CRAN Package Check Results for Package sybil

Last updated on 2015-04-19 17:48:51.

Flavor Version Tinstall Tcheck Ttotal Status Flags
r-devel-linux-x86_64-debian-clang 1.2.6 6.53 104.71 111.24 NOTE
r-devel-linux-x86_64-debian-gcc 1.2.6 6.46 101.98 108.44 NOTE
r-devel-linux-x86_64-fedora-clang 1.2.6 231.83 NOTE
r-devel-linux-x86_64-fedora-gcc 1.2.6 218.36 NOTE
r-devel-osx-x86_64-clang 1.2.6 237.43 NOTE
r-devel-windows-ix86+x86_64 1.2.6 28.00 164.00 192.00 NOTE
r-patched-linux-x86_64 1.2.6 6.53 103.40 109.93 NOTE
r-patched-solaris-sparc 1.2.6 1353.20 NOTE
r-patched-solaris-x86 1.2.6 303.30 NOTE
r-release-linux-x86_64 1.2.6 6.40 128.86 135.26 NOTE
r-release-osx-x86_64-mavericks 1.2.6 ERROR
r-release-osx-x86_64-snowleopard 1.2.6 NOTE
r-release-windows-ix86+x86_64 1.2.6 13.00 161.00 174.00 NOTE
r-oldrel-windows-ix86+x86_64 1.2.6 20.00 186.00 206.00 NOTE

Check Details

Version: 1.2.6
Check: dependencies in R code
Result: NOTE
    'library' or 'require' call to ‘parallel’ in package code.
     Please use :: or requireNamespace() instead.
     See section 'Suggested packages' in the 'Writing R Extensions' manual.
Flavors: r-devel-linux-x86_64-debian-clang, r-devel-linux-x86_64-debian-gcc, r-devel-linux-x86_64-fedora-clang, r-devel-linux-x86_64-fedora-gcc, r-devel-osx-x86_64-clang, r-devel-windows-ix86+x86_64, r-patched-linux-x86_64, r-patched-solaris-sparc, r-patched-solaris-x86, r-release-linux-x86_64, r-release-osx-x86_64-mavericks, r-release-osx-x86_64-snowleopard, r-release-windows-ix86+x86_64, r-oldrel-windows-ix86+x86_64

Version: 1.2.6
Check: package dependencies
Result: NOTE
    Package suggested but not available for checking: ‘cplexAPI’
Flavors: r-devel-linux-x86_64-fedora-clang, r-devel-linux-x86_64-fedora-gcc, r-devel-osx-x86_64-clang, r-devel-windows-ix86+x86_64, r-patched-solaris-sparc, r-patched-solaris-x86, r-release-windows-ix86+x86_64, r-oldrel-windows-ix86+x86_64

Version: 1.2.6
Check: package dependencies
Result: NOTE
    Packages suggested but not available for checking:
     ‘glpkAPI’ ‘cplexAPI’ ‘clpAPI’
Flavor: r-release-osx-x86_64-mavericks

Version: 1.2.6
Check: Rd cross-references
Result: NOTE
    Package unavailable to check Rd xrefs: ‘glpkAPI’
Flavor: r-release-osx-x86_64-mavericks

Version: 1.2.6
Check: examples
Result: ERROR
    Running examples in ‘sybil-Ex.R’ failed
    The error most likely occurred in:
    
    > ### Name: SYBIL_SETTINGS
    > ### Title: Set and Get sybil Parameters
    > ### Aliases: SYBIL_SETTINGS SOLVER METHOD TOLERANCE MAXIMUM ALGORITHM
    > ### OPT_DIRECTION USE_NAMES PATH_TO_MODEL SOLVER_CTRL_PARM
    > ### Keywords: optimize
    >
    > ### ** Examples
    >
    > ## show all current parameters
    > SYBIL_SETTINGS()
    $SOLVER
    [1] "glpkAPI"
    
    $METHOD
    [1] "simplex"
    
    $TOLERANCE
    [1] 1e-06
    
    $MAXIMUM
    [1] 1000
    
    $ALGORITHM
    [1] "fba"
    
    $OPT_DIRECTION
    [1] "max"
    
    $USE_NAMES
    [1] FALSE
    
    $PATH_TO_MODEL
    [1] "."
    
    $SOLVER_CTRL_PARM
     NA
    1 NA
    
    >
    > ## show current setting for "SOLVER"
    > SYBIL_SETTINGS("SOLVER")
    [1] "glpkAPI"
    >
    > ## change current solver to glpkAPI
    > SYBIL_SETTINGS("SOLVER", "glpkAPI")
    Loading required package: glpkAPI
    Warning in library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE, :
     there is no package called ‘glpkAPI’
    Error in checkDefaultMethod(solver = value, method = "", probType = "", :
     package ‘glpkAPI’ not found
    Calls: SYBIL_SETTINGS -> checkDefaultMethod
    Execution halted
Flavor: r-release-osx-x86_64-mavericks

Version: 1.2.6
Check: running R code from vignettes
Result: WARN
    Errors in running code in vignettes:
    when running code in ‘sybil.Rnw’
     ...
    number of exchange reactions: 20
    
    > optL <- optimizeProb(Ec_core, algorithm = "fba", retOptSol = FALSE)
    Loading required package: glpkAPI
    Warning in library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE, :
     there is no package called ‘glpkAPI’
    
     When sourcing ‘sybil.R’:
    Error: package ‘glpkAPI’ not found
    Execution halted
Flavor: r-release-osx-x86_64-mavericks

Version: 1.2.6
Check: re-building of vignette outputs
Result: NOTE
    Error in re-building vignettes:
     ...
    sybil::fluxVar Flux Variability Analysis
    
    
    Type '?PKG::FOO' to inspect entries 'PKG::FOO', or 'TYPE?PKG::FOO' for
    entries like 'PKG::FOO-TYPE'.
    
    
    
    
    reading model description, ... OK
    reading metabolite list ... OK
    parsing reaction list ... OK
    GPR mapping ... OK
    sub systems ... OK
    prepare modelorg object ... OK
    validating object ... OK
    Loading required package: glpkAPI
    Warning in library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE, :
     there is no package called ‘glpkAPI’
    
    Error: processing vignette 'sybil.Rnw' failed with diagnostics:
     chunk 13
    Error in checkDefaultMethod(solver, method, pType) :
     package ‘glpkAPI’ not found
    Execution halted
Flavor: r-release-osx-x86_64-mavericks

Version: 1.2.6
Check: package dependencies
Result: NOTE
    Packages suggested but not available for checking: ‘cplexAPI’ ‘clpAPI’
Flavor: r-release-osx-x86_64-snowleopard