Error(s) in re-building vignettes:
  ...
--- re-building ‘rodeoVignette.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
/home/ripley/developerstudio12.6/bin/f95  -PIC  -O -libmil -xtarget=native -xcache=generic -nofstore  -c  /home/ripley/R/packages/tests32/rodeo.Rcheck/vign_test/rodeo/vignettes/vignetteData/fortran/functionsCode.f95 -o /home/ripley/R/packages/tests32/rodeo.Rcheck/vign_test/rodeo/vignettes/vignetteData/fortran/functionsCode.o
/home/ripley/developerstudio12.6/bin/f95  -PIC  -O -libmil -xtarget=native -xcache=generic -nofstore  -c  /tmp/Rtmp5kaG3d/working_dir/Rtmp0Uaq2m/rodeo19b2412e2463.f95 -o /tmp/Rtmp5kaG3d/working_dir/Rtmp0Uaq2m/rodeo19b2412e2463.o

module dimensions_and_indices
       ^                      
"/tmp/Rtmp5kaG3d/working_dir/Rtmp0Uaq2m/rodeo19b2412e2463.f95", Line = 3, Column = 8: ERROR: The compiler has detected errors in module "DIMENSIONS_AND_INDICES".  No module information file will be created for this module.

    integer, pointer:: bac => ivar0D(1)
                                      ^ 
"/tmp/Rtmp5kaG3d/working_dir/Rtmp0Uaq2m/rodeo19b2412e2463.f95", Line = 22, Column = 39: ERROR: Illegal pointer assignment.

    integer, pointer:: sub => ivar0D(2)
                                      ^ 
"/tmp/Rtmp5kaG3d/working_dir/Rtmp0Uaq2m/rodeo19b2412e2463.f95", Line = 23, Column = 39: ERROR: Illegal pointer assignment.

    integer, pointer:: mu => ipar0D(1)
                                     ^ 
"/tmp/Rtmp5kaG3d/working_dir/Rtmp0Uaq2m/rodeo19b2412e2463.f95", Line = 26, Column = 38: ERROR: Illegal pointer assignment.

    integer, pointer:: half => ipar0D(2)
                                       ^ 
"/tmp/Rtmp5kaG3d/working_dir/Rtmp0Uaq2m/rodeo19b2412e2463.f95", Line = 27, Column = 40: ERROR: Illegal pointer assignment.

    integer, pointer:: yield => ipar0D(3)
                                        ^ 
"/tmp/Rtmp5kaG3d/working_dir/Rtmp0Uaq2m/rodeo19b2412e2463.f95", Line = 28, Column = 41: ERROR: Illegal pointer assignment.

    integer, pointer:: vol => ipar0D(4)
                                      ^ 
"/tmp/Rtmp5kaG3d/working_dir/Rtmp0Uaq2m/rodeo19b2412e2463.f95", Line = 29, Column = 39: ERROR: Illegal pointer assignment.

    integer, pointer:: flow => ipar0D(5)
                                       ^ 
"/tmp/Rtmp5kaG3d/working_dir/Rtmp0Uaq2m/rodeo19b2412e2463.f95", Line = 30, Column = 40: ERROR: Illegal pointer assignment.

    integer, pointer:: sub_in => ipar0D(6)
                                         ^ 
"/tmp/Rtmp5kaG3d/working_dir/Rtmp0Uaq2m/rodeo19b2412e2463.f95", Line = 31, Column = 42: ERROR: Illegal pointer assignment.

    integer, pointer:: bac => ivar(1)
                                    ^ 
"/tmp/Rtmp5kaG3d/working_dir/Rtmp0Uaq2m/rodeo19b2412e2463.f95", Line = 38, Column = 37: ERROR: Illegal pointer assignment.

    integer, pointer:: sub => ivar(2)
                                    ^ 
"/tmp/Rtmp5kaG3d/working_dir/Rtmp0Uaq2m/rodeo19b2412e2463.f95", Line = 39, Column = 37: ERROR: Illegal pointer assignment.

    integer, pointer:: mu => ipar(1)
                                   ^ 
"/tmp/Rtmp5kaG3d/working_dir/Rtmp0Uaq2m/rodeo19b2412e2463.f95", Line = 42, Column = 36: ERROR: Illegal pointer assignment.

    integer, pointer:: half => ipar(2)
                                     ^ 
"/tmp/Rtmp5kaG3d/working_dir/Rtmp0Uaq2m/rodeo19b2412e2463.f95", Line = 43, Column = 38: ERROR: Illegal pointer assignment.

