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chemosensors log file (check_x86_64_linux)

Wed Mar  2 16:05:19 2016: Checking package chemosensors (SVN revision 55) ...
* using log directory ‘/mnt/building/build_2016-03-02-16-04/RF_PKG_CHECK/PKGS/chemosensors.Rcheck’
* using R version 3.2.4 beta (2016-03-01 r70257)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--as-cran’
* checking for file ‘chemosensors/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘chemosensors’ version ‘0.7.11’
* checking CRAN incoming feasibility ... NOTE
Maintainer: ‘Andrey Ziyatdinov ’
New submission

Package was archived on CRAN

CRAN repository db overrides:
  X-CRAN-Comment: Archived on 2016-01-27 as check problems were not
    corrected despite reminders.

No package encoding and non-ASCII characters in the following R files:
  R/ScenarioClass.R
    88:     # dummy assignment to get rid of errors from 'R CMD check' (no visible binding for global variable <80><98>label<80><99>)
  R/ScenarioClassMethods.R
    623:   # dummy assignment to get rid of errors from 'R CMD check' (no visible binding for global variable <80><98>gas<80><99>)
  R/SensorDynamicsClassMethods.R
    147:   # dummy assignment to get rid of errors from 'R CMD check' (no visible binding for global variable <80><98>gas<80><99>)

The Description field should not start with the package name,
  'This package' or similar.
* checking package namespace information ... OK
* checking package dependencies ... NOTE
  No repository set, so cyclic dependency check skipped
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for executable files ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘chemosensors’ can be installed ... [3s/3s] OK
* checking installed package size ... OK
* checking package directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking loading without being on the library search path ... OK
* checking use of S3 registration ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd line widths ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... WARNING
Undocumented code objects:
  ‘affinity’ ‘alpha’ ‘beta’ ‘ccol’ ‘checkConc’ ‘cmatrix’ ‘coeffNonneg’
  ‘coefnames’ ‘computeAffinity’ ‘conc2col’ ‘conc2df’ ‘conc2glab’
  ‘conc2lab’ ‘conc2tpoint’ ‘concMax’ ‘concMin’ ‘concSample’
  ‘concSampleDyn’ ‘concUnits’ ‘concUnitsInt’ ‘concUnitsSorption’ ‘csd’
  ‘dsd’ ‘dspace’ ‘enableDyn’ ‘enableSorption’ ‘gases’ ‘gcol’ ‘getConc’
  ‘getSensor’ ‘getTPoint’ ‘gind’ ‘gnames’ ‘idx’ ‘knum’ ‘lab2df’
  ‘label2df’ ‘logf’ ‘mapcol’ ‘modelName’ ‘ncoef’ ‘nconst’ ‘ndcomp’
  ‘ndvar’ ‘ngases’ ‘noisef’ ‘nsamples’ ‘nsensors’ ‘num’ ‘plotAffinity’
  ‘plotAffinityMap’ ‘plotAffinitySpace’ ‘plotBox’ ‘plotMixture’
  ‘plotPCA’ ‘plotPolar’ ‘plotPolarGases’ ‘plotResponse’ ‘plotSignal’
  ‘plotTimeline’ ‘scol’ ‘sdata.frame’ ‘sdata2df’ ‘sdata2feature’
  ‘sdata2pulse’ ‘set2lab’ ‘snames’ ‘ssd’ ‘tconst’ ‘trange’ ‘tunit’
  ‘type’
All user-level objects in a package should have documentation entries.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... WARNING
Undocumented arguments in documentation object 'ConcNoiseModel-class'
  ‘x’ ‘.Object’ ‘gases’ ‘gnames’ ‘concUnits’ ‘concUnitsInt’ ‘csd’
  ‘cntype’ ‘cnlogf’ ‘nsd’
Objects in \usage without \alias in documentation object 'ConcNoiseModel-class':
  ‘logf’ ‘\S4method{initialize}{ConcNoiseModel}’

Undocumented arguments in documentation object 'DriftNoiseModel-class'
  ‘x’ ‘.Object’ ‘num’ ‘datasetDriftNoiseModel’ ‘pck’ ‘dsd’ ‘ndcomp’
  ‘ndvar’ ‘dmodel’ ‘nsd’
Objects in \usage without \alias in documentation object 'DriftNoiseModel-class':
  ‘ndcomp’ ‘ndvar’ ‘dspace’ ‘\S4method{initialize}{DriftNoiseModel}’

Undocumented arguments in documentation object 'Scenario-class'
  ‘.Object’ ‘T’ ‘nT’ ‘V’ ‘nV’ ‘tunit’ ‘randomize’ ‘name’ ‘gases’
  ‘gnames’ ‘concUnits’ ‘concUnitsInt’ ‘seed’
Objects in \usage without \alias in documentation object 'Scenario-class':
  ‘\S4method{initialize}{Scenario}’

