[Rd] Recursive dependencies(Rcmdr)
Something might have slipped by me, but I got into the following situation
installing Rcmdr:
< install.packages("Rcmdr",depend=TRUE) >
Oodles of Output, until:
* Installing *source* package 'multcomp' ...
** R
** data
** inst
** preparing package for lazy loading
Error in dyn.load(x, as.logical(local), as.logical(now)) :
unable to load shared library
'/home/bs/pd/Rlibrary/mvtnorm/libs/mvtnorm.so':
/home/bs/pd/Rlibrary/mvtnorm/libs/mvtnorm.so: cannot open shared object file:
No such file or directory
Execution halted
Several oodles more for remaining packages
** building package indices ...
* DONE (strucchange)
The downloaded packages are in
/tmp/RtmpF23254/downloaded_packages
Warning messages:
1: installation of package 'multcomp' had non-zero exit status in:
install.packages("Rcmdr", depend = TRUE)
2: cannot create HTML package index in: tools:::unix.packages.html(.Library)
OK, so we start Rcmdr
> library(Rcmdr)
Loading required package: tcltk
Loading required package: car
it then detects that multcomp is missing and asks for permission to
install it, giving the same result.
The thing appears to be that multcomp depends on mvtnorm, but the
extra dependency goes undetected. Manual installation of the two
works.
A workaround is that John adds mvtnorm to the Suggested list for
Rcmdr, but I wonder if we couldn't do something smarter.
> version
_
platform x86_64-unknown-linux-gnu
arch x86_64
os linux-gnu
system x86_64, linux-gnu
status
major2
minor2.0
year 2005
month10
day 06
svn rev 35749
language R
> .libPaths()
[1] "/home/bs/pd/Rlibrary" "/usr/lib64/R/library"
--
O__ Peter Dalgaard Øster Farimagsgade 5, Entr.B
c/ /'_ --- Dept. of Biostatistics PO Box 2099, 1014 Cph. K
(*) \(*) -- University of Copenhagen Denmark Ph: (+45) 35327918
~~ - ([EMAIL PROTECTED]) FAX: (+45) 35327907
__
R-devel@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] Recursive dependencies(Rcmdr)
On Fri, 11 Nov 2005, Peter Dalgaard wrote:
Something might have slipped by me, but I got into the following situation
installing Rcmdr:
install.packages() does indeed have code to check for dependencies of
dependencies. I got the message
also installing the dependencies 'acepack', 'scatterplot3d', 'quadprog',
'fBasics', 'Hmisc', 'mlbench', 'randomForest', 'SparseM', 'xtable', 'oz',
'leaps', 'dynlm', 'e1071', 'tseries', 'chron', 'fCalendar', 'its', 'DAAG',
'abind', 'car', 'effects', 'lmtest', 'multcomp', 'mvtnorm', 'relimp',
'sandwich', 'strucchange', 'zoo'
The problem is the ordering. Rcmdr does have mvtnorm in the 'Suggests'
list, and has it after 'multcomp', and install.packages does not check
that the Suggests list does not have inter-dependencies.
So we do `do something smarter', but not smart enough.
< install.packages("Rcmdr",depend=TRUE) >
Oodles of Output, until:
* Installing *source* package 'multcomp' ...
** R
** data
** inst
** preparing package for lazy loading
Error in dyn.load(x, as.logical(local), as.logical(now)) :
unable to load shared library
'/home/bs/pd/Rlibrary/mvtnorm/libs/mvtnorm.so':
/home/bs/pd/Rlibrary/mvtnorm/libs/mvtnorm.so: cannot open shared object file:
No such file or directory
Execution halted
Several oodles more for remaining packages
** building package indices ...
* DONE (strucchange)
The downloaded packages are in
/tmp/RtmpF23254/downloaded_packages
Warning messages:
1: installation of package 'multcomp' had non-zero exit status in:
install.packages("Rcmdr", depend = TRUE)
2: cannot create HTML package index in: tools:::unix.packages.html(.Library)
OK, so we start Rcmdr
library(Rcmdr)
Loading required package: tcltk
Loading required package: car
it then detects that multcomp is missing and asks for permission to
install it, giving the same result.
