CRAN Package Check Results for Package BacArena

Last updated on 2020-04-09 09:48:02 CEST.

Check Details

Version: 1.8.1
Check: examples
Result: ERROR
    Running examples in 'BacArena-Ex.R' failed
    The error most likely occurred in:
    
    > base::assign(".ptime", proc.time(), pos = "CheckExEnv")
    > ### Name: HeatMapFeeding
    > ### Title: Function for plotting heatmap of feeding between two selected
    > ### cell models
    > ### Aliases: HeatMapFeeding HeatMapFeeding,Eval-method
    >
    > ### ** Examples
    >
    > sim <- sihumi_test
    > HeatMapFeeding(object = sim, speciesA = 1, speciesB = 2, var_nr = 78)
    Warning in BacArena::findFeeding3(object, time = t, mets = A$sub[1:var_nr], :
     sim_step 1 : No crossfeeding found. Try other metaboites or time points.
    Warning in BacArena::findFeeding3(object, time = t, mets = A$sub[1:var_nr], :
     sim_step 2 : No crossfeeding found. Try other metaboites or time points.
    Warning in BacArena::findFeeding3(object, time = t, mets = A$sub[1:var_nr], :
     sim_step 3 : No crossfeeding found. Try other metaboites or time points.
    Warning in BacArena::findFeeding3(object, time = t, mets = A$sub[1:var_nr], :
     sim_step 4 : No crossfeeding found. Try other metaboites or time points.
    Warning in BacArena::findFeeding3(object, time = t, mets = A$sub[1:var_nr], :
     sim_step 5 : No crossfeeding found. Try other metaboites or time points.
    Warning in BacArena::findFeeding3(object, time = t, mets = A$sub[1:var_nr], :
     sim_step 6 : No crossfeeding found. Try other metaboites or time points.
    Warning in BacArena::findFeeding3(object, time = t, mets = A$sub[1:var_nr], :
     sim_step 7 : No crossfeeding found. Try other metaboites or time points.
    Error in if (z[h, 1] == names(object@specs)[speciesA]) d[h, 1] <- 1 else if (z[h, :
     argument is of length zero
    Calls: HeatMapFeeding -> HeatMapFeeding
    Execution halted
Flavors: r-devel-linux-x86_64-debian-clang, r-devel-linux-x86_64-debian-gcc, r-patched-linux-x86_64

Version: 1.8.1
Check: re-building of vignette outputs
Result: WARN
    Error(s) in re-building vignettes:
     ...
    --- re-building 'BacArena-Introduction.Rmd' using rmarkdown
    Loading required package: sybil
    Loading required package: Matrix
    Loading required package: lattice
    Loading required package: ReacTran
    Loading required package: rootSolve
    Loading required package: deSolve
    Loading required package: shape
    BacArena paper: https://doi.org/10.1371/journal.pcbi.1005544
     Tutorials: https://bacarena.github.io
     Model import from SBML: https://github.com/euba/BacArena/wiki/Model-import
     Development and help: https://github.com/euba/bacarena
    Warning in simEnv(arena, time = 10) :
     If growth is limited by maximum weight for an organism (max_weight=TRUE) it is recommended to use minimize total flux (sec_obj='mtf').
    Quitting from lines 231-232 (BacArena-Introduction.Rmd)
    Error: processing vignette 'BacArena-Introduction.Rmd' failed with diagnostics:
    Faceting variables must have at least one value
    --- failed re-building 'BacArena-Introduction.Rmd'
    
    SUMMARY: processing the following file failed:
     'BacArena-Introduction.Rmd'
    
    Error: Vignette re-building failed.
    Execution halted
Flavors: r-devel-linux-x86_64-debian-clang, r-devel-linux-x86_64-debian-gcc, r-patched-linux-x86_64, r-patched-osx-x86_64

Version: 1.8.1
Check: installed package size
Result: NOTE
     installed size is 9.0Mb
     sub-directories of 1Mb or more:
     R 1.2Mb
     data 3.3Mb
     libs 3.8Mb
Flavors: r-devel-linux-x86_64-fedora-clang, r-devel-windows-ix86+x86_64, r-devel-windows-ix86+x86_64-gcc8, 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: 1.8.1
Check: dependencies in R code
Result: NOTE
    Namespace in Imports field not imported from: ‘glpkAPI’
     All declared Imports should be used.
Flavors: r-devel-linux-x86_64-fedora-clang, r-devel-linux-x86_64-fedora-gcc, r-patched-osx-x86_64, r-patched-solaris-x86, r-release-osx-x86_64, r-oldrel-osx-x86_64

