Package: DEqMS

Version: 1.1.7

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:DEqMS.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings DEqMS_1.1.7.tar.gz

StartedAt: 2019-04-09 00:24:40 -0400 (Tue, 09 Apr 2019)

EndedAt: 2019-04-09 00:29:33 -0400 (Tue, 09 Apr 2019)

EllapsedTime: 292.5 seconds

RetCode: 0

Status:  OK

CheckDir: DEqMS.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:DEqMS.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings DEqMS_1.1.7.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.9-bioc/meat/DEqMS.Rcheck’
* using R Under development (unstable) (2018-11-27 r75683)
* using platform: x86_64-apple-darwin15.6.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘DEqMS/DESCRIPTION’ ... OK
* this is package ‘DEqMS’ version ‘1.1.7’
* 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 ‘DEqMS’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Malformed Title field: should not end in a period.
* 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
Residualplot: no visible global function definition for ‘fitted’
Residualplot: no visible global function definition for ‘residuals’
VarianceScatterplot: no visible global function definition for ‘fitted’
peptideProfilePlot: no visible binding for global variable ‘variable’
peptideProfilePlot: no visible binding for global variable ‘value’
peptideProfilePlot: no visible binding for global variable ‘PSM_id’
peptideProfilePlot: no visible binding for global variable ‘Peptide’
spectraCounteBayes: no visible global function definition for ‘fitted’
Undefined global functions or variables:
  PSM_id Peptide fitted residuals value variable
Consider adding
  importFrom("stats", "fitted", "residuals")
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 files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
                            user system elapsed
medpolishSummary         112.662  0.324 114.866
farmsSummary              39.350  1.555  42.101
Residualplot              15.286  0.947  18.018
spectraCounteBayes        10.548  0.278  11.181
outputResult              10.064  0.274  10.792
VarianceScatterplot        9.897  0.284  10.626
VarianceBoxplot            9.759  0.310  10.508
equalMedianNormalization   9.608  0.283  12.495
medianSummary              8.714  0.261   9.461
medianSweeping             8.626  0.238   9.274
peptideProfilePlot         4.566  0.121   5.069
* 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/DEqMS.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 DEqMS
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* installing to library ‘/Library/Frameworks/R.framework/Versions/3.6/Resources/library’
* installing *source* package ‘DEqMS’ ...
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (DEqMS)

name	user	system	elapsed
Residualplot	15.286	0.947	18.018
VarianceBoxplot	9.759	0.310	10.508
VarianceScatterplot	9.897	0.284	10.626
equalMedianNormalization	9.608	0.283	12.495
farmsSummary	39.350	1.555	42.101
medianSummary	8.714	0.261	9.461
medianSweeping	8.626	0.238	9.274
medpolishSummary	112.662	0.324	114.866
outputResult	10.064	0.274	10.792
peptideProfilePlot	4.566	0.121	5.069
spectraCounteBayes	10.548	0.278	11.181