[Rd] seek() and gzfile() on 32-bit R2.12.0 in linux
I have installed both 32-bit and 64-bit versions of R2.12.0 (2010-06-15
r52300) on my Ubuntu 10.04 64-bit system. I observe the following behavior
when running the examples from base::connections. There appears to be a
problem with seek() on a .gz file when using a 32-bit installation of
R2.12.0, but the problem doesn't appear in the 64-bit installation. I
realize that seek() has been difficult in the past, and I don't want to open
old wounds, but is this a known problem? Is this easily fixable? I have a
package that relies on seek() when accessing gzipped files.
Using the 32-bit installation...
*> zz <- file("ex.data", "w") # open an output file connection
> cat("TITLE extra line", "2 3 5 7", "", "11 13 17", file = zz, sep =
"\n")
> cat("One more line\n", file = zz)
> close(zz)
> blah = file("ex.data", "r")
> seek(blah)
[1] 0
>
> zz <- gzfile("ex.gz", "w") # compressed file
> cat("TITLE extra line", "2 3 5 7", "", "11 13 17", file = zz, sep =
"\n")
> close(zz)
> blah = file("ex.gz", "r")
> seek(blah)
[1] 7.80707e+17
>
> zz <- bzfile("ex.bz2", "w") # bzip2-ed file
> cat("TITLE extra line", "2 3 5 7", "", "11 13 17", file = zz, sep =
"\n")
> close(zz)
> blah = file("ex.bz2", "r")
> seek(blah)
Error in seek.connection(blah) : 'seek' not enabled for this connection
>*
Using the 64-bit installation...
*> zz <- file("ex.data", "w") # open an output file connection
> cat("TITLE extra line", "2 3 5 7", "", "11 13 17", file = zz, sep = "\n")
> cat("One more line\n", file = zz)
> close(zz)
> blah = file("ex.data", "r")
> seek(blah)
[1] 0
>
> zz <- gzfile("ex.gz", "w") # compressed file
> cat("TITLE extra line", "2 3 5 7", "", "11 13 17", file = zz, sep = "\n")
> close(zz)
> blah = file("ex.gz", "r")
> seek(blah)
[1] 0
>
> zz <- bzfile("ex.bz2", "w") # bzip2-ed file
> cat("TITLE extra line", "2 3 5 7", "", "11 13 17", file = zz, sep = "\n")
> close(zz)
> blah = file("ex.bz2", "r")
> seek(blah)
Error in seek.connection(blah) : 'seek' not enabled for this connection
> *
thanks,
Brandon
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[Rd] seek() and gzfile() on 32-bit R2.12.0 in linux
Peter, thanks for your comments. The reason I have taken this issue to R-devel is from the advice of Kurt Hornik. An update to my package oro.nifti is being refused by CRAN because it fails on the _development_ version of R on 32-bit linux. As we have just discussed (and thanks to Matt's input), the problem is not with my package but with the development version of R. Hence, I wanted to alert to the R Core Development Team that the _unstable_ version of R appears to have a problem. Obviously, I would prefer to have my new version of oro.nifti accepted by CRAN... but at the moment I am in between a rock and a hard place. I agree that the 2.12.0 release of R is quite far in the future. Is there a possibility of relaxing the exclusion criteria for CRAN? cheers... Brandon Please notice that there is NO release of R 2.12.0 until some time around October. You are using a build from the UNSTABLE development branch. The stable branch is 2.11.1 with a release date of May 31. If Ubuntu is claiming that there is such a thing as a R 2.12.0 release, I'd say that they have a problem. Not that we don't welcome reports on problems in the development branch, but do notice that it is by definition UNSTABLE, and that bugs can come and go without notice. -pd __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
[Rd] R CMD check error in v2.12.0
I have received the following error for my package oro.nifti under "CRAN
checks" for r-devel-linux-ix86; i.e.,
http://www.r-project.org/nosvn/R.check/r-devel-linux-ix86/oro.nifti-00check.html
- using R version 2.12.0 Under development (unstable) (2010-06-12 r52259)
- using platform: i686-pc-linux-gnu (32-bit)
- using session charset: UTF-8
- checking for file oro.nifti/DESCRIPTION ... OK
- this is package oro.nifti version 0.1.4
- checking package name space information ... OK
- checking package dependencies ... OK
- checking if this is a source package ... OK
- checking for executable files ... OK
- checking whether package oro.nifti can be installed ... OK
- checking package directory ... OK
- checking for portable file names ... OK
- checking for sufficient/correct file permissions ... OK
- checking DESCRIPTION meta-information ... OK
- checking top-level files ... OK
- checking index information ... OK
- checking package subdirectories ... OK
- checking R files for non-ASCII characters ... OK
- checking R files for syntax errors ... OK
- checking whether the package can be loaded ... OK
- checking whether the package can be loaded with stated dependencies ...
OK
- checking whether the package can be unloaded cleanly ... OK
- checking whether the name space can be loaded with stated dependencies
... OK
- checking whether the name space can be unloaded cleanly ... OK
- checking for unstated dependencies in R code ... OK
- checking S3 generic/method consistency ... OK
- checking replacement functions ... OK
- checking foreign function calls ... OK
- checking R code for possible problems ... OK
- checking Rd files ... OK
- checking Rd metadata ... OK
- checking Rd cross-references ... OK
- checking for missing documentation entries ... OK
- checking for code/documentation mismatches ... OK
- checking Rd \usage sections ... OK
- checking Rd contents ... OK
- checking examples ... ERROR
Running examples in oro.nifti-Ex.R failed
The error most likely occurred in:
> ### Name: writeNIfTI
> ### Title: writeNIfTI
> ### Aliases: writeNIfTI
> ### Keywords: file
>
> ### ** Examples
>
> norm <- dnorm(seq(-5, 5, length=32), sd=2)
> norm <- (norm-min(norm)) / max(norm-min(norm))
> img <- outer(outer(norm, norm), norm)
> img <- round(255 * img)
> img[17:32,,] <- 255 - img[17:32,,]
> img.nifti <- nifti(img) # create NIfTI object
>
> writeNIfTI(img.nifti, "test-nifti-image-uint8", verbose=TRUE)
niftiExtension detected!
niftiAuditTrail detected!
vox_offset = 1392
*writing niftiExtension(s) at byte = 6.803919e+17 # <- LARGE NUMBER!
writing data at byte = 6.803919e+17 # <- LARGE NUMBER!*
> ## These files should be viewable in, for example, FSLview
> ## Make sure you adjust the min/max values for proper visualization
> data <- readNIfTI("test-nifti-image-uint8", verbose=TRUE)
fname = test-nifti-image-uint8
files = test-nifti-image-uint8.nii.gz
nii = test-nifti-image-uint8.nii.gz
vox_offset = 1392
niftiExtension detected!
Error in read.nifti.content(fname, gzipped = TRUE, verbose = verbose, :
-- extension size (esize) has overshot voxel offset --
Calls: readNIfTI -> read.nifti.content
Execution halted
Please draw your attention to the two lines annotated above. The line of
code that "looks a bit odd" above is
cat(" writing niftiExtension(s) at byte =", seek(fid), fill=TRUE)
...where fid is a call to file()... and this large number is causing the
subsequent read function to fail.
My questions are:
- Why would this error occur in 32-bit linux only for R 2.12.0?
- How can I test any fixes to this error given I am not running R in
32-bit linux?
Any suggestions would be welcome.
Thank-you,
Brandon
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