installing spam package is failing (spam_0.29-1)

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installing spam package is failing (spam_0.29-1)

chuckles the clone
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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Re: installing spam package is failing (spam_0.29-1)

Uwe Ligges-3


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
>>
>
>
>
>
>
>
>
>
>
>
>
> --
> 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.
>
> ______________________________________________
> [hidden email] mailing list
> https://stat.ethz.ch/mailman/listinfo/r-devel
>

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Re: installing spam package is failing (spam_0.29-1)

chuckles the clone
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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Re: installing spam package is failing (spam_0.29-1)

Steve Lianoglou-6
Hi Chuckles,

On Mon, Jul 16, 2012 at 3:05 PM, chuckles the clone
<[hidden email]> 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

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Re: installing spam package is failing (spam_0.29-1)

Tobias Verbeke-2
In reply to this post by chuckles the clone
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.
>
> ______________________________________________
> [hidden email] mailing list
> https://stat.ethz.ch/mailman/listinfo/r-devel
>

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Re: installing spam package is failing (spam_0.29-1)

chuckles the clone
Thank you for your snark but it was not necessary.

In fact I *have* read the "documentation". That's how I got R installed
in the first place. But I followed, again, the instructions on that page
and, again, I am still at version 2.13.1. (SEE BELOW)

Is there some other means of causing R to update to the latest version?
There is nothing at all in the "documentation" that suggests I should be
having this issue or what to do about it.

Thanks!


# apt-get install r-base
Reading package lists... Done
Building dependency tree
Reading state information... Done
r-base is already the newest version.
0 upgraded, 0 newly installed, 0 to remove and 4 not upgraded.

# apt-get install r-base-dev
Reading package lists... Done
Building dependency tree
Reading state information... Done
r-base-dev is already the newest version.
r-base-dev set to manually installed.
0 upgraded, 0 newly installed, 0 to remove and 4 not upgraded.
root:~#

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)
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Re: installing spam package is failing (spam_0.29-1)

Heather Turner-2
I expect what's happened is that you have installed R at some point,
then later updated Ubuntu, which caused the R repository you had stored
to be disabled.

Try running

sudo gedit /etc/apt/sources.list

If my guess is right, you will probably have something like

# deb http://<my.favorite.cran.mirror>/bin/linux/ubuntu natty/ #disabled
on upgrade to oneiric

Note that the whole line has been commented out! To fix, simply
uncomment and replace the old ubuntu version (e.g. natty) with your new
one (e.g. oneiric). Then, assuming you already have Michael Rutter's key
on your system, just run

sudo apt-get update && sudo apt-get upgrade

and you should be able to upgrade to 2.15.1

Best wishes,

Heather


On 17/07/12 07:34, chuckles the clone wrote:

> Thank you for your snark but it was not necessary.
>
> In fact I *have* read the "documentation". That's how I got R installed
> in the first place. But I followed, again, the instructions on that page
> and, again, I am still at version 2.13.1. (SEE BELOW)
>
> Is there some other means of causing R to update to the latest version?
> There is nothing at all in the "documentation" that suggests I should be
> having this issue or what to do about it.
>
> Thanks!
>
>
> # apt-get install r-base
> Reading package lists... Done
> Building dependency tree
> Reading state information... Done
> r-base is already the newest version.
> 0 upgraded, 0 newly installed, 0 to remove and 4 not upgraded.
>
> # apt-get install r-base-dev
> Reading package lists... Done
> Building dependency tree
> Reading state information... Done
> r-base-dev is already the newest version.
> r-base-dev set to manually installed.
> 0 upgraded, 0 newly installed, 0 to remove and 4 not upgraded.
> root:~#
>
> 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)
>
>
> --
> View this message in context: http://r.789695.n4.nabble.com/installing-spam-package-is-failing-spam-0-29-1-tp4636628p4636727.html
> Sent from the R devel mailing list archive at Nabble.com.
>
> ______________________________________________
> [hidden email] mailing list
> https://stat.ethz.ch/mailman/listinfo/r-devel
>

