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errors when installing packages (ubuntu)
3 messages · Roman Luštrik, Uwe Ligges, Reinhard Furrer
Looks like spam depends on R-2.10.x which the package maintainer (CCing) has not declared in the DESCRIPTION file. So either install R-2.10.1 and try again or use an older spam version from the CRAN archives for your old version of R. To Reinhard Furrer: can you please upload a new version with increased version number to CRAN that declares the dependency. Thank you. Best wishes, Uwe Ligges
On 09.01.2010 14:27, romunov wrote:
Hi List,
I'm having problems installing certain packages. When I try to install
fields, I get the output below. I have highlighted the what I perceive as
the first error (spam seems to be a dependency of fields). Can I assume this
is causing dependency problems for fields, which fails to install at the
end, or is there a deeper problem? I run Ubuntu Karmic Koala on R 2.9.2.
2> install.packages("fields")
Warning in install.packages("fields") :
argument 'lib' is missing: using
'/home/romunov/R/i486-pc-linux-gnu-library/2.9'
--- Please select a CRAN mirror for use in this session ---
Loading Tcl/Tk interface ... done
also installing the dependency ?spam?
trying URL 'http://cran.at.r-project.org/src/contrib/spam_0.20-2.tar.gz'
Content type 'application/x-gzip' length 470013 bytes (458 Kb)
opened URL
==================================================
downloaded 458 Kb
trying URL 'http://cran.at.r-project.org/src/contrib/fields_6.01.tar.gz'
Content type 'application/x-gzip' length 3670039 bytes (3.5 Mb)
opened URL
==================================================
downloaded 3.5 Mb
* Installing *source* package ?spam? ...
** libs
gfortran -fpic -g -O2 -c bckslvmodified.f -o bckslvmodified.o
gfortran -fpic -g -O2 -c cholmodified.f -o cholmodified.o
gfortran -fpic -g -O2 -c dist.f -o dist.o
gfortran -fpic -g -O2 -c fromsparsekit.f -o fromsparsekit.o
gfortran -fpic -g -O2 -c kronecker.f -o kronecker.o
gfortran -fpic -g -O2 -c spamown.f -o spamown.o
gfortran -fpic -g -O2 -c xybind.f -o xybind.o
gcc -std=gnu99 -shared -o spam.so bckslvmodified.o cholmodified.o dist.o
fromsparsekit.o kronecker.o spamown.o xybind.o -lgfortran -lm
-L/usr/lib/R/lib -lR
** 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"
Error in setOldClass(c("dist", "numeric")) :
inconsistent old-style class information for "numeric"; the class is
defined but does not extend "oldClass"
Error : unable to load R code in package 'spam'
ERROR: lazy loading failed for package ?spam?
* Removing ?/home/romunov/R/i486-pc-linux-gnu-library/2.9/spam?
* Installing *source* package ?fields? ...
** libs
gfortran -fpic -g -O2 -c css.f -o css.o
gfortran -fpic -g -O2 -c csstr.f -o csstr.o
gfortran -fpic -g -O2 -c cvrf.f -o cvrf.o
gfortran -fpic -g -O2 -c dchold.f -o dchold.o
gfortran -fpic -g -O2 -c dcopy.f -o dcopy.o
gfortran -fpic -g -O2 -c ddfind.f -o ddfind.o
gfortran -fpic -g -O2 -c ddot.f -o ddot.o
gfortran -fpic -g -O2 -c derrb.f -o derrb.o
gfortran -fpic -g -O2 -c dlv.f -o dlv.o
gfortran -fpic -g -O2 -c dmaket.f -o dmaket.o
gfortran -fpic -g -O2 -c drdfun.f -o drdfun.o
gfortran -fpic -g -O2 -c dsetup.f -o dsetup.o
gfortran -fpic -g -O2 -c evlpoly.f -o evlpoly.o
gfortran -fpic -g -O2 -c evlpoly2.f -o evlpoly2.o
gfortran -fpic -g -O2 -c expbs.f -o expbs.o
gfortran -fpic -g -O2 -c expfn.f -o expfn.o
gfortran -fpic -g -O2 -c gaspbs.f -o gaspbs.o
gfortran -fpic -g -O2 -c gaspfn.f -o gaspfn.o
gfortran -fpic -g -O2 -c gcvcss.f -o gcvcss.o
gfortran -fpic -g -O2 -c gcvfc.f -o gcvfc.o
gfortran -fpic -g -O2 -c hsort.f -o hsort.o
gfortran -fpic -g -O2 -c ifind.f -o ifind.o
gfortran -fpic -g -O2 -c igpoly.f -o igpoly.o
gfortran -fpic -g -O2 -c inpoly.f -o inpoly.o
gfortran -fpic -g -O2 -c lscv.f -o lscv.o
gfortran -fpic -g -O2 -c m2deb.f -o m2deb.o
gfortran -fpic -g -O2 -c mkpoly.f -o mkpoly.o
gfortran -fpic -g -O2 -c mltdrb.f -o mltdrb.o
gfortran -fpic -g -O2 -c mltdtd.f -o mltdtd.o
gfortran -fpic -g -O2 -c msort.f -o msort.o
gfortran -fpic -g -O2 -c multeb.f -o multeb.o
gfortran -fpic -g -O2 -c multgb.f -o multgb.o
