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###
### Running command:
###
###   D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:multiHiCcompare.install-out.txt --library=D:\biocbuild\bbs-3.15-bioc\R\library --no-vignettes --timings multiHiCcompare_1.13.0.tar.gz
###
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* using log directory 'D:/biocbuild/bbs-3.15-bioc/meat/multiHiCcompare.Rcheck'
* using R Under development (unstable) (2021-11-21 r81221)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'multiHiCcompare/DESCRIPTION' ... OK
* this is package 'multiHiCcompare' version '1.13.0'
* 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 whether package 'multiHiCcompare' 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
.count_manhattan: no visible global function definition for 'textxy'
cyclic_loess: no visible binding for global variable 'chr'
cyclic_loess: no visible binding for global variable 'region1'
cyclic_loess: no visible binding for global variable 'region2'
exportJuicebox: no visible binding for global variable 'logCPM'
exportJuicebox: no visible binding for global variable 'logFC'
exportJuicebox: no visible binding for global variable 'p.adj'
fastlo: no visible binding for global variable 'chr'
fastlo: no visible binding for global variable 'region1'
fastlo: no visible binding for global variable 'region2'
hic_exactTest: no visible binding for global variable 'chr'
hic_exactTest: no visible binding for global variable 'region1'
hic_exactTest: no visible binding for global variable 'region2'
hic_filter: no visible binding for global variable 'hg19_cyto'
hic_glm: no visible binding for global variable 'chr'
hic_glm: no visible binding for global variable 'region1'
hic_glm: no visible binding for global variable 'region2'
make_hicexp: no visible binding for global variable 'hg19_cyto'
make_hicexp: no visible binding for global variable 'region2'
make_hicexp: no visible binding for global variable 'region1'
make_hicexp: no visible binding for global variable 'chr'
perm_test: no visible binding for global variable 'chr'
perm_test: no visible global function definition for 'IRanges'
topDirs: no visible binding for global variable 'logCPM'
topDirs: no visible binding for global variable 'logFC'
topDirs: no visible binding for global variable 'p.adj'
Undefined global functions or variables:
  IRanges chr hg19_cyto logCPM logFC p.adj region1 region2 textxy
* 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 LazyData ... OK
* checking data for ASCII and uncompressed saves ... 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 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: 1 NOTE
See
  'D:/biocbuild/bbs-3.15-bioc/meat/multiHiCcompare.Rcheck/00check.log'
for details.

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###
### Running command:
###
###   D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD INSTALL multiHiCcompare
###
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* installing to library 'D:/biocbuild/bbs-3.15-bioc/R/library'
* installing *source* package 'multiHiCcompare' ...
** using staged installation
** R
** data
*** moving datasets to lazyload DB
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'multiHiCcompare'
    finding HTML links ... done
    HCT116_r1                               html  
    HCT116_r2                               html  
    HCT116_r3                               html  
    HCT116_r4                               html  
    HCT116_r5                               html  
    HCT116_r6                               html  
    Hicexp-class                            html  
    MD_composite                            html  
    MD_hicexp                               html  
    cyclic_loess                            html  
    exportJuicebox                          html  
    fastlo                                  html  
    hg19_cyto                               html  
    hg38_cyto                               html  
    hic_exactTest                           html  
    hic_filter                              html  
    hic_glm                                 html  
    hic_scale                               html  
    hic_table                               html  
    hicexp2                                 html  
    hicexp_diff                             html  
    make_hicexp                             html  
    manhattan_hicexp                        html  
    meta                                    html  
    normalized                              html  
    perm_test                               html  
    plot_counts                             html  
    plot_pvals                              html  
    pval_heatmap                            html  
    resolution                              html  
    results                                 html  
    show                                    html  
    smartApply                              html  
    topDirs                                 html  
** 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 (multiHiCcompare)
Making 'packages.html' ... done

R Under development (unstable) (2021-11-21 r81221) -- "Unsuffered Consequences"
Copyright (C) 2021 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64 (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(multiHiCcompare)
> 
> test_check("multiHiCcompare")
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 17 ]
> 
> proc.time()
   user  system elapsed 
  32.15    1.00   33.04