##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:exomePeak2.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings exomePeak2_1.6.1.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.14-bioc/meat/exomePeak2.Rcheck’
* using R version 4.1.3 (2022-03-10)
* using platform: x86_64-apple-darwin17.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘exomePeak2/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘exomePeak2’ version ‘1.6.1’
* 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 ‘exomePeak2’ 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 ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
Results,SummarizedExomePeak: no visible global function definition for
  ‘glm_M’
exomePeakCalling,MeripBamFileList: no visible global function
  definition for ‘metadata’
exomePeakCalling,MeripBamFileList: no visible global function
  definition for ‘%over%’
plotLfcGC,SummarizedExomePeak: no visible binding for global variable
  ‘GC_idx’
plotLfcGC,SummarizedExomePeak: no visible binding for global variable
  ‘Log2FC’
plotLfcGC,SummarizedExomePeak: no visible binding for global variable
  ‘Label’
plotReadsGC,SummarizedExomePeak: no visible binding for global variable
  ‘GC_cont’
plotReadsGC,SummarizedExomePeak: no visible binding for global variable
  ‘value’
plotSizeFactors,SummarizedExomePeak: no visible binding for global
  variable ‘samples’
plotSizeFactors,SummarizedExomePeak: no visible binding for global
  variable ‘size_factors’
plotSizeFactors,SummarizedExomePeak: no visible binding for global
  variable ‘Estimation_Methods’
Undefined global functions or variables:
  %over% Estimation_Methods GC_cont GC_idx Label Log2FC glm_M metadata
  samples size_factors value
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... WARNING
Codoc mismatches from documentation object 'exomePeakCalling-methods':
exomePeakCalling
  Code: function(merip_bams = NULL, txdb = NULL, bsgenome = NULL,
                 genome = NA, mod_annot = NULL, glm_type = c("DESeq2",
                 "NB", "Poisson"), background_method =
                 c("Gaussian_mixture", "m6Aseq_prior", "manual",
                 "all"), manual_background = NULL, correct_GC_bg =
                 TRUE, qtnorm = FALSE, gff_dir = NULL, fragment_length
                 = 100, binding_length = 25, step_length =
                 binding_length, min_peak_width = fragment_length/2,
                 max_peak_width = fragment_length * 100,
                 pc_count_cutoff = 5, bg_count_cutoff = 50, p_cutoff =
                 1e-05, p_adj_cutoff = NULL, log2FC_cutoff = 0,
                 parallel = 3, bp_param = NULL)
  Docs: function(merip_bams = NULL, txdb = NULL, bsgenome = NULL,
                 genome = NA, mod_annot = NULL, glm_type = c("DESeq2",
                 "NB", "Poisson"), background_method = c("all",
                 "Gaussian_mixture", "m6Aseq_prior", "manual"),
                 manual_background = NULL, correct_GC_bg = TRUE, qtnorm
                 = FALSE, gff_dir = NULL, fragment_length = 100,
                 binding_length = 25, step_length = binding_length,
                 min_peak_width = fragment_length/2, max_peak_width =
                 fragment_length * 100, pc_count_cutoff = 5,
                 bg_count_cutoff = 50, p_cutoff = 1e-05, p_adj_cutoff =
                 NULL, log2FC_cutoff = 0, parallel = 3, bp_param =
                 NULL)
  Mismatches in argument default values:
    Name: 'background_method' Code: c("Gaussian_mixture", "m6Aseq_prior", "manual", "all") Docs: c("all", "Gaussian_mixture", "m6Aseq_prior", "manual")

* checking Rd \usage sections ... WARNING
Undocumented arguments in documentation object 'exomePeakCalling-methods'
  ‘max_peak_width’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                             user system elapsed
exomePeak2                121.737  0.545 122.401
exomePeakCalling-methods   69.909  0.273  70.246
SummarizedExomePeak-class  43.949  0.897  44.912
glmM-methods                9.383  0.013   9.403
glmDM-methods               9.065  0.011   9.080
* 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 WARNINGs, 1 NOTE
See
  ‘/Users/biocbuild/bbs-3.14-bioc/meat/exomePeak2.Rcheck/00check.log’
for details.

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL exomePeak2
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.1/Resources/library’
* installing *source* package ‘exomePeak2’ ...
** 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 (exomePeak2)