BioC 3.5: CHECK report for sva on oaxaca

Package: sva

Version: 3.23.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings sva_3.23.0.tar.gz

StartedAt: 2017-03-04 09:49:35 -0800 (Sat, 04 Mar 2017)

EndedAt: 2017-03-04 09:52:24 -0800 (Sat, 04 Mar 2017)

EllapsedTime: 169.4 seconds

RetCode: 0

Status:  WARNINGS

CheckDir: sva.Rcheck

Warnings: 2

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings sva_3.23.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.5-bioc/meat/sva.Rcheck’
* using R Under development (unstable) (2017-02-15 r72177)
* using platform: x86_64-apple-darwin13.4.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘sva/DESCRIPTION’ ... OK
* this is package ‘sva’ version ‘3.23.0’
* 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 ‘sva’ 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
ComBat: no visible global function definition for ‘model.matrix’
ComBat: no visible binding for global variable ‘var’
ComBat: no visible global function definition for ‘par’
ComBat: no visible global function definition for ‘density’
ComBat: no visible global function definition for ‘plot’
ComBat: no visible global function definition for ‘lines’
ComBat: no visible global function definition for ‘dnorm’
ComBat: no visible global function definition for ‘qqnorm’
ComBat: no visible global function definition for ‘qqline’
ComBat: no visible global function definition for ‘rgamma’
ComBat: no visible global function definition for ‘qqplot’
ComBat: no visible global function definition for ‘title’
L: no visible global function definition for ‘dnorm’
aprior: no visible global function definition for ‘var’
bprior: no visible global function definition for ‘var’
edge.lfdr: no visible global function definition for ‘qnorm’
edge.lfdr: no visible global function definition for ‘density’
edge.lfdr: no visible global function definition for ‘smooth.spline’
edge.lfdr: no visible global function definition for ‘predict’
edge.lfdr: no visible global function definition for ‘dnorm’
f.pvalue: no visible global function definition for ‘pf’
fsva: no visible global function definition for ‘cor’
psva: no visible global function definition for ‘lmFit’
sva.class2Model: no visible global function definition for
  ‘model.matrix’
twostepsva.build: no visible global function definition for ‘cor’
Undefined global functions or variables:
  cor density dnorm lines lmFit model.matrix par pf plot predict qnorm
  qqline qqnorm qqplot rgamma smooth.spline title var
Consider adding
  importFrom("graphics", "lines", "par", "plot", "title")
  importFrom("stats", "cor", "density", "dnorm", "model.matrix", "pf",
             "predict", "qnorm", "qqline", "qqnorm", "qqplot", "rgamma",
             "smooth.spline", "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 'ComBat':
ComBat
  Code: function(dat, batch, mod = NULL, par.prior = TRUE, prior.plots
                 = FALSE, mean.only = FALSE)
  Docs: function(dat, batch, mod = NULL, par.prior = TRUE, prior.plots
                 = FALSE)
  Argument names in code not in docs:
    mean.only

* checking Rd \usage sections ... WARNING
Documented arguments not in \usage in documentation object 'ComBat':
  ‘mean.only’

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 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 ... NONE
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’
 OK
* 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: 2 WARNINGs, 1 NOTE
See
  ‘/Users/biocbuild/bbs-3.5-bioc/meat/sva.Rcheck/00check.log’
for details.

* installing *source* package ‘sva’ ...
** libs
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG   -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include   -fPIC  -Wall -mtune=core2 -g -O2  -c sva.c -o sva.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 sva.so sva.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-3.5-bioc/meat/sva.Rcheck/sva/libs
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (sva)