CRAN Package Check Results for Package nCal

Last updated on 2014-07-29 03:48:42.

Flavor Version Tinstall Tcheck Ttotal Status Flags
r-devel-linux-x86_64-debian-clang 13.12-01 2.19 68.09 70.28 NOTE
r-devel-linux-x86_64-debian-gcc 13.12-01 2.07 66.84 68.91 NOTE
r-devel-linux-x86_64-fedora-clang 13.12-01 150.23 NOTE
r-devel-linux-x86_64-fedora-gcc 13.12-01 137.68 NOTE
r-devel-osx-x86_64-clang 13.12-01 119.23 NOTE
r-devel-windows-ix86+x86_64 13.12-01 9.00 97.00 106.00 NOTE
r-patched-linux-x86_64 13.12-01 2.02 66.57 68.59 NOTE
r-patched-solaris-sparc 13.12-01 942.90 NOTE
r-patched-solaris-x86 13.12-01 289.50 NOTE
r-release-linux-ix86 13.12-01 2.60 88.18 90.77 NOTE
r-release-linux-x86_64 13.12-01 2.10 67.45 69.55 NOTE
r-release-osx-x86_64-mavericks 13.12-01 ERROR
r-release-osx-x86_64-snowleopard 13.12-01 OK
r-release-windows-ix86+x86_64 13.12-01 8.00 105.00 113.00 NOTE
r-oldrel-windows-ix86+x86_64 13.12-01 8.00 106.00 114.00 NOTE

Check Details

Version: 13.12-01
Check: dependencies in R code
Result: NOTE
    Packages in Depends field not imported from:
     drc gWidgets gdata
     These packages need to be imported from (in the NAMESPACE file)
     for when this namespace is loaded but not attached.
    See the information on DESCRIPTION files in the chapter Creating R
    packages of 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-ix86, r-release-linux-x86_64, r-release-osx-x86_64-mavericks, r-release-windows-ix86+x86_64, r-oldrel-windows-ix86+x86_64

Version: 13.12-01
Check: package dependencies
Result: NOTE
    Package suggested but not available for checking: rjags
Flavor: r-release-osx-x86_64-mavericks

Version: 13.12-01
Check: R code for possible problems
Result: NOTE
    bcrm: no visible global function definition for jags.model
    bcrm: no visible global function definition for coda.samples
Flavor: r-release-osx-x86_64-mavericks

Version: 13.12-01
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 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, error.model="gh_norm", informative.prior=TRUE, n.iter=1e4)
    Loading required package: rjags
    Warning in library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE, :
     there is no package called rjags
    Error in bcrm(log(fi) ~ expected_conc, dat, error.model = "gh_norm", informative.prior = TRUE, :
     rjags does not load successfully. Is JAGS installed?
    Execution halted
Flavor: r-release-osx-x86_64-mavericks