Prof. John C Nash
2010-Feb-03 17:50 UTC
[R-sig-Debian] Installation woes for rattle (and other packages)
Yesterday I wanted to try rattle on Ubuntu 9.04 Jaunty. I had (and still have)
it running
(though it complains on startup a bit -- I'll look into that later) on a
different bootup
on the same machine with 8.04 Hardy.
I got an error that libglade cannot be found, and various attempts to get glade
support
failed. I removed and reinstalled R -- same problem.
To avoid the issue of local setup being in conflict with R, I created a
VirtualBox
instance of a clean Ubuntu Jaunty. Same woes. To be really sure of things, I put
in a
virtual Debian lenny from debian-503-i386-netinst.iso
Since the Ubuntu cran2deb attempt gave same results as Debian lenny (though the
CRAN
repository was a little different, but cran2deb repository the same), I'll
only include
the Debian run. I also tried the install on a separate machine (real) running
8.04 Hardy
and got a similar broken packages message. So similar results on 4 systems.
What follows below (rather long!) is my set of attempts to get rattle and other
things
running on the Debian Lenny. Some of the attempts at the end are in the
"desperation"
category, but they may indicate that packages are broken, and the debian
wrappings are not
to blame.
Any suggestions of where the problem lies? I'd be happy to learn I've
done something silly
that is easily fixed.
JN
Note: in the following, my mailer appears to be wrapping the lines.
debian 503 installation on VBox -- note a kernel failure on first reboot which
cleared
after it was booted single user and disk fsck was run.
(user/password)
apt-get install wajig joe leafpad
visudo
add
user ALL=(ALL) ALL
Adjusted sources.list to:
#
# deb cdrom:[Debian GNU/Linux 5.0.3 _Lenny_ - Official i386 NETINST Binary-1
0090906-12:06]/ lenny main
#deb cdrom:[Debian GNU/Linux 5.0.3 _Lenny_ - Official i386 NETINST Binary-1
20090906-12:06]/ lenny main
deb http://probability.ca/cran/bin/linux/debian lenny-cran/
deb http://debian.cran.r-project.org/cran2deb/debian-i386 testing/
deb http://debian.yorku.ca/debian/ lenny main
deb-src http://debian.yorku.ca/debian/ lenny main
deb http://security.debian.org/ lenny/updates main
deb-src http://security.debian.org/ lenny/updates main
deb http://volatile.debian.org/debian-volatile lenny/volatile main
deb-src http://volatile.debian.org/debian-volatile lenny/volatile main
-------------------------------------
Put in keys:
gpg --keyserver subkeys.pgp.net --recv-key 381BA480
gpg -a --export 381BA480 > jranke_cran.asc
apt-key add jranke_cran.asc
Downloaded key.asc for cran2deb and then
sudo apt-key add key.asc
apt-get update
apt-get upgrade
Try to put in R
wajig install r-base
debian:/home/user# wajig install r-base
Reading package lists... Done
Building dependency tree
Reading state information... Done
The following extra packages will be installed:
binutils build-essential dpatch dpkg-dev fakeroot g++ g++-4.3 gcc gcc-4.3
gfortran
gfortran-4.3 libblas-dev libbz2-dev libc6-dev libgomp1 libjpeg62-dev
liblapack-dev libncurses5-dev libpaper-utils libpcre3-dev libpcrecpp0
libpng12-dev
libreadline5-dev libstdc++6-4.3-dev libtimedate-perl linux-libc-dev
make patchutils r-base-core r-base-dev r-base-html r-cran-boot r-cran-class
r-cran-cluster r-cran-codetools r-cran-foreign r-cran-kernsmooth
r-cran-lattice r-cran-mass r-cran-matrix r-cran-mgcv r-cran-nlme r-cran-nnet
r-cran-rpart r-cran-spatial r-cran-survival r-doc-html r-recommended tcl8.5
tk8.5 zlib1g-dev
Suggested packages:
binutils-doc curl debian-keyring g++-multilib g++-4.3-multilib gcc-4.3-doc
libstdc++6-4.3-dbg gcc-multilib manpages-dev autoconf automake1.9 libtool flex
bison gdb gcc-doc gcc-4.3-multilib libmudflap0-4.3-dev gcc-4.3-locales
libgcc1-dbg
libgomp1-dbg libmudflap0-dbg gfortran-multilib gfortran-doc
gfortran-4.3-multilib gfortran-4.3-doc libgfortran3-dbg glibc-doc
libstdc++6-4.3-doc
make-doc ess r-doc-info r-doc-pdf r-mathlib cdbs debhelper
tclreadline
The following NEW packages will be installed:
binutils build-essential dpatch dpkg-dev fakeroot g++ g++-4.3 gcc gcc-4.3
gfortran
gfortran-4.3 libblas-dev libbz2-dev libc6-dev libgomp1 libjpeg62-dev
liblapack-dev libncurses5-dev libpaper-utils libpcre3-dev libpcrecpp0
libpng12-dev
libreadline5-dev libstdc++6-4.3-dev libtimedate-perl linux-libc-dev
make patchutils r-base r-base-core r-base-dev r-base-html r-cran-boot
r-cran-class
r-cran-cluster r-cran-codetools r-cran-foreign r-cran-kernsmooth
r-cran-lattice r-cran-mass r-cran-matrix r-cran-mgcv r-cran-nlme r-cran-nnet
r-cran-rpart r-cran-spatial r-cran-survival r-doc-html r-recommended tcl8.5
tk8.5 zlib1g-dev
0 upgraded, 52 newly installed, 0 to remove and 0 not upgraded.
