Re: [R] writeMat error
Hi, a follow up on this as well: I've fixed the below bug in
writeMat(). R.matlab v1.2.4 is now available on CRAN. Please update.
Henrik
On Wed, Oct 1, 2008 at 12:55 PM, Henrik Bengtsson [EMAIL PROTECTED] wrote:
Hi.
On Sat, Sep 27, 2008 at 5:17 AM, Steele, Dr Douglas [EMAIL PROTECTED] wrote:
Hi
I am using Ubuntu 8.04 64 bit, R as below, Matlab 7.6.0. I would like to
transfer mat files back and forward between R and Matlab. Whilst I have
used Matlab for years its been a long time since I have used R (hence
question may be a bit simple)
Running code
A - c(1:10)
dim(A) - c(2,5)
library(R.matlab)
writeMat('A.mat', A=A)
Does not appear to generate any mat file either in local directory or in
/tmp/R*
It *is* created in the *current* directory. If there are no errors,
then it should be there. Use can use getwd() to see which this is,
e.g.
library(R.matlab);
A - c(1:10);
dim(A) - c(2,5);
writeMat(A.mat, A=A);
print(getwd());
[1] C:/Users/foo/braju.com.R/R.matlab
print(list.files())
[1] A.mat
res - readMat(A.mat);
str(res)
List of 1
$ A: int [1:2, 1:5] 1 2 3 4 5 6 7 8 9 10
- attr(*, header)=List of 3
..$ description: chr MATLAB 5.0 MAT-file, Platform: windows,
Software: R v2.7.2, Created on: Wed Oct 01 12:40:23 2008
..$ version: chr 5
..$ endian : chr little
I tried both current version of R.matlab and older version because of bug
https://stat.ethz.ch/pipermail/r-help/2008-September/173432.html
Correct. You should use install the old R.matlab v1.2.1, because
v1.2.3 (as well as v1.2.2) contains a bug which is still to be fixed.
A - matrix(1:27, ncol=3)
B - as.matrix(1:10)
fn - paste(tempfile(), .mat, sep=)
writeMat(fn, A=A, B=B)
data - readMat(fn)
print(data)
unlink(fn)
This is from example(writeMat). It works this far, correct? You
should see 'data' being reported. The unlink() command is there such
that the example script cleans up after itself, i.e. it delete the
temporary MAT file. Skip that last command if you want to grab the
file.
onWrite - function(x)
writeBin(x$length, con=x$con, size=4, endian=big);
writeMat(fn, A=A, B=B, onWrite=onWrite)
Do *not* use these latter commands. They are modifications of
original example code that is only used to illustrate for advanced
users how to send a MAT structure over a connection. As indicated by
the example code:
## Not run:
# When writing to a stream connection the receiver needs to know in
# beforehand how many bytes are available. This can be done by using
# the 'onWrite' argument.
onWrite - function(x)
writeBin(x$length, con=x$con, size=4, endian=little);
writeMat(con, A=A, B=B, onWrite=onWrite)
## End(Not run)
they are within a Not run block, which in R means that they are not
necessarily intended to be executed. If you run the example code with
example(writeMat) that code will not be executed. You obviously
cut'n'paste here, but didn't you see the above comments. How you do
view you help(), i.e. typically help(writeMat) will display those
comments? FYI, the first argument 'con' (supposed to indicate a
connection) is on purpose non-existing and not the same as the 'fn'
argument (pathname) in the preceeding code.
Does generate a file in /tmp/Rtmpjhfjxw
-rw-r--r-- 1 dst dst 396 2008-09-27 12:46 file643c9869.mat
When I try to read it into Matlab I get
??? Error using == load
Unable to read MAT-file /tmp/Rtmpjhfjxw/file643c9869.mat
File may be corrupt.
Yes, but that is because you use that latter code. Before writing the
MAT structure, it writes the byte size of the structure to the file,
which is not part of the MAT file format. You don't want this. This
is only intended for sending MAT structure over a connection.
