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This page was generated on 2021-10-22 12:05:04 -0400 (Fri, 22 Oct 2021).

CHECK results for msmsTests on merida1

To the developers/maintainers of the msmsTests package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/msmsTests.git to
reflect on this report. See How and When does the builder pull? When will my changes propagate? here for more information.
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raw results

Package 1217/2075HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
msmsTests 1.31.0  (landing page)
Josep Gregori i Font
Snapshot Date: 2021-10-21 14:50:08 -0400 (Thu, 21 Oct 2021)
git_url: https://git.bioconductor.org/packages/msmsTests
git_branch: master
git_last_commit: 9021056
git_last_commit_date: 2021-05-19 11:59:53 -0400 (Wed, 19 May 2021)
nebbiolo2Linux (Ubuntu 20.04.2 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
riesling1Windows Server 2019 Standard / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
merida1macOS 10.14.6 Mojave / x86_64  OK    OK    OK    NA  

Summary

Package: msmsTests
Version: 1.31.0
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:msmsTests.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings msmsTests_1.31.0.tar.gz
StartedAt: 2021-10-22 06:31:43 -0400 (Fri, 22 Oct 2021)
EndedAt: 2021-10-22 06:35:16 -0400 (Fri, 22 Oct 2021)
EllapsedTime: 212.6 seconds
RetCode: 0
Status:   OK  
CheckDir: msmsTests.Rcheck
Warnings: 0

Command output

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### Running command:
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###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:msmsTests.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings msmsTests_1.31.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.14-bioc/meat/msmsTests.Rcheck’
* using R version 4.1.1 Patched (2021-08-22 r80813)
* using platform: x86_64-apple-darwin17.0 (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 ‘1.31.0’
* 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 ‘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 points poisson quasi text
Consider adding
  importFrom("graphics", "abline", "grid", "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.pois   11.018  0.123  11.152
test.results    10.919  0.028  10.961
res.volcanoplot 10.803  0.025  10.838
msms.glm.qlll   10.591  0.058  10.661
pval.by.fc       8.333  0.021   8.362
* 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-3.14-bioc/meat/msmsTests.Rcheck/00check.log’
for details.



Installation output

msmsTests.Rcheck/00install.out

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### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL msmsTests
###
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* installing to library ‘/Library/Frameworks/R.framework/Versions/4.1/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)

Tests output


Example timings

msmsTests.Rcheck/msmsTests-Ex.timings

nameusersystemelapsed
msms.edgeR0.6880.0090.699
msms.glm.pois11.018 0.12311.152
msms.glm.qlll10.591 0.05810.661
msms.spk0.0100.0040.014
pval.by.fc8.3330.0218.362
res.volcanoplot10.803 0.02510.838
test.results10.919 0.02810.961