Undocumented arguments in documentation object 'SensorArray-class'
  ‘object’ ‘index’ ‘concUnits’ ‘gases’ ‘type’ ‘n’ ‘.Object’
  ‘enableSorption’ ‘nsensors’ ‘gnames’ ‘concUnitsInt’
  ‘concUnitsIntSorption’ ‘knum’ ‘model’ ‘datasetSensorModel’
  ‘datasetDistr’ ‘datasetSensorNoiseModel’ ‘pck’ ‘Conc0’ ‘Conc’ ‘dat’
  ‘sndata’ ‘coefsd’
Objects in \usage without \alias in documentation object 'SensorArray-class':
  ‘getSensor’ ‘affinity’ ‘\S4method{initialize}{SensorArray}’

Undocumented arguments in documentation object 'SensorDynamics-class'
  ‘x’ ‘.Object’ ‘num’ ‘gases’ ‘gnames’ ‘concUnits’ ‘concUnitsInt’
  ‘tunit’ ‘ntconst’ ‘trange’
Objects in \usage without \alias in documentation object 'SensorDynamics-class':
  ‘nconst’ ‘trange’ ‘tconst’ ‘\S4method{initialize}{SensorDynamics}’

Undocumented arguments in documentation object 'SensorModel-class'
  ‘x’ ‘.Object’ ‘nsensors’ ‘num’ ‘gases’ ‘gnames’ ‘concUnits’
  ‘concUnitsInt’ ‘datasetSensorModel’ ‘datasetDistr’ ‘pck’ ‘coefsd’
  ‘model’ ‘coeffNonneg’ ‘coeffNonnegTransform’ ‘Conc0’ ‘Conc’ ‘dat’
  ‘tunit’ ‘beta’
Objects in \usage without \alias in documentation object 'SensorModel-class':
  ‘coeffNonneg’ ‘\S4method{initialize}{SensorModel}’

Undocumented arguments in documentation object 'SensorNoiseModel-class'
  ‘x’ ‘.Object’ ‘num’ ‘gases’ ‘gnames’ ‘concUnits’ ‘concUnitsInt’
  ‘datasetSensorNoiseModel’ ‘pck’ ‘ssd’ ‘sntype’ ‘snf’ ‘sndata’ ‘nsd’
Objects in \usage without \alias in documentation object 'SensorNoiseModel-class':
  ‘noisef’ ‘\S4method{initialize}{SensorNoiseModel}’

Undocumented arguments in documentation object 'SorptionModel-class'
  ‘x’ ‘.Object’ ‘gases’ ‘gnames’ ‘concUnits’ ‘concUnitsSorption’
  ‘datasetSorptionModel’ ‘pck’ ‘knum’ ‘srdata’ ‘Qequal’ ‘Knorm’ ‘Kmin’
  ‘Kmax’ ‘alpha’
Objects in \usage without \alias in documentation object 'SorptionModel-class':
  ‘knum’ ‘concUnitsSorption’ ‘\S4method{initialize}{SorptionModel}’

Undocumented arguments in documentation object 'class-methods'
  ‘x’ ‘...’
Objects in \usage without \alias in documentation object 'class-methods':
  ‘print’

Undocumented arguments in documentation object 'compute-methods'
  ‘object’ ‘method’ ‘norm’ ‘...’
Objects in \usage without \alias in documentation object 'compute-methods':
  ‘computeAffinity’

Undocumented arguments in documentation object 'get-methods'
  ‘x’ ‘object’ ‘...’ ‘sensor.names’ ‘type’
Objects in \usage without \alias in documentation object 'get-methods':
  ‘alpha’ ‘beta’ ‘modelName’ ‘tunit’ ‘enableSorption’ ‘enableDyn’ ‘num’
  ‘idx’ ‘gases’ ‘gind’ ‘ngases’ ‘gnames’ ‘coefficients’ ‘coef’
  ‘nsensors’ ‘snames’ ‘concUnits’ ‘concUnitsInt’ ‘type’ ‘coefnames’
  ‘ncoef’

Undocumented arguments in documentation object 'model-methods'
  ‘object’ ‘...’ ‘concUnits’ ‘type’ ‘n’ ‘gases’ ‘conc’ ‘sdata’ ‘set’
  ‘cf’ ‘coef’ ‘sensors’
Objects in \usage without \alias in documentation object 'model-methods':
  ‘concMin’ ‘concMax’ ‘concSample’ ‘concSampleDyn’ ‘predict’ ‘getConc’

