Re: [Rd] Too long pathname in bitmap() crashes R on WinXP
Thanks. /Henrik On 3/31/07, Prof Brian Ripley [EMAIL PROTECTED] wrote: It is also possible to trigger this on Unix: a buffer in postscript() is PATH_MAX when it should be 2*PATH_MAX + 2. I'll fix this in 2.5.0 alpha (there is also a potential issue inside the Windows' runcmd that needs fixing). On Fri, 30 Mar 2007, Henrik Bengtsson wrote: Hi, using too long pathnames for bitmap() crash R on WinXP. I've verified that this is the case with R version 2.4.1 Patched (2007-03-25 r40958) and R version 2.5.0 alpha (2007-03-30 r40957). I cannot reproduce it on Linux. REPRODUCIBLE EXAMPLE: % Rterm --vanilla # Tell R where Ghostscript is gsexe - C:/gs/gs8.54/bin/gswin32c.exe; gsexe - C:/Program Files/gs/gs8.56/bin/gswin32c.exe; gsexe - shortPathName(gsexe); Sys.putenv(R_GSCMD=gsexe); # Total length of pathname (R crashes when it is too long) n - 130; # Output path path - tempdir(); # Filename name - paste(rep(a, n-5-nchar(path)), collapse=); filename - paste(name, png, sep=.); # Full pathname pathname - file.path(path, filename); print(pathname); stopifnot(nchar(pathname) == n); bitmap(pathname); plot(1); dev.off(); R crash with dev.off(), but the PNG file is still created. # MORE DETAILED EXAMPLE: n - 130; path - tempdir(); name - paste(rep(a, n-5-nchar(path)), collapse=); filename - paste(name, png, sep=.); pathname - file.path(path, filename); print(pathname); # Tell R where Ghostscript is gsexe - C:/gs/gs8.54/bin/gswin32c.exe; gsexe - C:/Program Files/gs/gs8.56/bin/gswin32c.exe; gsexe - shortPathName(gsexe); cmd - paste(gsexe, -dNOPAUSE -dBATCH -q -sDEVICE=png256 -r72 -g432x432 -sOutputFile=, pathname, sep=); print(cmd); print(nchar(cmd)); tmp - tempfile(); postscript(file=tmp, width=6, height=6, pointsize=9, paper=special, horizontal=FALSE, print.it=TRUE, command=cmd); plot(1); dev.off(); It seems to have to do with the length of 'cmd' (since the possible pathname length varies with the length of 'gsexe' used). Any ideas? /Henrik __ 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] Matrix package: compilation error
Trying to compile the package Matrix_0.9975-11.tar.gz with newest R-2.5.0 alpha (2007-03-31 r40986) on FreeBSD 7.0-CURRENT (i386) I get the following error: - R CMD INSTALL Matrix_0.9975-11.tar.gz * Installing to library '/usr/local/lib/R/library' * Installing *source* package 'Matrix' ... ** libs ** arch - Makefile, line 10: Missing dependency operator Makefile, line 12: Need an operator Makefile, line 14: Need an operator make: fatal errors encountered -- cannot continue ERROR: compilation failed for package 'Matrix' ** Removing '/usr/local/lib/R/library/Matrix' - Under FreeBSD I have installed the LAPACK package (3.0.2) with library at location /usr/local/lib/liblapack.so.4 Is it possible that the Makefile of package Matrix fails because of that? Any help is appreciated, Rainer Hurling __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
[Rd] Problem with S4 inheritance: unexpected re-initialization?
