Package: alsace

Version: 1.22.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:alsace.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings alsace_1.22.0.tar.gz

StartedAt: 2020-04-15 00:19:27 -0400 (Wed, 15 Apr 2020)

EndedAt: 2020-04-15 00:20:47 -0400 (Wed, 15 Apr 2020)

EllapsedTime: 79.2 seconds

RetCode: 0

Status:  OK

CheckDir: alsace.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:alsace.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings alsace_1.22.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.10-bioc/meat/alsace.Rcheck’
* using R version 3.6.3 (2020-02-29)
* using platform: x86_64-apple-darwin15.6.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘alsace/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘alsace’ version ‘1.22.0’
* 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 ‘alsace’ 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
'library' or 'require' call to ‘lattice’ in package code.
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
getPeakTable : clusterPeaks: no visible global function definition for
  ‘stripplot’
getPeakTable : clusterPeaks : <anonymous>: no visible global function
  definition for ‘panel.stripplot’
getPeakTable : clusterPeaks : <anonymous>: no visible global function
  definition for ‘panel.abline’
Undefined global functions or variables:
  panel.abline panel.stripplot stripplot
* 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 or elapsed time > 5s
               user system elapsed
components   14.074  0.714  14.904
teaMerged     7.267  0.177   7.469
correctPeaks  6.383  0.240   6.682
doALS         6.522  0.097   6.690
fitpeaks      5.337  0.162   5.536
* 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-3.10-bioc/meat/alsace.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 alsace
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* installing to library ‘/Library/Frameworks/R.framework/Versions/3.6/Resources/library’
* installing *source* package ‘alsace’ ...
** 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 (alsace)

name	user	system	elapsed
components	14.074	0.714	14.904
correctPeaks	6.383	0.240	6.682
correctRT	3.388	0.133	3.567
doALS	6.522	0.097	6.690
filterPeaks	0.062	0.002	0.065
fitpeaks	5.337	0.162	5.536
getAllPeaks	0.050	0.002	0.054
getPeakTable	2.585	0.115	2.713
opa	1.326	0.057	1.386
preprocess	0.122	0.008	0.130
showALSresult	0.097	0.006	0.104
tea	0.120	0.012	0.133
teaMerged	7.267	0.177	7.469
windows	0.127	0.012	0.140