(This is same error message as above link and occurs with old and current
version of R.matlab)
Any advice would be very helpful
Hope this helps
Henrik
Regards
Douglas
sessionInfo()
R version 2.6.2 (2008-02-08)
x86_64-pc-linux-gnu
locale:
LC_CTYPE=en_GB.UTF-8;LC_NUMERIC=C;LC_TIME=en_GB.UTF-8;LC_COLLATE=en_GB.UTF-8;LC_MONETARY=en_GB.UTF-8;LC_MESSAGES=en_GB.UTF-8;LC_PAPER=en_GB.UTF-8;LC_NAME=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=en_GB.UTF-8;LC_IDENTIFICATION=C
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] R.matlab_1.2.1R.oo_1.4.6R.methodsS3_1.0.3
loaded via a namespace (and not attached):
[1] rcompgen_0.1-17
The University of Aberdeen is a charity registered in Scotland, No SC013683.
__
R-help@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
__
R-help@r-project.org
Re: [R] writeMat error
Hi.
On Sat, Sep 27, 2008 at 5:17 AM, Steele, Dr Douglas [EMAIL PROTECTED] wrote:
Hi
I am using Ubuntu 8.04 64 bit, R as below, Matlab 7.6.0. I would like to
transfer mat files back and forward between R and Matlab. Whilst I have used
Matlab for years its been a long time since I have used R (hence question may
be a bit simple)
Running code
A - c(1:10)
dim(A) - c(2,5)
library(R.matlab)
writeMat('A.mat', A=A)
Does not appear to generate any mat file either in local directory or in
/tmp/R*
It *is* created in the *current* directory. If there are no errors,
then it should be there. Use can use getwd() to see which this is,
e.g.
library(R.matlab);
A - c(1:10);
dim(A) - c(2,5);
writeMat(A.mat, A=A);
print(getwd());
[1] C:/Users/foo/braju.com.R/R.matlab
print(list.files())
[1] A.mat
res - readMat(A.mat);
str(res)
List of 1
$ A: int [1:2, 1:5] 1 2 3 4 5 6 7 8 9 10
- attr(*, header)=List of 3
..$ description: chr MATLAB 5.0 MAT-file, Platform: windows,
Software: R v2.7.2, Created on: Wed Oct 01 12:40:23 2008
..$ version: chr 5
..$ endian : chr little
I tried both current version of R.matlab and older version because of bug
https://stat.ethz.ch/pipermail/r-help/2008-September/173432.html
Correct. You should use install the old R.matlab v1.2.1, because
v1.2.3 (as well as v1.2.2) contains a bug which is still to be fixed.
A - matrix(1:27, ncol=3)
B - as.matrix(1:10)
fn - paste(tempfile(), .mat, sep=)
writeMat(fn, A=A, B=B)
data - readMat(fn)
print(data)
unlink(fn)
This is from example(writeMat). It works this far, correct? You
should see 'data' being reported. The unlink() command is there such
that the example script cleans up after itself, i.e. it delete the
temporary MAT file. Skip that last command if you want to grab the
file.
onWrite - function(x)
writeBin(x$length, con=x$con, size=4, endian=big);
writeMat(fn, A=A, B=B, onWrite=onWrite)
Do *not* use these latter commands. They are modifications of
original example code that is only used to illustrate for advanced
users how to send a MAT structure over a connection. As indicated by
the example code:
## Not run:
# When writing to a stream connection the receiver needs to know in
# beforehand how many bytes are available. This can be done by using
# the 'onWrite' argument.
onWrite - function(x)
writeBin(x$length, con=x$con, size=4, endian=little);
writeMat(con, A=A, B=B, onWrite=onWrite)
## End(Not run)
they are within a Not run block, which in R means that they are not
necessarily intended to be executed. If you run the example code with
example(writeMat) that code will not be executed. You obviously
cut'n'paste here, but didn't you see the above comments. How you do
view you help(), i.e. typically help(writeMat) will display those
comments? FYI, the first argument 'con' (supposed to indicate a
connection) is on purpose non-existing and not the same as the 'fn'
argument (pathname) in the preceeding code.
Does generate a file in /tmp/Rtmpjhfjxw
-rw-r--r-- 1 dst dst 396 2008-09-27 12:46 file643c9869.mat
When I try to read it into Matlab I get
??? Error using == load
Unable to read MAT-file /tmp/Rtmpjhfjxw/file643c9869.mat
File may be corrupt.
