CRAN Package Check Results for Package nCal

Last updated on 2014-10-22 04:47:20.

Flavor Version Tinstall Tcheck Ttotal Status Flags
r-devel-linux-x86_64-debian-clang 13.12-01 2.25 63.14 65.39 NOTE
r-devel-linux-x86_64-debian-gcc 13.12-01 2.01 63.17 65.18 NOTE
r-devel-linux-x86_64-fedora-clang 13.12-01 136.58 NOTE
r-devel-linux-x86_64-fedora-gcc 13.12-01 131.06 NOTE
r-devel-osx-x86_64-clang 13.12-01 117.86 NOTE
r-devel-windows-ix86+x86_64 13.12-01 8.00 92.00 100.00 NOTE
r-patched-linux-x86_64 13.12-01 2.07 64.58 66.65 NOTE
r-patched-solaris-sparc 13.12-01 2054.60 NOTE
r-patched-solaris-x86 13.12-01 1931.00 ERROR
r-release-linux-ix86 13.12-01 2.61 87.46 90.06 NOTE
r-release-linux-x86_64 13.12-01 2.16 68.16 70.32 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 9.00 97.00 106.00 NOTE
r-oldrel-windows-ix86+x86_64 13.12-01 9.00 107.00 116.00 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: 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’
    drm.fit: no visible global function definition for ‘drmc’
    drm.fit: no visible global function definition for ‘drm’
    drm.fit: no visible global function definition for ‘LL.5’
    drm.fit: no visible global function definition for ‘LL.4’
    ncalGUI: no visible global function definition for ‘gwindow’
    ncalGUI: no visible global function definition for ‘glabel’
    ncalGUI: no visible global function definition for ‘ggroup’
    ncalGUI: no visible global function definition for ‘gfilebrowse’
    ncalGUI: no visible global function definition for ‘gradio’
    ncalGUI: no visible global function definition for ‘gedit’
    ncalGUI: no visible global function definition for ‘svalue<-’
    ncalGUI : <anonymous>: no visible global function definition for
     ‘svalue<-’
    ncalGUI : <anonymous>: no visible global function definition for
     ‘svalue’
    ncalGUI : call.getConc.fun: no visible global function definition for
     ‘enabled<-’
    ncalGUI : call.getConc.fun: no visible global function definition for
     ‘svalue<-’
    ncalGUI : call.getConc.fun: no visible global function definition for
     ‘dispose’
    ncalGUI : call.getConc.fun: no visible global function definition for
     ‘svalue’
    ncalGUI : call.getConc.fun: no visible global function definition for
     ‘gwindow’
    ncalGUI : call.getConc.fun: no visible global function definition for
     ‘gtext’
    ncalGUI : call.getConc.fun: no visible global function definition for
     ‘insert’
    ncalGUI : call.getConc.fun: no visible global function definition for
     ‘visible<-’
    ncalGUI : update.status.fun: no visible global function definition for
     ‘svalue’
    ncalGUI : update.status.fun: no visible global function definition for
     ‘enabled<-’
    ncalGUI : update.status.fun: no visible global function definition for
     ‘svalue<-’
    ncalGUI: no visible global function definition for ‘addSpring’
    ncalGUI: no visible global function definition for ‘gbutton’
    ncalGUI: no visible global function definition for ‘addSpace’
    ncalGUI: no visible global function definition for ‘enabled<-’
    ncalGUI.2: no visible global function definition for ‘gwindow’
    ncalGUI.2: no visible global function definition for ‘gstatusbar’
    ncalGUI.2: no visible global function definition for ‘ggroup’
    ncalGUI.2: no visible global function definition for ‘glabel’
    ncalGUI.2: no visible global function definition for ‘gfilebrowse’
    ncalGUI.2: no visible global function definition for ‘gedit’
    ncalGUI.2: no visible global function definition for ‘gradio’
    ncalGUI.2 : update.status.fun: no visible global function definition
     for ‘svalue’
    ncalGUI.2 : update.status.fun: no visible global function definition
     for ‘svalue<-’
    ncalGUI.2 : process.fun: no visible global function definition for
     ‘svalue’
    ncalGUI.2 : process.fun: no visible global function definition for
     ‘svalue<-’
    ncalGUI.2 : process.fun: no visible global function definition for
     ‘dispose’
    ncalGUI.2 : process.fun: no visible global function definition for
     ‘gwindow’
    ncalGUI.2 : process.fun: no visible global function definition for
     ‘gedit’
    ncalGUI.2 : process.fun: no visible global function definition for
     ‘addHandlerChanged’
    ncalGUI.2: no visible global function definition for ‘svalue<-’
    ncalGUI.2: no visible global function definition for
     ‘addHandlerChanged’
    ncalGUI.2: no visible global function definition for ‘addSpring’
    ncalGUI.2: no visible global function definition for ‘gbutton’
    ncalGUI.2: no visible global function definition for ‘addSpace’
    ncalGUI.2 : <anonymous>: no visible global function definition for
     ‘dispose’
    read.luminex.fixed.sheet.xls: no visible global function definition for
     ‘xls2sep’
    read.luminex.sheet.xls: no visible global function definition for
     ‘xls2sep’
    read.luminex.xls: no visible global function definition for
     ‘sheetNames’
    ss.fct.via.LL4: no visible global function definition for ‘drm’
    ss.fct.via.LL4: no visible global function definition for ‘LL.4’
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

