[Rd] summary of Surv object crashes R 2.2.0 (PR#8203)
Full_Name: Victor Moreno Version: 2.2.0 OS: windows Submission from: (NULL) (213.151.99.160) summary of an object class Surv (package survival) hangs and closes R 2.2.0 I would like to have Surv objects in a data frame to build models easier: t<-rexp(100) s<-rbinom(100,1,.3) surv<-Surv(t,s) x1<-rnorm(100,10,2) x2<-rnorm(100,10,2) dat<-data.frame(surv,x1,x2) coxph(surv~.,data=dat) so far no problems, but R crashes if I write summary(dat) I checked that the problem is in summary(surv) Tested on previous versions of R (1.9.0, 2.1.0) in a friend's computer) gives no results, but doesn't crash R __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
[Rd] 8 char labels in read.spss
I was wondering why it is possible to read long labels from the CVS files but not from the SPSS files. I did not have much time to search for the code but I found: in foreign_0.8-10 source file var.h.in > /* Definition of the max length of a short string value, generally >eight characters. */ > #define MAX_SHORT_STRING ((SIZEOF_DOUBLE)>=8 ? ((SIZEOF_DOUBLE)+1)/2*2 > : 8) > #define MIN_LONG_STRING (MAX_SHORT_STRING+1) > > /* FYI: It is a bad situation if sizeof(R_flt64) < MAX_SHORT_STRING: >then short string missing values can be truncated in system files >because there's only room for as many characters as can fit in a >R_flt64. */ > #if MAX_SHORT_STRING > 8 > #error MAX_SHORT_STRING must be less than 8. > #endif I am am right then there was a restriction in the year 2000 because the files are from the year 2000. Now there are some questions: Did I found the right code? is it possible that anybody could recompile this with long value names or where is the best manual for a quick start in compiling packages. I found a couple of weeks before a tread where anybody wrote a complete way for building packages. He described all problems of him and there were a lot of hints for the first steps, but I am not able to find it again - I don't know the search terms which I used before :-( with regards Knut __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
[Rd] Post processing need for installing packages in rpms.
Hello,
I maintain some packages in Fedora Extras for R related modules.
Until R 2.2.0 I used for post processing (both after installing and
removing the package) the following lines:
%{_bindir}/R CMD perl %{_libdir}/R/share/perl/build-help.pl --htmllists
cat %{_libdir}/R/library/*/CONTENTS > %{_libdir}/R/doc/html/search/index.txt
Typically %{_bindir} is /usr/bin and %{_libdir} is /usr/lib or
/usr/lib64
The purpose of those lines is to enable the access to the module
documentation from R help. The first refers to html and the second to the
text help variant.
With R 2.2.0 build-help.pl no longer has the --htmllists option. Is
there any easy replacement, or is there any other method to achieve the same
results?
FWIW, I have searched trough the release notes as well as through the
documentation for sys admins and for package developers without any
success.
Best regards,
--
José Abílio
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Re: [Rd] Post processing need for installing packages in rpms.
On Tue, 11 Oct 2005, [UTF-8] José Matos wrote:
Hello,I maintain some packages in Fedora Extras for R related modules.
Until R 2.2.0 I used for post processing (both after installing
andremoving the package) the following lines:
%{_bindir}/R CMD perl %{_libdir}/R/share/perl/build-help.pl --htmllistscat
%{_libdir}/R/library/*/CONTENTS > %{_libdir}/R/doc/html/search/index.txt
Typically %{_bindir} is /usr/bin and %{_libdir} is /usr/lib or/usr/lib64
The purpose of those lines is to enable the access to the
moduledocumentation from R help. The first refers to html and the second to
thetext help variant.
With R 2.2.0 build-help.pl no longer has the --htmllists option. Isthere
any easy replacement, or is there any other method to achieve the sameresults?
It is no longer needed: the information is now built by R at runtime.
FWIW, I have searched trough the release notes as well as through
thedocumentation for sys admins and for package developers without anysuccess.
For an outsider it might not be obvious that the NEWS entry
o R_HOME/doc/html/packages.html is now remade by R not Perl code.
This may result in small changes in layout and a change in
encoding (to UTF-8 where supported).
refers to this. (Note that build-help.pl --htmllists was never documented
as part of R's API.)
I checked Martyn Plummer's R.spec on CRAN, but that is out-of-date.
Please look at the R.spec in his current SRPM, which works for me.