Dear all,
To explain my problem I am attaching a demonstration package myclasspkg:
I have the following two S4 classes with similar inheritance:
SubSubClassA - SubClassB - BaseClass
SubSubClassB - SubClassB - BaseClass
In R I am calling the following functions:
library(myclasspkg)
subA -
new(SubClassA,filename=OutSubA,filedir=/Volumes/CoreData/CRAN/Workspaces/rclasspkg,mytitle=TitleSubA)
subsubA -
new(SubSubClassA,filename=MyFileName,filedir=/Volumes/CoreData/CRAN/Workspaces/rclasspkg,subA=subA)
subsubB -
new(SubSubClassB,filename=MyFileNameB,filedir=/Volumes/CoreData/CRAN/Workspaces/rclasspkg,subA=subA)
Creating subsubA works fine and gives the correct result:
subsubA -
new(SubSubClassA,filename=MyFileName,filedir=/Volumes/CoreData/CRAN/Workspaces/rclasspkg,subA=subA)
[1] --initialize:SubSubClassA--
[1] SubSubClassA:init:class(.Object) = SubSubClassA
[1] --initialize:SubClassB--
[1] SubClassB:init:class(.Object) = SubSubClassA
[1] --initialize:BaseClass--
[1] BaseClass:init:class(.Object) = SubSubClassA
[1] --pathFile--
[1] BaseClass:init:dirfile =
/Volumes/CoreData/CRAN/Workspaces/rclasspkg/MyFileName
[1] --setValidity:BaseClass--
[1] BaseClass:val:class(object) = SubClassB
[1] BaseClass:val:dirfile =
/Volumes/CoreData/CRAN/Workspaces/rclasspkg/MyFileName
[1] BaseClass:val:filedir = /Volumes/CoreData/CRAN/Workspaces/rclasspkg
[1] --setValidity:SubClassB--
[1] SubClassB:val:class(object) = SubClassB
[1] SubClassB:val:filename = MyFileName
[1] BaseClass:val:dirfile =
/Volumes/CoreData/CRAN/Workspaces/rclasspkg/MyFileName
[1] --setValidity:SubSubClassA--
[1] SubSubClassA:val:class(.Object) = SubSubClassA
In contrast, when trying to create subsubB, it seems that setValidity
re-initializes SubClassB:
subsubB -
new(SubSubClassB,filename=MyFileNameB,filedir=/Volumes/CoreData/CRAN/Workspaces/rclasspkg,subA=subA)
[1] --initialize:SubSubClassB--
[1] SubSubClassB:init:class(.Object) = SubSubClassB
[1] SubSubClassB:init:subsubnameB = subsubNameB
[1] --initialize:SubClassB--
[1] SubClassB:init:class(.Object) = SubSubClassB
[1] --initialize:BaseClass--
[1] BaseClass:init:class(.Object) = SubSubClassB
[1] --pathFile--
[1] BaseClass:init:dirfile =
/Volumes/CoreData/CRAN/Workspaces/rclasspkg/MyFileNameB
[1] --setValidity:BaseClass--
[1] --initialize:SubClassB--
[1] SubClassB:init:class(.Object) = SubClassB
[1] --initialize:BaseClass--
[1] BaseClass:init:class(.Object) = SubClassB
[1] --pathFile--
Error in if (dirname(filename) != .) { :
argument is of length zero
Can someone tell me why the first case works fine, but the second case not?
Probably, I am making some mistake, but since two weeks I am unable to
find it.
Thank you in advance.
P.S.: I am running R-2.5.0 on Intel-Mac OS 10.4.8.