gfortran -fpic -g -O2 -c multrb.f -o multrb.o
gfortran -fpic -g -O2 -c radbas.f -o radbas.o
gfortran -fpic -g -O2 -c radfn2.f -o radfn2.o
gfortran -fpic -g -O2 -c radfun.f -o radfun.o
gfortran -fpic -g -O2 -c rcss.f -o rcss.o
gfortran -fpic -g -O2 -c rcssr.f -o rcssr.o
gfortran -fpic -g -O2 -c rcsswt.f -o rcsswt.o
gfortran -fpic -g -O2 -c sortm.f -o sortm.o
gcc -std=gnu99 -shared -o fields.so css.o csstr.o cvrf.o dchold.o dcopy.o
ddfind.o ddot.o derrb.o dlv.o dmaket.o drdfun.o dsetup.o evlpoly.o
evlpoly2.o expbs.o expfn.o gaspbs.o gaspfn.o gcvcss.o gcvfc.o hsort.o
ifind.o igpoly.o inpoly.o lscv.o m2deb.o mkpoly.o mltdrb.o mltdtd.o msort.o
multeb.o multgb.o multrb.o radbas.o radfn2.o radfun.o rcss.o rcssr.o
rcsswt.o sortm.o -lgfortran -lm -L/usr/lib/R/lib -lR
** R
** data
** preparing package for lazy loading
Warning in library(pkg, character.only = TRUE, logical.return = TRUE,
lib.loc = lib.loc) :
there is no package called 'spam'
Error : package 'spam' could not be loaded
ERROR: lazy loading failed for package ?fields?
* Removing ?/home/romunov/R/i486-pc-linux-gnu-library/2.9/fields?
The downloaded packages are in
?/tmp/RtmpOUIANP/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
[[alternative HTML version deleted]]
______________________________________________ R-help at 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.
All, as a temporary fix (until the new version is on CRAN), one can install spam version spam_0.20-0 available on http://user.math.uzh.ch/furrer/software/spam/ During the installation, a couple warnings appear, but on can ignore those... I'll post a new version soon. Best, Reinhard
Uwe Ligges wrote:
Looks like spam depends on R-2.10.x which the package maintainer (CCing) has not declared in the DESCRIPTION file. So either install R-2.10.1 and try again or use an older spam version from the CRAN archives for your old version of R. To Reinhard Furrer: can you please upload a new version with increased version number to CRAN that declares the dependency. Thank you. Best wishes, Uwe Ligges On 09.01.2010 14:27, romunov wrote:
Hi List,
I'm having problems installing certain packages. When I try to install
fields, I get the output below. I have highlighted the what I perceive as
the first error (spam seems to be a dependency of fields). Can I
assume this
is causing dependency problems for fields, which fails to install at the
end, or is there a deeper problem? I run Ubuntu Karmic Koala on R 2.9.2.
2> install.packages("fields")
Warning in install.packages("fields") :
argument 'lib' is missing: using
'/home/romunov/R/i486-pc-linux-gnu-library/2.9'
--- Please select a CRAN mirror for use in this session ---
Loading Tcl/Tk interface ... done
also installing the dependency ?spam?
trying URL 'http://cran.at.r-project.org/src/contrib/spam_0.20-2.tar.gz'
Content type 'application/x-gzip' length 470013 bytes (458 Kb)
opened URL
==================================================
downloaded 458 Kb
trying URL 'http://cran.at.r-project.org/src/contrib/fields_6.01.tar.gz'
Content type 'application/x-gzip' length 3670039 bytes (3.5 Mb)
opened URL
==================================================
downloaded 3.5 Mb
* Installing *source* package ?spam? ...
** libs
gfortran -fpic -g -O2 -c bckslvmodified.f -o bckslvmodified.o
gfortran -fpic -g -O2 -c cholmodified.f -o cholmodified.o
gfortran -fpic -g -O2 -c dist.f -o dist.o
gfortran -fpic -g -O2 -c fromsparsekit.f -o fromsparsekit.o
gfortran -fpic -g -O2 -c kronecker.f -o kronecker.o
gfortran -fpic -g -O2 -c spamown.f -o spamown.o
gfortran -fpic -g -O2 -c xybind.f -o xybind.o
gcc -std=gnu99 -shared -o spam.so bckslvmodified.o cholmodified.o dist.o
fromsparsekit.o kronecker.o spamown.o xybind.o -lgfortran -lm
-L/usr/lib/R/lib -lR
** 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"
Error in setOldClass(c("dist", "numeric")) :
inconsistent old-style class information for "numeric"; the class is
defined but does not extend "oldClass"
Error : unable to load R code in package 'spam'
ERROR: lazy loading failed for package ?spam?
