -O3 -pipe  -g -c bckslvmodified.f -o bckslvmodified.o
gfortran   -fpic  -O3 -pipe  -g -c cholmodified.f -o cholmodified.o
gfortran   -fpic  -O3 -pipe  -g -c dist.f -o dist.o
gfortran   -fpic  -O3 -pipe  -g -c fromsparsekit.f -o fromsparsekit.o
gfortran   -fpic  -O3 -pipe  -g -c kronecker.f -o kronecker.o
gfortran   -fpic  -O3 -pipe  -g -c permutation.f -o permutation.o
gfortran   -fpic  -O3 -pipe  -g -c rowcolstats.f -o rowcolstats.o
gfortran   -fpic  -O3 -pipe  -g -c spamown.f -o spamown.o
gfortran   -fpic  -O3 -pipe  -g -c spamown2.f -o spamown2.o
gfortran   -fpic  -O3 -pipe  -g -c xybind.f -o xybind.o
gcc -shared -o spam.so bckslvmodified.o cholmodified.o dist.o
fromsparsekit.o kronecker.o permutation.o rowcolstats.o s\
pamown.o spamown2.o xybind.o -lgfortran -lm -lquadmath -L/usr/lib/R/lib -lR
installing to /usr/local/lib/R/site-library/spam/libs
** R
** data
**  moving datasets to lazyload DB
** demo
** inst

** preparing package for lazy loading
Creating a new generic function for "print" in "spam"
Creating a new generic function for "summary" in "spam"
Creating a new generic function for "diag" in "spam"
Creating a new generic function for "diag<-" in "spam"
Creating a new generic function for "t" in "spam"
Creating a new generic function for "as.matrix" in "spam"
Creating a new generic function for "all.equal" in "spam"
Creating a new generic function for "isSymmetric" in "spam"
Creating a new generic function for "diff" in "spam"
Error in setGeneric(f, where = where) :
  must supply a function skeleton, explicitly or via an existing function
Error : unable to load R code in package 'spam'
ERROR: lazy loading failed for package ?spam?
* removing ?/usr/local/lib/R/site-library/spam?
ERROR: dependency ?spam? is not available for package ?fields?
* removing ?/usr/local/lib/R/site-library/fields?

The downloaded packages are in
	?/tmp/RtmpauQxtX/downloaded_packages?
Warning messages:
1: In install.packages("fields") :
  installation of package 'spam' had non-zero exit status
2: In install.packages("fields") :
  installation of package 'fields' had non-zero exit
status
> 










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On 16.07.2012 12:44, chuckles the clone wrote:
> The primary error seems to be:
>
>   "Creating a new generic function for "diff" in
"spam"
>     Error in setGeneric(f, where = where) :
>       must supply a function skeleton, explicitly or via an existing
> function"
>
> And the full output follows. Any thoughts on what may be happening
> and/or how to work around the problem?

Is the R-2.15.1 and are all other packages updated?

We do not see this problem in the CRAN checks:

http://cran.r-project.org/web/checks/check_results_spam.html

Uwe Ligges


> Thanks!
>
>> install.packages('fields')
> Installing package(s) into ?/usr/local/lib/R/site-library?
> (as ?lib? is unspecified)
> --- Please select a CRAN mirror for use in this session ---
> CRAN mirror
>
>   1: Argentina (La Plata)      2: Argentina (Mendoza)
> [...]
>
> Selection: 1
> also installing the dependency ?spam?
>
> trying URL
>
'http://mirror.fcaglp.unlp.edu.ar/CRAN/src/contrib/spam_0.29-1.tar.gz'
> Content type 'application/x-gzip' length 396179 bytes (386 Kb)
> opened URL
> =================================================> downloaded 386 Kb
>
> trying URL
>
'http://mirror.fcaglp.unlp.edu.ar/CRAN/src/contrib/fields_6.6.3.tar.gz'
> Content type 'application/x-gzip' length 2488570 bytes (2.4 Mb)
> opened URL
> =================================================> downloaded 2.4 Mb
>
> * installing *source* package ?spam? ...
> ** libs
> gfortran   -fpic  -O3 -pipe  -g -c bckslvmodified.f -o bckslvmodified.o
> gfortran   -fpic  -O3 -pipe  -g -c cholmodified.f -o cholmodified.o
> gfortran   -fpic  -O3 -pipe  -g -c dist.f -o dist.o
> gfortran   -fpic  -O3 -pipe  -g -c fromsparsekit.f -o fromsparsekit.o
> gfortran   -fpic  -O3 -pipe  -g -c kronecker.f -o kronecker.o
> gfortran   -fpic  -O3 -pipe  -g -c permutation.f -o permutation.o
> gfortran   -fpic  -O3 -pipe  -g -c rowcolstats.f -o rowcolstats.o
> gfortran   -fpic  -O3 -pipe  -g -c spamown.f -o spamown.o
> gfortran   -fpic  -O3 -pipe  -g -c spamown2.f -o spamown2.o
> gfortran   -fpic  -O3 -pipe  -g -c xybind.f -o xybind.o
> gcc -shared -o spam.so bckslvmodified.o cholmodified.o dist.o
> fromsparsekit.o kronecker.o permutation.o rowcolstats.o s\
> pamown.o spamown2.o xybind.o -lgfortran -lm -lquadmath -L/usr/lib/R/lib -lR
> installing to /usr/local/lib/R/site-library/spam/libs
> ** R
> ** data
> **  moving datasets to lazyload DB
> ** demo
> ** inst
>
> ** preparing package for lazy loading
> Creating a new generic function for "print" in "spam"
> Creating a new generic function for "summary" in "spam"
> Creating a new generic function for "diag" in "spam"
> Creating a new generic function for "diag<-" in
"spam"
> Creating a new generic function for "t" in "spam"
> Creating a new generic function for "as.matrix" in
"spam"
> Creating a new generic function for "all.equal" in
"spam"
> Creating a new generic function for "isSymmetric" in
"spam"
> Creating a new generic function for "diff" in "spam"
> Error in setGeneric(f, where = where) :
>    must supply a function skeleton, explicitly or via an existing function
> Error : unable to load R code in package 'spam'
> ERROR: lazy loading failed for package ?spam?
> * removing ?/usr/local/lib/R/site-library/spam?
> ERROR: dependency ?spam? is not available for package ?fields?
> * removing ?/usr/local/lib/R/site-library/fields?
>
> The downloaded packages are in
> 	?/tmp/RtmpauQxtX/downloaded_packages?
> Warning messages:
> 1: In install.packages("fields") :
>    installation of package 'spam' had non-zero exit status
> 2: In install.packages("fields") :
>    installation of package 'fields' had non-zero exit status
>>
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> View this message in context:
http://r.789695.n4.nabble.com/installing-spam-package-is-failing-spam-0-29-1-tp4636628.html
> Sent from the R devel mailing list archive at Nabble.com.
>
> ______________________________________________
> R-devel at r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/r-devel
>