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Re: installing spam package is failing (spam_0.29-1)

chuckles the clone
Thanks! But no. sources.list already contains:
deb http://http://cran.cnr.Berkeley.edu/bin/linux/ubuntu oneiric/

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. )
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Re: installing spam package is failing (spam_0.29-1)

Peter Dalgaard-2

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.
>
> ______________________________________________
> [hidden email] 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: [hidden email]  Priv: [hidden email]

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Re: installing spam package is failing (spam_0.29-1)

chuckles the clone
In reply to this post by chuckles the clone

also, it does not help to remove and re-install r-base. as far as apt-get is concerned, version 2.13.1 is the latest.

# apt-get --purge remove r-base-dev
Reading package lists... Done
Building dependency tree
Reading state information... Done
The following packages will be REMOVED:
  r-base-dev*
0 upgraded, 0 newly installed, 1 to remove and 4 not upgraded.
After this operation, 36.9 kB disk space will be freed.
Do you want to continue [Y/n]? y
(Reading database ... 47129 files and directories currently installed.)
Removing r-base-dev ...

# apt-get --purge remove r-base
Reading package lists... Done
Building dependency tree
Reading state information... Done
The following packages were automatically installed and are no longer required:
  gfortran-4.6 libblas-dev libxml-parser-perl patchutils libncurses5-dev cdbs
  libreadline6-dev libpcrecpp0 intltool liblapack-dev libtinfo-dev
  python-scour gfortran libpcre3-dev dh-translations libjpeg62-dev dpatch
  libbz2-dev libreadline-dev libpng12-dev
Use 'apt-get autoremove' to remove them.
The following packages will be REMOVED:
  r-base*
0 upgraded, 0 newly installed, 1 to remove and 4 not upgraded.
After this operation, 77.8 kB disk space will be freed.
Do you want to continue [Y/n]? y
(Reading database ... 47126 files and directories currently installed.)
Removing r-base ...

# apt-get install r-base
Reading package lists... Done
Building dependency tree
Reading state information... Done
The following packages were automatically installed and are no longer required:
  gfortran-4.6 libblas-dev libxml-parser-perl patchutils libncurses5-dev cdbs
  libreadline6-dev libpcrecpp0 intltool liblapack-dev libtinfo-dev
  python-scour gfortran libpcre3-dev dh-translations libjpeg62-dev dpatch
  libbz2-dev libreadline-dev libpng12-dev
Use 'apt-get autoremove' to remove them.
Suggested packages:
  ess r-doc-info r-doc-pdf
The following NEW packages will be installed:
  r-base
0 upgraded, 1 newly installed, 0 to remove and 4 not upgraded.
Need to get 0 B/9,560 B of archives.
After this operation, 77.8 kB of additional disk space will be used.
debconf: unable to initialize frontend: Dialog
debconf: (Dialog frontend will not work on a dumb terminal, an emacs shell buffer, or without a controlling terminal.)
debconf: falling back to frontend: Readline
Selecting previously deselected package r-base.
(Reading database ... 47122 files and directories currently installed.)
Unpacking r-base (from .../r-base_2.13.1-1_all.deb) ...
Setting up r-base (2.13.1-1) ...
# apt-get install r-base-dev
Reading package lists... Done
Building dependency tree

Reading state information... Done
The following NEW packages will be installed:
  r-base-dev
0 upgraded, 1 newly installed, 0 to remove and 4 not upgraded.
Need to get 0 B/3,546 B of archives.
After this operation, 36.9 kB of additional disk space will be used.
debconf: unable to initialize frontend: Dialog
debconf: (Dialog frontend will not work on a dumb terminal, an emacs shell buffer, or without a controlling terminal.)
debconf: falling back to frontend: Readline
Selecting previously deselected package r-base-dev.
(Reading database ... 47126 files and directories currently installed.)
Unpacking r-base-dev (from .../r-base-dev_2.13.1-1_all.deb) ...
Setting up r-base-dev (2.13.1-1) ...
#





