Package: msmsTests

Version: 1.25.0

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_1.25.0.tar.gz

StartedAt: 2020-01-16 06:45:58 -0500 (Thu, 16 Jan 2020)

EndedAt: 2020-01-16 06:50:02 -0500 (Thu, 16 Jan 2020)

EllapsedTime: 243.7 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_1.25.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.11-bioc/meat/msmsTests.Rcheck’
* using R Under development (unstable) (2019-12-14 r77572)
* 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 ‘1.25.0’
* 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 (user + system) or elapsed time > 5s
                  user system elapsed
msms.glm.qlll   13.337  0.098  13.434
test.results    13.376  0.031  13.474
res.volcanoplot 13.299  0.028  13.513
msms.glm.pois   12.178  0.245  12.424
pval.by.fc      10.931  0.025  11.172
* 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-3.11-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/4.0/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	0.829	0.041	0.870
msms.glm.pois	12.178	0.245	12.424
msms.glm.qlll	13.337	0.098	13.434
msms.spk	0.010	0.004	0.015
pval.by.fc	10.931	0.025	11.172
res.volcanoplot	13.299	0.028	13.513
test.results	13.376	0.031	13.474