--
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__
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Re: [Rd] 8 char labels in read.spss
On Tue, 11 Oct 2005, Knut Krueger wrote: > I was wondering why it is possible to read long labels from the CVS > files but not from the SPSS files. The SPSS file formats are not documented, and so we rely on the code from PSPP. At the time, PSPP did not read long variable names. It now does, so it would be possible for someone update the SPSS-reading code to handle long variable names. This is much more complicated than just changing a #define; the long variable names are stored in a different part of the file. I don't expect anyone on R-core to get around to this any time soon. If you want to try, the current PSPP code is at http://savannah.gnu.org/projects/pspp -thomas > I did not have much time to search for the code but I found: > > in foreign_0.8-10 source file var.h.in > >> /* Definition of the max length of a short string value, generally >>eight characters. */ >> #define MAX_SHORT_STRING ((SIZEOF_DOUBLE)>=8 ? ((SIZEOF_DOUBLE)+1)/2*2 >> : 8) >> #define MIN_LONG_STRING (MAX_SHORT_STRING+1) >> >> /* FYI: It is a bad situation if sizeof(R_flt64) < MAX_SHORT_STRING: >>then short string missing values can be truncated in system files >>because there's only room for as many characters as can fit in a >>R_flt64. */ >> #if MAX_SHORT_STRING > 8 >> #error MAX_SHORT_STRING must be less than 8. >> #endif > > I am am right then there was a restriction in the year 2000 because the > files are from the year 2000. > > Now there are some questions: > Did I found the right code? > is it possible that anybody could recompile this with long value names > or where is the best manual for a quick start in compiling packages. > > > I found a couple of weeks before a tread where anybody wrote a complete > way for building packages. > He described all problems of him and there were a lot of hints for the > first steps, but I am not able to find it again - I don't know the > search terms which I used before :-( > > > with regards > Knut > > __ > R-devel@r-project.org mailing list > https://stat.ethz.ch/mailman/listinfo/r-devel > Thomas Lumley Assoc. Professor, Biostatistics [EMAIL PROTECTED] University of Washington, Seattle __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] Post processing need for installing packages in rpms.
Prof Brian Ripley wrote:
> On Tue, 11 Oct 2005, [UTF-8] José Matos wrote:
>
>> Hello,I maintain some packages in Fedora Extras for R related
>> modules.
>>Until R 2.2.0 I used for post processing (both after installing
>>andremoving the package) the following lines:
>> %{_bindir}/R CMD perl %{_libdir}/R/share/perl/build-help.pl
>> --htmllistscat %{_libdir}/R/library/*/CONTENTS >
>> %{_libdir}/R/doc/html/search/index.txt
>>Typically %{_bindir} is /usr/bin and %{_libdir} is /usr/lib
>>or/usr/lib64 The purpose of those lines is to enable the access to
>>the moduledocumentation from R help. The first refers to html and
>>the second to thetext help variant. With R 2.2.0 build-help.pl no
>>longer has the --htmllists option. Isthere any easy replacement,
>>or is there any other method to achieve the sameresults?
>
> It is no longer needed: the information is now built by R at runtime.
It is good to know that. My work becomes easier now. :-)
>>FWIW, I have searched trough the release notes as well as through
>>thedocumentation for sys admins and for package developers without
>>anysuccess.
>
> For an outsider it might not be obvious that the NEWS entry
>
> o R_HOME/doc/html/packages.html is now remade by R not Perl code.
> This may result in small changes in layout and a change in
> encoding (to UTF-8 where supported).
>
> refers to this. (Note that build-help.pl --htmllists was never documented
> as part of R's API.)
Actually I notice that line, it looked suspicious but then I got
distracted by the last sentence and I have focused on the layout changes.
"A posteriori" it is easy to justify most of our failures. :-)
> I checked Martyn Plummer's R.spec on CRAN, but that is out-of-date.
> Please look at the R.spec in his current SRPM, which works for me.
Where do I get it?
I checked the spec files in
http://cran.at.r-project.org/bin/linux/redhat/SRPMS/R.spec
http://cran.at.r-project.org/bin/linux/redhat/SRPMS/R-2.2.0-2.fc3.src.rpm
since they have different dates, and they both show the same line with the
--htmlists parameter:
# Update package indices
%{_bindir}/R CMD perl %{_libdir}/R/share/perl/build-help.pl --htmllists
> /dev/null 2>/dev/null
[Last line was wrapped by my email composer.]
--
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Re: [Rd] Post processing need for installing packages in rpms.
On Tue, 2005-10-11 at 13:11 +0100, Prof Brian Ripley wrote:
> On Tue, 11 Oct 2005, [UTF-8] José Matos wrote:
>
> > Hello,I maintain some packages in Fedora Extras for R related
> > modules.