Need to get 52.8MB of archives.
After this operation, 135MB of additional disk space will be used.
Do you want to continue [Y/n]?
Get:1 http://probability.ca lenny-cran/ r-base-core 2.10.1-2~lennycran.0
[13.3MB]
Get:2 http://security.debian.org lenny/updates/main libc6-dev 2.7-18lenny2
[3388kB]
Get:3 http://debian.cran.r-project.org testing/ r-cran-mass 7.3-5-1cran1 [790kB]
Get:4 http://debian.yorku.ca lenny/main binutils 2.18.1~cvs20080103-7 [2686kB]
Get:5 http://debian.cran.r-project.org testing/ r-cran-lattice 0.18-3-1cran1
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Get:6 http://debian.cran.r-project.org testing/ r-cran-matrix 0.999375-33-1cran2
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Get:7 http://debian.cran.r-project.org testing/ r-cran-mgcv 1.6-1-1cran2 [665kB]
Get:8 http://debian.cran.r-project.org testing/ r-cran-survival 2.35-8-1cran2
[2440kB]
Get:9 http://debian.yorku.ca lenny/main linux-libc-dev 2.6.26-21 [751kB]
Get:10 http://debian.yorku.ca lenny/main libgomp1 4.3.2-1.1 [13.2kB]
Get:11 http://debian.yorku.ca lenny/main gcc-4.3 4.3.2-1.1 [2747kB]
Get:12 http://debian.cran.r-project.org testing/ r-cran-class 7.3-1-1cran3
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Get:13 http://debian.cran.r-project.org testing/ r-cran-nnet 7.3-1-1cran5
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Get:14 http://debian.cran.r-project.org testing/ r-cran-spatial 7.3-1-1cran4
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Get:15 http://debian.yorku.ca lenny/main gcc 4:4.3.2-2 [5008B]
Get:16 http://debian.yorku.ca lenny/main libstdc++6-4.3-dev 4.3.2-1.1 [1389kB]
Get:17 http://debian.yorku.ca lenny/main g++-4.3 4.3.2-1.1 [3414kB]
Get:18 http://probability.ca lenny-cran/ r-cran-boot 1.2.41-1~lennycran.2.10.1
[441kB]
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1.12.1-2~lennycran.2.10.1 [351kB]
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0.8.38-1~lennycran.2.10.1 [158kB]
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2.23-3-2~lennycran.2.10.1
[58.4kB]
Get:22 http://probability.ca lenny-cran/ r-cran-nlme 3.1.96-1~lennycran.2.10.1
[1558kB]
Get:23 http://debian.yorku.ca lenny/main g++ 4:4.3.2-2 [1368B]
Get:24 http://debian.yorku.ca lenny/main make 3.81-5 [382kB]
Get:25 http://probability.ca lenny-cran/ r-cran-rpart 3.1.45-2~lennycran.2.10.1
[158kB]
Get:26 http://debian.yorku.ca lenny/main libtimedate-perl 1.1600-9 [32.9kB]
Get:27 http://debian.yorku.ca lenny/main dpkg-dev 1.14.28 [771kB]
Get:28 http://probability.ca lenny-cran/ r-cran-codetools
0.2-2-2~lennycran.2.10.1
[42.0kB]
Get:29 http://probability.ca lenny-cran/ r-recommended 2.10.1-2~lennycran.0
[2676B]
Get:30 http://probability.ca lenny-cran/ r-base 2.10.1-2~lennycran.0 [34.0kB]
Get:31 http://probability.ca lenny-cran/ r-base-dev 2.10.1-2~lennycran.0 [3504B]
Get:32 http://probability.ca lenny-cran/ r-doc-html 2.10.1-2~lennycran.0 [579kB]
Get:33 http://debian.yorku.ca lenny/main build-essential 11.4 [7118B]