    integer, pointer:: yield => ipar(3)
                                      ^ 
"/tmp/Rtmp5kaG3d/working_dir/Rtmp0Uaq2m/rodeo19b2412e2463.f95", Line = 44, Column = 39: ERROR: Illegal pointer assignment.

    integer, pointer:: vol => ipar(4)
                                    ^ 
"/tmp/Rtmp5kaG3d/working_dir/Rtmp0Uaq2m/rodeo19b2412e2463.f95", Line = 45, Column = 37: ERROR: Illegal pointer assignment.

    integer, pointer:: flow => ipar(5)
                                     ^ 
"/tmp/Rtmp5kaG3d/working_dir/Rtmp0Uaq2m/rodeo19b2412e2463.f95", Line = 46, Column = 38: ERROR: Illegal pointer assignment.

    integer, pointer:: sub_in => ipar(6)
                                       ^ 
"/tmp/Rtmp5kaG3d/working_dir/Rtmp0Uaq2m/rodeo19b2412e2463.f95", Line = 47, Column = 40: ERROR: Illegal pointer assignment.

    integer, pointer:: growth => ipro(1)
                                       ^ 
"/tmp/Rtmp5kaG3d/working_dir/Rtmp0Uaq2m/rodeo19b2412e2463.f95", Line = 50, Column = 40: ERROR: Illegal pointer assignment.

    integer, pointer:: inout => ipro(2)
                                      ^ 
"/tmp/Rtmp5kaG3d/working_dir/Rtmp0Uaq2m/rodeo19b2412e2463.f95", Line = 51, Column = 39: ERROR: Illegal pointer assignment.

  use dimensions_and_indices
      ^                      
"/tmp/Rtmp5kaG3d/working_dir/Rtmp0Uaq2m/rodeo19b2412e2463.f95", Line = 60, Column = 7: ERROR: "DIMENSIONS_AND_INDICES" is specified as the module name on a USE statement, but the compiler cannot find it.

  double precision, dimension(NVAR*NBOX), intent(in):: var
                              ^                            
"/tmp/Rtmp5kaG3d/working_dir/Rtmp0Uaq2m/rodeo19b2412e2463.f95", Line = 65, Column = 31: ERROR: IMPLICIT NONE is specified in the local scope, therefore an explicit type must be specified for data object "NVAR".

  double precision, dimension(NPAR*NBOX), intent(in):: par
                              ^                            
"/tmp/Rtmp5kaG3d/working_dir/Rtmp0Uaq2m/rodeo19b2412e2463.f95", Line = 66, Column = 31: ERROR: IMPLICIT NONE is specified in the local scope, therefore an explicit type must be specified for data object "NPAR".

  double precision, dimension(NPRO*NBOX), intent(out):: pro
                              ^                             
"/tmp/Rtmp5kaG3d/working_dir/Rtmp0Uaq2m/rodeo19b2412e2463.f95", Line = 70, Column = 31: ERROR: IMPLICIT NONE is specified in the local scope, therefore an explicit type must be specified for data object "NPRO".

    ivar= (ivar0D - 1) * NBOX + iBox
    ^                                
"/tmp/Rtmp5kaG3d/working_dir/Rtmp0Uaq2m/rodeo19b2412e2463.f95", Line = 94, Column = 5: ERROR: IMPLICIT NONE is specified in the local scope, therefore an explicit type must be specified for data object "IVAR".
           ^                         
"/tmp/Rtmp5kaG3d/working_dir/Rtmp0Uaq2m/rodeo19b2412e2463.f95", Line = 94, Column = 12: ERROR: IMPLICIT NONE is specified in the local scope, therefore an explicit type must be specified for data object "IVAR0D".

    ipar= (ipar0D - 1) * NBOX + iBox
    ^                                
"/tmp/Rtmp5kaG3d/working_dir/Rtmp0Uaq2m/rodeo19b2412e2463.f95", Line = 95, Column = 5: ERROR: IMPLICIT NONE is specified in the local scope, therefore an explicit type must be specified for data object "IPAR".
           ^                         
"/tmp/Rtmp5kaG3d/working_dir/Rtmp0Uaq2m/rodeo19b2412e2463.f95", Line = 95, Column = 12: ERROR: IMPLICIT NONE is specified in the local scope, therefore an explicit type must be specified for data object "IPAR0D".