> >Until R 2.2.0 I used for post processing (both after installing
> > andremoving the package) the following lines:
> > %{_bindir}/R CMD perl %{_libdir}/R/share/perl/build-help.pl --htmllistscat
> > %{_libdir}/R/library/*/CONTENTS > %{_libdir}/R/doc/html/search/index.txt
> >Typically %{_bindir} is /usr/bin and %{_libdir} is /usr/lib
> > or/usr/lib64
> >The purpose of those lines is to enable the access to the
> > moduledocumentation from R help. The first refers to html and the second to
> > thetext help variant.
> >With R 2.2.0 build-help.pl no longer has the --htmllists option.
> > Isthere any easy replacement, or is there any other method to achieve the
> > sameresults?
>
> It is no longer needed: the information is now built by R at runtime.
>
> >FWIW, I have searched trough the release notes as well as through
> > thedocumentation for sys admins and for package developers without
> > anysuccess.
>
> For an outsider it might not be obvious that the NEWS entry
>
> o R_HOME/doc/html/packages.html is now remade by R not Perl code.
> This may result in small changes in layout and a change in
> encoding (to UTF-8 where supported).
>
> refers to this. (Note that build-help.pl --htmllists was never documented
> as part of R's API.)
>
> I checked Martyn Plummer's R.spec on CRAN, but that is out-of-date.
> Please look at the R.spec in his current SRPM, which works for me.
Sorry about that. I had forgotten that I put a lone spec file in there.
I have removed it, since it seems likely that I will do the same thing
in the future.
The perl hack used to be required because rpmbuild installs R in a build
root which is different from the final installation directory. The
reason you don't see an error message from the post install script is
because it is redirected to /dev/null. I'll fix this in the next
version.
Martyn
---
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Re: [Rd] Catching warning and error output
Dear R developers, since nobody has pointed me to an existing solution so far, here is a more specific suggestion. Attached you will find two patches against R version 2.2.0. The first patch does two things: 1) Add a function R_WriteErrConsole similar to R_WriteConsole, and a corresponding ptr_R_WriteErrConsole. 2) Make inError, inWarning, and inPrintWarnings from errors.c accessible (read-only) in R_ext/Error.h I believe these changes to be minimally invasive. I did not test-compile on windows, but the change in gnuwin32 should be trivial. The second patch adds a test/example to tests/Embedding, showing how this added API can be used to identify warnings and errors in the output stream. If you need any further comments / different format of patches, or anything else in order to evaluate this proposal, please let me know. Thanks! Thomas __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
[Rd] Compile problem R 2.2.0 + Solaris 10 x86
Hi!
I'm trying to compile R (32-bit) on Solaris 10 x86
using Sun Studio 10 + Sun Perflib (for BLAS and
LAPACK) but encountered issues with undefined symbol
"bratio". Appreciate any help.
Compiler options (from configure output):
==
R is now configured for i386-pc-solaris2.10
Source directory: .
Installation directory:/usr/local
C compiler:cc -g -O -xtarget=opteron
-D__NO_MATH_INLINES -g -O -xtarget=opteron
C++ compiler: CC -gO -xtarget=opteron
-gO -xtarget=opteron
Fortran compiler: f77 -g -O
-xtarget=opteron -gO -xtarget=opteron
Interfaces supported: X11
External libraries:readline, BLAS(SunPerf)
Additional capabilities: PNG, JPEG, MBCS, NLS
Options enabled: R profiling
Recommended packages: yes
configure: WARNING: you cannot build DVI versions of
the R manuals
configure: WARNING: you cannot build PDF versions of
the R manuals
==
Compile error:
==
...
