Error(s) in re-building vignettes:
--- re-building ‘Delay_difference.Rmd’ using rmarkdown
dyld: lazy symbol binding failed: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

dyld: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

Error: processing vignette 'Delay_difference.Rmd' failed with diagnostics:
pandoc document conversion failed with error 6
--- failed re-building ‘Delay_difference.Rmd’

--- re-building ‘MSEtool.Rmd’ using rmarkdown
Loading required package: DLMtool
Loading required package: snowfall
Loading required package: snow

Attaching package: 'MSEtool'

The following objects are masked from 'package:DLMtool':

    avail, userguide

dyld: lazy symbol binding failed: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

dyld: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

Error: processing vignette 'MSEtool.Rmd' failed with diagnostics:
pandoc document conversion failed with error 6
--- failed re-building ‘MSEtool.Rmd’

--- re-building ‘SCA.Rmd’ using rmarkdown
dyld: lazy symbol binding failed: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

dyld: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

Error: processing vignette 'SCA.Rmd' failed with diagnostics:
pandoc document conversion failed with error 6
--- failed re-building ‘SCA.Rmd’

--- re-building ‘SRA_scope.Rmd’ using rmarkdown
dyld: lazy symbol binding failed: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

dyld: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

Error: processing vignette 'SRA_scope.Rmd' failed with diagnostics:
pandoc document conversion failed with error 6
--- failed re-building ‘SRA_scope.Rmd’

--- re-building ‘Surplus_production.Rmd’ using rmarkdown
dyld: lazy symbol binding failed: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

dyld: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

Error: processing vignette 'Surplus_production.Rmd' failed with diagnostics:
pandoc document conversion failed with error 6
--- failed re-building ‘Surplus_production.Rmd’

--- re-building ‘VPA.Rmd’ using rmarkdown
dyld: lazy symbol binding failed: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

dyld: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

Error: processing vignette 'VPA.Rmd' failed with diagnostics:
pandoc document conversion failed with error 6
--- failed re-building ‘VPA.Rmd’

--- re-building ‘multiMSE.Rmd’ using rmarkdown
Loading required package: DLMtool
Loading required package: snowfall
Loading required package: snow

Attaching package: 'MSEtool'

The following objects are masked from 'package:DLMtool':

    avail, userguide

MOM-class               package:MSEtool                R Documentation

_C_l_a_s_s "_M_O_M"

_D_e_s_c_r_i_p_t_i_o_n:

     An object containing all the parameters needed to control a
     multi-stock, multi-fleet MSE which can be build from component
     Stock, Fleet, Obs, and Imp objects.

_D_e_t_a_i_l_s:

     Almost all of these inputs are a vector of length 2 which
     describes the upper and lower bounds of a uniform distribution
     from which to sample the parameter.

_S_l_o_t_s:

     'Name' Name of the operating model

     'Agency' Name of the agency responsible for the management of the
          fishery. Character string

     'Region' Name of the general geographic region of the fishery.
          Character string

     'Sponsor' Name of the organization who sponsored the OM. Character
          string

     'Latitude' Latitude (decimal degrees). Negative values represent
          the South of the Equator. Numeric. Single value

     'Longitude' Longitude (decimal degrees). Negative values represent
          the West of the Prime Meridian. Numeric. Single value

     'nsim' The number of simulations

     'proyears' The number of projected years

     'interval' The assessment interval - how often would you like to
          update the management system?

     'pstar' The percentile of the sample of the management
          recommendation for each method

     'maxF' Maximum instantaneous fishing mortality rate that may be
          simulated for any given age class

     'reps' Number of samples of the management recommendation for each
          method. Note that when this is set to 1, the mean value of
          the data inputs is used.

     'cpars' A hierarcical list nstock then nfleet long of custom
          parameters. Time series are a matrix nsim rows by nyears
          columns. Single parameters are a vector nsim long

     'seed' A random seed to ensure users can reproduce results exactly

     'Source' A reference to a website or article from which parameters
          were taken to define the operating model

     'Stocks' List of stock objects

     'Fleets' List of Fleet objects

     'Obs' Hierarchical List of Observation model objects Level 1 is
          stock, level 2 is fleet

     'Imps' Hierarchical List of Implementation model objects Level 1
          is stock, level 2 is fleet

     'CatchFrac' A list nstock long, of matrices nsim x nfleet
          representing the fraction of current catches of the various
          fleets to each stock (each matrix is nsim by nfleet long and
          rows sum to 1 for each stock)

     'Allocation' A list nstock long, of matrices nsim x nfleet
          representing the fraction of future TACs of the various
          fleets to each stock (each matrix is nsim by nfleet long and
          rows sum to 1 for each stock).

     'Efactor' A list nstock long, of current effort factors by fleet
          (default is 1 - same as current effort)

     'Complexes' A list of stock complexes. Each position is a vector
          of stock numbers (as they appear in StockPars) for which data
          should be aggregated and TAC recommendations split among
          stocks according to vulnerable biomass

     'SexPars' A list of slots that control sex-specific dynamics

     'Rel' A list of biological / ecological relationships among stocks
          over-ridden if an MP of class 'MP_F" is supplied that is a
          multi-fleet MP.

_O_b_j_e_c_t_s _f_r_o_m _t_h_e _C_l_a_s_s:

     Objects can be created by calls of the form 'new('MOM',
     Stock_list, Fleet_list, Obs_list, Imp_list)'.

