Package: DSS

Version: 2.26.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings DSS_2.26.0.tar.gz

StartedAt: 2018-04-12 03:05:54 -0400 (Thu, 12 Apr 2018)

EndedAt: 2018-04-12 03:08:37 -0400 (Thu, 12 Apr 2018)

EllapsedTime: 163.3 seconds

RetCode: 0

Status:  WARNINGS

CheckDir: DSS.Rcheck

Warnings: 1

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings DSS_2.26.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.6-bioc/meat/DSS.Rcheck’
* using R version 3.4.4 (2018-03-15)
* using platform: x86_64-apple-darwin15.6.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘DSS/DESCRIPTION’ ... OK
* this is package ‘DSS’ version ‘2.26.0’
* 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 for sufficient/correct file permissions ... OK
* checking whether package ‘DSS’ 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 ... NOTE
Namespaces in Imports field not imported from:
  ‘graphics’ ‘stats’
  All declared Imports should be used.
Package in Depends field not imported from: ‘splines’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
DMLfit.multiFactor: no visible global function definition for
  ‘model.matrix’
DMLtest.multiFactor.Contrast: no visible global function definition for
  ‘pnorm’
DMLtest.multiFactor.Contrast: no visible global function definition for
  ‘p.adjust’
DMLtest.multiFactor.coef: no visible global function definition for
  ‘pnorm’
DMLtest.multiFactor.coef: no visible global function definition for
  ‘p.adjust’
callDML: no visible global function definition for ‘pnorm’
callDMR: no visible global function definition for ‘pnorm’
compute.baseSigma.notrend: no visible global function definition for
  ‘IQR’
compute.baseSigma.trend: no visible global function definition for
  ‘IQR’
compute.waldStat.Smooth: no visible global function definition for
  ‘pnorm’
compute.waldStat.Smooth: no visible global function definition for
  ‘p.adjust’
compute.waldStat.noSmooth: no visible global function definition for
  ‘pnorm’
compute.waldStat.noSmooth: no visible global function definition for
  ‘p.adjust’
dispersion.shrinkage.BSseq : plik.logN: no visible global function
  definition for ‘dnorm’
dispersion.shrinkage.BSseq: no visible global function definition for
  ‘optimize’
est.phi0: no visible binding for global variable ‘var’
est.prior.BSseq.logN: no visible global function definition for
  ‘median’
est.prior.BSseq.logN: no visible global function definition for ‘IQR’
est.trend: no visible global function definition for ‘median’
est.trend: no visible global function definition for ‘quantile’
est.trend: no visible binding for global variable ‘median’
est.trend: no visible global function definition for ‘isoreg’
est.trend: no visible global function definition for ‘smooth.spline’
est.trend: no visible global function definition for ‘predict’
estDispersion.multiFactor: no visible global function definition for
  ‘median’
estDispersion.multiFactor: no visible global function definition for
  ‘IQR’
estDispersion.multiFactor : get.phi : obj: no visible global function
  definition for ‘dnorm’
estDispersion.multiFactor : get.phi: no visible global function
  definition for ‘optimize’
estNormFactors.lr: no visible global function definition for ‘quantile’
estNormFactors.lr: no visible global function definition for ‘median’
estNormFactors.median: no visible binding for global variable ‘median’
estNormFactors.quantile : <anonymous>: no visible global function
  definition for ‘quantile’
locfdr: no visible global function definition for ‘median’
locfdr: no visible global function definition for ‘quantile’
locfdr: no visible global function definition for ‘hist’
locfdr: no visible global function definition for ‘ns’
locfdr: no visible global function definition for ‘glm’
locfdr: no visible binding for global variable ‘poisson’
locfdr: no visible global function definition for ‘poly’
locfdr: no visible global function definition for ‘lm’
locfdr: no visible global function definition for ‘qnorm’
locfdr: no visible global function definition for ‘dnorm’
locfdr: no visible global function definition for ‘approx’
locfdr: no visible global function definition for ‘par’
locfdr: no visible global function definition for ‘lines’
locfdr: no visible global function definition for ‘title’
locfdr: no visible global function definition for ‘points’
locfdr: no visible global function definition for ‘matplot’
locfdr: no visible global function definition for ‘abline’
locfdr: no visible global function definition for ‘text’
locmle: no visible global function definition for ‘median’
locmle: no visible global function definition for ‘quantile’
locmle: no visible global function definition for ‘qnorm’
locmle: no visible global function definition for ‘pnorm’
locmle: no visible global function definition for ‘dnorm’
lrTest: no visible global function definition for ‘dnbinom’
lrTest: no visible global function definition for ‘pchisq’
makeContrast: no visible global function definition for ‘terms’
rnegbinom: no visible global function definition for ‘rpois’
rnegbinom: no visible global function definition for ‘rgamma’
scv: no visible global function definition for ‘var’
showOneDMR: no visible global function definition for ‘par’
showOneDMR: no visible global function definition for ‘plot’
showOneDMR: no visible global function definition for ‘box’
showOneDMR: no visible global function definition for ‘axis’
showOneDMR: no visible global function definition for ‘mtext’
showOneDMR: no visible global function definition for ‘lines’
showOneDMR: no visible global function definition for ‘rect’
shrink.dispersion.notrend: no visible global function definition for
  ‘median’
shrink.dispersion.notrend: no visible global function definition for
  ‘IQR’
shrink.dispersion.notrend : get.phi: no visible global function
  definition for ‘optimize’
shrink.dispersion.trend: no visible global function definition for
  ‘IQR’
shrink.dispersion.trend : get.phi: no visible global function
  definition for ‘optimize’
waldTest: no visible global function definition for ‘pnorm’
waldTest: no visible global function definition for ‘median’
waldTest: no visible global function definition for ‘IQR’
Undefined global functions or variables:
  IQR abline approx axis box dnbinom dnorm glm hist isoreg lines lm
  matplot median model.matrix mtext ns optimize p.adjust par pchisq
  plot pnorm points poisson poly predict qnorm quantile rect rgamma
  rpois smooth.spline terms text title var
Consider adding
  importFrom("graphics", "abline", "axis", "box", "hist", "lines",
             "matplot", "mtext", "par", "plot", "points", "rect", "text",
             "title")
  importFrom("stats", "IQR", "approx", "dnbinom", "dnorm", "glm",
             "isoreg", "lm", "median", "model.matrix", "optimize",
             "p.adjust", "pchisq", "pnorm", "poisson", "poly", "predict",
             "qnorm", "quantile", "rgamma", "rpois", "smooth.spline",
             "terms", "var")
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 ... WARNING
Codoc mismatches from documentation object 'callDML':
callDML
  Code: function(DMLresult, delta = 0.1, p.threshold = 1e-05)
  Docs: function(DMLresult, delta = 0, p.threshold = 1e-05)
  Mismatches in argument default values:
    Name: 'delta' Code: 0.1 Docs: 0