cc -g -O -xtarget=opteron -L/opt/SUNWspro/lib
-L/usr/lib -L/usr/sfw/lib -L/opt/sfw/lib -o R.bin
Rmain.o CConverters.o CommandLineArgs.o Rdynload.o
Renviron.o RNG.o apply.o arithmetic.o apse.o array.o
attrib.o base.o bind.o builtin.o character.o
coerce.o colors.o complex.o connections.o context.o
cov.o cum.o dcf.o datetime.o debug.o deparse.o
deriv.o dotcode.o dounzip.o dstruct.o duplicate.o
engine.o envir.o errors.o eval.o format.o fourier.o
gevents.o gram.o gram-ex.o graphics.o identical.o
internet.o iosupport.o lapack.o list.o logic.o
main.o mapply.o match.o memory.o model.o names.o
objects.o optim.o optimize.o options.o par.o paste.o
pcre.o platform.o plot.o plot3d.o plotmath.o print.o
printarray.o printvector.o printutils.o qsort.o
random.o regex.o registration.o relop.o saveload.o
scan.o seq.o serialize.o size.o sort.o source.o
split.o sprintf.o startup.o subassign.o subscript.o
subset.o summary.o sysutils.o unique.o util.o
version.o vfonts.o xxxpr.o ../unix/libunix.a
../appl/libappl.a ../nmath/libnmath.a
-xlic_lib=sunperf -lsunmath -Rreg
-R/opt/SUNWspro/lib/sse2:/opt/SUNWspro/lib
-L/opt/SUNWspro/lib/sse2 -L/opt/SUNWspro/prod/lib/sse2
-L/opt/SUNWspro/prod/lib -L/usr/ccs/lib -lfui -lfai
-lfsu -lsunmath -lmtsk -lm ../extra/zlib/libz.a
../extra/bzip2/libbz2.a ../extra/pcre/libpcre.a
../extra/intl/libintl.a -lreadline -lncurses -lnsl
-lsocket -ldl -lm
Undefined first referenced
symbol in file
bratio
../nmath/libnmath.a(pbeta.o)
ld: fatal: Symbol referencing errors. No output
written to R.bin
*** Error code 1
make: Fatal error: Command failed for target `R.bin'
Current working directory
/tmp/apps/R-2.2.0-32/src/main
*** Error code 1
The following command caused the error:
make install-bin-local
make: Fatal error: Command failed for target `R'
Current working directory
/tmp/apps/R-2.2.0-32/src/main
*** Error code 1
The following command caused the error:
for d in scripts include extra appl nmath unix main
modules library; do \
(cd ${d} && make R) || exit 1; \
done
make: Fatal error: Command failed for target `R'
Current working directory /tmp/apps/R-2.2.0-32/src
*** Error code 1
The following command caused the error:
for d in m4 tools doc etc share src tests po; do \
(cd ${d} && make R) || exit 1; \
done
make: Fatal error: Command failed for target `R'
==
Thanks.
Regards,
Daniel
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[Rd] Error: .First.lib failed for 'SBMLodeSolveR'
Dear R-developers,
I am getting the following error message (see bottom of e-mail) and can't make
a clue out of it.
The zzz.R file contains
.First.lib <- function(lib, pkg) library.dynam("SBMLodeSolveR",pkg,lib)
.Last.lib <- function(libpath) library.dynam.unload("SBMLodeSolveR", libpath)
There is a SBMLodeSolveR.so file in the src directory which works if loaded
with
dyn.load("/data/devel/SBMLodeSolveR/SBMLodeSolveR/src/SBMLodeSolveR.so")
The error/warning messages are:
* checking S3 generic/method consistency ... WARNING
Error: .First.lib failed for 'SBMLodeSolveR'
Call sequence:
2: stop(gettextf(".First.lib failed for '%s'", libraryPkgName(package)),
domain = NA)
1: library(package, lib.loc = lib.loc, character.only = TRUE, verbose = FALSE)
Execution halted
See section 'Generic functions and methods' of the 'Writing R Extensions'
manual.
* checking replacement functions ... WARNING
Error: .First.lib failed for 'SBMLodeSolveR'
Call sequence:
2: stop(gettextf(".First.lib failed for '%s'", libraryPkgName(package)),
domain = NA)
1: library(package, lib.loc = lib.loc, character.only = TRUE, verbose = FALSE)
Execution halted
In R, the argument of a replacement function which corresponds to the right
hand side must be named 'value'.
* checking foreign function calls ... WARNING
Error: .First.lib failed for 'SBMLodeSolveR'
Call sequence:
2: stop(gettextf(".First.lib failed for '%s'", libraryPkgName(package)),
domain = NA)
1: library(package, lib.loc = lib.loc, character.only = TRUE, verbose = FALSE)
Execution halted
See section 'System and foreign language interfaces' of the 'Writing R
Extensions' manual.