The thing appears to be that multcomp depends on mvtnorm, but the
extra dependency goes undetected. Manual installation of the two
works.
A workaround is that John adds mvtnorm to the Suggested list for
Rcmdr, but I wonder if we couldn't do something smarter.
version
_
platform x86_64-unknown-linux-gnu
arch x86_64
os linux-gnu
system x86_64, linux-gnu
status
major2
minor2.0
year 2005
month10
day 06
svn rev 35749
language R
.libPaths()
[1] "/home/bs/pd/Rlibrary" "/usr/lib64/R/library"
--
O__ Peter Dalgaard Øster Farimagsgade 5, Entr.B
c/ /'_ --- Dept. of Biostatistics PO Box 2099, 1014 Cph. K
(*) \(*) -- University of Copenhagen Denmark Ph: (+45) 35327918
~~ - ([EMAIL PROTECTED]) FAX: (+45) 35327907
__
R-devel@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-devel
--
Brian D. Ripley, [EMAIL PROTECTED]
Professor of Applied Statistics, http://www.stats.ox.ac.uk/~ripley/
University of Oxford, Tel: +44 1865 272861 (self)
1 South Parks Road, +44 1865 272866 (PA)
Oxford OX1 3TG, UKFax: +44 1865 272595__
R-devel@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] Recursive dependencies(Rcmdr)
Dear Brian and Peter,
I guess that this problem didn't surface before because most use of the
Rcmdr package is on Windows using the package binaries.
I think that I can simply remove mvtnorm (and probably some others as well)
from the Rcmdr dependencies. I'll check more carefully when I have some
time, but I believe that mtvnorm is there just for multcomp, and its
inclusion probably dates to a period before dependencies were resolved by
install.packages().
Thanks for bringing this to my attention.
John
John Fox
Department of Sociology
McMaster University
Hamilton, Ontario
Canada L8S 4M4
905-525-9140x23604
http://socserv.mcmaster.ca/jfox
> -Original Message-
> From: [EMAIL PROTECTED]
> [mailto:[EMAIL PROTECTED] On Behalf Of Prof Brian Ripley
> Sent: Friday, November 11, 2005 10:45 AM
> To: Peter Dalgaard
> Cc: r-devel@stat.math.ethz.ch
> Subject: Re: [Rd] Recursive dependencies(Rcmdr)
>
> On Fri, 11 Nov 2005, Peter Dalgaard wrote:
>
> > Something might have slipped by me, but I got into the following
> > situation installing Rcmdr:
>
> install.packages() does indeed have code to check for
> dependencies of dependencies. I got the message
>
> also installing the dependencies 'acepack', 'scatterplot3d',
> 'quadprog', 'fBasics', 'Hmisc', 'mlbench', 'randomForest',
> 'SparseM', 'xtable', 'oz', 'leaps', 'dynlm', 'e1071',
> 'tseries', 'chron', 'fCalendar', 'its', 'DAAG', 'abind',
> 'car', 'effects', 'lmtest', 'multcomp', 'mvtnorm', 'relimp',
> 'sandwich', 'strucchange', 'zoo'
>
> The problem is the ordering. Rcmdr does have mvtnorm in the
> 'Suggests'
> list, and has it after 'multcomp', and install.packages does
> not check that the Suggests list does not have inter-dependencies.
>
> So we do `do something smarter', but not smart enough.
>
> >
> > < install.packages("Rcmdr",depend=TRUE) >
> >
> > Oodles of Output, until:
> >
> > * Installing *source* package 'multcomp' ...
> > ** R
> > ** data
> > ** inst
> > ** preparing package for lazy loading
> > Error in dyn.load(x, as.logical(local), as.logical(now)) :
> >unable to load shared library
> '/home/bs/pd/Rlibrary/mvtnorm/libs/mvtnorm.so':
> > /home/bs/pd/Rlibrary/mvtnorm/libs/mvtnorm.so: cannot open shared
> > object file: No such file or directory Execution halted
> >
> > Several oodles more for remaining packages
> >
> > ** building package indices ...
