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
>
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[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 :
require(boot)
Rprof( memory.profiling = TRUE)
Rprof(NULL)
for(i in 1:2){
Rprof( memory.profiling = TRUE, append = TRUE)
example(boot)
Rprof(NULL)
}
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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[Rd] Probem with argument "append" in "Rprof"
[forgot to attach the second patch in the first mail, sorry.]
Hello,
Appending information to the profiler's output seems to generate
problems. Here is a small example of code :
require(boot)
Rprof( memory.profiling = TRUE)
Rprof(NULL)
for(i in 1:2){
Rprof( memory.profiling = TRUE, append = TRUE)
example(boot)
Rprof(NULL)
}
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),
--- Rprof 2007-03-31 21:23:16.0 +0100
+++ /tmp/R-devel/src/scripts/Rprof 2007-03-31 19:58:29.0 +0100
@@ -57,12 +57,11 @@
%totalcounts = ();
while (<>) {
-if (/.*sample\.interval=/) {
- s/.*sample\.interval=//;
+if (/^sample\.interval=/) {
+ s/sample\.interval=//;
$sample = $_ / 1e6;
} else {
chomp;
- s/[^\"]*\"/"/;
@line = split(/ /);
%names = ();
$leaf = @line[0];
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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
Re: [Rd] Probem with argument "append" in "Rprof"
And now I realize I gave the patches in the wrong order, let me try
again
Cheers,
Romain
Romain Francois wrote:
> [forgot to attach the second patch in the first mail, sorry.]
>
> Hello,
>
> Appending information to the profiler's output seems to generate
> problems. Here is a small example of code :
>
>
> require(boot)
> Rprof( memory.profiling = TRUE)
> Rprof(NULL)
> for(i in 1:2){
> Rprof( memory.profiling = TRUE, append = TRUE)
> example(boot)
> Rprof(NULL)
> }
>
>
> 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)
>
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--- /tmp/R-devel/src/library/utils/R/summRprof.R 2006-10-05 07:54:38.0 +0100
+++ summRprof.R 2007-03-31 21:10:31.0 +0100
@@ -32,8 +32,10 @@
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"){
@@ -119,6 +121,7 @@
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),
--- /tmp/R-devel/src/scripts/Rprof 2007-03-31 19:58:29.0 +0100
+++ Rprof 2007-03-31 21:23:16.0 +0100
@@ -57,11 +57,12 @@
%totalcounts = ();
while (<>) {
-if (/^sample\.interval=/) {
- s/sample\.interval=//;
+if (/.*sample\.interval=/) {
+ s/.*sample\.interval=//;
$sample = $_ / 1e6;
} else {
chomp;
+ s/[^\"]*\"/"/;
@line = split(/ /);
%names = ();
$leaf = @line[0];
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