*
Eryk
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Re: [Rd] Catching warning and error output
> since nobody has pointed me to an existing solution so far, here is a more > specific suggestion. Attached you will find two patches against R version > 2.2.0. Sorry, seems the attachments were stripped (at least they don't show up in the archive). Here are links to the two diffs in question: http://rkward.sourceforge.net/temp/classify_output_patch.diff http://rkward.sourceforge.net/temp/classify_output_test.diff Thomas __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] summary of Surv object crashes R 2.2.0 (PR#8203)
This hasn't crashed R. It is almost certainly stack overflow due to excessive recursion (which is what happens on Linux, and in R-patched on Windows). (Note to people tempted to raise the evaluation limit in R: please check against the stack size. We've raised the latter to 10Mb on Windows to compensate.) I get > summary(surv) Error: evaluation nested too deeply: infinite recursion / options(expressions=)? The issue is that surv is a matrix, and summary.matrix calls summary.data.frame which calls summary.matrix on the matrix column And this happens because there is an as.data.frame method for class Surv. You probably got a useful error message in 2.1.0: I did. The current code come from r33884 | maechler | 2005-04-11 11:37:04 +0100 (Mon, 11 Apr 2005) | 1 line summary(data.frame(I())) which is clearly not enough. When Martin gets back perhaps he can remind us why unclass() was not good enough here. I think we need > summary.matrix function (object, ...) summary.data.frame(data.frame(unclass(object)), ...) since there is no other way to guarantee that data.frame splits the matrix up into columns. But a summary.Surv method would be a good idea. On Tue, 11 Oct 2005 [EMAIL PROTECTED] wrote: > Full_Name: Victor Moreno > Version: 2.2.0 > OS: windows > Submission from: (NULL) (213.151.99.160) > > > summary of an object class Surv (package survival) hangs and closes R 2.2.0 > > I would like to have Surv objects in a data frame to build models easier: > > t<-rexp(100) > s<-rbinom(100,1,.3) > surv<-Surv(t,s) > x1<-rnorm(100,10,2) > x2<-rnorm(100,10,2) > dat<-data.frame(surv,x1,x2) > coxph(surv~.,data=dat) > > so far no problems, but R crashes if I write > > summary(dat) > > I checked that the problem is in > summary(surv) > > Tested on previous versions of R (1.9.0, 2.1.0) in a friend's computer) > gives no results, but doesn't crash R -- 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] Compile problem R 2.2.0 + Solaris 10 x86
I can't solve this as I think the problem occurred earlier. bratio is
defined in src/nmath/toms708.o included in src/nmath/libmath.a
Take a look at what was built in src/nmath.
On Wed, 12 Oct 2005, Daniel Wong wrote:
> Hi!
>
> I'm trying to compile R (32-bit) on Solaris 10 x86
> using Sun Studio 10 + Sun Perflib (for BLAS and
> LAPACK) but encountered issues with undefined symbol
> "bratio". Appreciate any help.
>
> Compiler options (from configure output):
> ==
> R is now configured for i386-pc-solaris2.10
>
> Source directory: .
> Installation directory:/usr/local
>
> C compiler:cc -g -O -xtarget=opteron
> -D__NO_MATH_INLINES -g -O -xtarget=opteron
> C++ compiler: CC -gO -xtarget=opteron
> -gO -xtarget=opteron
> Fortran compiler: f77 -g -O
> -xtarget=opteron -gO -xtarget=opteron
>
> Interfaces supported: X11
> External libraries:readline, BLAS(SunPerf)
> Additional capabilities: PNG, JPEG, MBCS, NLS
> Options enabled: R profiling
>
> Recommended packages: yes
>
> configure: WARNING: you cannot build DVI versions of
> the R manuals
> configure: WARNING: you cannot build PDF versions of
> the R manuals
> ==
>
> Compile error:
> ==
> ...
> cc -g -O -xtarget=opteron -L/opt/SUNWspro/lib
> -L/usr/lib -L/usr/sfw/lib -L/opt/sfw/lib -o R.bin
> Rmain.o CConverters.o CommandLineArgs.o Rdynload.o
> Renviron.o RNG.o apply.o arithmetic.o apse.o array.o
> attrib.o base.o bind.o builtin.o character.o
> coerce.o colors.o complex.o connections.o context.o
> cov.o cum.o dcf.o datetime.o debug.o deparse.o
> deriv.o dotcode.o dounzip.o dstruct.o duplicate.o
> engine.o envir.o errors.o eval.o format.o fourier.o