> > * DONE (strucchange)
> >
> > The downloaded packages are in
> >/tmp/RtmpF23254/downloaded_packages
> > Warning messages:
> > 1: installation of package 'multcomp' had non-zero exit status in:
> > install.packages("Rcmdr", depend = TRUE)
> > 2: cannot create HTML package index in:
> > tools:::unix.packages.html(.Library)
> >
> >
> > OK, so we start Rcmdr
> >
> >> library(Rcmdr)
> > Loading required package: tcltk
> > Loading required package: car
> >
> > it then detects that multcomp is missing and asks for permission to
> > install it, giving the same result.
> >
> > The thing appears to be that multcomp depends on mvtnorm, but the
> > extra dependency goes undetected. Manual installation of the two
> > works.
> >
> > A workaround is that John adds mvtnorm to the Suggested list for
> > Rcmdr, but I wonder if we couldn't do something smarter.
> >
> >> version
> > _
> > platform x86_64-unknown-linux-gnu
> > arch x86_64
> > os linux-gnu
> > system x86_64, linux-gnu
> > status
> > major2
> > minor2.0
> > year 2005
> > month10
> > day 06
> > svn rev 35749
> > language R
> >> .libPaths()
> > [1] "/home/bs/pd/Rlibrary" "/usr/lib64/R/library"
> >
> > --
> > O__ Peter Dalgaard Øster Farimagsgade 5, Entr.B
> > c/ /'_ --- Dept. of Biostatistics PO Box 2099, 1014 Cph. K
> > (*) \(*) -- University of Copenhagen Denmark Ph:
> (+45) 35327918
> > ~~ - ([EMAIL PROTECTED])
> FAX: (+45) 35327907
> >
> > __
> > R-devel@r-project.org mailing list
> > https://stat.ethz.ch/mailman/listinfo/r-devel
> >
> >
>
> --
> Brian D. Ripley, [EMAIL PROTECTED]
> Professor of Applied Statistics, http://www.stats.ox.ac.uk/~ripley/
> University of Oxford, Tel: +44 1865 272861 (self)
> 1 South Parks Road, +44 1865 272866 (PA)
> Oxford OX1 3TG, UKFax: +44 1865 272595
__
R-devel@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-devel
[Rd] configure on solaris 2.9 with non GNU compilers (PR#8300)
Full_Name: Toby Muhlhofer Version: 2.2.0, 2.1.1 OS: Solaris 2.9 Submission from: (NULL) (128.83.62.46) I'm trying to compile R on a Solaris machine. The default C compiler is cc (although gcc is available) and the default Fortran compiler is f95 (although g77 is available). Without defining the F77 environment variable, configure defaults to f95 as a Fortran compiler and eventually fails with the following output: - checking whether mixed C/Fortran code can be run... configure: WARNING: cannot run mixed C/Fortan code configure: error: Maybe check LDFLAGS for paths to Fortran libraries? - Setting LDFLAGS to the path where the Fortran libraries sit makes the C compiler complain. If I give the value g77 (or the full path to g77) to F77, there are two interesting issues: 1) - defining F77 to be g77 checking whether we are using the GNU Fortran 77 compiler... no checking whether g77 accepts -g... yes - Why does configure think we are not using the GNU Fortran 77 compiler? But more importantly 2) - checking how to get verbose linking output from g77... configure: WARNING: compilation failed checking for Fortran libraries of g77... checking how to get verbose linking output from cc... -### checking for C libraries of cc... -L/usr/local/lib -lthread checking for dummy main to link with Fortran libraries... none checking for Fortran name-mangling scheme... configure: error: cannot compile a simple Fortran program - I tried to compile a simple "Hello World" program with either Fortran compiler and both work without a problem. __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