Best regards
Christian
_._._._._._._._._._._._._._._._
C.h.i.s.t.i.a.n S.t.r.a.t.o.w.a
V.i.e.n.n.a A.u.s.t.r.i.a
_._._._._._._._._._._._._._._._
myclasspkg_0.1.1.tar.gz
Description: GNU Zip compressed data
__
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Re: [Rd] Matrix package: compilation error
This is because of the GNUism in Matrix/src/Makefile ## get rid of this, once we have 'Depends: R (= 2.5.0)': ifeq (, $(findstring -lRlapack, $(LAPACK_LIBS))) SOURCES_LAPACK = else SOURCES_LAPACK = zpotf2.f zpotrf.f zlacgv.f endif I guess you know what you need to do to fix it for BSD make? On Sat, 31 Mar 2007, Rainer Hurling wrote: Trying to compile the package Matrix_0.9975-11.tar.gz with newest R-2.5.0 alpha (2007-03-31 r40986) on FreeBSD 7.0-CURRENT (i386) I get the following error: - R CMD INSTALL Matrix_0.9975-11.tar.gz * Installing to library '/usr/local/lib/R/library' * Installing *source* package 'Matrix' ... ** libs ** arch - Makefile, line 10: Missing dependency operator Makefile, line 12: Need an operator Makefile, line 14: Need an operator make: fatal errors encountered -- cannot continue ERROR: compilation failed for package 'Matrix' ** Removing '/usr/local/lib/R/library/Matrix' - Under FreeBSD I have installed the LAPACK package (3.0.2) with library at location /usr/local/lib/liblapack.so.4 Is it possible that the Makefile of package Matrix fails because of that? Not used unless you asked for it during R's configure. -- 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] Matrix package: compilation error
Rainer == Rainer Hurling [EMAIL PROTECTED] on Sat, 31 Mar 2007 19:03:44 +0200 writes: Rainer Trying to compile the package Rainer Matrix_0.9975-11.tar.gz Rainer with newest R-2.5.0 alpha Rainer (2007-03-31 r40986) on FreeBSD 7.0-CURRENT (i386) does FreeBSD use a make that is 'GNU make' compatible? Matrix/DESCRIPTION has a line which says -- SystemRequirements: GNU make -- Regards, Martin Maechler, ETH Zurich Rainer I get the following error: Rainer - Rainer R CMD INSTALL Matrix_0.9975-11.tar.gz Rainer * Installing to library '/usr/local/lib/R/library' Rainer * Installing *source* package 'Matrix' ... Rainer ** libs Rainer ** arch - Rainer Makefile, line 10: Missing dependency operator Rainer Makefile, line 12: Need an operator Rainer Makefile, line 14: Need an operator Rainer make: fatal errors encountered -- cannot continue Rainer ERROR: compilation failed for package 'Matrix' Rainer ** Removing '/usr/local/lib/R/library/Matrix' Rainer - Rainer Under FreeBSD I have installed the LAPACK package (3.0.2) with library Rainer at location Rainer /usr/local/lib/liblapack.so.4 Rainer Is it possible that the Makefile of package Matrix fails because of that? Rainer Any help is appreciated, Rainer Rainer Hurling Rainer __ Rainer R-devel@r-project.org mailing list Rainer 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] Matrix package: compilation error
Thanks, Brian and Martin, I think you are both right, Matrix tries to use BSD make (/usr/bin/make) on FreeBSD instead of GNU make (/usr/local/bin/gmake). Sorry, but I don't know how to persuade the configure script to use gmake :-( Rainer Prof Brian Ripley schrieb: This is because of the GNUism in Matrix/src/Makefile ## get rid of this, once we have 'Depends: R (= 2.5.0)': ifeq (, $(findstring -lRlapack, $(LAPACK_LIBS))) SOURCES_LAPACK = else SOURCES_LAPACK = zpotf2.f zpotrf.f zlacgv.f endif I guess you know what you need to do to fix it for BSD make? On Sat, 31 Mar 2007, Rainer Hurling wrote: Trying to compile the package Matrix_0.9975-11.tar.gz with newest R-2.5.0 alpha (2007-03-31 r40986) on FreeBSD 7.0-CURRENT (i386) I get the following error: - R CMD INSTALL Matrix_0.9975-11.tar.gz * Installing to library '/usr/local/lib/R/library' * Installing *source* package 'Matrix' ... ** libs ** arch - Makefile, line 10: Missing dependency operator Makefile, line 12: Need an operator Makefile, line 14: Need an operator make: fatal errors encountered -- cannot continue ERROR: compilation failed for package 'Matrix' ** Removing '/usr/local/lib/R/library/Matrix' - Under FreeBSD I have installed the LAPACK package (3.0.2) with library at location /usr/local/lib/liblapack.so.4 Is it possible that the Makefile of package Matrix fails because of that? Not used unless you asked for it during R's configure. __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] Matrix package: compilation error