> gevents.o gram.o gram-ex.o graphics.o identical.o
> internet.o iosupport.o lapack.o list.o logic.o
> main.o mapply.o match.o memory.o model.o names.o
> objects.o optim.o optimize.o options.o par.o paste.o
> pcre.o platform.o plot.o plot3d.o plotmath.o print.o
> printarray.o printvector.o printutils.o qsort.o
> random.o regex.o registration.o relop.o saveload.o
> scan.o seq.o serialize.o size.o sort.o source.o
> split.o sprintf.o startup.o subassign.o subscript.o
> subset.o summary.o sysutils.o unique.o util.o
> version.o vfonts.o xxxpr.o ../unix/libunix.a
> ../appl/libappl.a ../nmath/libnmath.a
> -xlic_lib=sunperf -lsunmath -Rreg
> -R/opt/SUNWspro/lib/sse2:/opt/SUNWspro/lib
> -L/opt/SUNWspro/lib/sse2 -L/opt/SUNWspro/prod/lib/sse2
> -L/opt/SUNWspro/prod/lib -L/usr/ccs/lib -lfui -lfai
> -lfsu -lsunmath -lmtsk -lm ../extra/zlib/libz.a
> ../extra/bzip2/libbz2.a ../extra/pcre/libpcre.a
> ../extra/intl/libintl.a -lreadline -lncurses -lnsl
> -lsocket -ldl -lm
> Undefined first referenced
> symbol in file
> bratio
> ../nmath/libnmath.a(pbeta.o)
> ld: fatal: Symbol referencing errors. No output
> written to R.bin
> *** Error code 1
> make: Fatal error: Command failed for target `R.bin'
> Current working directory
> /tmp/apps/R-2.2.0-32/src/main
> *** Error code 1
> The following command caused the error:
> make install-bin-local
> make: Fatal error: Command failed for target `R'
> Current working directory
> /tmp/apps/R-2.2.0-32/src/main
> *** Error code 1
> The following command caused the error:
> for d in scripts include extra appl nmath unix main
> modules library; do \
> (cd ${d} && make R) || exit 1; \
> done
> make: Fatal error: Command failed for target `R'
> Current working directory /tmp/apps/R-2.2.0-32/src
> *** Error code 1
> The following command caused the error:
> for d in m4 tools doc etc share src tests po; do \
> (cd ${d} && make R) || exit 1; \
> done
> make: Fatal error: Command failed for target `R'
> ==
>
> Thanks.
>
> Regards,
>
> Daniel
>
>
>
> __
> Meet your soulmate!
>
> __
> 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
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Re: [Rd] Error: .First.lib failed for 'SBMLodeSolveR'
What is 'SBMLodeSolveR'?
The standard advice is to check that you can install and load the package
before you try R CMD check on it. That way you may get a more informative
error message. You may also need to try loading after having started R
with R_DEFAULT_PACKAGES=NULL.
On Tue, 11 Oct 2005, nwew wrote:
> Dear R-developers,
>
> I am getting the following error message (see bottom of e-mail) and can't make
> a clue out of it.
>
> The zzz.R file contains
> .First.lib <- function(lib, pkg) library.dynam("SBMLodeSolveR",pkg,lib)
> .Last.lib <- function(libpath) library.dynam.unload("SBMLodeSolveR", libpath)
>
> There is a SBMLodeSolveR.so file in the src directory which works if loaded
> with
> dyn.load("/data/devel/SBMLodeSolveR/SBMLodeSolveR/src/SBMLodeSolveR.so")
>
> The error/warning messages are:
>
> * checking S3 generic/method consistency ... WARNING
> Error: .First.lib failed for 'SBMLodeSolveR'
> Call sequence:
> 2: stop(gettextf(".First.lib failed for '%s'", libraryPkgName(package)),
> domain = NA)
> 1: library(package, lib.loc = lib.loc, character.only = TRUE, verbose = FALSE)
> Execution halted
> See section 'Generic functions and methods' of the 'Writing R Extensions'
> manual.
> * checking replacement functions ... WARNING
> Error: .First.lib failed for 'SBMLodeSolveR'
> Call sequence:
> 2: stop(gettextf(".First.lib failed for '%s'", libraryPkgName(package)),
> domain = NA)
> 1: library(package, lib.loc = lib.loc, character.only = TRUE, verbose = FALSE)
> Execution halted
> In R, the argument of a replacement function which corresponds to the right
> hand side must be named 'value'.
> * checking foreign function calls ... WARNING
> Error: .First.lib failed for 'SBMLodeSolveR'
> Call sequence:
> 2: stop(gettextf(".First.lib failed for '%s'", libraryPkgName(package)),
> domain = NA)
> 1: library(package, lib.loc = lib.loc, character.only = TRUE, verbose = FALSE)
> Execution halted
> See section 'System and foreign language interfaces' of the 'Writing R
> Extensions' manual.
