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BioC 3.4: CHECK report for snm on morelia

This page was generated on 2016-09-21 03:50:50 -0700 (Wed, 21 Sep 2016).

Package 1134/1257HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
snm 1.21.0
John D. Storey
Snapshot Date: 2016-09-19 19:15:14 -0700 (Mon, 19 Sep 2016)
URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/snm
Last Changed Rev: 117081 / Revision: 121152
Last Changed Date: 2016-05-03 14:30:44 -0700 (Tue, 03 May 2016)
zin1 Linux (Ubuntu 16.04 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
moscato1 Windows Server 2008 R2 Standard (64-bit) / x64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository
morelia Mac OS X Mavericks (10.9.5) / x86_64  OK  OK [ OK ] OK UNNEEDED, same version exists in internal repository

Summary

Package: snm
Version: 1.21.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings snm_1.21.0.tar.gz
StartedAt: 2016-09-20 13:16:41 -0700 (Tue, 20 Sep 2016)
EndedAt: 2016-09-20 13:21:06 -0700 (Tue, 20 Sep 2016)
EllapsedTime: 265.6 seconds
RetCode: 0
Status:  OK 
CheckDir: snm.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings snm_1.21.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.4-bioc/meat/snm.Rcheck’
* using R version 3.3.1 (2016-06-21)
* using platform: x86_64-apple-darwin13.4.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘snm/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘snm’ version ‘1.21.0’
* 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 for sufficient/correct file permissions ... 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
* 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 sizes of PDF files under ‘inst/doc’ ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
                 user system elapsed
sim.refDesign 112.056  10.11 122.497
snm            95.832   5.55 102.066
* 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
  ‘/Users/biocbuild/bbs-3.4-bioc/meat/snm.Rcheck/00check.log’
for details.


snm.Rcheck/00install.out:

* installing *source* package ‘snm’ ...
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (snm)

snm.Rcheck/snm-Ex.timings:

nameusersystemelapsed
fitted.snm0.0010.0000.001
plot.snm0.0000.0000.001
sim.doubleChannel000
sim.preProcessed2.9190.1573.077
sim.refDesign112.056 10.110122.497
sim.singleChannel0.0010.0000.001
snm 95.832 5.550102.066
summary.snm0.0010.0000.001