Get:34 http://debian.yorku.ca lenny/main dpatch 2.0.30 [88.2kB]
Get:35 http://debian.yorku.ca lenny/main fakeroot 1.11 [114kB]
Get:36 http://debian.yorku.ca lenny/main gfortran-4.3 4.3.2-1.1 [3503kB]
Get:37 http://probability.ca lenny-cran/ r-base-html 2.10.1-2~lennycran.0
[81.5kB]
Get:38 http://debian.yorku.ca lenny/main gfortran 4:4.3.2-2 [1124B]
Get:39 http://debian.yorku.ca lenny/main libblas-dev 1.2-2 [223kB]
Get:40 http://debian.yorku.ca lenny/main libbz2-dev 1.0.5-1 [31.7kB]
Get:41 http://debian.yorku.ca lenny/main libjpeg62-dev 6b-14 [186kB]
Get:42 http://debian.yorku.ca lenny/main liblapack-dev 3.1.1-1 [3001kB]
Get:43 http://debian.yorku.ca lenny/main libncurses5-dev 5.7+20081213-1 [1546kB]
Get:44 http://debian.yorku.ca lenny/main libpaper-utils 1.1.23+nmu1 [17.6kB]
Get:45 http://debian.yorku.ca lenny/main libpcrecpp0 7.6-2.1 [93.6kB]
Get:46 http://debian.yorku.ca lenny/main libpcre3-dev 7.6-2.1 [256kB]
Get:47 http://debian.yorku.ca lenny/main zlib1g-dev 1:1.2.3.3.dfsg-12 [157kB]
Get:48 http://debian.yorku.ca lenny/main libpng12-dev 1.2.27-2+lenny2 [247kB]
Get:49 http://debian.yorku.ca lenny/main libreadline5-dev 5.2-3.1 [222kB]
Get:50 http://debian.yorku.ca lenny/main patchutils 0.2.31-4 [93.7kB]
Get:51 http://debian.yorku.ca lenny/main tcl8.5 8.5.3-2 [1541kB]
Get:52 http://debian.yorku.ca lenny/main tk8.5 8.5.3-4 [1110kB]
Fetched 52.8MB in 2min46s (316kB/s)
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debian:/home/user# R
R version 2.10.1 (2009-12-14)
Copyright (C) 2009 The R Foundation for Statistical Computing
ISBN 3-900051-07-0
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.
Natural language support but running in an English locale
R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.
Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.
> q()
Save workspace image? [y/n/c]: n
Seems OK, so try rattle
wajig install r-cran-rattle
debian:/home/user# wajig install r-cran-rattle
Reading package lists... Done
Building dependency tree
Reading state information... Done
Some packages could not be installed. This may mean that you have
requested an impossible situation or if you are using the unstable
distribution that some required packages have not yet been created
or been moved out of Incoming.
The following information may help to resolve the situation:
The following packages have unmet dependencies:
r-cran-rattle: Depends: r-cran-rgtk2 but it is not going to be installed
Depends: r-cran-pmml but it is not going to be installed
E: Broken packages
debian:/home/user#
Try install.packages in R -- very long process.
debian:/home/user# R
R version 2.10.1 (2009-12-14)
Copyright (C) 2009 The R Foundation for Statistical Computing
ISBN 3-900051-07-0
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.
Natural language support but running in an English locale
R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.
Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.
