Package: snm

Version: 1.26.0

Command: rm -rf snm.buildbin-libdir snm.Rcheck && mkdir snm.buildbin-libdir snm.Rcheck && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=snm.buildbin-libdir snm_1.26.0.tar.gz >snm.Rcheck\00install.out 2>&1 && cp snm.Rcheck\00install.out snm-install.out && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD check --library=snm.buildbin-libdir --install="check:snm-install.out" --force-multiarch --no-vignettes --timings snm_1.26.0.tar.gz

StartedAt: 2018-04-12 03:17:34 -0400 (Thu, 12 Apr 2018)

EndedAt: 2018-04-12 03:28:06 -0400 (Thu, 12 Apr 2018)

EllapsedTime: 632.2 seconds

RetCode: 0

Status:  OK

CheckDir: snm.Rcheck

Warnings: 0

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### Running command:
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###   rm -rf snm.buildbin-libdir snm.Rcheck && mkdir snm.buildbin-libdir snm.Rcheck && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=snm.buildbin-libdir snm_1.26.0.tar.gz >snm.Rcheck\00install.out 2>&1 && cp snm.Rcheck\00install.out snm-install.out  &&  C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD check --library=snm.buildbin-libdir --install="check:snm-install.out" --force-multiarch --no-vignettes --timings snm_1.26.0.tar.gz
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* using log directory 'C:/Users/biocbuild/bbs-3.6-bioc/meat/snm.Rcheck'
* using R version 3.4.4 (2018-03-15)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'snm/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'snm' version '1.26.0'
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking whether package 'snm' can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking 'build' 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
* loading checks for arch 'i386'
** 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
* loading checks for arch 'x64'
** 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 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 ... NOTE
buildBasisSplineMatrix : <anonymous>: no visible global function
  definition for 'predict'
calcArrayEffects : <anonymous>: no visible global function definition
  for 'predict'
edge.glr: no visible global function definition for 'pf'
edge.qvalue: no visible global function definition for 'smooth.spline'
edge.qvalue: no visible global function definition for 'predict'
fit.model: no visible binding for global variable 'weighted.mean'
fit.model: no visible global function definition for 'residuals'
getSpanningSet: no visible global function definition for 'quantile'
make.ref.model.matrices: no visible global function definition for
  'model.matrix'
make.ref.model.matrices: no visible global function definition for
  'as.formula'
make.snm.obj: no visible global function definition for 'model.matrix'
sim.doubleChannel: no visible global function definition for 'rchisq'
sim.doubleChannel: no visible global function definition for 'runif'
sim.doubleChannel: no visible global function definition for 'rnorm'
sim.doubleChannel: no visible binding for global variable 'rnorm'
sim.doubleChannel: no visible global function definition for
  'model.matrix'
sim.function.var: no visible global function definition for
  'model.matrix'
sim.intensity.dep: no visible global function definition for
  'model.matrix'
sim.intensity.dep: no visible global function definition for 'predict'
sim.preProcessed: no visible global function definition for 'rchisq'
sim.preProcessed: no visible global function definition for 'runif'
sim.preProcessed: no visible global function definition for 'rnorm'
sim.preProcessed: no visible binding for global variable 'rnorm'
sim.preProcessed: no visible global function definition for
  'model.matrix'
sim.probe.specific: no visible global function definition for
  'model.matrix'
sim.refDesign: no visible global function definition for 'rchisq'
sim.refDesign: no visible global function definition for 'runif'
sim.refDesign: no visible binding for global variable 'rnorm'
sim.refDesign: no visible global function definition for 'rnorm'
sim.refDesign: no visible global function definition for 'model.matrix'
sim.singleChannel: no visible global function definition for 'rchisq'
sim.singleChannel: no visible global function definition for 'runif'
sim.singleChannel: no visible global function definition for 'rnorm'
sim.singleChannel: no visible binding for global variable 'rnorm'
sim.singleChannel: no visible global function definition for
  'model.matrix'
snm.diagnostic.plot: no visible global function definition for 'par'
snm.diagnostic.plot: no visible global function definition for 'plot'
snm.diagnostic.plot: no visible global function definition for 'axis'
snm.diagnostic.plot : <anonymous>: no visible global function
  definition for 'points'
snm.diagnostic.plot: no visible global function definition for 'hist'
snm.diagnostic.plot: no visible global function definition for 'abline'
snm.diagnostic.plot: no visible global function definition for 'mtext'
snm.diagnostic.plot: no visible global function definition for 'title'
snm.plot: no visible global function definition for 'model.matrix'
snm.plot: no visible global function definition for 'rainbow'
snm.plot: no visible global function definition for 'plot'
snm.plot: no visible global function definition for 'points'
snm.plot: no visible global function definition for 'par'
snm.plot: no visible global function definition for 'abline'
snm.plot: no visible global function definition for 'fitted'
snm.plot: no visible global function definition for 'hist'
snm.plot: no visible global function definition for 'mtext'
snm.plot: no visible global function definition for 'title'
Undefined global functions or variables:
  abline as.formula axis fitted hist model.matrix mtext par pf plot
  points predict quantile rainbow rchisq residuals rnorm runif
  smooth.spline title weighted.mean
Consider adding
  importFrom("grDevices", "rainbow")
  importFrom("graphics", "abline", "axis", "hist", "mtext", "par",
             "plot", "points", "title")
  importFrom("stats", "as.formula", "fitted", "model.matrix", "pf",
             "predict", "quantile", "rchisq", "residuals", "rnorm",
             "runif", "smooth.spline", "weighted.mean")
to your NAMESPACE file.
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking installed files from 'inst/doc' ... OK
* checking files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
Examples with CPU or elapsed time > 5s
                user system elapsed
sim.refDesign 142.16    8.4  150.57
snm           126.26   10.0  136.31
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
                user system elapsed
sim.refDesign 139.34   3.36  142.76
snm           119.22   2.22  121.49
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in 'inst/doc' ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 1 NOTE
See
  'C:/Users/biocbuild/bbs-3.6-bioc/meat/snm.Rcheck/00check.log'
for details.

install for i386

* installing *source* package 'snm' ...
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
  converting help for package 'snm'
    finding HTML links ... done
    fitted.snm                              html  
    plot.snm                                html  
    sim.doubleChannel                       html  
    sim.preProcessed                        html  
    sim.refDesign                           html  
    sim.singleChannel                       html  
    snm-internal                            html  
    snm                                     html  
    summary.snm                             html  
** building package indices
** installing vignettes
** testing if installed package can be loaded
In R CMD INSTALL

install for x64

* installing *source* package 'snm' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'snm' as snm_1.26.0.zip
* DONE (snm)
In R CMD INSTALL
In R CMD INSTALL