Version: 13.12-01
Check: examples
Result: ERROR
    Running examples in ‘nCal-Ex.R’ failed
    The error most likely occurred in:
    
    > ### Name: ncal
    > ### Title: Main function for the nCal package
    > ### Aliases: nCal ncal rumi ncal.formula ncal.character ncalGUI
    > ### Keywords: distribution
    >
    > ### ** Examples
    >
    >
    > #begin=Sys.time()
    >
    > # basic example
    >
    > # simulate a dataset
    > 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=0.2)
    > dat.std=data.frame(fi, expected_conc=exp(rep(log.conc,each=n.replicate)), analyte="Test",
    + assay_id="Run 1", sample_id=NA, well_role="Standard", dilution=rep(3**(9:0), each=n.replicate),
    + replicate=rep(1:n.replicate, 10))
    > # add unknown
    > dat.unk=rbind(
    + data.frame(fi=exp(6.75), expected_conc=NA, analyte="Test", assay_id="Run 1", sample_id=1,
    + well_role="Unknown", dilution=1, replicate=1)
    + , data.frame(fi=exp(6.70), expected_conc=NA, analyte="Test", assay_id="Run 1", sample_id=2,
    + well_role="Unknown", dilution=1, replicate=1)
    + , data.frame(fi=exp(3), expected_conc=NA, analyte="Test", assay_id="Run 1", sample_id=3,
    + well_role="Unknown", dilution=1, replicate=1)
    + , data.frame(fi=exp(4.4), expected_conc=NA, analyte="Test", assay_id="Run 1", sample_id=4,
    + well_role="Unknown", dilution=10, replicate=1)
    + )
    > dat=rbind(dat.std, dat.unk)
    >
    >
    > # does drm fit
    > out = ncal(log(fi)~expected_conc, dat, return.fits = TRUE, plot.se.profile=TRUE)
    > fit=attr(out, "fits")[[1]]
    >
    > # does jags fit and collect 1e5 posterior samples, it may be better to set n.iter higher
    > out.norm = ncal(log(fi)~expected_conc, dat, bcrm.fit=TRUE, bcrm.model="norm",
    + return.fits = TRUE, plot.se.profile=TRUE,
    + control.jags=list(n.iter=1e5), n.iter=1e4, verbose=FALSE)
    Loading required package: rjags
    Loading required package: coda
    Loading required package: lattice
    Linked to JAGS 3.4.0
    Loaded modules: basemod,bugs
     Running jags
Flavor: r-patched-solaris-x86

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