> install.packages("rattle", dependencies=TRUE)
Warning in install.packages("rattle", dependencies = TRUE) :
argument 'lib' is missing: using
'/usr/local/lib/R/site-library'
--- Please select a CRAN mirror for use in this session ---
Loading Tcl/Tk interface ... done
Warning: dependencies ?Biobase?, ??, ?marray?, ?affy?, ?Rgraphviz? are not
available
also installing the dependencies ?splancs?, ?misc3d?, ?gam?, ?geoR?,
?RandomFields?,
?Rmpi?, ?nws?, ?tweedie?, ?sets?, ?slam?, ?Rglpk?, ?Rsymphony?, ?RBGL?,
?fields?, ?sm?,
?rpanel?, ?kinship?, ?snow?, ?rpvm?, ?rlecuyer?, ?rsprng?, ?statmod?, ?Ecdat?,
?maxLik?,
?ape?, ?flexmix?, ?rmeta?, ?lpSolve?, ?quadprog?, ?relations?, ?TSP?, ?RSQLite?,
?graph?,
?spam?, ?spatstat?, ?PBSmapping?, ?RArcInfo?, ?logspline?, ?plm?, ?sem?,
?rgenoud?,
?snowFT?, ?mboost?, ?fUtilities?, ?Formula?, ?ineq?, ?mlogit?, ?np?, ?pscl?,
?sampleSelection?, ?urca?, ?HSAUR?, ?clue?, ?seriation?, ?multicore?, ?igraph?,
?biglm?,
?scatterplot3d?, ?robustbase?, ?mix?, ?spdep?, ?maptools?, ?tkrplot?, ?rgl?,
?sgeostat?,
?mapproj?, ?tcltk2?, ?tree?, ?maps?, ?quantreg?, ?oz?, ?sp?, ?DBI?, ?VGAM?,
?MCMCpack?,
?coda?, ?gee?, ?systemfit?, ?anchors?, ?survey?, ?mlmRev?, ?MEMSS?, ?numDeriv?,
?ergm?,
?latentnet?, ?degreenet?, ?abind?, ?shapes?, ?multcomp?, ?fCalendar?, ?fSeries?,
?fts?,
?its?, ?tis?, ?tseries?, ?xts?, ?lmtest?, ?AER?, ?dynlm?, ?proto?, ?digest?,
?gpclib?,
?randomSurvivalForest?, ?vcd?, ?flexclust?, ?isa2?, ?leaps?, ?proxy?, ?gclus?,
?mvtnorm?,
?mlbench?, ?SparseM?, ?xtable?, ?RUnit?, ?timeSeries?, ?akima?, ?mclust?,
?trimcluster?,
?prabclus?, ?caTools?, ?gWidgets?, ?chron?, ?acepack?, ?TeachingDemos?,
?Design?,
?subselect?, ?latticeExtra?, ?gWidgetstcltk?, ?hexbin?, ?deldir?, ?tripack?,
?DAAG?,
?VIM?, ?mitools?, ?Zelig?, ?lme4?, ?sna?, ?statnet?, ?modeltools?, ?coin?,
?zoo?,
?sandwich?, ?strucchange?, ?ipred?, ?gridBase?, ?ggplot2?, ?RColorBrewer?,
?plyr?,
?bitops?, ?pmml?, ?RGtk2?, ?ada?, ?amap?, ?arules?, ?biclust?, ?cairoDevice?,
?car?,
?cba?, ?colorspace?, ?doBy?, ?e1071?, ?ellipse?, ?fEcofin?, ?fBasics?, ?fpc?,
?gdata?,
?gtools?, ?gplots?, ?gWidgetsRGtk2?, ?Hmisc?, ?kernlab?, ?latticist?, ?mice?,
?network?,
?odfWeave?, ?party?, ?playwith?, ?randomForest?, ?reshape?, ?rggobi?, ?ROCR?,
?RODBC?,
?RSvgDevice?, ?timeDate?, ?XML?
trying URL
'http://probability.ca/cran/src/contrib/splancs_2.01-25.tar.gz'
Content type 'application/x-gzip' length 108419 bytes (105 Kb)
opened URL
=================================================downloaded 105 Kb
trying URL 'http://probability.ca/cran/src/contrib/misc3d_0.7-0.tar.gz'
Content type 'application/x-gzip' length 60237 bytes (58 Kb)
opened URL
=================================================downloaded 58 Kb
trying URL 'http://probability.ca/cran/src/contrib/gam_1.01.tar.gz'
Content type 'application/x-gzip' length 92920 bytes (90 Kb)
opened URL
=================================================downloaded 90 Kb
trying URL 'http://probability.ca/cran/src/contrib/geoR_1.6-27.tar.gz'
Content type 'application/x-gzip' length 466130 bytes (455 Kb)
opened URL
=================================================downloaded 455 Kb
trying URL
'http://probability.ca/cran/src/contrib/RandomFields_1.3.41.tar.gz'
Content type 'application/x-gzip' length 325440 bytes (317 Kb)
opened URL
=================================================downloaded 317 Kb
trying URL 'http://probability.ca/cran/src/contrib/Rmpi_0.5-8.tar.gz'
Content type 'application/x-gzip' length 87528 bytes (85 Kb)
opened URL
=================================================downloaded 85 Kb
trying URL 'http://probability.ca/cran/src/contrib/nws_1.7.0.0.tar.gz'
Content type 'application/x-gzip' length 98040 bytes (95 Kb)
opened URL
=================================================downloaded 95 Kb
trying URL 'http://probability.ca/cran/src/contrib/tweedie_2.0.2.tar.gz'
Content type 'application/x-gzip' length 108077 bytes (105 Kb)
opened URL
=================================================downloaded 105 Kb
