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### Running command:
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###   /Library/Frameworks/R.framework/Resources/bin/R CMD build --keep-empty-dirs --no-resave-data breakpointR
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* checking for file ‘breakpointR/DESCRIPTION’ ... OK
* preparing ‘breakpointR’:
* checking DESCRIPTION meta-information ... OK
* installing the package to build vignettes
* creating vignettes ... ERROR
--- re-building ‘breakpointR.Rnw’ using knitr
breakpointr            package:breakpointR             R Documentation

_M_a_i_n _f_u_n_c_t_i_o_n _f_o_r _t_h_e '_b_r_e_a_k_p_o_i_n_t_R' _p_a_c_k_a_g_e

_D_e_s_c_r_i_p_t_i_o_n:

     This function is an easy-to-use wrapper to find breakpoints with
     'runBreakpointr' in parallel, write the results to file, plot
     results and find hotspots.

_U_s_a_g_e:

     breakpointr(
       inputfolder,
       outputfolder,
       configfile = NULL,
       numCPU = 1,
       reuse.existing.files = FALSE,
       windowsize = 1e+06,
       binMethod = "size",
       multi.sizes = NULL,
       pairedEndReads = FALSE,
       pair2frgm = FALSE,
       chromosomes = NULL,
       min.mapq = 10,
       filtAlt = FALSE,
       genoT = "fisher",
       trim = 10,
       peakTh = 0.33,
       zlim = 3.291,
       background = 0.05,
       minReads = 10,
       maskRegions = NULL,
       callHotSpots = FALSE,
       conf = 0.99
     )
     
_A_r_g_u_m_e_n_t_s:

inputfolder: Folder with BAM files.

outputfolder: Folder to output the results. If it does not exist it
          will be created.

configfile: A file specifying the parameters of this function (without
          'inputfolder', 'outputfolder' and 'configfile'). Having the
          parameters in a file can be handy if many samples with the
          same parameter settings are to be run. If a 'configfile' is
          specified, it will take priority over the command line
          parameters.

  numCPU: The numbers of CPUs that are used. Should not be more than
          available on your machine.

reuse.existing.files: A logical indicating whether or not existing
          files in 'outputfolder' should be reused.

windowsize: The window size used to calculate deltaWs, either number of
          reads or genomic size depending on 'binMethod'.

binMethod: Method used to calculate optimal number of reads in the
          window ("size", "reads"). By default 'binMethod='size''.

multi.sizes: User defined multiplications of the original window size.

pairedEndReads: Set to 'TRUE' if you have paired-end reads in your
          file.

pair2frgm: Set to 'TRUE' if every paired-end read should be merged into
          a single fragment.

chromosomes: If only a subset of the chromosomes should be binned,
          specify them here.

min.mapq: Minimum mapping quality when importing from BAM files.

 filtAlt: Set to 'TRUE' if you want to filter out alternative
          alignments defined in 'XA' tag.

   genoT: A method ('fisher' or 'binom') to genotype regions defined by
          a set of breakpoints.

    trim: The amount of outliers in deltaWs removed to calculate the
          stdev (10 will remove top 10% and bottom 10% of deltaWs).

  peakTh: The treshold that the peak deltaWs must pass to be considered
          a breakpoint (e.g. 0.33 is 1/3 of max(deltaW)).

    zlim: The number of stdev that the deltaW must pass the peakTh
          (ensures only significantly higher peaks are considered).

background: The percent (e.g. 0.05 = 5%) of background reads allowed
          for WW or CC genotype calls.

minReads: The minimal number of reads between two breaks required for
          genotyping.

maskRegions: List of regions to be excluded from the analysis
          (tab-separated file: chromosomes start end).

callHotSpots: Search for regions of high abundance of breakpoints in
          single cells.

    conf: Desired confidence interval of localized breakpoints.

_V_a_l_u_e:

     'NULL'

_A_u_t_h_o_r(_s):

     David Porubsky, Aaron Taudt, Ashley Sanders

_E_x_a_m_p_l_e_s:

     ## Not run:
     
     ## The following call produces plots and genome browser files for all BAM files in "my-data-folder"
     breakpointr(inputfolder="my-data-folder", outputfolder="my-output-folder")
     ## End(Not run)
     

Error: processing vignette 'breakpointR.Rnw' failed with diagnostics:
Running 'texi2dvi' on 'breakpointR.tex' failed.
LaTeX errors:
! Package xcolor Error: Undefined color `fgcolor'.

See the xcolor package documentation for explanation.
Type  H <return>  for immediate help.
 ...                                              
! Emergency stop.
 ...                                              
                                                  
l.58 ...}{rgb}{0.941, 0.941, 0.941}\color{fgcolor}
                                                  \begin{kframe}
!  ==> Fatal error occurred, no output PDF file produced!
--- failed re-building ‘breakpointR.Rnw’

SUMMARY: processing the following file failed:
  ‘breakpointR.Rnw’

Error: Vignette re-building failed.
Execution halted