BioC 3.3: CHECK report for simulatorZ on zin2

Package: simulatorZ

Version: 1.6.0

Command: /home/biocbuild/bbs-3.3-bioc/R/bin/R CMD check --no-vignettes --timings simulatorZ_1.6.0.tar.gz

StartedAt: 2016-10-13 06:53:55 -0700 (Thu, 13 Oct 2016)

EndedAt: 2016-10-13 06:56:27 -0700 (Thu, 13 Oct 2016)

EllapsedTime: 152.3 seconds

RetCode: 0

Status:  OK

CheckDir: simulatorZ.Rcheck

Warnings: 0

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### Running command:
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###   /home/biocbuild/bbs-3.3-bioc/R/bin/R CMD check --no-vignettes --timings simulatorZ_1.6.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.3-bioc/meat/simulatorZ.Rcheck’
* using R version 3.3.1 (2016-06-21)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘simulatorZ/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘simulatorZ’ version ‘1.6.0’
* 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 ‘simulatorZ’ 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:
  ‘IRanges’ ‘S4Vectors’
  All declared Imports should be used.
Packages in Depends field not imported from:
  ‘BiocGenerics’ ‘methods’
  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
fastCox: no visible global function definition for ‘pnorm’
geneFilter: no visible global function definition for ‘cor’
plusMinus: no visible binding for global variable ‘sd’
plusMinus: no visible binding for global variable ‘quantile’
rowCoxTests: no visible global function definition for ‘pnorm’
simTime: no visible global function definition for ‘runif’
Undefined global functions or variables:
  cor pnorm quantile runif sd
Consider adding
  importFrom("stats", "cor", "pnorm", "quantile", "runif", "sd")
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 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
Examples with CPU or elapsed time > 5s
               user system elapsed
geneFilter   10.797  0.124  10.938
zmatrix       5.575  0.079   5.667
simTime       5.472  0.068   5.547
simBootstrap  5.166  0.048   5.219
getTrueModel  4.989  0.084   5.078
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘runTests.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 NOTEs
See
  ‘/home/biocbuild/bbs-3.3-bioc/meat/simulatorZ.Rcheck/00check.log’
for details.

* installing *source* package ‘simulatorZ’ ...
** libs
g++ -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -Wall -c coxformatrices.cpp -o coxformatrices.o
g++ -shared -L/home/biocbuild/bbs-3.3-bioc/R/lib -L/usr/local/lib -o simulatorZ.so coxformatrices.o -L/home/biocbuild/bbs-3.3-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.3-bioc/meat/simulatorZ.Rcheck/simulatorZ/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 (simulatorZ)

name	user	system	elapsed
cvSubsets	1.586	0.036	2.204
funCV	1.097	0.028	1.123
geneFilter	10.797	0.124	10.938
getTrueModel	4.989	0.084	5.078
masomenos	0.827	0.016	0.843
plusMinus	0.864	0.020	0.885
rowCoxTests	0.83	0.00	0.83
simBootstrap	5.166	0.048	5.219
simData	3.983	0.064	4.054
simTime	5.472	0.068	5.547
zmatrix	5.575	0.079	5.667