Package: flowStats

Version: 3.45.2

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:flowStats.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings flowStats_3.45.2.tar.gz

StartedAt: 2020-01-16 04:32:46 -0500 (Thu, 16 Jan 2020)

EndedAt: 2020-01-16 04:38:14 -0500 (Thu, 16 Jan 2020)

EllapsedTime: 328.3 seconds

RetCode: 0

Status:  WARNINGS

CheckDir: flowStats.Rcheck

Warnings: 4

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:flowStats.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings flowStats_3.45.2.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.11-bioc/meat/flowStats.Rcheck’
* using R Under development (unstable) (2019-12-14 r77572)
* using platform: x86_64-apple-darwin15.6.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘flowStats/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘flowStats’ version ‘3.45.2’
* package encoding: UTF-8
* 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 ‘flowStats’ 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
Missing object imported by a ':::' call: ‘flowWorkspace:::.isBooleanGate.graphNEL’
Unexported objects imported by ':::' calls:
  ‘flowCore:::checkClass’ ‘flowCore:::copyFlowSet’
  ‘flowCore:::findTimeChannel’ ‘flowCore:::inPolygon’
  ‘flowViz:::evalError’ ‘flowViz:::plotType’
  See the note in ?`:::` about the use of this operator.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
.plotGPAprocess: no visible binding for global variable ‘whichS’
.plotGPAprocess: no visible binding for global variable ‘cluster’
.plotWorkFlow: no visible binding for global variable ‘cluster’
.plotWorkFlow: no visible binding for global variable ‘bogus’
.usingSVD: no visible binding for global variable ‘params’
density1d_simple: no visible binding for global variable ‘y’
normQA: no visible binding for global variable ‘group’
normQA: no visible binding for global variable ‘hasPeak’
Undefined global functions or variables:
  bogus cluster group hasPeak params whichS y
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... WARNING
Missing link or links in documentation object 'autoGate.Rd':
  ‘[flowCore:norm2Filter-class]{norm2Filter}’

Missing link or links in documentation object 'lymphGate.Rd':
  ‘[flowCore:norm2Filter-class]{norm2Filter}’

See section 'Cross-references' in the 'Writing R Extensions' manual.

* checking for missing documentation entries ... WARNING
Undocumented S4 methods:
  generic '%in%' and siglist 'flowFrame,norm2Filter'
All user-level objects in a package (including S4 classes and methods)
should have documentation entries.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
* checking for code/documentation mismatches ... WARNING
Codoc mismatches from documentation object 'spillover-flowSet':
\S4method{spillover}{flowSet}
  Code: function(x, unstained = NULL, fsc = "FSC-A", ssc = "SSC-A",
                 patt = NULL, method = "median", stain_match =
                 c("intensity", "ordered", "regexpr"), useNormFilt =
                 FALSE, prematched = FALSE, exact_match = FALSE)
  Docs: function(x, unstained = NULL, fsc = "FSC-A", ssc = "SSC-A",
                 patt = NULL, method = "median", stain_match =
                 c("intensity", "ordered", "regexpr"), useNormFilt =
                 FALSE, prematched = FALSE)
  Argument names in code not in docs:
    exact_match

Codoc mismatches from documentation object 'warpSet':
warpSet
  Code: function(x, ...)
  Docs: function(x, stains, grouping = NULL, monwrd = TRUE, subsample =
                 NULL, peakNr = NULL, clipRange = 0.01, nbreaks = 11,
                 fres, bwFac = 2, warpFuns = FALSE, target = NULL, ...)
  Argument names in docs not in code:
    stains grouping monwrd subsample peakNr clipRange nbreaks fres
    bwFac warpFuns target
  Mismatches in argument names:
    Position: 2 Code: ... Docs: stains

* 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 ... WARNING
  Warning: package needs dependence on R (>= 2.10)
* 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
warpSet   26.638  9.610  36.397
gaussNorm  8.310  1.300   9.621
rangeGate  5.215  0.868   6.267
gpaSet     5.660  0.317   5.980
lymphGate  4.720  0.509   5.233
density1d  4.299  0.866   5.166
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’
 OK
* 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: 4 WARNINGs, 2 NOTEs
See
  ‘/Users/biocbuild/bbs-3.11-bioc/meat/flowStats.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 flowStats
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* installing to library ‘/Library/Frameworks/R.framework/Versions/4.0/Resources/library’
* installing *source* package ‘flowStats’ ...
** 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 (flowStats)

R Under development (unstable) (2019-12-14 r77572) -- "Unsuffered Consequences"
Copyright (C) 2019 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin15.6.0 (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> library(testthat)
> library(flowStats)
> 
> test_check("flowStats")

Estimating landmarks for channel CD4 ...
Registering curves for parameter CD4 ...
══ testthat results  ═══════════════════════════════════════════════════════════
[ OK: 23 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 0 ]
> 
> proc.time()
   user  system elapsed 
 26.203   4.408  24.324 

name	user	system	elapsed
autoGate	2.975	0.228	3.204
binByRef	1.375	0.229	1.604
calcPBChiSquare	1.032	0.193	1.225
calcPearsonChi	1.438	0.156	1.606
curv1Filter-class	0.478	0.036	0.514
curv2Filter-class	2.574	0.494	3.068
curvPeaks	0.962	0.243	1.205
density1d	4.299	0.866	5.166
gate_singlet	0.000	0.000	0.001
gaussNorm	8.310	1.300	9.621
gpaSet	5.660	0.317	5.980
iProcrustes	0.276	0.005	0.283
idFeaturesByBackgating	2.036	0.033	2.070
landmarkMatrix	1.209	0.250	1.458
lymphGate	4.720	0.509	5.233
norm2Filter-class	0.186	0.012	0.199
normalize	0.001	0.001	0.002
overton_like	0.018	0.010	0.028
plotBins	1.189	0.213	1.402
proBin	0.914	0.156	1.070
quadrantGate	0.000	0.000	0.001
rangeGate	5.215	0.868	6.267
warpSet	26.638	9.610	36.397