* checking Rd \usage sections ... OK
* 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 line endings in C/C++/Fortran sources/headers ... OK
* checking compiled code ... 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
* checking for unstated dependencies in vignettes ... NOTE
'library' or 'require' call not declared from: ‘edgeR’
* 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 WARNING, 3 NOTEs
See
  ‘/Users/biocbuild/bbs-3.6-bioc/meat/DSS.Rcheck/00check.log’
for details.

* installing *source* package ‘DSS’ ...
** libs
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG   -I/usr/local/include   -fPIC  -Wall -g -O2  -c compute_var_smooth.c -o compute_var_smooth.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG   -I/usr/local/include   -fPIC  -Wall -g -O2  -c filter.c -o filter.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG   -I/usr/local/include   -fPIC  -Wall -g -O2  -c nitem.c -o nitem.o
clang++ -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/Library/Frameworks/R.framework/Resources/lib -L/usr/local/lib -o DSS.so compute_var_smooth.o filter.o nitem.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-3.6-bioc/meat/DSS.Rcheck/DSS/libs
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (DSS)

name	user	system	elapsed
DMLfit.multiFactor	2.70	0.06	2.80
DMLtest	0.001	0.000	0.001
DMLtest.multiFactor	0.002	0.001	0.002
DSS.DE	0.745	0.011	0.766
RRBS	0.026	0.006	0.031
SeqCountSet-class	0.290	0.002	0.307
callDML	0.002	0.001	0.002
callDMR	0.002	0.000	0.002
design	0.023	0.006	0.029
dispersion	0.462	0.011	0.479
estDispersion	0.346	0.010	0.359
estNormFactors	0.012	0.002	0.015
makeBSseqData	1.983	0.069	2.077
normalizationFactor	0.004	0.001	0.006
seqData	0.004	0.002	0.006
showOneDMR	0.001	0.000	0.000
waldTest	0.773	0.014	0.798