[Rd] 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
>
--
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@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] installing spam package is failing (spam_0.29-1)
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/. -- 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@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] installing spam package is failing (spam_0.29-1)
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. __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] installing spam package is failing (spam_0.29-1)
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. ) -- 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@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] installing spam package is failing (spam_0.29-1)
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) ... # -- View this message in context: http://r.789695.n4.nabble.com/installing-spam-package-is-failing-spam-0-29-1-tp4636628p4636920.html Sent from the R devel mailing list archive at Nabble.com. __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] installing spam package is failing (spam_0.29-1)
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/ -- View this message in context: http://r.789695.n4.nabble.com/installing-spam-package-is-failing-spam-0-29-1-tp4636628p4636929.html Sent from the R devel mailing list archive at Nabble.com. __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] installing spam package is failing (spam_0.29-1)
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: -- View this message in context: http://r.789695.n4.nabble.com/installing-spam-package-is-failing-spam-0-29-1-tp4636628p4636972.html Sent from the R devel mailing list archive at Nabble.com. __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] installing spam package is failing (spam_0.29-1)
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. -- View this message in context: http://r.789695.n4.nabble.com/installing-spam-package-is-failing-spam-0-29-1-tp4636628p4636973.html Sent from the R devel mailing list archive at Nabble.com. __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] installing spam package is failing (spam_0.29-1)
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! -- View this message in context: http://r.789695.n4.nabble.com/installing-spam-package-is-failing-spam-0-29-1-tp4636628p4636974.html Sent from the R devel mailing list archive at Nabble.com. __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] installing spam package is failing (spam_0.29-1)
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! -- View this message in context: http://r.789695.n4.nabble.com/installing-spam-package-is-failing-spam-0-29-1-tp4636628p4636975.html Sent from the R devel mailing list archive at Nabble.com. __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] installing spam package is failing (spam_0.29-1)
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. -- View this message in context: http://r.789695.n4.nabble.com/installing-spam-package-is-failing-spam-0-29-1-tp4636628p4636981.html Sent from the R devel mailing list archive at Nabble.com. __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
