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###
### Running command:
###
###   /home/biocbuild/R/R/bin/R CMD check --install=check:flowPloidy.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings flowPloidy_1.37.1.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.23-bioc/meat/flowPloidy.Rcheck’
* using R Under development (unstable) (2025-02-19 r87757)
* using platform: aarch64-unknown-linux-gnu
* R was compiled by
    aarch64-unknown-linux-gnu-gcc (GCC) 14.2.0
    GNU Fortran (GCC) 14.2.0
* running under: openEuler 24.03 (LTS-SP1)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘flowPloidy/DESCRIPTION’ ... OK
* this is package ‘flowPloidy’ version ‘1.37.1’
* 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 ‘flowPloidy’ 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 code 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 loading without being on the library search path ... 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
fhMetadata : <anonymous>: no visible global function definition for
  ‘quantile’
Undefined global functions or variables:
  quantile
Consider adding
  importFrom("stats", "quantile")
to your NAMESPACE file.
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... NOTE
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  FlowHist.Rd: read.FCS, flowFrame
  fhDoCV.Rd: deltaMethod
  fhDoNLS.Rd: nlsLM
  fhMetadata.Rd: read.FCS
  findPeaks.Rd: runmax, runmean
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... WARNING
Codoc mismatches from Rd file 'FlowHist.Rd':
FlowHist
  Code: function(file, channel, bins = 256, analyze = TRUE, linearity =
                 "variable", debris = "SC", samples = 2, pick = FALSE,
                 standards = 0, g2 = TRUE, debrisLimit = 40,
                 truncate_max_range = TRUE, trimRaw = 0, nameField =
                 "GUID", ...)
  Docs: function(file, channel, bins = 256, analyze = TRUE, linearity =
                 "variable", debris = "SC", samples = 2, pick = FALSE,
                 standards = 0, g2 = TRUE, debrisLimit = 40,
                 truncate_max_range = TRUE, trimRaw = 0, ...)
  Argument names in code not in docs:
    nameField
  Mismatches in argument names:
    Position: 14 Code: nameField Docs: ...

Codoc mismatches from Rd file 'plot.FlowHist.Rd':
plot.FlowHist
  Code: function(x, init = FALSE, nls = TRUE, comps = TRUE, main =
                 fhName(x), ...)
  Docs: function(x, init = FALSE, nls = TRUE, comps = TRUE, main =
                 fhFile(x), ...)
  Mismatches in argument default values:
    Name: 'main' Code: fhName(x) Docs: fhFile(x)

Codoc mismatches from Rd file 'plotFH.Rd':
plotFH
  Code: function(fh, main = fhName(fh), ...)
  Docs: function(fh, main = fhFile(fh), ...)
  Mismatches in argument default values:
    Name: 'main' Code: fhName(fh) Docs: fhFile(fh)

* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’
 OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 1 WARNING, 2 NOTEs
See
  ‘/home/biocbuild/bbs-3.23-bioc/meat/flowPloidy.Rcheck/00check.log’
for details.

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###
### Running command:
###
###   /home/biocbuild/R/R/bin/R CMD INSTALL flowPloidy
###
##############################################################################
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* installing to library ‘/home/biocbuild/R/R-devel_2025-02-19/site-library’
* installing *source* package ‘flowPloidy’ ...
** this is package ‘flowPloidy’ version ‘1.37.1’
** 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 (flowPloidy)

R Under development (unstable) (2025-02-19 r87757) -- "Unsuffered Consequences"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: aarch64-unknown-linux-gnu

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(flowPloidy)
> 
> test_check("flowPloidy")
FlowHist object '188-15.LMD'
channel: FL3.INT.LIN
2 samples
bins: 256
linearity: variable
debris: SC
7 model components: a1, a2, a_s, b1, b_s, SC, AG
12 parameters: a1P, a_mean, a_stddev, a2P, linearity, a_sP, b1P, b_mean, b_stddev, b_sP, SCaP, AP
5 special parameters: xx, SCvals, DBvals, TRvals, QDvals
Model fit

Analysis
========

Counts
------
 a1_count  a2_count a_s_count  b1_count b_s_count 
  1442.99    336.58      0.00   2820.64    405.87 

Peak Sizes
----------
a_mean b_mean 
 99.04 136.12 

CVs
---
a_CV b_CV 
 2.2  2.0 

RCS: 1.589 
FlowHist object '222.LMD'
channel: FL3.INT.LIN
2 samples
bins: 256
linearity: variable
debris: SC
8 model components: a1, a2, a_s, b1, b2, b_s, SC, AG
13 parameters: a1P, a_mean, a_stddev, a2P, linearity, a_sP, b1P, b_mean, b_stddev, b2P, b_sP, SCaP, AP
5 special parameters: xx, SCvals, DBvals, TRvals, QDvals
Model fitting not complete

RCS: NA 
FlowHist object '240+S.LMD'
channel: FL3.INT.LIN
2 samples
bins: 256
linearity: variable
debris: MC
7 model components: a1, a2, a_s, b1, b_s, MC, AG
13 parameters: a1P, a_mean, a_stddev, a2P, linearity, a_sP, b1P, b_mean, b_stddev, b_sP, MCaP, k, AP
5 special parameters: xx, MCvals, DBvals, TRvals, QDvals
Model fit

Analysis
========

Counts
------
 a1_count  a2_count a_s_count  b1_count b_s_count 
   664.23      0.00    195.73   3269.65      0.00 

Peak Sizes
----------
a_mean b_mean 
 77.10 160.79 

CVs
---
a_CV b_CV 
 4.8  7.7 

RCS: 2.22 
FlowHist object '08.328'
channel: FL2.A
2 samples
bins: 256
linearity: variable
debris: SC
0 model components: 
0 parameters: 
0 special parameters: 
Model fitting not complete

RCS: NA 
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 26 ]
> 
> proc.time()
   user  system elapsed 
  4.310   0.164   4.478