> *
>
>
> Eryk
>
> __
> 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
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[Rd] Manual page example of plot.window needs fixing
I was looking at the example on the manual page of plot.window, and
noticed that it needs fixing - names(eurodist) should now be
labels(eurodist):
--- /home/rsb/topics/R-2.2.0/src/library/graphics/man/plot.window.Rd
2005-04-18 12:18:59.0 +0200
+++ plot.window.Rd 2005-10-11 21:08:57.0 +0200
@@ -48,6 +48,6 @@
ry <- range(y <- -loc[,2])
plot(x, y, type="n", asp=1, xlab="", ylab="")
abline(h = pretty(rx, 10), v = pretty(ry, 10), col = "lightgray")
-text(x, y, names(eurodist), cex=0.8)
+text(x, y, labels(eurodist), cex=0.8)
}
\keyword{aplot}
with reference to Prof. Ripley's message of 5 May:
http://finzi.psych.upenn.edu/R/Rhelp02a/archive/55417.html
--
Roger Bivand
Economic Geography Section, Department of Economics, Norwegian School of
Economics and Business Administration, Helleveien 30, N-5045 Bergen,
Norway. voice: +47 55 95 93 55; fax +47 55 95 95 43
e-mail: [EMAIL PROTECTED]
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[Rd] MiKTeX/yap/Ghostcript issues with R-generated postscript
Hello, I wonder if anybody has encountered this problem? While MiKTeX/yap/Ghostscript seems to work fine on most TeX files that I have tested (including a great deal of postscript graphics), there is one file where the graphics works ok for all postscript files except one, the only one that is generated by R. I get an error "Some postscript specials could not be rendered", and the details of the error message are in the attached file. This same dvi file displays fine under Linux. I'm using yap from MiKTeX 2.4 with the "most popular" installation option. Any tips would be appreciated, Dominick Error: /undefined in [EMAIL PROTECTED] Operand stack: --nostringval-- PermitFileReading --nostringval-- PermitFileWriting --nostringval-- Execution stack: %interp_exit .runexec2 --nostringval-- --nostringval-- --nostringval-- 2 %stopped_push --nostringval-- --nostringval-- --nostringval-- false 1 %stopped_push 1 3 %oparray_pop 1 3 %oparray_pop 1 3 %oparray_pop 1 3 %oparray_pop .runexec2 --nostringval-- --nostringval-- --nostringval-- 2 %stopped_push --nostringval-- Dictionary stack: --dict:1125/1686(ro)(G)-- --dict:0/20(G)-- --dict:71/200(L)-- --dict:95/300(L)-- --dict:63/200(L)-- Current allocation mode is local MiKTeX GPL Ghostscript 8.15: Unrecoverable error, exit code 1 __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] Manual page example of plot.window needs fixing
Yes, thanks will fix in R-patched shortly.
Some grep-ing shows that there is another example in optim.Rd.
On Tue, 11 Oct 2005, Roger Bivand wrote:
> I was looking at the example on the manual page of plot.window, and
> noticed that it needs fixing - names(eurodist) should now be
> labels(eurodist):
>
> --- /home/rsb/topics/R-2.2.0/src/library/graphics/man/plot.window.Rd
> 2005-04-18 12:18:59.0 +0200
> +++ plot.window.Rd 2005-10-11 21:08:57.0 +0200
> @@ -48,6 +48,6 @@
> ry <- range(y <- -loc[,2])
> plot(x, y, type="n", asp=1, xlab="", ylab="")
> abline(h = pretty(rx, 10), v = pretty(ry, 10), col = "lightgray")
> -text(x, y, names(eurodist), cex=0.8)
> +text(x, y, labels(eurodist), cex=0.8)
> }
> \keyword{aplot}
>
> with reference to Prof. Ripley's message of 5 May:
>
> http://finzi.psych.upenn.edu/R/Rhelp02a/archive/55417.html
>
> --
> Roger Bivand
> Economic Geography Section, Department of Economics, Norwegian School of
> Economics and Business Administration, Helleveien 30, N-5045 Bergen,
> Norway. voice: +47 55 95 93 55; fax +47 55 95 95 43
> e-mail: [EMAIL PROTECTED]
>
> __
> 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
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Re: [Rd] 8 char labels in read.spss
Thomas Lumley schrieb: > On Tue, 11 Oct 2005, Knut Krueger wrote: > >> I was wondering why it is possible to read long labels from the CVS >> files but not from the SPSS files. > > > The SPSS file formats are not documented, and so we rely on the code > from PSPP. At the time, PSPP did not read long variable names. It > now does, so it would be possible for someone update the SPSS-reading > code to handle long variable names. This is much more complicated > than just changing a #define; the long variable names are stored in a > different part of the file. > > I don't expect anyone on R-core to get around to this any time soon. > If you want to try, the current PSPP code is at >http://savannah.gnu.org/projects/pspp Thanks for your reply, unfortunatlley the link is broken and gnu.org is linking to the same page http://www.gnu.org/software/pspp/pspp.html ... Knut __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] 8 char labels in read.spss
