Package: DEqMS

Version: 1.0.1

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_1.0.1.tar.gz

StartedAt: 2019-04-15 23:26:34 -0400 (Mon, 15 Apr 2019)

EndedAt: 2019-04-15 23:30:42 -0400 (Mon, 15 Apr 2019)

EllapsedTime: 248.5 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_1.0.1.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.8-bioc/meat/DEqMS.Rcheck’
* using R version 3.5.3 (2019-03-11)
* 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 ‘1.0.1’
* 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
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’
Undefined global functions or variables:
  PSM_id Peptide value variable
* 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         111.669  0.341 113.135
farmsSummary              38.652  1.656  40.717
equalMedianNormalization  12.173  0.652  13.361
spectraCounteBayes         7.727  0.286   8.245
plotFitCurve               7.637  0.261   8.021
outputResult               7.177  0.265   7.740
medianSummary              7.060  0.247   8.037
medianSweeping             5.955  0.195   6.334
* 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-3.8-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/3.5/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
equalMedianNormalization	12.173	0.652	13.361
farmsSummary	38.652	1.656	40.717
medianSummary	7.060	0.247	8.037
medianSweeping	5.955	0.195	6.334
medpolishSummary	111.669	0.341	113.135
outputResult	7.177	0.265	7.740
peptideProfilePlot	1.902	0.094	2.185
plotFitCurve	7.637	0.261	8.021
spectraCounteBayes	7.727	0.286	8.245