No, it is R version 2.13.1
This is the latest version apt-get is getting.
Is there some advanced technique for obtaining version 2.15.1 ?

root:~# cat /etc/motd
Welcome to Ubuntu 11.10 (GNU/Linux 3.0.0-16-virtual x86_64)

root:~# apt-get upgrade R
Reading package lists... Done
Building dependency tree
Reading state information... Done
The following packages have been kept back:
  landscape-client libgeos-c1 linux-image-virtual linux-virtual
0 upgraded, 0 newly installed, 0 to remove and 4 not upgraded.
root:~# R --version
R version 2.13.1 (2011-07-08)
Copyright (C) 2011 The R Foundation for Statistical Computing
ISBN 3-900051-07-0
Platform: x86_64-pc-linux-gnu (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under the terms of the
GNU General Public License version 2.
For more information about these matters see
http://www.gnu.org/licenses/.



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Hi Chuckles,

On Mon, Jul 16, 2012 at 3:05 PM, chuckles the clone
<frobnutz at sogetthis.com> wrote:
> No, it is R version 2.13.1
> This is the latest version apt-get is getting.
> Is there some advanced technique for obtaining version 2.15.1 ?
If you consider "reading the docs" as an advanced technique, then yes:

http://cran.cnr.Berkeley.edu/bin/linux/ubuntu/

HTH,
-steve

-- 
Steve Lianoglou
Graduate Student: Computational Systems Biology
 | Memorial Sloan-Kettering Cancer Center
 | Weill Medical College of Cornell University
Contact Info: http://cbio.mskcc.org/~lianos/contact

Hi Chuckles,

On 07/16/2012 09:05 PM, chuckles the clone wrote:
> No, it is R version 2.13.1
> This is the latest version apt-get is getting.
> Is there some advanced technique for obtaining version 2.15.1 ?
Have a look here:

http://cran.r-project.org/bin/linux/ubuntu/

HTH,
Tobias
> root:~# cat /etc/motd
> Welcome to Ubuntu 11.10 (GNU/Linux 3.0.0-16-virtual x86_64)
>
> root:~# apt-get upgrade R
> Reading package lists... Done
> Building dependency tree
> Reading state information... Done
> The following packages have been kept back:
>    landscape-client libgeos-c1 linux-image-virtual linux-virtual
> 0 upgraded, 0 newly installed, 0 to remove and 4 not upgraded.
> root:~# R --version
> R version 2.13.1 (2011-07-08)
> Copyright (C) 2011 The R Foundation for Statistical Computing
> ISBN 3-900051-07-0
> Platform: x86_64-pc-linux-gnu (64-bit)
>
> R is free software and comes with ABSOLUTELY NO WARRANTY.
> You are welcome to redistribute it under the terms of the
> GNU General Public License version 2.
> For more information about these matters see
> http://www.gnu.org/licenses/.
>
>
>
> --
> View this message in context:
http://r.789695.n4.nabble.com/installing-spam-package-is-failing-spam-0-29-1-tp4636628p4636676.html
> Sent from the R devel mailing list archive at Nabble.com.
>
> ______________________________________________
> R-devel at r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/r-devel
>

On Jul 18, 2012, at 20:02 , chuckles the clone wrote:
> Thanks! But no. sources.list already contains:
> deb http://http://cran.cnr.Berkeley.edu/bin/linux/ubuntu oneiric/
If it is actually spelled like that, that may be the cause of your problem.
Fixing what needs, I see that there is indeed a

http://cran.cnr.berkeley.edu/bin/linux/ubuntu/oneiric/r-base-core_2.15.1-1oneiric0_amd64.deb

file and several of its friends in that directory.
> 
> Re-running any sort of apt-get results in the same failure to upgrade R.
> 
> Is there some way of installing a version of this "spam" library
which
> is compatible with the version of R that apt-get insists on installing?
> 
> (also, who decided to name this thing "spam"? i suppose it seemed
> cute at the time but it is virtually impossible to google for. )
> 
> 
> --
> View this message in context:
http://r.789695.n4.nabble.com/installing-spam-package-is-failing-spam-0-29-1-tp4636628p4636918.html
> Sent from the R devel mailing list archive at Nabble.com.
> 
> ______________________________________________
> R-devel at r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/r-devel
-- 
Peter Dalgaard, Professor,
Center for Statistics, Copenhagen Business School
Solbjerg Plads 3, 2000 Frederiksberg, Denmark
Phone: (+45)38153501
Email: pd.mes at cbs.dk  Priv: PDalgd at gmail.com