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###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:DegCre.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings DegCre_1.2.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.20-bioc/meat/DegCre.Rcheck’
* using R version 4.4.2 (2024-10-31)
* using platform: x86_64-apple-darwin20
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    GNU Fortran (GCC) 12.2.0
* running under: macOS Monterey 12.7.6
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘DegCre/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘DegCre’ version ‘1.2.0’
* 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 ‘DegCre’ 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 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
calcPadjsAndEtpFun: multiple local function definitions for ‘tpFun’
  with different formal arguments
convDegCreResListToCreGeneScoreGR: no visible global function
  definition for ‘calcAdjAssocProbOR’
Undefined global functions or variables:
  calcAdjAssocProbOR
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... WARNING
Missing link or links in Rd file 'convDegCreResListToCreGeneScoreGR.Rd':
  ‘calcAdjAssocProbOR’

See section 'Cross-references' in the 'Writing R Extensions' manual.
* 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 files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                                     user system elapsed
optimizeAlphaDegCre                21.235  0.385  27.698
plotBrowserDegCre                  20.707  0.554  26.635
degCrePRAUC                        18.594  1.979  25.490
plotExpectedAssocsPerDeg           11.242  0.166  14.560
getExpectAssocPerDEG               11.217  0.181  14.602
calcAssocProbOR                     6.050  0.148   7.451
calcRawAssocProbOR                  5.550  0.158   6.894
runDegCre                           5.604  0.087   8.051
plotDegCreAssocProbVsDist           5.505  0.115   7.208
getDistBinNullAssocProb             5.347  0.113   7.210
collapseDegCreToGene                4.819  0.160   6.101
convertdegCreResListToGInteraction  4.753  0.080   5.906
convertDegCreDataFrame              4.641  0.111   5.662
convDegCreResListToCreGeneScoreGR   4.578  0.074   5.497
plotDegCreBinHeuristic              4.343  0.094   5.630
* 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, 1 NOTE
See
  ‘/Users/biocbuild/bbs-3.20-bioc/meat/DegCre.Rcheck/00check.log’
for details.

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###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL DegCre
###
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* installing to library ‘/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library’
* installing *source* package ‘DegCre’ ...
** using staged installation
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
*** copying figures
** 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 (DegCre)

R version 4.4.2 (2024-10-31) -- "Pile of Leaves"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin20

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.

> # This file is part of the standard setup for testthat.
> # It is recommended that you do not modify it.
> #
> # Where should you do additional test configuration?
> # Learn more about the roles of various files in:
> # * https://r-pkgs.org/testing-design.html#sec-tests-files-overview
> # * https://testthat.r-lib.org/articles/special-files.html
> 
> library(testthat)
> library(DegCre)

> 
> test_check("DegCre")
Processing associations for gene collapse
Using GeneSymb as gene name column.
Minimum display region size = 29091 bp.
All smaller regions will be expanded.
ACOT7 promoters have been merged for plotting.
HES2 promoters have been merged for plotting.
ERRFI1 promoters have been merged for plotting.
SLC2A5 promoters have been merged for plotting.
GPR157 promoters have been merged for plotting.
SPSB1 promoters have been merged for plotting.
arches[arches1]
heatmapLegend[heatmapLegend1]
signal[signal1_h]
yaxis[yaxis1]
genomeLabel[genomeLabel1]
genes[genes1]
genes[genes2]
text[text1]
text[text2]
text[text2]
Analyzing 34169 DegGR to CreGR hits for optimal distance bin size.
Hit distance bin n = 2277
Small last bin resolved.
Running over 16 hit distance thresholds
Adjusting association probability for distance.
Calculation of assoc probabilities over hit bins complete.
Assoc FDR calculation complete.
DegCre calculations complete.
[ FAIL 0 | WARN 3 | SKIP 0 | PASS 38 ]

[ FAIL 0 | WARN 3 | SKIP 0 | PASS 38 ]
> 
> proc.time()
   user  system elapsed 
145.656   4.112 201.240