[R] [R-pkgs] package installation fails (RandomFields)
I have been unable to install the package RandomFields. I am using R 2.9.0-4 on Ubuntu 9.04. To install, I use the command: sudo R CMD INSTALL RandomFields_1.3.37.tar.gz The output follows below. Any help Would be appreciated. D. Hoysak Brandon University * Installing to library ‘/usr/local/lib/R/site-library’ * Installing *source* package ‘RandomFields’ ... ** libs g++ -I/usr/share/R/include -g -fpic -g -O2 -c D.H.cc -o D.H.o In file included from D.H.cc:27: RFsimu.h:38: warning: ‘typedef’ was ignored in this declaration RFsimu.h:261: warning: ‘typedef’ was ignored in this declaration RFsimu.h:309: warning: ‘typedef’ was ignored in this declaration g++ -I/usr/share/R/include -g -fpic -g -O2 -c Hyperfcts.cc -o Hyperfcts.o In file included from Hyperfcts.cc:27: RFsimu.h:38: warning: ‘typedef’ was ignored in this declaration RFsimu.h:261: warning: ‘typedef’ was ignored in this declaration RFsimu.h:309: warning: ‘typedef’ was ignored in this declaration Hyperfcts.cc: In function ‘int checkNinit_co(covinfo_type*, int*, int, SimulationType, bool)’: Hyperfcts.cc:145: warning: deprecated conversion from string constant to ‘char*’ Hyperfcts.cc:145: warning: deprecated conversion from string constant to ‘char*’ Hyperfcts.cc:145: warning: deprecated conversion from string constant to ‘char*’ Hyperfcts.cc:145: warning: deprecated conversion from string constant to ‘char*’ Hyperfcts.cc:145: warning: deprecated conversion from string constant to ‘char*’ Hyperfcts.cc: In function ‘int checkNinit_Stein(covinfo_type*, int*, int, SimulationType, bool)’: Hyperfcts.cc:261: warning: deprecated conversion from string constant to ‘char*’ Hyperfcts.cc:261: warning: deprecated conversion from string constant to ‘char*’ Hyperfcts.cc:261: warning: deprecated conversion from string constant to ‘char*’ Hyperfcts.cc:261: warning: deprecated conversion from string constant to ‘char*’ Hyperfcts.cc:261: warning: deprecated conversion from string constant to ‘char*’ Hyperfcts.cc:261: warning: deprecated conversion from string constant to ‘char*’ g++ -I/usr/share/R/include -g -fpic -g -O2 -c MPP.cc -o MPP.o In file included from MPP.cc:32: RFsimu.h:38: warning: ‘typedef’ was ignored in this declaration RFsimu.h:261: warning: ‘typedef’ was ignored in this declaration RFsimu.h:309: warning: ‘typedef’ was ignored in this declaration g++ -I/usr/share/R/include -g -fpic -g -O2 -c MPPFcts.cc -o MPPFcts.o In file included from MPPFcts.cc:48: RFsimu.h:38: warning: ‘typedef’ was ignored in this declaration RFsimu.h:261: warning: ‘typedef’ was ignored in this declaration RFsimu.h:309: warning: ‘typedef’ was ignored in this declaration g++ -I/usr/share/R/include -g -fpic -g -O2 -c RFCovFcts.cc -o RFCovFcts.o In file included from RFCovFcts.cc:47: RFsimu.h:38: warning: ‘typedef’ was ignored in this declaration RFsimu.h:261: warning: ‘typedef’ was ignored in this declaration RFsimu.h:309: warning: ‘typedef’ was ignored in this declaration g++ -I/usr/share/R/include -g -fpic -g -O2 -c RFcircembed.cc -o RFcircembed.o In file included from RFcircembed.cc:33: RFsimu.h:38: warning: ‘typedef’ was ignored in this declaration RFsimu.h:261: warning: ‘typedef’ was ignored in this declaration RFsimu.h:309: warning: ‘typedef’ was ignored in this declaration RFcircembed.cc: In function ‘void SetParamCircEmbed(int*, int*, double*, double*, int*, int*, double*, int*, int*, double*, int*)’: RFcircembed.cc:114: warning: deprecated conversion from string constant to ‘char*’ RFcircembed.cc: In function ‘void SetParamLocal(int*, int*, double*, double*, int*, double*, int*, double*, int*)’: RFcircembed.cc:124: warning: deprecated conversion from string constant to ‘char*’ g++ -I/usr/share/R/include -g -fpic -g -O2 -c RFdirect.cc -o RFdirect.o In file included from RFdirect.cc:28: RFsimu.h:38: warning: ‘typedef’ was ignored in this declaration RFsimu.h:261: warning: ‘typedef’ was ignored in this declaration RFsimu.h:309: warning: ‘typedef’ was ignored in this declaration g++ -I/usr/share/R/include -g -fpic -g -O2 -c RFempvario.cc -o RFempvario.o In file included from RFempvario.cc:28: RFsimu.h:38: warning: ‘typedef’ was ignored in this declaration RFsimu.h:261: warning: ‘typedef’ was ignored in this declaration RFsimu.h:309: warning: ‘typedef’ was ignored in this declaration g++ -I/usr/share/R/include -g -fpic -g -O2 -c RFgetNset.cc -o RFgetNset.o In file included from RFgetNset.cc:36: RFsimu.h:38: warning: ‘typedef’ was ignored in this declaration RFsimu.h:261: warning: ‘typedef’ was ignored in this declaration RFsimu.h:309: warning: ‘typedef’ was ignored in this declaration RFgetNset.cc: In function ‘SEXPREC* TooLarge(int*, int)’: RFgetNset.cc:1081: warning: deprecated conversion from string constant to ‘char*’ RFgetNset.cc:1081: warning: deprecated conversion from string constant to ‘char*’ RFgetNset.cc: In function ‘SEXPREC* GetModelInfo(covinfo_type*, int, int, long int)’: RFgetNset.cc:1106: warning: deprecated conversion from string
Re: [R] [R-pkgs] package installation fails (RandomFields)
[[ NOTE: This accidentally was approved to go to R-packages,
it should never have gone there, and I have deleted it
from the archives.
Please *only* reply to R-help (and the OP)!
]]
DH == Drew Hoysak hoy...@wcgwave.ca
on Wed, 10 Jun 2009 14:40:32 -0500 writes:
DH I have been unable to install the package RandomFields. I am using R
DH 2.9.0-4 on Ubuntu 9.04.
How exactly did you install R? Just as ubuntu package?
{probably, given the somewhat particular version number}
DH To install, I use the command:
DH sudo R CMD INSTALL RandomFields_1.3.37.tar.gz
DH The output follows below. Any help Would be appreciated.
DH D. Hoysak
DH Brandon University
DH * Installing to library ‘/usr/local/lib/R/site-library’
DH * Installing *source* package ‘RandomFields’ ...
DH ** libs
DH g++ -I/usr/share/R/include -g -fpic -g -O2 -c D.H.cc -o D.H.o
DH In file included from D.H.cc:27:
DH RFsimu.h:38: warning: ‘typedef’ was ignored in this declaration
DH RFsimu.h:261: warning: ‘typedef’ was ignored in this declaration
DH RFsimu.h:309: warning: ‘typedef’ was ignored in this declaration
[..]
[..]
DH RFsimu.h:309: warning: ‘typedef’ was ignored in this declaration
DH g++ -I/usr/share/R/include -g -fpic -g -O2 -c win_linux_aux.cc -o
DH win_linux_aux.o
DH g++ -shared -o RandomFields.so D.H.o Hyperfcts.o MPP.o MPPFcts.o
DH RFCovFcts.o RFcircembed.o RFdirect.o RFempvario.o RFgetNset.o
DH RFhyperplan.o RFinitNerror.o RFnugget.o RFother.o RFsimu.o RFspectral.o
DH RFtbm.o Xempvario.o addownfctns.o auxiliary.o avltr.o extremes.o
DH modelling.o win_linux_aux.o -llapack -L/usr/lib/R/lib -lR
DH /usr/bin/ld: cannot find -llapack
^
This looks like a setup problem of the R installation you have;
I'd guess that you would also see problems installing other R
packages that rely on LAPACK.