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Re: installing spam package is failing (spam_0.29-1)

Steve Lianoglou-6
In reply to this post by chuckles the clone
Hello Chuckles the Clone,

On Wed, Jul 18, 2012 at 2:02 PM, chuckles the clone
<[hidden email]> wrote:
> Thanks! But no. sources.list already contains:
> deb http://http://cran.cnr.Berkeley.edu/bin/linux/ubuntu oneiric/

Could you please copy/paste your /etc/apt/sources.list file here? I
guess what you wrote above is a typo, but it's also wrong -- it would
be easier for us to help you that way, I reckon.

> 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?

You could likely just install it yourself via a call to
`install.packages('spam')`

I reckon you will probably need to `sudo apt-get install r-base-dev`
since it seems (I didn't d/l the package to check) that you'll have to
compile fortran/c code.

Which means you'll also need gcc/gfortran installed.

> (also, who decided to name this thing "spam"? i suppose it seemed
> cute at the time but it is virtually impossible to google for. )

That would be the author of the package.

--
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

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Re: installing spam package is failing (spam_0.29-1)

chuckles the clone
Hello!

No, doing a hand-install of the spam package fails in the same way as
when it is installed via installing the fields package. ie, in exactly the same
way as seen in the initial post in this thread.

Apparently the latest version of "spam" is incompatible with the version
of R that I have installed. I am hoping that if I can't upgrade R, that I can
find a down-graded spam.

The line from my sources.list was cut-and-pasted from a previous suggestion.
Perhaps it is a typo? In any case, here is my entire sources.list.

If it matters, I'm running this on an Amazon EC2 cloud machine.

I'm sorry if these seem like particularly lame questions, but I rarely use
apt-get and have never seen this issue before.

Thanks!


## modifications made here will not survive a re-bundle.
## if you wish to make changes you can:
## a.) add 'apt_preserve_sources_list: true' to /etc/cloud/cloud.cfg
##     or do the same in user-data
## b.) add sources in /etc/apt/sources.list.d
## c.) make changes to template file /etc/cloud/templates/sources.list.tmpl
#

# See http://help.ubuntu.com/community/UpgradeNotes for how to upgrade to
# newer versions of the distribution.
deb http://us-west-1.ec2.archive.ubuntu.com/ubuntu/ oneiric main
deb-src http://us-west-1.ec2.archive.ubuntu.com/ubuntu/ oneiric main

## Major bug fix updates produced after the final release of the
## distribution.
deb http://us-west-1.ec2.archive.ubuntu.com/ubuntu/ oneiric-updates main
deb-src http://us-west-1.ec2.archive.ubuntu.com/ubuntu/ oneiric-updates main

## N.B. software from this repository is ENTIRELY UNSUPPORTED by the Ubuntu
## team. Also, please note that software in universe WILL NOT receive any
## review or updates from the Ubuntu security team.
deb http://us-west-1.ec2.archive.ubuntu.com/ubuntu/ oneiric universe
deb-src http://us-west-1.ec2.archive.ubuntu.com/ubuntu/ oneiric universe
deb http://us-west-1.ec2.archive.ubuntu.com/ubuntu/ oneiric-updates universe
deb-src http://us-west-1.ec2.archive.ubuntu.com/ubuntu/ oneiric-updates universe

## N.B. software from this repository is ENTIRELY UNSUPPORTED by the Ubuntu
## team, and may not be under a free licence. Please satisfy yourself as to
## your rights to use the software. Also, please note that software in
## multiverse WILL NOT receive any review or updates from the Ubuntu
## security team.
# deb http://us-west-1.ec2.archive.ubuntu.com/ubuntu/ oneiric multiverse
# deb-src http://us-west-1.ec2.archive.ubuntu.com/ubuntu/ oneiric multiverse
# deb http://us-west-1.ec2.archive.ubuntu.com/ubuntu/ oneiric-updates multiverse
# deb-src http://us-west-1.ec2.archive.ubuntu.com/ubuntu/ oneiric-updates multiverse

