Package: DEqMS

Version: 1.1.7

Command: /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD check --install=check:DEqMS.install-out.txt --library=/home/biocbuild/bbs-3.9-bioc/R/library --no-vignettes --timings DEqMS_1.1.7.tar.gz

StartedAt: 2019-04-08 23:59:17 -0400 (Mon, 08 Apr 2019)

EndedAt: 2019-04-09 00:03:50 -0400 (Tue, 09 Apr 2019)

EllapsedTime: 273.4 seconds

RetCode: 0

Status:  OK

CheckDir: DEqMS.Rcheck

Warnings: 0

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### Running command:
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###   /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD check --install=check:DEqMS.install-out.txt --library=/home/biocbuild/bbs-3.9-bioc/R/library --no-vignettes --timings DEqMS_1.1.7.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.9-bioc/meat/DEqMS.Rcheck’
* using R Under development (unstable) (2019-03-18 r76245)
* using platform: x86_64-pc-linux-gnu (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         100.801  0.041 101.181
farmsSummary              38.633  0.198  41.483
Residualplot              15.348  0.352  16.379
VarianceBoxplot           11.132  0.084  11.467
spectraCounteBayes        10.958  0.055  11.192
VarianceScatterplot       10.915  0.060  11.282
outputResult              10.318  0.104  10.742
equalMedianNormalization  10.017  0.056  11.206
medianSummary              9.323  0.092   9.815
medianSweeping             9.132  0.076   9.530
* 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
  ‘/home/biocbuild/bbs-3.9-bioc/meat/DEqMS.Rcheck/00check.log’
for details.

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### Running command:
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###   /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD INSTALL DEqMS
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* installing to library ‘/home/biocbuild/bbs-3.9-bioc/R/library’
* installing *source* package ‘DEqMS’ ...
** using staged installation
** 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 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 (DEqMS)

name	user	system	elapsed
Residualplot	15.348	0.352	16.379
VarianceBoxplot	11.132	0.084	11.467
VarianceScatterplot	10.915	0.060	11.282
equalMedianNormalization	10.017	0.056	11.206
farmsSummary	38.633	0.198	41.483
medianSummary	9.323	0.092	9.815
medianSweeping	9.132	0.076	9.530
medpolishSummary	100.801	0.041	101.181
outputResult	10.318	0.104	10.742
peptideProfilePlot	4.570	0.036	4.842
spectraCounteBayes	10.958	0.055	11.192