DH collect2: ld returned 1 exit status
DH make: *** [RandomFields.so] Error 1
DH ERROR: compilation failed for package ‘RandomFields’
DH * Removing ‘/usr/local/lib/R/site-library/RandomFields’
__
R-help@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
Re: [R] [R-pkgs] package installation fails (RandomFields)
Drew, Wrong list -- please use r-help. Re-directing from r-packages. On 10 June 2009 at 14:40, Drew Hoysak wrote: | I have been unable to install the package RandomFields. I am using R | 2.9.0-4 on Ubuntu 9.04. | | To install, I use the command: | sudo R CMD INSTALL RandomFields_1.3.37.tar.gz | | | The output follows below. Any help Would be appreciated. | | D. Hoysak | Brandon University | | | * Installing to library ‘/usr/local/lib/R/site-library’ | * Installing *source* package ‘RandomFields’ ... | ** libs | g++ -I/usr/share/R/include -g -fpic -g -O2 -c D.H.cc -o D.H.o [...] | g++ -shared -o RandomFields.so D.H.o Hyperfcts.o MPP.o MPPFcts.o | RFCovFcts.o RFcircembed.o RFdirect.o RFempvario.o RFgetNset.o | RFhyperplan.o RFinitNerror.o RFnugget.o RFother.o RFsimu.o RFspectral.o | RFtbm.o Xempvario.o addownfctns.o auxiliary.o avltr.o extremes.o | modelling.o win_linux_aux.o -llapack -L/usr/lib/R/lib -lR | /usr/bin/ld: cannot find -llapack ^ Did you install r-base-dev, which then pulls in libblas-dev and liblapack-dev (or their libatlas-* equivalents) as well as a bunch of other -dev packages? If no do 'sudo apt-get install r-base-dev' and try again. Dirk | collect2: ld returned 1 exit status | make: *** [RandomFields.so] Error 1 | ERROR: compilation failed for package ‘RandomFields’ | * Removing ‘/usr/local/lib/R/site-library/RandomFields’ | | ___ | R-packages mailing list | r-packa...@r-project.org | https://stat.ethz.ch/mailman/listinfo/r-packages | | __ | R-help@r-project.org mailing list | https://stat.ethz.ch/mailman/listinfo/r-help | PLEASE do read the posting guide http://www.R-project.org/posting-guide.html | and provide commented, minimal, self-contained, reproducible code. -- Three out of two people have difficulties with fractions. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] [R-pkgs] package installation fails (RandomFields)
The offending lines don't look right to me:
38 typedef struct key_type;
261 typedef struct mpp_storage;
309 typedef struct cov_fct;
Shouldn't they be 'typedef struct struct_name typedefed_name'?
Later in the file there are proper typedef's for these things.
Bill Dunlap
TIBCO Software Inc - Spotfire Division
wdunlap tibco.com
-Original Message-
From: r-help-boun...@r-project.org
[mailto:r-help-boun...@r-project.org] On Behalf Of Martin Maechler
Sent: Thursday, June 11, 2009 12:42 AM
To: Drew Hoysak
Cc: r-help@r-project.org
Subject: Re: [R] [R-pkgs] package installation fails (RandomFields)
[[ NOTE: This accidentally was approved to go to R-packages,
it should never have gone there, and I have deleted it
from the archives.
Please *only* reply to R-help (and the OP)!
]]
DH == Drew Hoysak hoy...@wcgwave.ca
on Wed, 10 Jun 2009 14:40:32 -0500 writes:
DH I have been unable to install the package
RandomFields. I am using R
DH 2.9.0-4 on Ubuntu 9.04.
How exactly did you install R? Just as ubuntu package?
{probably, given the somewhat particular version number}
DH To install, I use the command:
DH sudo R CMD INSTALL RandomFields_1.3.37.tar.gz
DH The output follows below. Any help Would be appreciated.
DH D. Hoysak
DH Brandon University
DH * Installing to library '/usr/local/lib/R/site-library'
DH * Installing *source* package 'RandomFields' ...
DH ** libs
DH g++ -I/usr/share/R/include -g -fpic -g -O2 -c D.H.cc -o D.H.o
DH In file included from D.H.cc:27:
DH RFsimu.h:38: warning: 'typedef' was ignored in this
declaration
DH RFsimu.h:261: warning: 'typedef' was ignored in this
declaration
DH RFsimu.h:309: warning: 'typedef' was ignored in this
declaration
[..]
[..]