trying URL 'http://probability.ca/cran/src/contrib/sets_1.0-2.tar.gz'
Content type 'application/x-gzip' length 374103 bytes (365 Kb)
opened URL
=================================================downloaded 365 Kb
trying URL 'http://probability.ca/cran/src/contrib/slam_0.1-9.tar.gz'
Content type 'application/x-gzip' length 14121 bytes (13 Kb)
opened URL
=================================================downloaded 13 Kb
trying URL 'http://probability.ca/cran/src/contrib/Rglpk_0.3-3.tar.gz'
Content type 'application/x-gzip' length 3229592 bytes (3.1 Mb)
opened URL
=================================================downloaded 3.1 Mb
trying URL
'http://probability.ca/cran/src/contrib/Rsymphony_0.1-9.tar.gz'
Content type 'application/x-gzip' length 9884047 bytes (9.4 Mb)
opened URL
=================================================downloaded 9.4 Mb
trying URL 'http://probability.ca/cran/src/contrib/RBGL_1.22.0.tar.gz'
Content type 'application/x-gzip' length 1898148 bytes (1.8 Mb)
opened URL
=================================================downloaded 1.8 Mb
trying URL 'http://probability.ca/cran/src/contrib/fields_6.01.tar.gz'
Content type 'application/x-gzip' length 3670039 bytes (3.5 Mb)
opened URL
=================================================downloaded 3.5 Mb
trying URL 'http://probability.ca/cran/src/contrib/sm_2.2-3.tar.gz'
Content type 'application/x-gzip' length 152308 bytes (148 Kb)
opened URL
=================================================downloaded 148 Kb
trying URL 'http://probability.ca/cran/src/contrib/rpanel_1.0-5.tar.gz'
Content type 'application/x-gzip' length 695870 bytes (679 Kb)
opened URL
=================================================downloaded 679 Kb
trying URL
'http://probability.ca/cran/src/contrib/kinship_1.1.0-23.tar.gz'
Content type 'application/x-gzip' length 1229419 bytes (1.2 Mb)
opened URL
=================================================downloaded 1.2 Mb
trying URL 'http://probability.ca/cran/src/contrib/snow_0.3-3.tar.gz'
Content type 'application/x-gzip' length 18618 bytes (18 Kb)
opened URL
=================================================downloaded 18 Kb
trying URL 'http://probability.ca/cran/src/contrib/rpvm_1.0.2.tar.gz'
Content type 'application/x-gzip' length 62737 bytes (61 Kb)
opened URL
=================================================downloaded 61 Kb
trying URL
'http://probability.ca/cran/src/contrib/rlecuyer_0.3-1.tar.gz'
Content type 'application/x-gzip' length 10525 bytes (10 Kb)
opened URL
=================================================
... could not capture all output
hecking mpi.h presence... no
checking for mpi.h... no
configure: error: "Cannot find mpi.h header file"
ERROR: configuration failed for package ?Rmpi?
* removing ?/usr/local/lib/R/site-library/Rmpi?
* installing *source* package ?nws? ...
** R
pointer and integer
tcltkimg.c:463: warning: implicit declaration of function ?Tk_CreateImageType?
tcltkimg.c:463: error: ?RplotImageType? undeclared (first use in this function)
tcltkimg.c:465: warning: implicit declaration of function ?Tcl_PkgProvide?
tcltkimg.c: In function ?Rplot_SafeInit?:
tcltkimg.c:469: error: expected declaration specifiers before ?Tcl_Interp?
tcltkimg.c:470: warning: type of ?interp? defaults to ?int?
make: *** [tcltkimg.o] Error 1
ERROR: compilation failed for package ?tkrplot?
* removing ?/usr/local/lib/R/site-library/tkrplot?
* installing *source* package ?rgl? ...
checking for gcc... gcc -std=gnu99
checking for C compiler default output file name... a.out
checking whether the C compiler works... yes
** preparing package for lazy loading
** help
*** installing help indices
** building package indices ...
* DONE (bitops)
* installing *source* package ?RGtk2? ...
checking for pkg-config... /usr/bin/pkg-config
checking pkg-config is at least version 0.9.0... yes
checking for LIBGLADE... no
configure: WARNING: libglade not found
checking for INTROSPECTION... no
checking for GTK... no
configure: error: GTK version 2.8.0 required
ERROR: configuration failed for package ?RGtk2?
