CRAN Package Check Results for Package nCal

Last updated on 2017-07-31 01:47:07.

Check Details

Version: 2016.7-31
Check: package dependencies
Result: NOTE
    Package suggested but not available for checking: ‘rjags’
Flavor: r-release-osx-x86_64

Version: 2016.7-31
Check: examples
Result: ERROR
    Running examples in ‘nCal-Ex.R’ failed
    The error most likely occurred in:
    
    > ### Name: bcrm
    > ### Title: Bayesian Concentration-Response Model
    > ### Aliases: bcrm getVarComponent.bcrm vcov.bcrm coef.bcrm plot.bcrm
    > ### print.bcrm get.single.fit
    > ### Keywords: distribution
    >
    > ### ** Examples
    >
    >
    >
    > set.seed(1)
    > log.conc=log(1e4)-log(3)*9:0
    > n.replicate=2
    > fi=simulate1curve (p.eotaxin[1,], rep(log.conc,each=n.replicate), sd.e=0.3)
    > dat.std=data.frame(fi, expected_conc=exp(rep(log.conc,each=n.replicate)), analyte="test",
    + assay_id="assay1", sample_id=NA, well_role="Standard", dilution=rep(3**(9:0), each=n.replicate))
    > # add unknown
    > dat.unk=rbind(
    + data.frame(fi=exp(6.75), expected_conc=NA, analyte="test", assay_id="assay1",
    + sample_id=1, well_role="Unknown", dilution=1)
    + , data.frame(fi=exp(6.70), expected_conc=NA, analyte="test", assay_id="assay1",
    + sample_id=2, well_role="Unknown", dilution=1)
    + , data.frame(fi=exp(3), expected_conc=NA, analyte="test", assay_id="assay1",
    + sample_id=3, well_role="Unknown", dilution=1)
    + , data.frame(fi=exp(4.4), expected_conc=NA, analyte="test", assay_id="assay1",
    + sample_id=4, well_role="Unknown", dilution=10)
    + )
    > dat=rbind(dat.std, dat.unk)
    > # second plate
    > fi=simulate1curve (p.eotaxin[2,], rep(log.conc,each=n.replicate), sd.e=0.3)
    > dat.std=data.frame(fi, expected_conc=exp(rep(log.conc,each=n.replicate)), analyte="test",
    + assay_id="assay2", sample_id=NA, well_role="Standard", dilution=rep(3**(9:0), each=n.replicate))
    > # add unknown
    > dat.unk=rbind(
    + data.frame(fi=exp(6.75), expected_conc=NA, analyte="test", assay_id="assay2",
    + sample_id=1, well_role="Unknown", dilution=1)
    + , data.frame(fi=exp(6.70), expected_conc=NA, analyte="test", assay_id="assay2",
    + sample_id=2, well_role="Unknown", dilution=1)
    + , data.frame(fi=exp(3), expected_conc=NA, analyte="test", assay_id="assay2",
    + sample_id=3, well_role="Unknown", dilution=1)
    + , data.frame(fi=exp(4.4), expected_conc=NA, analyte="test", assay_id="assay2",
    + sample_id=4, well_role="Unknown", dilution=10)
    + )
    > dat=rbind(dat, dat.std, dat.unk)
    >
    > fits = bcrm(log(fi)~expected_conc, dat, parameterization="gh", error.model="norm",
    + prior="cytokine", n.iter=6e3)
    Error in loadNamespace(name) : there is no package called ‘rjags’
    [1] "jags.model fails, try with a different seed"
    Error in loadNamespace(name) : there is no package called ‘rjags’
    [1] "jags.model fails, try with a different seed"
    Error in loadNamespace(name) : there is no package called ‘rjags’
    [1] "jags.model fails, try with a different seed"
    > par(mfrow=c(1,2))
    > plot(fits)
    Error in plot.window(...) : need finite 'xlim' values
    Calls: plot -> plot.default -> localWindow -> plot.window
    In addition: Warning messages:
    1: In min(x) : no non-missing arguments to min; returning Inf
    2: In max(x) : no non-missing arguments to max; returning -Inf
    3: In min(x) : no non-missing arguments to min; returning Inf
    4: In max(x) : no non-missing arguments to max; returning -Inf
    Execution halted
Flavor: r-release-osx-x86_64

Version: 2016.7-31
Check: tests
Result: ERROR
     Running ‘doRUnit.R’ [14s/21s]
    Running the tests in ‘tests/doRUnit.R’ failed.
    Last 13 lines of output:
     Number of failures: 1
    
    
     1 Test Suite :
     nCal unit testing - 3 test functions, 2 errors, 1 failure
     ERROR in test.5PL: Error in 0:(ncol(single.fit$coefficients) - 1) : argument of length 0
     FAILURE in test.bcrm: Error in checkEqualsNumeric(mean(fits$median.coef), 4.01789, tolerance = tolerance.jags) :
     'is.NA' value mismatch: 0 in current 1 in target
    
     ERROR in test.ncal: Error in 0:(ncol(single.fit$coefficients) - 1) : argument of length 0
     Error:
    
     unit testing failed (#test failures: 1, #R errors: 2)
    
     Execution halted
Flavor: r-release-osx-x86_64

Version: 2016.7-31
Check: re-building of vignette outputs
Result: WARN
    Error in re-building vignettes:
     ...
    Warning: running command 'kpsewhich framed.sty' had status 1
    Warning in test_latex_pkg("framed", system.file("misc", "framed.sty", package = "knitr")) :
     unable to find LaTeX package 'framed'; will use a copy from knitr
    Error in loadNamespace(name) : there is no package called 'rjags'
    Error in loadNamespace(name) : there is no package called 'rjags'
    Error in loadNamespace(name) : there is no package called 'rjags'
    Quitting from lines 100-102 (nCal-vignette.Rnw)
    Error: processing vignette 'nCal-vignette.Rnw' failed with diagnostics:
    argument of length 0
    Execution halted
Flavor: r-release-osx-x86_64

Version: 2016.7-31
Check: for code/documentation mismatches
Result: FAIL
    Check process probably crashed or hung up for 20 minutes ... killed
    Most likely this happened in the example checks (?),
    if not, ignore the following last lines of example output:
    
    ======== End of example output (where/before crash/hang up occured ?) ========
Flavor: r-oldrel-windows-ix86+x86_64