_A_u_t_h_o_r(_s):

     T. Carruthers and A. Hordyk


MMSE-class               package:MSEtool               R Documentation

_C_l_a_s_s "_M_M_S_E"

_D_e_s_c_r_i_p_t_i_o_n:

     A Multi Management Strategy Evaluation object that contains
     information about simulation conditions and performance of MPs for
     a multi-stock, multi-fleet operating model.

_S_l_o_t_s:

     'Name' Name of the MMSE object. Single value. Character string

     'nyears' The number of years for the historical simulation. Single
          value. Positive integer

     'proyears' The number of years for the projections - closed loop
          simulations. Single value. Positive integer

     'nMPs' Number of management procedures simulation tested. Single
          value. Positive integer.

     'MPs' The names of the MPs that were tested. Vector of length
          nMPs. Character strings.

     'MPcond' The MP condition. Character ('bystock': an MP per stock,
          'byfleet' and MP per stock and fleet, 'MMP' an MP for all
          stocks and fleets)

     'MPrefs' The names of the MPs applied for each stock (row) and
          fleet (column). An array.

     'nsim' Number of simulations. Single value. Positive integer

     'nstocks' Number of stocks. Single value. Positive integer

     'nfleets' Number of fleets. Single value. Positive integer

     'Snames' Names of the stocks

     'Fnames' Names of the fleets (matrix nstocks x nfleets)

     'Stocks' The stock operating model objects. List of Stocks

     'Fleets' The fleet operating model objects. Hierarchical list,
          fleets nested in stocks.

     'Obss' The fleet specific observation error operating model
          objects. Hierarchical list, fleets nested in stocks.

     'Imps' The fleet soecific implementation error operating model
          objects. Hierarchical list, fleets nested in stocks.

     'OM' A table of sampled parameters of the operating model. Data
          frame of nsim rows.

     'Obs' A table of sampled parameters of the observation model. Data
          frame of nsim rows.

     'B_BMSY' Simulated biomass relative to BMSY over the projection.
          An array with dimensions: nsim, nMPs, proyears. Non-negative
          real numbers

     'F_FMSY' Simulated fishing mortality rate relative to FMSY over
          the projection. An array with dimensions: nsim, nMPs,
          proyears. Non-negative real numbers

     'B' Simulated stock biomass over the projection. An array with
          dimensions: nsim, nMPs, proyears. Non-negative real numbers

     'SSB' Simulated spawning stock biomass over the projection. An
          array with dimensions: nsim, nMPs, proyears. Non-negative
          real numbers

     'VB' Simulated vulnerable biomass over the projection. An array
          with dimensions: nsim, nMPs, proyears. Non-negative real
          numbers

     'FM' Simulated fishing mortality rate over the projection. An
          array with dimensions: nsim, nMPs, proyears. Non-negative
          real numbers

     'C' Simulated catches (taken) over the projection. An array with
          dimensions: nsim, nMPs, proyears. Non-negative real numbers

     'TAC' Simulated Total Allowable Catch (prescribed) over the
          projection (this is NA for input controls). An array with
          dimensions: nsim, nMPs, proyears. Non-negative real numbers

     'SSB_hist' Simulated historical spawning stock biomass. An array
          with dimensions: nsim, nages, nyears, nareas. Non-negative
          real numbers

     'CB_hist' Simulated historical catches in weight. An array with
          dimensions: nsim, nages, nyears, nareas. Non-negative real
          numbers

     'FM_hist' Simulated historical fishing mortality rate. An array
          with dimensions: nsim, nages, nyears, nareas. Non-negative
          real numbers

     'Effort' Simulated relative fishing effort in the projection
          years. An array with dimensions: nsim, nMPs, proyears.
          Non-negative real numbers

     'PAA' Population at age in last projection year. An array with
          dimensions: nsim, nMPs, nages. Non-negative real numbers

     'CAA' Catch at age in last projection year. An array with
          dimensions: nsim, nMPs, nages. Non-negative real numbers

     'CAL' Catch at length in last projection year. An array with
          dimensions: nsim, nMPs, nCALbins. Non-negative real numbers

     'CALbins' Mid-points of the catch-at-length bins. Vector of length
          nCALbins. Positive real numbers.

     'MSY_P' Array of projected MSY by year with dimensions: nsim,
          nstock, nMP, proyears.

     'FMSY_P' Array of projected FMSY by year with dimensions: nsim,
          nstock, nMP, proyears.

     'SSBMSY_P' Array of projected Spawning Stock Biomass at MSY by
          year with dimensions: nsim, nstock, nMP, proyears.

     'Misc' Miscellanenous output such as posterior predictive data

_O_b_j_e_c_t_s _f_r_o_m _t_h_e _C_l_a_s_s:

     Objects can be created by calls of the form 'new('MMSE', Name,
     nyears, proyears, nMPs, MPs, nsim, OMtable, Obs, B_BMSYa, F_FMSYa,
     Ba, FMa, Ca, OFLa, Effort, PAA, CAA, CAL, CALbins)'

_A_u_t_h_o_r(_s):

     T. Carruthers


dyld: lazy symbol binding failed: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

dyld: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

Error: processing vignette 'multiMSE.Rmd' failed with diagnostics:
pandoc document conversion failed with error 6
--- failed re-building ‘multiMSE.Rmd’

SUMMARY: processing the following files failed:
  ‘Delay_difference.Rmd’ ‘MSEtool.Rmd’ ‘SCA.Rmd’ ‘SRA_scope.Rmd’
  ‘Surplus_production.Rmd’ ‘VPA.Rmd’ ‘multiMSE.Rmd’

Error: Vignette re-building failed.
Execution halted