DH RFsimu.h:309: warning: 'typedef' was ignored in this
declaration
DH g++ -I/usr/share/R/include -g -fpic -g -O2 -c
win_linux_aux.cc -o
DH win_linux_aux.o
DH g++ -shared -o RandomFields.so D.H.o Hyperfcts.o
MPP.o MPPFcts.o
DH RFCovFcts.o RFcircembed.o RFdirect.o RFempvario.o RFgetNset.o
DH RFhyperplan.o RFinitNerror.o RFnugget.o RFother.o
RFsimu.o RFspectral.o
DH RFtbm.o Xempvario.o addownfctns.o auxiliary.o avltr.o
extremes.o
DH modelling.o win_linux_aux.o -llapack -L/usr/lib/R/lib -lR
DH /usr/bin/ld: cannot find -llapack
^
This looks like a setup problem of the R installation you have;
I'd guess that you would also see problems installing other R
packages that rely on LAPACK.
DH collect2: ld returned 1 exit status
DH make: *** [RandomFields.so] Error 1
DH ERROR: compilation failed for package 'RandomFields'
DH * Removing '/usr/local/lib/R/site-library/RandomFields'
__
R-help@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide
http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
__
R-help@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
Re: [R] [R-pkgs] package installation fails (RandomFields)
William Dunlap wrote:
The offending lines don't look right to me:
38 typedef struct key_type;
261 typedef struct mpp_storage;
309 typedef struct cov_fct;
Shouldn't they be 'typedef struct struct_name typedefed_name'?
Later in the file there are proper typedef's for these things.
In that case, can you please report it to the RandomFields maintainer?
Thank you very much,
Uwe Ligges
Bill Dunlap
TIBCO Software Inc - Spotfire Division
wdunlap tibco.com
-Original Message-
From: r-help-boun...@r-project.org
[mailto:r-help-boun...@r-project.org] On Behalf Of Martin Maechler
Sent: Thursday, June 11, 2009 12:42 AM
To: Drew Hoysak
Cc: r-help@r-project.org
Subject: Re: [R] [R-pkgs] package installation fails (RandomFields)
[[ NOTE: This accidentally was approved to go to R-packages,
it should never have gone there, and I have deleted it
from the archives.
Please *only* reply to R-help (and the OP)!
]]
DH == Drew Hoysak hoy...@wcgwave.ca
on Wed, 10 Jun 2009 14:40:32 -0500 writes:
DH I have been unable to install the package
RandomFields. I am using R
DH 2.9.0-4 on Ubuntu 9.04.
How exactly did you install R? Just as ubuntu package?
{probably, given the somewhat particular version number}
DH To install, I use the command:
DH sudo R CMD INSTALL RandomFields_1.3.37.tar.gz
DH The output follows below. Any help Would be appreciated.
DH D. Hoysak
DH Brandon University
DH * Installing to library '/usr/local/lib/R/site-library'
DH * Installing *source* package 'RandomFields' ...
DH ** libs
DH g++ -I/usr/share/R/include -g -fpic -g -O2 -c D.H.cc -o D.H.o
DH In file included from D.H.cc:27:
DH RFsimu.h:38: warning: 'typedef' was ignored in this
declaration
DH RFsimu.h:261: warning: 'typedef' was ignored in this
declaration
DH RFsimu.h:309: warning: 'typedef' was ignored in this
declaration
[..]
[..]
DH RFsimu.h:309: warning: 'typedef' was ignored in this
declaration
DH g++ -I/usr/share/R/include -g -fpic -g -O2 -c
win_linux_aux.cc -o
DH win_linux_aux.o
DH g++ -shared -o RandomFields.so D.H.o Hyperfcts.o
MPP.o MPPFcts.o
DH RFCovFcts.o RFcircembed.o RFdirect.o RFempvario.o RFgetNset.o
DH RFhyperplan.o RFinitNerror.o RFnugget.o RFother.o
RFsimu.o RFspectral.o
DH RFtbm.o Xempvario.o addownfctns.o auxiliary.o avltr.o
extremes.o
DH modelling.o win_linux_aux.o -llapack -L/usr/lib/R/lib -lR
DH /usr/bin/ld: cannot find -llapack
^
This looks like a setup problem of the R installation you have;
I'd guess that you would also see problems installing other R
packages that rely on LAPACK.
DH collect2: ld returned 1 exit status
DH make: *** [RandomFields.so] Error 1
DH ERROR: compilation failed for package 'RandomFields'
DH * Removing '/usr/local/lib/R/site-library/RandomFields'
__
R-help@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide
http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
__
R-help@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
__
R-help@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
Re: [R] [R-pkgs] package installation fails (RandomFields) - SOLVED
Thanks to all who replied so quickly. Installing liblapack-dev solved the problem and I can now install RandomFields. Drew Hoysak Brandon University __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
