* using log directory 'd:/Rcompile/CRANpkg/local/2.8/aCGH.Spline.Rcheck'
* using R version 2.8.1 (2008-12-22)
* using session charset: ISO8859-1
* checking for file 'aCGH.Spline/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'aCGH.Spline' version '1.0'
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking whether package 'aCGH.Spline' can be installed ... OK
* checking package directory ... OK
* checking for portable file names ... 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 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 cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* creating aCGH.Spline-Ex.R ... OK
* checking examples ... OK
* creating aCGH.Spline-manual.tex ... OK
* checking aCGH.Spline-manual.tex using pdflatex ... ERROR
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
LaTeX errors found:
! Missing $ inserted.
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                $
l.79 ..."FeatureExtraction.txt" or Nimblegen "SEG_
                                                  MNT.txt" files)\\
! LaTeX Error: Command \end{list} invalid in math mode.

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! LaTeX Error: Something's wrong--perhaps a missing \item.

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! LaTeX Error: Something's wrong--perhaps a missing \item.

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! Missing $ inserted.
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l.80 \end{Note}
               
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l.585 ... Nimblegen "SEG_MNT.txt" file.}{nim.read}
                                                  
! Extra }, or forgotten $.
<recently read> \egroup 
                        
l.585 ... Nimblegen "SEG_MNT.txt" file.}{nim.read}
                                                  
! LaTeX Error: Command \end{list} invalid in math mode.

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! LaTeX Error: Something's wrong--perhaps a missing \item.

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! LaTeX Error: Something's wrong--perhaps a missing \item.

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! Missing $ inserted.
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l.585 ... Nimblegen "SEG_MNT.txt" file.}{nim.read}
                                                  
! Missing } inserted.
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                }
l.585 ... Nimblegen "SEG_MNT.txt" file.}{nim.read}
                                                  
! Missing $ inserted.
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l.588 Function to read a Nimblgen "SEG_
                                       MNT.txt" file.
! LaTeX Error: Command \end{list} invalid in math mode.

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! LaTeX Error: Something's wrong--perhaps a missing \item.

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! LaTeX Error: Something's wrong--perhaps a missing \item.

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! Missing $ inserted.
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l.589 \end{Description}
                       
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l.597 \item[\code{file}] - Nimblegen "SEG_
                                          MNT.txt" file to read.
! LaTeX Error: Command \end{list} invalid in math mode.

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l.598 \end{ldescription}
                        
! Missing $ inserted.
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l.601 ...n reads the contains of a Nimblegen "SEG_
                                                  MNT.txt" file into a ".tem...
! LaTeX Error: Command \end{list} invalid in math mode.

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! LaTeX Error: Something's wrong--perhaps a missing \item.

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! LaTeX Error: Something's wrong--perhaps a missing \item.

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! Missing $ inserted.
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l.602 \end{Details}
                   
! Missing $ inserted.
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l.615 ... is currently no option to output a "SEG_
                                                  MNT.txt" format, however, ...
! LaTeX Error: Command \end{list} invalid in math mode.

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Type  H <return>  for immediate help.
 ...                                              
! LaTeX Error: Something's wrong--perhaps a missing \item.

See the LaTeX manual or LaTeX Companion for explanation.
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! LaTeX Error: Something's wrong--perhaps a missing \item.

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! Missing $ inserted.
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                $
l.616 \end{Note}