## Uncomment the following two lines to add software from the 'backports'
## repository.
## N.B. software from this repository may not have been tested as
## extensively as that contained in the main release, although it includes
## newer versions of some applications which may provide useful features.
## Also, please note that software in backports WILL NOT receive any review
## or updates from the Ubuntu security team.
# deb http://us-west-1.ec2.archive.ubuntu.com/ubuntu/ oneiric-backports main restricted universe multiverse
# deb-src http://us-west-1.ec2.archive.ubuntu.com/ubuntu/ oneiric-backports main restricted universe multiverse

## Uncomment the following two lines to add software from Canonical's
## 'partner' repository.
## This software is not part of Ubuntu, but is offered by Canonical and the
## respective vendors as a service to Ubuntu users.
# deb http://archive.canonical.com/ubuntu oneiric partner
# deb-src http://archive.canonical.com/ubuntu oneiric partner

deb http://security.ubuntu.com/ubuntu oneiric-security main
deb-src http://security.ubuntu.com/ubuntu oneiric-security main
deb http://security.ubuntu.com/ubuntu oneiric-security universe
deb-src http://security.ubuntu.com/ubuntu oneiric-security universe
# deb http://security.ubuntu.com/ubuntu oneiric-security multiverse
# deb-src http://security.ubuntu.com/ubuntu oneiric-security multiverse


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




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Re: installing spam package is failing (spam_0.29-1)

Peter Dalgaard-2

On Jul 18, 2012, at 20:35 , chuckles the clone wrote:

>
> The line from my sources.list was cut-and-pasted from a previous suggestion.
> Perhaps it is a typo? In any case, here is my entire sources.list.

In that case, the obvious current suggestion is to lose the double http:// in the last line and retry.

--
Peter Dalgaard, Professor,
Center for Statistics, Copenhagen Business School
Solbjerg Plads 3, 2000 Frederiksberg, Denmark
Phone: (+45)38153501
Email: [hidden email]  Priv: [hidden email]

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Re: installing spam package is failing (spam_0.29-1)

chuckles the clone
Well, it looks like part of the problem is that there's an r-base
on us-west-1.ec2.archive.ubuntu.com which apt-get I suppose
must be thinking is the latest.




# apt-cache showpkg r-base
Package: r-base
Versions:
2.13.1-1 (/var/lib/apt/lists/us-west-1.ec2.archive.ubuntu.com_ubuntu_dists_oneiric_universe_binary-amd64_Packages) (/va\
\
r/lib/dpkg/status)
 Description Language: en
                 File: /var/lib/apt/lists/us-west-1.ec2.archive.ubuntu.com_ubuntu_dists_oneiric_universe_i18n_Translati\
\
on-en
                  MD5: e8de27c34fdd57ca1c4480d402910df7
 Description Language:
                 File: /var/lib/apt/lists/us-west-1.ec2.archive.ubuntu.com_ubuntu_dists_oneiric_universe_binary-amd64_P\
\
ackages
                  MD5: e8de27c34fdd57ca1c4480d402910df7


Reverse Depends:
  r-base-core:i386,r-base 1.4.1-1
  texmacs,r-base
  science-numericalcomputation,r-base
  science-meteorology,r-base
  r-doc-info,r-base 1.4.1-1
  r-doc-html,r-base 1.4.1-1
  r-base-html,r-base 1.4.1-1
  r-base-core,r-base 1.4.1-1
  med-physics,r-base
  ess,r-base
Dependencies:
2.13.1-1 - r-base-core (2 2.13.1-1) r-recommended (5 2.13.1-1) ess (0 (null)) r-doc-info (16 (null)) r-doc-pdf (0 (null\
\
)) r-base-html (0 (null)) r-doc-html (0 (null)) r-base:i386 (0 (null))
Provides:
2.13.1-1 -
Reverse Provides:

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Re: installing spam package is failing (spam_0.29-1)

chuckles the clone
If I comment out everything in the sources.list file *except* the cran entry, apt-get fails this way:

# apt-get --reinstall -V install r-base
Reading package lists... Done
Building dependency tree
Reading state information... Done
Reinstallation of r-base is not possible, it cannot be downloaded.
0 upgraded, 0 newly installed, 0 to remove and 1 not upgraded.


