[Rd] R CMD check error in v2.12.0

From: Brandon Whitcher <bwhitcher_at_gmail.com>
Date: Wed, 16 Jun 2010 15:08:06 +0100


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

   > ### 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, :

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:

Any suggestions would be welcome.

Thank-you,

Brandon

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