Version: 1.8.1
Check: examples
Result: ERROR
    Running examples in ‘BacArena-Ex.R’ failed
    The error most likely occurred in:
    
    > ### Name: HeatMapFeeding
    > ### Title: Function for plotting heatmap of feeding between two selected
    > ### cell models
    > ### Aliases: HeatMapFeeding HeatMapFeeding,Eval-method
    >
    > ### ** Examples
    >
    > sim <- sihumi_test
    > HeatMapFeeding(object = sim, speciesA = 1, speciesB = 2, var_nr = 78)
    Warning in BacArena::findFeeding3(object, time = t, mets = A$sub[1:var_nr], :
     sim_step 1 : No crossfeeding found. Try other metaboites or time points.
    Warning in BacArena::findFeeding3(object, time = t, mets = A$sub[1:var_nr], :
     sim_step 2 : No crossfeeding found. Try other metaboites or time points.
    Warning in BacArena::findFeeding3(object, time = t, mets = A$sub[1:var_nr], :
     sim_step 3 : No crossfeeding found. Try other metaboites or time points.
    Warning in BacArena::findFeeding3(object, time = t, mets = A$sub[1:var_nr], :
     sim_step 4 : No crossfeeding found. Try other metaboites or time points.
    Warning in BacArena::findFeeding3(object, time = t, mets = A$sub[1:var_nr], :
     sim_step 5 : No crossfeeding found. Try other metaboites or time points.
    Warning in BacArena::findFeeding3(object, time = t, mets = A$sub[1:var_nr], :
     sim_step 6 : No crossfeeding found. Try other metaboites or time points.
    Warning in BacArena::findFeeding3(object, time = t, mets = A$sub[1:var_nr], :
     sim_step 7 : No crossfeeding found. Try other metaboites or time points.
    Error in if (z[h, 1] == names(object@specs)[speciesA]) d[h, 1] <- 1 else if (z[h, :
     argument is of length zero
    Calls: HeatMapFeeding -> HeatMapFeeding
    Execution halted
Flavors: r-devel-linux-x86_64-fedora-clang, r-devel-linux-x86_64-fedora-gcc, r-patched-osx-x86_64, r-patched-solaris-x86

Version: 1.8.1
Check: re-building of vignette outputs
Result: WARN
    Error(s) in re-building vignettes:
    --- re-building ‘BacArena-Introduction.Rmd’ using rmarkdown
    Loading required package: sybil
    Loading required package: Matrix
    Loading required package: lattice
    Loading required package: ReacTran
    Loading required package: rootSolve
    Loading required package: deSolve
    Loading required package: shape
    BacArena paper: https://doi.org/10.1371/journal.pcbi.1005544
     Tutorials: https://bacarena.github.io
     Model import from SBML: https://github.com/euba/BacArena/wiki/Model-import
     Development and help: https://github.com/euba/bacarena
    Warning in simEnv(arena, time = 10) :
     If growth is limited by maximum weight for an organism (max_weight=TRUE) it is recommended to use minimize total flux (sec_obj='mtf').
    Quitting from lines 231-232 (BacArena-Introduction.Rmd)
    Error: processing vignette 'BacArena-Introduction.Rmd' failed with diagnostics:
    Faceting variables must have at least one value
    --- failed re-building ‘BacArena-Introduction.Rmd’
    
    SUMMARY: processing the following file failed:
     ‘BacArena-Introduction.Rmd’
    
    Error: Vignette re-building failed.
    Execution halted
Flavors: r-devel-linux-x86_64-fedora-clang, r-devel-linux-x86_64-fedora-gcc, r-devel-windows-ix86+x86_64, r-devel-windows-ix86+x86_64-gcc8

Version: 1.8.1
Check: running examples for arch ‘i386’
Result: ERROR
    Running examples in 'BacArena-Ex.R' failed
    The error most likely occurred in:
    