* Removing ?/home/romunov/R/i486-pc-linux-gnu-library/2.9/spam?
* Installing *source* package ?fields? ...
** libs
gfortran -fpic -g -O2 -c css.f -o css.o
gfortran -fpic -g -O2 -c csstr.f -o csstr.o
gfortran -fpic -g -O2 -c cvrf.f -o cvrf.o
gfortran -fpic -g -O2 -c dchold.f -o dchold.o
gfortran -fpic -g -O2 -c dcopy.f -o dcopy.o
gfortran -fpic -g -O2 -c ddfind.f -o ddfind.o
gfortran -fpic -g -O2 -c ddot.f -o ddot.o
gfortran -fpic -g -O2 -c derrb.f -o derrb.o
gfortran -fpic -g -O2 -c dlv.f -o dlv.o
gfortran -fpic -g -O2 -c dmaket.f -o dmaket.o
gfortran -fpic -g -O2 -c drdfun.f -o drdfun.o
gfortran -fpic -g -O2 -c dsetup.f -o dsetup.o
gfortran -fpic -g -O2 -c evlpoly.f -o evlpoly.o
gfortran -fpic -g -O2 -c evlpoly2.f -o evlpoly2.o
gfortran -fpic -g -O2 -c expbs.f -o expbs.o
gfortran -fpic -g -O2 -c expfn.f -o expfn.o
gfortran -fpic -g -O2 -c gaspbs.f -o gaspbs.o
gfortran -fpic -g -O2 -c gaspfn.f -o gaspfn.o
gfortran -fpic -g -O2 -c gcvcss.f -o gcvcss.o
gfortran -fpic -g -O2 -c gcvfc.f -o gcvfc.o
gfortran -fpic -g -O2 -c hsort.f -o hsort.o
gfortran -fpic -g -O2 -c ifind.f -o ifind.o
gfortran -fpic -g -O2 -c igpoly.f -o igpoly.o
gfortran -fpic -g -O2 -c inpoly.f -o inpoly.o
gfortran -fpic -g -O2 -c lscv.f -o lscv.o
gfortran -fpic -g -O2 -c m2deb.f -o m2deb.o
gfortran -fpic -g -O2 -c mkpoly.f -o mkpoly.o
gfortran -fpic -g -O2 -c mltdrb.f -o mltdrb.o
gfortran -fpic -g -O2 -c mltdtd.f -o mltdtd.o
gfortran -fpic -g -O2 -c msort.f -o msort.o
gfortran -fpic -g -O2 -c multeb.f -o multeb.o
gfortran -fpic -g -O2 -c multgb.f -o multgb.o
gfortran -fpic -g -O2 -c multrb.f -o multrb.o
gfortran -fpic -g -O2 -c radbas.f -o radbas.o
gfortran -fpic -g -O2 -c radfn2.f -o radfn2.o
gfortran -fpic -g -O2 -c radfun.f -o radfun.o
gfortran -fpic -g -O2 -c rcss.f -o rcss.o
gfortran -fpic -g -O2 -c rcssr.f -o rcssr.o
gfortran -fpic -g -O2 -c rcsswt.f -o rcsswt.o
gfortran -fpic -g -O2 -c sortm.f -o sortm.o
gcc -std=gnu99 -shared -o fields.so css.o csstr.o cvrf.o dchold.o dcopy.o
ddfind.o ddot.o derrb.o dlv.o dmaket.o drdfun.o dsetup.o evlpoly.o
evlpoly2.o expbs.o expfn.o gaspbs.o gaspfn.o gcvcss.o gcvfc.o hsort.o
ifind.o igpoly.o inpoly.o lscv.o m2deb.o mkpoly.o mltdrb.o mltdtd.o
msort.o
multeb.o multgb.o multrb.o radbas.o radfn2.o radfun.o rcss.o rcssr.o
rcsswt.o sortm.o -lgfortran -lm -L/usr/lib/R/lib -lR
** R
** data
** preparing package for lazy loading
Warning in library(pkg, character.only = TRUE, logical.return = TRUE,
lib.loc = lib.loc) :
there is no package called 'spam'
Error : package 'spam' could not be loaded
ERROR: lazy loading failed for package ?fields?
* Removing ?/home/romunov/R/i486-pc-linux-gnu-library/2.9/fields?
The downloaded packages are in
?/tmp/RtmpOUIANP/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
[[alternative HTML version deleted]]
______________________________________________ R-help at 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.