CRAN Package Check Results for Package nCal

Last updated on 2017-08-21 11:47:52.

Flavor Version Tinstall Tcheck Ttotal Status Flags
r-devel-linux-x86_64-debian-clang 2016.7-31 4.88 95.80 100.69 OK
r-devel-linux-x86_64-debian-gcc 2016.7-31 4.56 94.03 98.58 OK
r-devel-linux-x86_64-fedora-clang 2016.7-31 204.46 OK
r-devel-linux-x86_64-fedora-gcc 2016.7-31 201.75 OK
r-devel-windows-ix86+x86_64 2016.7-31 15.00 141.00 156.00 OK
r-patched-linux-x86_64 2016.7-31 4.69 93.74 98.43 OK
r-patched-solaris-x86 2016.7-31 255.30 OK
r-release-linux-x86_64 2016.7-31 4.88 95.13 100.01 OK
r-release-windows-ix86+x86_64 2016.7-31 20.00 147.00 167.00 OK
r-release-osx-x86_64 2016.7-31 ERROR
r-oldrel-windows-ix86+x86_64 2016.7-31 13.00 129.00 142.00 OK
r-oldrel-osx-x86_64 2016.7-31 OK

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