* removing ?/usr/local/lib/R/site-library/RGtk2?
checking for sqlext.h... no
configure: error: "ODBC headers sql.h and sqlext.h not found"
ERROR: configuration failed for package ?RODBC?
* removing ?/usr/local/lib/R/site-library/RODBC?
* installing *source* package ?RSvgDevice? ...
** libs
* DONE (spatstat)
* installing *source* package ?snowFT? ...
** R
** preparing package for lazy loading
Error : package 'rpvm' required by 'snowFT' could not be found
ERROR: lazy loading failed for package ?snowFT?
* removing ?/usr/local/lib/R/site-library/snowFT?
* installing *source* package ?mlogit? ...
** R
** demo
** preparing package for lazy loading
Warning in library(pkg, character.only = TRUE, logical.return = TRUE, lib.loc =
lib.loc) :
there is no package called 'rgl'
Error : package 'rgl' could not be loaded
ERROR: lazy loading failed for package ?shapes?
* removing ?/usr/local/lib/R/site-library/shapes?
* installing *source* package ?multcomp? ...
** R
** data
** moving datasets to lazyload DB
building package indices ...
* DONE (gdata)
* installing *source* package ?gWidgetsRGtk2? ...
** R
** inst
** preparing package for lazy loading
Error in loadNamespace(i, c(lib.loc, .libPaths())) :
there is no package called 'RGtk2'
ERROR: lazy loading failed for package ?gWidgetsRGtk2?
* removing ?/usr/local/lib/R/site-library/gWidgetsRGtk2?
* installing *source* package ?odfWeave? ...
** R
** inst
** preparing package for lazy loading
Warning in library(pkg, character.only = TRUE, logical.return = TRUE, lib.loc =
lib.loc) :
there is no package called 'XML'
Error : package 'XML' could not be loaded
ERROR: lazy loading failed for package ?odfWeave?
* removing ?/usr/local/lib/R/site-library/odfWeave?
* installing *source* package ?reshape? ...
* DONE (fSeries)
* installing *source* package ?VIM? ...
** R
** data
** inst
** preparing package for lazy loading
Loading Tcl/Tk interface ... done
Warning in library(pkg, character.only = TRUE, logical.return = TRUE, lib.loc =
lib.loc) :
there is no package called 'tkrplot'
Error : package 'tkrplot' could not be loaded
ERROR: lazy loading failed for package ?VIM?
* removing ?/usr/local/lib/R/site-library/VIM?
* installing *source* package ?strucchange? ...
** R
** data
** moving datasets to lazyload DB
** building package indices ...
* DONE (latticist)
* installing *source* package ?playwith? ...
** libs
gcc -std=gnu99 -I/usr/share/R/include -fpic -g -O2 -c interrupt.c -o
interrupt.o
gcc -std=gnu99 -shared -o playwith.so interrupt.o -L/usr/lib/R/lib -lR
** R
** demo
** inst
** preparing package for lazy loading
Warning in library(pkg, character.only = TRUE, logical.return = TRUE, lib.loc =
lib.loc) :
there is no package called 'cairoDevice'
Error : package 'cairoDevice' could not be loaded
ERROR: lazy loading failed for package ?playwith?
* removing ?/usr/local/lib/R/site-library/playwith?
* installing *source* package ?rattle? ...
** R
** data
** moving datasets to lazyload DB
** inst
** preparing package for lazy loading
Error : package 'pmml' required by 'rattle' co
----------------
The downloaded packages are in
?/tmp/RtmpRtEt2L/downloaded_packages?
There were 20 warnings (use warnings() to see them)
> pointer and integer
Error: unexpected symbol in " pointer and"
> tcltkimg.c:463: warning: implicit declaration of function
?Tk_CreateImageType?
Error: unexpected symbol in "tcltkimg.c:463: warning: implicit
declaration"
> tcltkimg.c:463: error: ?RplotImageType? undeclared (first use in this
function)
Error: unexpected input in "tcltkimg.c:463: error:
> tcltkimg.c:465: warning: implicit declaration of function ?Tcl_PkgProvide?
Error: unexpected symbol in "tcltkimg.c:465: warning: implicit
declaration"
> tcltkimg.c: In function ?Rplot_SafeInit?:
Error: unexpected 'function' in "tcltkimg.c: In function"
> tcltkimg.c:469: error: expected declaration specifiers before ?Tcl_Interp?
Error: unexpected symbol in "tcltkimg.c:469: error: expected
declaration"
> tcltkimg.c:470: warning: type of ?interp? defaults to ?int?