Thomas Lumley schrieb: > On Tue, 11 Oct 2005, Knut Krueger wrote: > >> I was wondering why it is possible to read long labels from the CVS >> files but not from the SPSS files. > > > The SPSS file formats are not documented, and so we rely on the code > from PSPP. I found a definition of the SPSS files. http://www.wotsit.org/download.asp?f=spssdata but they recommend to use the spss input/output dll to ensure upward compatbility Regards Knut __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] 8 char labels in read.spss
Thomas Lumley schrieb: > On Tue, 11 Oct 2005, Knut Krueger wrote: > >> Thanks for your reply, >> unfortunatlley the link is broken >> and gnu.org is linking to the same page >> http://www.gnu.org/software/pspp/pspp.html ... >> > > It works for me now (as it did then) Mc Murpey was working ... seems that the server did not answer just in the 5 minutes I tried it Regards Knut > > > -thomas > > -- with regards Knut Krueger http://www.biostatistic.de __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] MiKTeX/yap/Ghostcript issues with R-generated postscript
Dominick Samperi wrote: > Hello, > > I wonder if anybody has encountered this problem? > > While MiKTeX/yap/Ghostscript seems to work fine on most TeX files that I > have > tested (including a great deal of postscript graphics), there is one > file where the > graphics works ok for all postscript files except one, the only one that > is generated > by R. I get an error "Some postscript specials could not be rendered", > and the > details of the error message are in the attached file. > > This same dvi file displays fine under Linux. > > I'm using yap from MiKTeX 2.4 with the "most popular" installation option. > Hmmm, has not happened for me within the last couple of years I was using R + MikTeX 2.4 ... Can you specify a reproducible example for the R code that produces that PostScript file, please? [Wild guess: Maybe you forgot to close the device by dev.off()?] Uwe Ligges > Any tips would be appreciated, > Dominick > > > > > Error: /undefined in [EMAIL PROTECTED] > Operand stack: >--nostringval-- PermitFileReading --nostringval-- PermitFileWriting > --nostringval-- > Execution stack: >%interp_exit .runexec2 --nostringval-- --nostringval-- > --nostringval-- 2 %stopped_push --nostringval-- --nostringval-- > --nostringval-- false 1 %stopped_push 1 3 %oparray_pop 1 3 > %oparray_pop 1 3 %oparray_pop 1 3 %oparray_pop .runexec2 > --nostringval-- --nostringval-- --nostringval-- 2 %stopped_push > --nostringval-- > Dictionary stack: >--dict:1125/1686(ro)(G)-- --dict:0/20(G)-- --dict:71/200(L)-- > --dict:95/300(L)-- --dict:63/200(L)-- > Current allocation mode is local > MiKTeX GPL Ghostscript 8.15: Unrecoverable error, exit code 1 > > > > > __ > R-devel@r-project.org mailing list > https://stat.ethz.ch/mailman/listinfo/r-devel __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] 8 char labels in read.spss
On Tue, 11 Oct 2005, Knut Krueger wrote: > > I found a definition of the SPSS files. > http://www.wotsit.org/download.asp?f=spssdata > but they recommend to use the spss input/output dll to ensure upward > compatbility > "Well, they would say that, wouldn't they" (Rice-Davis 1963) Unfortunately, that document is an old file format. It doesn't describe record 7 subtype 13, which is where the long variable names live. -thomas __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] MiKTeX/yap/Ghostcript issues with R-generated postscript
Uwe Ligges wrote: > Dominick Samperi wrote: > >> Hello, >> >> I wonder if anybody has encountered this problem? >> >> While MiKTeX/yap/Ghostscript seems to work fine on most TeX files >> that I have >> tested (including a great deal of postscript graphics), there is one >> file where the >> graphics works ok for all postscript files except one, the only one >> that is generated >> by R. I get an error "Some postscript specials could not be >> rendered", and the >> details of the error message are in the attached file. >> >> This same dvi file displays fine under Linux. >> >> I'm using yap from MiKTeX 2.4 with the "most popular" installation >> option. >> > > > Hmmm, has not happened for me within the last couple of years I was > using R + MikTeX 2.4 ... > > Can you specify a reproducible example for the R code that produces > that PostScript file, please? > [Wild guess: Maybe you forgot to close the device by dev.off()?] > > Uwe Ligges Thank you Uwe, Your wild guess is correct! I was not closing the device, and the postscript file indeed did not have proper trailers. I am surprised that this did not cause problems on the Linux side... Dominick __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
