Package: msmsTests

Version: 1.22.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:msmsTests.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings msmsTests_1.22.0.tar.gz

StartedAt: 2019-10-16 04:53:01 -0400 (Wed, 16 Oct 2019)

EndedAt: 2019-10-16 04:56:54 -0400 (Wed, 16 Oct 2019)

EllapsedTime: 232.6 seconds

RetCode: 0

Status:  OK

CheckDir: msmsTests.Rcheck

Warnings: 0

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:msmsTests.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings msmsTests_1.22.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.9-bioc/meat/msmsTests.Rcheck’
* using R version 3.6.1 (2019-07-05)
* using platform: x86_64-apple-darwin15.6.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘msmsTests/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘msmsTests’ version ‘1.22.0’
* 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 ‘msmsTests’ 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
Packages in Depends field not imported from:
  ‘MSnbase’ ‘msmsEDA’
  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
glm.pois: no visible global function definition for ‘glm’
glm.pois: no visible global function definition for ‘as.formula’
glm.pois: no visible global function definition for ‘poisson’
glm.pois: no visible global function definition for ‘coef’
glm.pois: no visible global function definition for ‘anova’
msms.edgeR: no visible global function definition for ‘exprs’
msms.edgeR: no visible global function definition for ‘pData’
msms.edgeR: no visible global function definition for ‘model.matrix’
msms.edgeR: no visible global function definition for ‘as.formula’
msms.glm.pois: no visible global function definition for ‘exprs’
msms.glm.pois: no visible global function definition for ‘pData’
msms.glm.qlll: no visible global function definition for ‘exprs’
msms.glm.qlll: no visible global function definition for ‘pData’
qp.test: no visible global function definition for ‘glm’
qp.test: no visible global function definition for ‘as.formula’
qp.test: no visible global function definition for ‘quasi’
qp.test: no visible binding for global variable ‘mu’
qp.test: no visible global function definition for ‘coef’
qp.test: no visible global function definition for ‘anova’
res.volcanoplot: no visible global function definition for ‘plot’
res.volcanoplot: no visible global function definition for ‘grid’
res.volcanoplot: no visible global function definition for ‘abline’
res.volcanoplot: no visible global function definition for ‘points’
res.volcanoplot: no visible global function definition for ‘text’
test.results: no visible global function definition for ‘exprs’
test.results: no visible global function definition for ‘p.adjust’
Undefined global functions or variables:
  abline anova as.formula coef exprs glm grid model.matrix mu p.adjust
  pData plot points poisson quasi text
Consider adding
  importFrom("graphics", "abline", "grid", "plot", "points", "text")
  importFrom("stats", "anova", "as.formula", "coef", "glm",
             "model.matrix", "p.adjust", "poisson", "quasi")
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 contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking sizes of PDF files under ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
                  user system elapsed
test.results    14.660  0.081  14.782
msms.glm.qlll   14.394  0.034  14.456
res.volcanoplot 14.329  0.031  14.402
msms.glm.pois   13.520  0.055  13.613
pval.by.fc      11.974  0.062  12.072
* 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
  ‘/Users/biocbuild/bbs-3.9-bioc/meat/msmsTests.Rcheck/00check.log’
for details.

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL msmsTests
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* installing to library ‘/Library/Frameworks/R.framework/Versions/3.6/Resources/library’
* installing *source* package ‘msmsTests’ ...
** using staged installation
** R
** data
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (msmsTests)

name	user	system	elapsed
msms.edgeR	0.771	0.029	0.800
msms.glm.pois	13.520	0.055	13.613
msms.glm.qlll	14.394	0.034	14.456
msms.spk	0.013	0.006	0.022
pval.by.fc	11.974	0.062	12.072
res.volcanoplot	14.329	0.031	14.402
test.results	14.660	0.081	14.782