Error: unexpected symbol in "tcltkimg.c:470: warning: type of"
> make: *** [tcltkimg.o] Error 1
Error: unexpected '^' in "make: **"
> ERROR: compilation failed for package ?tkrplot?
Error: unexpected symbol in "ERROR: compilation failed"
> * removing ?/usr/local/lib/R/site-library/tkrplot?
Error: unexpected '*' in "*"
> * installing *source* package ?rgl? ...
Error: unexpected '*' in "*"
> checking for gcc... gcc -std=gnu99
Error: unexpected 'for' in "checking for"
> checking for C compiler default output file name... a.out
Error: unexpected 'for' in "checking for"
> checking whether the C compiler works... yes
Error: unexpected symbol in "checking whether"
>
Try update.packages()
Updated foreign, rpart
> install.packages("rattle")
Warning in install.packages("rattle") :
argument 'lib' is missing: using
'/usr/local/lib/R/site-library'
also installing the dependencies ?XML?, ?pmml?
trying URL 'http://probability.ca/cran/src/contrib/XML_2.6-0.tar.gz'
Content type 'application/x-gzip' length 680366 bytes (664 Kb)
opened URL
=================================================downloaded 664 Kb
trying URL 'http://probability.ca/cran/src/contrib/pmml_1.2.21.tar.gz'
Content type 'application/x-gzip' length 41585 bytes (40 Kb)
opened URL
=================================================downloaded 40 Kb
trying URL 'http://probability.ca/cran/src/contrib/rattle_2.5.20.tar.gz'
Content type 'application/x-gzip' length 976700 bytes (953 Kb)
opened URL
=================================================downloaded 953 Kb
* installing *source* package ?XML? ...
checking for gcc... gcc
checking for C compiler default output file name... a.out
checking whether the C compiler works... yes
checking whether we are cross compiling... no
checking for suffix of executables...
checking for suffix of object files... o
checking whether we are using the GNU C compiler... yes
checking whether gcc accepts -g... yes
checking for gcc option to accept ANSI C... none needed
checking how to run the C preprocessor... gcc -E
checking for sed... /bin/sed
checking for pkg-config... /usr/bin/pkg-config
checking for xml2-config... no
Cannot find xml2-config
ERROR: configuration failed for package ?XML?
* removing ?/usr/local/lib/R/site-library/XML?
* installing *source* package ?pmml? ...
** R
** preparing package for lazy loading
Warning in library(pkg, character.only = TRUE, logical.return = TRUE, lib.loc =
lib.loc) :
there is no package called 'XML'
Error : package 'XML' could not be loaded
ERROR: lazy loading failed for package ?pmml?
* removing ?/usr/local/lib/R/site-library/pmml?
* installing *source* package ?rattle? ...
** R
** data
** moving datasets to lazyload DB
** inst
** preparing package for lazy loading
Error : package 'pmml' required by 'rattle' could not be found
ERROR: lazy loading failed for package ?rattle?
* removing ?/usr/local/lib/R/site-library/rattle?
The downloaded packages are in
?/tmp/RtmpRtEt2L/downloaded_packages?
Warning messages:
1: In install.packages("rattle") :
installation of package 'XML' had non-zero exit status
2: In install.packages("rattle") :
installation of package 'pmml' had non-zero exit status
3: In install.packages("rattle") :
installation of package 'rattle' had non-zero exit status
>
>
debian:/home/user# sudo apt-get install r-cran-pmml
Reading package lists... Done
Building dependency tree
Reading state information... Done
Some packages could not be installed. This may mean that you have
requested an impossible situation or if you are using the unstable
distribution that some required packages have not yet been created
or been moved out of Incoming.
The following information may help to resolve the situation:
The following packages have unmet dependencies:
r-cran-pmml: Depends: r-cran-xml but it is not going to be installed
E: Broken packages
debian:/home/user# sudo apt-get install r-cran-xml
Reading package lists... Done
Building dependency tree
Reading state information... Done
Some packages could not be installed. This may mean that you have
requested an impossible situation or if you are using the unstable
distribution that some required packages have not yet been created
or been moved out of Incoming.