      par(p%mu) * monod(var(v%sub), par(p%half)) * var(v%bac)&
          ^                                                    
"/tmp/Rtmp5kaG3d/working_dir/Rtmp0Uaq2m/rodeo19b2412e2463.f95", Line = 99, Column = 11: ERROR: IMPLICIT NONE is specified in the local scope, therefore an explicit type must be specified for data object "P".
                            ^                                  
"/tmp/Rtmp5kaG3d/working_dir/Rtmp0Uaq2m/rodeo19b2412e2463.f95", Line = 99, Column = 29: ERROR: IMPLICIT NONE is specified in the local scope, therefore an explicit type must be specified for data object "V".

    ivar= (ivar0D - 1) * NBOX + iBox
    ^                                
"/tmp/Rtmp5kaG3d/working_dir/Rtmp0Uaq2m/rodeo19b2412e2463.f95", Line = 114, Column = 5: ERROR: IMPLICIT NONE is specified in the local scope, therefore an explicit type must be specified for data object "IVAR".
           ^                         
"/tmp/Rtmp5kaG3d/working_dir/Rtmp0Uaq2m/rodeo19b2412e2463.f95", Line = 114, Column = 12: ERROR: IMPLICIT NONE is specified in the local scope, therefore an explicit type must be specified for data object "IVAR0D".

    ipar= (ipar0D - 1) * NBOX + iBox
    ^                                
"/tmp/Rtmp5kaG3d/working_dir/Rtmp0Uaq2m/rodeo19b2412e2463.f95", Line = 115, Column = 5: ERROR: IMPLICIT NONE is specified in the local scope, therefore an explicit type must be specified for data object "IPAR".
           ^                         
"/tmp/Rtmp5kaG3d/working_dir/Rtmp0Uaq2m/rodeo19b2412e2463.f95", Line = 115, Column = 12: ERROR: IMPLICIT NONE is specified in the local scope, therefore an explicit type must be specified for data object "IPAR0D".

    ipro= (ipro0D - 1) * NBOX + iBox
    ^                                
"/tmp/Rtmp5kaG3d/working_dir/Rtmp0Uaq2m/rodeo19b2412e2463.f95", Line = 116, Column = 5: ERROR: IMPLICIT NONE is specified in the local scope, therefore an explicit type must be specified for data object "IPRO".
           ^                         
"/tmp/Rtmp5kaG3d/working_dir/Rtmp0Uaq2m/rodeo19b2412e2463.f95", Line = 116, Column = 12: ERROR: IMPLICIT NONE is specified in the local scope, therefore an explicit type must be specified for data object "IPRO0D".

       pro(r%growth) * (1d0) +  pro(r%inout) * (-var(v%bac))&
           ^                                                  
"/tmp/Rtmp5kaG3d/working_dir/Rtmp0Uaq2m/rodeo19b2412e2463.f95", Line = 120, Column = 12: ERROR: IMPLICIT NONE is specified in the local scope, therefore an explicit type must be specified for data object "R".
                                                     ^        
"/tmp/Rtmp5kaG3d/working_dir/Rtmp0Uaq2m/rodeo19b2412e2463.f95", Line = 120, Column = 54: ERROR: IMPLICIT NONE is specified in the local scope, therefore an explicit type must be specified for data object "V".

       pro(r%growth) * (-1d0 / par(p%yield)) +  pro(r%inout) *&
                                   ^                            
"/tmp/Rtmp5kaG3d/working_dir/Rtmp0Uaq2m/rodeo19b2412e2463.f95", Line = 123, Column = 36: ERROR: IMPLICIT NONE is specified in the local scope, therefore an explicit type must be specified for data object "P".

f90comp: 128 SOURCE LINES
f90comp: 38 ERRORS, 0 WARNINGS, 0 OTHER MESSAGES, 0 ANSI
*** Error code 2
make: Fatal error: Command failed for target `/tmp/Rtmp5kaG3d/working_dir/Rtmp0Uaq2m/rodeo19b2412e2463.o'
Current working directory /tmp/Rtmp5kaG3d/working_dir/Rtmp0Uaq2m
Quitting from lines 408-408 (rodeoVignette.Rmd) 
Error: processing vignette 'rodeoVignette.Rmd' failed with diagnostics:
Compilation failed.
--- failed re-building ‘rodeoVignette.Rmd’

SUMMARY: processing the following file failed:
  ‘rodeoVignette.Rmd’

Error: Vignette re-building failed.
Execution halted