Yes, but that is because you use that latter code. Before writing the
MAT structure, it writes the byte size of the structure to the file,
which is not part of the MAT file format. You don't want this. This
is only intended for sending MAT structure over a connection.
(This is same error message as above link and occurs with old and current
version of R.matlab)
Any advice would be very helpful
Hope this helps
Henrik
Regards
Douglas
sessionInfo()
R version 2.6.2 (2008-02-08)
x86_64-pc-linux-gnu
locale:
LC_CTYPE=en_GB.UTF-8;LC_NUMERIC=C;LC_TIME=en_GB.UTF-8;LC_COLLATE=en_GB.UTF-8;LC_MONETARY=en_GB.UTF-8;LC_MESSAGES=en_GB.UTF-8;LC_PAPER=en_GB.UTF-8;LC_NAME=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=en_GB.UTF-8;LC_IDENTIFICATION=C
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] R.matlab_1.2.1R.oo_1.4.6R.methodsS3_1.0.3
loaded via a namespace (and not attached):
[1] rcompgen_0.1-17
The University of Aberdeen is a charity registered in Scotland, No SC013683.
__
R-help@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
__
R-help@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
[R] writeMat error
Hi
I am using Ubuntu 8.04 64 bit, R as below, Matlab 7.6.0. I would like to
transfer mat files back and forward between R and Matlab. Whilst I have used
Matlab for years its been a long time since I have used R (hence question may
be a bit simple)
Running code
A - c(1:10)
dim(A) - c(2,5)
library(R.matlab)
writeMat('A.mat', A=A)
Does not appear to generate any mat file either in local directory or in /tmp/R*
I tried both current version of R.matlab and older version because of bug
https://stat.ethz.ch/pipermail/r-help/2008-September/173432.html
A - matrix(1:27, ncol=3)
B - as.matrix(1:10)
fn - paste(tempfile(), .mat, sep=)
writeMat(fn, A=A, B=B)
data - readMat(fn)
print(data)
unlink(fn)
onWrite - function(x)
writeBin(x$length, con=x$con, size=4, endian=big);
writeMat(fn, A=A, B=B, onWrite=onWrite)
Does generate a file in /tmp/Rtmpjhfjxw
-rw-r--r-- 1 dst dst 396 2008-09-27 12:46 file643c9869.mat
When I try to read it into Matlab I get
??? Error using == load
Unable to read MAT-file /tmp/Rtmpjhfjxw/file643c9869.mat
File may be corrupt.
(This is same error message as above link and occurs with old and current
version of R.matlab)
Any advice would be very helpful
Regards
Douglas
sessionInfo()
R version 2.6.2 (2008-02-08)
x86_64-pc-linux-gnu
locale:
LC_CTYPE=en_GB.UTF-8;LC_NUMERIC=C;LC_TIME=en_GB.UTF-8;LC_COLLATE=en_GB.UTF-8;LC_MONETARY=en_GB.UTF-8;LC_MESSAGES=en_GB.UTF-8;LC_PAPER=en_GB.UTF-8;LC_NAME=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=en_GB.UTF-8;LC_IDENTIFICATION=C
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] R.matlab_1.2.1R.oo_1.4.6R.methodsS3_1.0.3
loaded via a namespace (and not attached):
[1] rcompgen_0.1-17
The University of Aberdeen is a charity registered in Scotland, No SC013683.
__
R-help@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
Re: [R] : writeMat
Hi,
that's the information about R and R.matlab:
*R version 2.6.2 (2008-02-08)
x86_64-pc-linux-gnu
locale:
C
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] R.matlab_1.2.3R.oo_1.4.5R.methodsS3_1.0.3 MASS_7.2-44
loaded via a namespace (and not attached):
[1] rcompgen_0.1-17
*
The matlab's version i'm using is* Matlab.7.6.0. *and the error matlab
gives me is:
*??? Error using == load
Unable to read MAT-file /home/erola/Dades/Saccharomyces cerevisiae/A.mat
File may be corrupt.*
I tried to put in matlab preferences -v6 saving, but it doesn't work.
I have the same Matlab's version that a month ago, I thought that it was
all the same but I have a problem with my computer and I have to reinstall
all again, and somethimg is been changed, but I don't know what.
Thank you.