The following information may help to resolve the situation:
The following packages have unmet dependencies:
r-cran-xml: Depends: libxml2 (>= 2.7.4) but 2.6.32.dfsg-5+lenny1 is to be
installed
E: Broken packages
debian:/home/user#
Dirk Eddelbuettel
2010-Feb-03 18:42 UTC
[R-sig-Debian] Installation woes for rattle (and other packages)
On 3 February 2010 at 12:50, Prof. John C Nash wrote: | Yesterday I wanted to try rattle on Ubuntu 9.04 Jaunty. I had (and still have) it running | (though it complains on startup a bit -- I'll look into that later) on a different bootup | on the same machine with 8.04 Hardy. | | I got an error that libglade cannot be found, and various attempts to get glade support | failed. I removed and reinstalled R -- same problem. | | To avoid the issue of local setup being in conflict with R, I created a VirtualBox | instance of a clean Ubuntu Jaunty. Same woes. To be really sure of things, I put in a | virtual Debian lenny from debian-503-i386-netinst.iso | | Since the Ubuntu cran2deb attempt gave same results as Debian lenny (though the CRAN | repository was a little different, but cran2deb repository the same), I'll only include | the Debian run. I also tried the install on a separate machine (real) running 8.04 Hardy | and got a similar broken packages message. So similar results on 4 systems. There is no such thing as Ubuntu cran2deb. You are forcing something that is not supported. [Lots of stuff deleted] | The following packages have unmet dependencies: | r-cran-rattle: Depends: r-cran-rgtk2 but it is not going to be installed | Depends: r-cran-pmml but it is not going to be installed | E: Broken packages This apt telling you that is cannot install rgtk2 and pmml because of conflicts. It could give you more details if you asked. As for installing Rattle by hand on Ubuntu:> install.packages("rattle", dependencies=TRUE)I would suggest to set dependencies to FALSE. Moreover, it you look more closely, only pmml is _required_. So start with that. Afterwards, rattle has a number of _suggested_ packages several of which Ubuntu should have pre-built: r-cran-rgtk2 r-cran-car r-cran-colorspace [...] I would start with those and then add those packages that are missing. We will help you best as we can with whichever packages are missing. But please consider switching from a chainsaw to a scalpel. Hth, Dirk -- Three out of two people have difficulties with fractions.
Paul Johnson
2010-Feb-03 18:46 UTC
[R-sig-Debian] Installation woes for rattle (and other packages)
Works for me on Ubuntu Karmic 9.10, same as it did in previous Ubuntu.> .help.ESS <- help > options(STERM='iESS', editor='emacsclient') > library(rattle)Loading required package: pmml Loading required package: XML Rattle: Graphical interface for data mining using R. Version 2.5.15 Copyright (c) 2006-2010 Togaware Pty Ltd. Type 'rattle()' to shake, rattle, and roll your data.> rattle() >Is the version of Rattle you get the same? I recall at one time I grabbed it from the owner's site, not CRAN? Note in your output you have lots and lots of failures because various devel packages for your OS are missing, and those cascade across the build. In order to build packages, you need to have a few more tools. You need the -dev parts of packages. For example, it appears to me you are missing tk-dev tcl-dev libgtk2.0-dev If you get that stuff installed, then the only "trick" is to teach R how to find it. many are automatic, not all. (see below re mpi) I'd suggest you run install.packages with the option (dep=T) so it tries to get all recommended/required packages. Then watch for the FIRST build error and fix that first, then re-install. For some of your errors, I know the answers.> hecking mpi.h presence... no > checking for mpi.h... no > configure: error: "Cannot find mpi.h header file" > ERROR: configuration failed for package ?Rmpi? > * removing ?/usr/local/lib/R/site-library/Rmpi? > * installing *source* package ?nws? ... > ** R >The install command needs to know which mpi library you want to use. To build on mine, I do install.packages("nws",configure.args="--with-mpi=/usr/lib/openmpi") because that's the mpi I want. You need to install the openmpi support (including the -dev packages)> Error : package 'tkrplot' could not be loaded > ERROR: lazy loading failed for package ?VIM? > * removing ?/usr/local/lib/R/site-library/VIM? > * installing *source* package ?strucchange? ...That happens because your workstation doesn't have the devel package for tk or tcl installed when tkrplot tries to build. I'd suggest you pick packages at the beginning of your failures, try to install them one at a time, and DO NOT go on until each one succeeds. Usually you have to install some deb devel packages, then re-try the install. It looks to me like the mpi or pmml things might need the first attention. I assure you, this is all possible. Here's what I get today, for example:> install.packages("pmml", dep=T)trying URL 'http://cran.case.edu/src/contrib/pmml_1.2.21.tar.gz' Content type 'application/x-gzip' length 41585 bytes (40 Kb) opened URL =================================================downloaded 40 Kb * installing *source* package ?pmml? ... ** R ** preparing package for lazy loading ** help *** installing help indices ** building package indices ... * DONE (pmml) The downloaded packages are in ?/tmp/RtmpUu915a/downloaded_packages? -- Paul E. Johnson Professor, Political Science 1541 Lilac Lane, Room 504 University of Kansas