Undocumented arguments in documentation object 'noise-methods'
  ‘x’ ‘object’ ‘value’
Objects in \usage without \alias in documentation object 'noise-methods':
  ‘csd’ ‘ssd’ ‘dsd’

Undocumented arguments in documentation object 'plot-methods'
  ‘x’ ‘y’ ‘...’ ‘conc’ ‘sdata’ ‘set’ ‘scenario’ ‘feature’ ‘air’ ‘mod’
  ‘center’ ‘scale’ ‘pc’ ‘object’ ‘polar’ ‘geom’ ‘main’ ‘xlab’ ‘ylab’
  ‘xlim’ ‘ylim’ ‘graphics’ ‘ret’ ‘concUnits’ ‘leg’ ‘lwd’ ‘lty’ ‘col’
  ‘bty’ ‘type’ ‘gases’ ‘n’ ‘las2’ ‘axes’ ‘nlevels’ ‘pal’ ‘start’ ‘end’
  ‘gamma’ ‘cf’ ‘sf’ ‘sensors’ ‘scales’ ‘gcol’ ‘sensor.names’ ‘idx’
  ‘sensor’ ‘gas’ ‘size’ ‘alpha’
Objects in \usage without \alias in documentation object 'plot-methods':
  ‘plot’ ‘plotPolar’ ‘plotPCA’ ‘plotBox’ ‘plotResponse’ ‘plotMixture’
  ‘plotSignal’ ‘plotPolarGases’ ‘plotTimeline’ ‘plotAffinity’
  ‘plotAffinityMap’ ‘plotAffinitySpace’ ‘ccol’ ‘gcol’ ‘scol’ ‘mapcol’

Undocumented arguments in documentation object 'scenario-methods'
  ‘x’ ‘...’ ‘object’ ‘conc’ ‘sdata’ ‘feature’ ‘df’ ‘unique’ ‘step’
  ‘lab’ ‘value’ ‘nsamples’ ‘pal’ ‘tpoint’ ‘cf’ ‘sf’
Objects in \usage without \alias in documentation object 'scenario-methods':
  ‘sdata.frame’ ‘nsamples’ ‘cmatrix’ ‘checkConc’ ‘sdata2feature’
  ‘sdata2df’ ‘conc2df’ ‘conc2lab’ ‘conc2glab’ ‘conc2col’ ‘getTPoint’
  ‘conc2tpoint’ ‘lab2df’ ‘label2df’ ‘set2lab’

Undocumented arguments in documentation object 'enableDyn<-'
  ‘object’ ‘value’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking examples ... ERROR
Running examples in ‘chemosensors-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: UNIMANsorption
> ### Title: Dataset UNIMANsorption.
> ### Aliases: UNIMANsorption
> ### Keywords: data
> 
> ### ** Examples
> 
> 
> data(UNIMANsorption, package="chemosensors")
> 
> # print the list of loaded data variables
> str(UNIMANsorption)
List of 1
 $ qkc: num [1:17, 1:3, 1:4] 10.02 9.51 9.52 6.57 9.19 ...
  ..- attr(*, "dimnames")=List of 3
  .. ..$ : chr [1:17] "1" "2" "3" "4" ...
  .. ..$ : chr [1:3] "A" "B" "C"
  .. ..$ : chr [1:4] "Q" "K" "KCmin" "KCmax"
> 
> dim(UNIMANsorption$qkc)
[1] 17  3  4
> 
> str(UNIMANsorption$qkc)
 num [1:17, 1:3, 1:4] 10.02 9.51 9.52 6.57 9.19 ...
 - attr(*, "dimnames")=List of 3
  ..$ : chr [1:17] "1" "2" "3" "4" ...
  ..$ : chr [1:3] "A" "B" "C"
  ..$ : chr [1:4] "Q" "K" "KCmin" "KCmax"
> 
> ### Langmuir parameter K
> K <- UNIMANsorption$qkc[, , "K"]
> 
> mf <- melt(K, varnames = c("sensor", "gas"))
> 
> p1 <- qplot(sensor, value, data = mf, geom = "line", color = gas) +
+   ylab("Langmuir parameter K")
> p1
> 
> p2 <- qplot(sensor, value, data = mf, geom = "bar", stat = "identity") + 
+   facet_grid(gas ~ ., scale = "free_y") + 
+   ylab("Langmuir parameter K")
Warning: `stat` is deprecated
> p2
Error: stat_count() must not be used with a y aesthetic.
Execution halted
* checking PDF version of manual ... OK
* DONE

Status: 1 ERROR, 2 WARNINGs, 2 NOTEs
See
  ‘/mnt/building/build_2016-03-02-16-04/RF_PKG_CHECK/PKGS/chemosensors.Rcheck/00check.log’
for details.

Run time: 72.5 seconds.

Additional Logs:   00install.out
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