On Tue, Sep 9, 2008 at 8:58 PM, Henrik Bengtsson [EMAIL PROTECTED]wrote:
Hi,
On Tue, Sep 9, 2008 at 9:53 AM, erola pairo [EMAIL PROTECTED] wrote:
I write a .mat file using the writeMat() command, but when i try to load
it
in Matlab it says that file may be corrupt. I did it a month ago and it
worked. It exists any option that I can change for making the file
readable
to Matlab?
A - c(1:10)
dim(A) - c(2,5)
library(R.matlab)
writeMat('A.mat', A=A)
And what matlab say is:
file may be corrupt
you need to provide much more information that this. Please see the
posting guides for the list (see footer), and provide sessionInfo() so
we know what version of R and R.matlab you are using. What version of
Matlab are you using? If it worked a month ago, what have you changed
since then?
Cheers
Henrik
(author of R.matlab)
Regards
[[alternative HTML version deleted]]
__
R-help@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide
http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
[[alternative HTML version deleted]]
__
R-help@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
Re: [R] : writeMat
Hi,
I've managed to reproduce the error with R.matlab v1.2.2 and Matlab
v7.4.0.287 (R2007a).
There seems to be a bug introduced in R.matlab v1.2.2 (2008-07-12). In
this version we tried to optimize the speed of writeMat(), and
something failed (although all tests show the generated files loads
fine with readMat() in R). You have probably updated R.matlab to this
version, which is why it worked before.
Until I identify and fix the bug, you can roll back to an earlier
version that I have verified works. Start a fresh R session and
install R.matlab v.1.2.1 as follows:
source(http://www.braju.com/R/hbLite.R;);
installPackages(http://www.braju.com/R/repos/R.matlab_1.2.1.tar.gz;);
(Windows users should replace *.tar.gz with *.zip).
Let me know if this helps and thanks for reporting the bug
Henrik
PS. It's time to update your R installation. DS.
On Wed, Sep 10, 2008 at 9:47 AM, erola pairo [EMAIL PROTECTED] wrote:
Hi,
that's the information about R and R.matlab:
R version 2.6.2 (2008-02-08)
x86_64-pc-linux-gnu
locale:
C
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] R.matlab_1.2.3R.oo_1.4.5R.methodsS3_1.0.3 MASS_7.2-44
loaded via a namespace (and not attached):
[1] rcompgen_0.1-17
The matlab's version i'm using is Matlab.7.6.0. and the error matlab gives
me is:
??? Error using == load
Unable to read MAT-file /home/erola/Dades/Saccharomyces cerevisiae/A.mat
File may be corrupt.
I tried to put in matlab preferences -v6 saving, but it doesn't work.
I have the same Matlab's version that a month ago, I thought that it was
all the same but I have a problem with my computer and I have to reinstall
all again, and somethimg is been changed, but I don't know what.
Thank you.
On Tue, Sep 9, 2008 at 8:58 PM, Henrik Bengtsson [EMAIL PROTECTED]
wrote:
Hi,
On Tue, Sep 9, 2008 at 9:53 AM, erola pairo [EMAIL PROTECTED] wrote:
I write a .mat file using the writeMat() command, but when i try to load
it
in Matlab it says that file may be corrupt. I did it a month ago and it
worked. It exists any option that I can change for making the file
readable
to Matlab?
A - c(1:10)
dim(A) - c(2,5)
library(R.matlab)
writeMat('A.mat', A=A)
And what matlab say is:
file may be corrupt
you need to provide much more information that this. Please see the
posting guides for the list (see footer), and provide sessionInfo() so
we know what version of R and R.matlab you are using. What version of
Matlab are you using? If it worked a month ago, what have you changed
since then?
Cheers
Henrik
(author of R.matlab)
Regards
[[alternative HTML version deleted]]
__
R-help@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide
http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
__
R-help@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
[R] : writeMat
I write a .mat file using the writeMat() command, but when i try to load it
in Matlab it says that file may be corrupt. I did it a month ago and it
worked. It exists any option that I can change for making the file readable
to Matlab?
A - c(1:10)
dim(A) - c(2,5)
library(R.matlab)
writeMat('A.mat', A=A)
And what matlab say is:
file may be corrupt
Regards
[[alternative HTML version deleted]]
__
R-help@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