    > ### Name: HeatMapFeeding
    > ### Title: Function for plotting heatmap of feeding between two selected
    > ### cell models
    > ### Aliases: HeatMapFeeding HeatMapFeeding,Eval-method
    >
    > ### ** Examples
    >
    > sim <- sihumi_test
    > HeatMapFeeding(object = sim, speciesA = 1, speciesB = 2, var_nr = 78)
    Warning in BacArena::findFeeding3(object, time = t, mets = A$sub[1:var_nr], :
     sim_step 1 : No crossfeeding found. Try other metaboites or time points.
    Warning in BacArena::findFeeding3(object, time = t, mets = A$sub[1:var_nr], :
     sim_step 2 : No crossfeeding found. Try other metaboites or time points.
    Warning in BacArena::findFeeding3(object, time = t, mets = A$sub[1:var_nr], :
     sim_step 3 : No crossfeeding found. Try other metaboites or time points.
    Warning in BacArena::findFeeding3(object, time = t, mets = A$sub[1:var_nr], :
     sim_step 4 : No crossfeeding found. Try other metaboites or time points.
    Warning in BacArena::findFeeding3(object, time = t, mets = A$sub[1:var_nr], :
     sim_step 5 : No crossfeeding found. Try other metaboites or time points.
    Warning in BacArena::findFeeding3(object, time = t, mets = A$sub[1:var_nr], :
     sim_step 6 : No crossfeeding found. Try other metaboites or time points.
    Warning in BacArena::findFeeding3(object, time = t, mets = A$sub[1:var_nr], :
     sim_step 7 : No crossfeeding found. Try other metaboites or time points.
    Error in if (z[h, 1] == names(object@specs)[speciesA]) d[h, 1] <- 1 else if (z[h, :
     argument is of length zero
    Calls: HeatMapFeeding -> HeatMapFeeding
    Execution halted
Flavors: r-devel-windows-ix86+x86_64, r-devel-windows-ix86+x86_64-gcc8

Version: 1.8.1
Check: running examples for arch ‘x64’
Result: ERROR
    Running examples in 'BacArena-Ex.R' failed
    The error most likely occurred in:
    
    > ### Name: HeatMapFeeding
    > ### Title: Function for plotting heatmap of feeding between two selected
    > ### cell models
    > ### Aliases: HeatMapFeeding HeatMapFeeding,Eval-method
    >
    > ### ** Examples
    >
    > sim <- sihumi_test
    > HeatMapFeeding(object = sim, speciesA = 1, speciesB = 2, var_nr = 78)
    Warning in BacArena::findFeeding3(object, time = t, mets = A$sub[1:var_nr], :
     sim_step 1 : No crossfeeding found. Try other metaboites or time points.
    Warning in BacArena::findFeeding3(object, time = t, mets = A$sub[1:var_nr], :
     sim_step 2 : No crossfeeding found. Try other metaboites or time points.
    Warning in BacArena::findFeeding3(object, time = t, mets = A$sub[1:var_nr], :
     sim_step 3 : No crossfeeding found. Try other metaboites or time points.
    Warning in BacArena::findFeeding3(object, time = t, mets = A$sub[1:var_nr], :
     sim_step 4 : No crossfeeding found. Try other metaboites or time points.
    Warning in BacArena::findFeeding3(object, time = t, mets = A$sub[1:var_nr], :
     sim_step 5 : No crossfeeding found. Try other metaboites or time points.
    Warning in BacArena::findFeeding3(object, time = t, mets = A$sub[1:var_nr], :
     sim_step 6 : No crossfeeding found. Try other metaboites or time points.
    Warning in BacArena::findFeeding3(object, time = t, mets = A$sub[1:var_nr], :
     sim_step 7 : No crossfeeding found. Try other metaboites or time points.
    Error in if (z[h, 1] == names(object@specs)[speciesA]) d[h, 1] <- 1 else if (z[h, :
     argument is of length zero
    Calls: HeatMapFeeding -> HeatMapFeeding
    Execution halted
Flavors: r-devel-windows-ix86+x86_64, r-devel-windows-ix86+x86_64-gcc8

Version: 1.8.1
Check: re-building of vignette outputs
Result: WARN
    Error(s) in re-building vignettes:
     ...
    --- re-building ‘BacArena-Introduction.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.
    Loading required package: sybil
    Loading required package: Matrix
    Loading required package: lattice
    Loading required package: ReacTran
    Loading required package: rootSolve
    Loading required package: deSolve
    Loading required package: shape
    BacArena paper: https://doi.org/10.1371/journal.pcbi.1005544
     Tutorials: https://bacarena.github.io
     Model import from SBML: https://github.com/euba/BacArena/wiki/Model-import
     Development and help: https://github.com/euba/bacarena
    Warning in simEnv(arena, time = 10) :
     If growth is limited by maximum weight for an organism (max_weight=TRUE) it is recommended to use minimize total flux (sec_obj='mtf').
    Quitting from lines 231-232 (BacArena-Introduction.Rmd)
    Error: processing vignette 'BacArena-Introduction.Rmd' failed with diagnostics:
    Faceting variables must have at least one value
    --- failed re-building ‘BacArena-Introduction.Rmd’
    
    SUMMARY: processing the following file failed:
     ‘BacArena-Introduction.Rmd’
    
    Error: Vignette re-building failed.
    Execution halted
Flavor: r-patched-solaris-x86