Hi Rainer, check the following post for an alternative solution: http://tolstoy.newcastle.edu.au/R/help/06/01/18908.html if you would like more detailed instructions, let me know. Andrew On Sat, Mar 31, 2007 at 10:10:45PM +0200, Rainer Hurling wrote: Thanks, Brian and Martin, I think you are both right, Matrix tries to use BSD make (/usr/bin/make) on FreeBSD instead of GNU make (/usr/local/bin/gmake). Sorry, but I don't know how to persuade the configure script to use gmake :-( Rainer Prof Brian Ripley schrieb: This is because of the GNUism in Matrix/src/Makefile ## get rid of this, once we have 'Depends: R (= 2.5.0)': ifeq (, $(findstring -lRlapack, $(LAPACK_LIBS))) SOURCES_LAPACK = else SOURCES_LAPACK = zpotf2.f zpotrf.f zlacgv.f endif I guess you know what you need to do to fix it for BSD make? On Sat, 31 Mar 2007, Rainer Hurling wrote: Trying to compile the package Matrix_0.9975-11.tar.gz with newest R-2.5.0 alpha (2007-03-31 r40986) on FreeBSD 7.0-CURRENT (i386) I get the following error: - R CMD INSTALL Matrix_0.9975-11.tar.gz * Installing to library '/usr/local/lib/R/library' * Installing *source* package 'Matrix' ... ** libs ** arch - Makefile, line 10: Missing dependency operator Makefile, line 12: Need an operator Makefile, line 14: Need an operator make: fatal errors encountered -- cannot continue ERROR: compilation failed for package 'Matrix' ** Removing '/usr/local/lib/R/library/Matrix' - Under FreeBSD I have installed the LAPACK package (3.0.2) with library at location /usr/local/lib/liblapack.so.4 Is it possible that the Makefile of package Matrix fails because of that? Not used unless you asked for it during R's configure. __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel -- Andrew Robinson Department of Mathematics and StatisticsTel: +61-3-8344-9763 University of Melbourne, VIC 3010 Australia Fax: +61-3-8344-4599 http://www.ms.unimelb.edu.au/~andrewpr http://blogs.mbs.edu/fishing-in-the-bay/ __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
[Rd] Probem with argument append in Rprof
Hello,
Appending information to the profiler's output seems to generate
problems. Here is a small example of code :
code r
require(boot)
Rprof( memory.profiling = TRUE)
Rprof(NULL)
for(i in 1:2){
Rprof( memory.profiling = TRUE, append = TRUE)
example(boot)
Rprof(NULL)
}
/code
The problem is that the file Rprof.out contains more than once the
header information:
$ grep sample.interval= Rprof.out
memory profiling: sample.interval=2
memory profiling: sample.interval=2
memory profiling: sample.interval=2
and `summaryRprof` or `R CMD Rprof` are not dealing with it
idx - grep( sample, rownames( smp - summaryRprof()[[1]] ) );
smp[idx, ]
self.time self.pct total.time total.pct
sample.interval=2 00 0.04 0.1
`sample.interval=2` is incorrectly considered as a function.
This is not too much of a big deal, but then if I ask for memory
profiling information as well, I get nothing:
summaryRprof( mem = stats)
Error in tapply(1:1L, list(index = c(sample.interval=2:profiling:, :
arguments must have same length
summaryRprof( mem = tseries)
Error in data.frame(..., check.names = FALSE) :
arguments imply differing number of rows: 1, 1490
summaryRprof( mem = both)
Error in apply(sapply(strsplit(memstuff, :), as.numeric), 1, diff) :
dim(X) must have a positive length
$ R CMD Rprof Rprof.out
Each sample represents seconds.
Total run time: 0 seconds.
Total seconds: time spent in function and callees.
Self seconds: time spent in function alone.
% total % self
totalseconds selfsecondsname
Illegal division by zero at /usr/local/lib/R/bin/Rprof line 91, line
1491.
A quick fix could be to ignore all the lines containing sample.interval=
except the first one, but then if someone wants to actually change the
interval argument in Rprof, it would not be correct. I attach a patch
against R-devel/src/library/utils/R/summRprof.R to do that anyway, but I
will look at a better solution.
