CRAN Package Check Results for Package MSEtool

Last updated on 2020-04-25 01:53:08 CEST.

Flavor Version Tinstall Tcheck Ttotal Status Flags
r-devel-linux-x86_64-debian-clang 1.5.0 173.86 215.41 389.27 OK
r-devel-linux-x86_64-debian-gcc 1.5.0 185.35 161.44 346.79 OK
r-devel-linux-x86_64-fedora-clang 1.5.0 508.50 NOTE
r-devel-linux-x86_64-fedora-gcc 1.5.0 563.86 OK
r-devel-windows-ix86+x86_64 1.5.0 336.00 361.00 697.00 NOTE
r-patched-linux-x86_64 1.5.0 170.45 208.93 379.38 OK
r-patched-osx-x86_64 1.5.0 WARN
r-patched-solaris-x86 1.5.0 527.30 NOTE
r-release-linux-x86_64 1.5.0 177.58 188.42 366.00 OK
r-release-windows-ix86+x86_64 1.5.0 314.00 346.00 660.00 NOTE
r-release-osx-x86_64 1.5.0 NOTE
r-oldrel-windows-ix86+x86_64 1.5.0 220.00 260.00 480.00 NOTE
r-oldrel-osx-x86_64 1.5.0 NOTE

Check Details

Version: 1.5.0
Check: installed package size
Result: NOTE
     installed size is 31.4Mb
     sub-directories of 1Mb or more:
     R 1.4Mb
     doc 1.1Mb
     libs 28.4Mb
Flavors: r-devel-linux-x86_64-fedora-clang, r-devel-windows-ix86+x86_64, r-patched-osx-x86_64, r-patched-solaris-x86, r-release-windows-ix86+x86_64, r-release-osx-x86_64, r-oldrel-windows-ix86+x86_64, r-oldrel-osx-x86_64

Version: 1.5.0
Check: re-building of vignette outputs
Result: WARN
    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
    
    _<08>C_<08>l_<08>a_<08>s_<08>s "_<08>M_<08>O_<08>M"
    
    _<08>D_<08>e_<08>s_<08>c_<08>r_<08>i_<08>p_<08>t_<08>i_<08>o_<08>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.
    
    _<08>D_<08>e_<08>t_<08>a_<08>i_<08>l_<08>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.
    
    _<08>S_<08>l_<08>o_<08>t_<08>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.
    
    _<08>O_<08>b_<08>j_<08>e_<08>c_<08>t_<08>s _<08>f_<08>r_<08>o_<08>m _<08>t_<08>h_<08>e _<08>C_<08>l_<08>a_<08>s_<08>s:
    
     Objects can be created by calls of the form 'new('MOM',
     Stock_list, Fleet_list, Obs_list, Imp_list)'.
    
    _<08>A_<08>u_<08>t_<08>h_<08>o_<08>r(_<08>s):
    
     T. Carruthers and A. Hordyk
    
    
    MMSE-class package:MSEtool R Documentation
    
    _<08>C_<08>l_<08>a_<08>s_<08>s "_<08>M_<08>M_<08>S_<08>E"
    
    _<08>D_<08>e_<08>s_<08>c_<08>r_<08>i_<08>p_<08>t_<08>i_<08>o_<08>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.
    
    _<08>S_<08>l_<08>o_<08>t_<08>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
    
    _<08>O_<08>b_<08>j_<08>e_<08>c_<08>t_<08>s _<08>f_<08>r_<08>o_<08>m _<08>t_<08>h_<08>e _<08>C_<08>l_<08>a_<08>s_<08>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)'
    
    _<08>A_<08>u_<08>t_<08>h_<08>o_<08>r(_<08>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
Flavor: r-patched-osx-x86_64