Yes, I have successfully done the apt-key thing.


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Re: installing spam package is failing (spam_0.29-1)

chuckles the clone
I suppose since the package system is completely borked, I'll have to build from sources.

But there doesn't seem to be any documentation clarifying what sources I need.
  r-base-core  ?
  r-base          ?  
  r-base-dev  ?

Those will probably be the minimum? But are there other packages that are needed
to get the basic engine up and running?


Thanks!
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Re: installing spam package is failing (spam_0.29-1)

chuckles the clone
Still, it would be a lot easier if there were just a version of the "spam"
library that was known to work with this release of R.  Has anyone successfully
installed this "spam" thing? How did you do it?

Thanks!
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Re: installing spam package is failing (spam_0.29-1)

Dirk Eddelbuettel
In reply to this post by chuckles the clone

For Pete's sake, could you please stop spamming the r-devel list?

We have a dedicated list r-sig-debian for questions related to R on
Debian/Ubuntu.  Please use it.

And as as far as I can tell, Peter already told you what's up:

   deb http://http://cran.cnr.Berkeley.edu/bin/linux/ubuntu oneiric/
       ^^^^^^^^^^^^

Not a valid url.  Once you have told apt/dpkg about additional sources, the
rest takes care of its own as higher package versions win:

edd@max:~$ apt-cache policy r-base-core
r-base-core:
  Installed: 2.15.1-1precise2
  Candidate: 2.15.1-1precise2
  Version table:
 *** 2.15.1-1precise2 0
        500 http://cran.r-project.org/bin/linux/ubuntu/ precise/ Packages
        100 /var/lib/dpkg/status
     2.15.0-1precise0 0
        500 http://cran.r-project.org/bin/linux/ubuntu/ precise/ Packages
     2.14.1-1 0
        500 http://us.archive.ubuntu.com/ubuntu/ precise/universe amd64 Packages
edd@max:~$


Dirk, one of several volunteers making sure the above "just works"

--
Dirk Eddelbuettel | [hidden email] | http://dirk.eddelbuettel.com

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Re: installing spam package is failing (spam_0.29-1)

chuckles the clone
No, I repaired that immediately and tried again. It failed in the same way, re-installing the
old version. I tried commenting out everything in the sources list except the CRAN archive
and then R could not be installed.

Sorry, no. I does not "just work".

From what I can tell, the initial install was done from one of the ubuntu, not CRAN,
repositories. And the version there was 2.13. Once that has happened, it does not
appear to be possible to upgrade to 2.15 at all.


As a result, I am upgrading my ENTIRE INSTALLATION of ubuntu. In hopes that that
might kick something in the broken apt-get repository and maybe I'll get a new version
of R.



But still, this is all JUST SO I CAN INSTALL THE "SPAM" PACKAGE! The spam package dependencies
are broken such that it does not "just work". The latest "spam" package CANNOT be installed
on R version 2.13 AND YET IT TRIES AND THERE DOES NOT SEEM TO BE ANY WAY TO CAUSE
AN EARLIER VERSION TO BE INSTALLED INSTEAD.


I'm sorry that attempting to get your just-works system to install does not work to the point
where I have to ask for assistance. But it does not. And there is no documentation which
even poorly describes what is happening here. So I have no recourse but to ask. I am happy
it works for you as a maintainer and apologise that it does not for me, a user.
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Re: installing spam package is failing (spam_0.29-1)

braverock
On 07/18/2012 08:56 PM, chuckles the clone wrote:
> As a result, I am upgrading my ENTIRE INSTALLATION of ubuntu. In hopes that
> that might kick something in the broken apt-get repository and maybe I'll get a
> new version of R.
And then please take this discussion to r-sig-debian.

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