I am not fluent enough in Perl to do the same in the Rprof script, it
looks like it does not handle the memory profiling information anyway. I
am about to learn Perl, so I guess it could be a useful way to do it. I
also attach a patch against R-devel/src/scripts/Rprof that would at
least get rid of the memory profiling information (if any). This is not
as good as dealing with it, but ... this is the first time I ever touch
a Perl script.
Cheers,
Romain
version
_
platform
i686-pc-linux-gnu
arch
i686
os
linux-gnu
system i686,
linux-gnu
status Under development
(unstable)
major
2
minor 6.0
year
2007
month
03
day
30
svn rev
40983
language
R
version.string R version 2.6.0 Under development (unstable) (2007-03-30
r40983)
--
Mango Solutions
data analysis that delivers
Tel: +44(0) 1249 467 467
Fax: +44(0) 1249 467 468
Mob: +44(0) 7813 526 123
--- summRprof.R 2007-03-31 21:10:31.0 +0100
+++ /tmp/R-devel/src/library/utils/R/summRprof.R 2006-10-05 07:54:38.0 +0100
@@ -32,10 +32,8 @@
repeat({
chunk-readLines(filename,n=chunksize)
- chunk - chunk[ -grep(sample\\.interval=, chunk) ]
if (length(chunk)==0)
break
-
if (memory.profiling){
memprefix-attr(regexpr(:[0-9]+:[0-9]+:[0-9]+:[0-9]+:,chunk),match.length)
if (memory==both){
@@ -121,7 +119,6 @@
repeat({
chunk-readLines(filename,n=chunksize)
- chunk - chunk[ -grep(sample\\.interval=, chunk) ]
if (length(chunk)==0)
break
memprefix-attr(regexpr(:[0-9]+:[0-9]+:[0-9]+:[0-9]+:,chunk),
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Re: [Rd] Matrix package: compilation error
Thank you Andrew, 'setenv MAKE gmake' did it. Now I can use latest spdep package :-) Rainer Andrew Robinson schrieb: Hi Rainer, check the following post for an alternative solution: http://tolstoy.newcastle.edu.au/R/help/06/01/18908.html if you would like more detailed instructions, let me know. Andrew On Sat, Mar 31, 2007 at 10:10:45PM +0200, Rainer Hurling wrote: Thanks, Brian and Martin, I think you are both right, Matrix tries to use BSD make (/usr/bin/make) on FreeBSD instead of GNU make (/usr/local/bin/gmake). Sorry, but I don't know how to persuade the configure script to use gmake :-( Rainer Prof Brian Ripley schrieb: This is because of the GNUism in Matrix/src/Makefile ## get rid of this, once we have 'Depends: R (= 2.5.0)': ifeq (, $(findstring -lRlapack, $(LAPACK_LIBS))) SOURCES_LAPACK = else SOURCES_LAPACK = zpotf2.f zpotrf.f zlacgv.f endif I guess you know what you need to do to fix it for BSD make? On Sat, 31 Mar 2007, Rainer Hurling wrote: Trying to compile the package Matrix_0.9975-11.tar.gz with newest R-2.5.0 alpha (2007-03-31 r40986) on FreeBSD 7.0-CURRENT (i386) I get the following error: - R CMD INSTALL Matrix_0.9975-11.tar.gz * Installing to library '/usr/local/lib/R/library' * Installing *source* package 'Matrix' ... ** libs ** arch - Makefile, line 10: Missing dependency operator Makefile, line 12: Need an operator Makefile, line 14: Need an operator make: fatal errors encountered -- cannot continue ERROR: compilation failed for package 'Matrix' ** Removing '/usr/local/lib/R/library/Matrix' - Under FreeBSD I have installed the LAPACK package (3.0.2) with library at location /usr/local/lib/liblapack.so.4 Is it possible that the Makefile of package Matrix fails because of that? Not used unless you asked for it during R's configure. __ 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
