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###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:HiCExperiment.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings HiCExperiment_1.6.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.20-bioc/meat/HiCExperiment.Rcheck’
* using R version 4.4.2 (2024-10-31)
* using platform: aarch64-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 Ventura 13.7.1
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘HiCExperiment/DESCRIPTION’ ... OK
* this is package ‘HiCExperiment’ version ‘1.6.0’
* 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 ‘HiCExperiment’ 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 whether startup messages can be suppressed ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... NOTE
Foreign function call to a different package:
  .Call("_H5Fis_hdf5", ..., PACKAGE = "rhdf5")
See chapter ‘System and foreign language interfaces’ in the ‘Writing R
Extensions’ manual.
* checking R code for possible problems ... NOTE
File ‘HiCExperiment/R/zzz.R’:
  .onLoad calls:
    packageStartupMessage("Consider using the `HiContacts` package to perform advanced genomic operations \non `HiCExperiment` objects.\n\nRead \"Orchestrating Hi-C analysis with Bioconductor\" online book to learn more:\nhttps://js2264.github.io/OHCA/")

See section ‘Good practice’ in '?.onAttach'.

.pairs2gi: no visible global function definition for ‘read.delim’
.pairs2gi: no visible global function definition for ‘tail’
Undefined global functions or variables:
  read.delim tail
Consider adding
  importFrom("utils", "read.delim", "tail")
to your NAMESPACE file.
* 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 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
import-methods    72.629  9.705  80.786
HiCExperiment     17.416  1.785  22.070
AggrHiCExperiment 15.010  1.335  17.817
HicproFile-class   4.770  0.560   7.888
export-methods     4.728  0.543   6.191
HicFile-class      3.075  0.429   5.427
CoolFile-class     3.019  0.480   5.344
* 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: 2 NOTEs
See
  ‘/Users/biocbuild/bbs-3.20-bioc/meat/HiCExperiment.Rcheck/00check.log’
for details.

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###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL HiCExperiment
###
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* installing to library ‘/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library’
* installing *source* package ‘HiCExperiment’ ...
** 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 (HiCExperiment)

R version 4.4.2 (2024-10-31) -- "Pile of Leaves"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: aarch64-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/tests.html
> # * https://testthat.r-lib.org/reference/test_package.html#special-files
> 
> library(testthat)
> library(HiCExperiment)
Consider using the `HiContacts` package to perform advanced genomic operations 
on `HiCExperiment` objects.

Read "Orchestrating Hi-C analysis with Bioconductor" online book to learn more:
https://js2264.github.io/OHCA/
> 
> test_check("HiCExperiment")
see ?HiContactsData and browseVignettes('HiContactsData') for documentation
loading from cache
see ?HiContactsData and browseVignettes('HiContactsData') for documentation
loading from cache
see ?HiContactsData and browseVignettes('HiContactsData') for documentation
loading from cache
see ?HiContactsData and browseVignettes('HiContactsData') for documentation
loading from cache
see ?HiContactsData and browseVignettes('HiContactsData') for documentation
loading from cache
see ?HiContactsData and browseVignettes('HiContactsData') for documentation
loading from cache
resolutions(1): 1000

resolutions(5): 1000 2000 4000 8000 16000

resolutions(1): 1000

resolutions(5): 1000 2000 4000 8000 16000

CoolFile object
.mcool file: /Users/biocbuild/Library/Caches/org.R-project.R/R/ExperimentHub/c600771c3c5f_7751 
resolution: 1000 
pairs file: 
metadata(0):
see ?HiContactsData and browseVignettes('HiContactsData') for documentation
loading from cache
`HiCExperiment` object with 8,757,906 contacts over 763 regions 
-------
fileName: "/Users/biocbuild/Library/Caches/org.R-project.R/R/ExperimentHub/c6006ad7b8a8_7752" 
focus: "II" 
resolutions(5): 1000 2000 4000 8000 16000
active resolution: 16000 
interactions: 267709 
scores(3): count balanced test 
topologicalFeatures: compartments(0) borders(0) loops(0) viewpoints(0) centromeres(16) test(0) 
pairsFile: /Users/biocbuild/Library/Caches/org.R-project.R/R/ExperimentHub/c60011681905_7753 
metadata(1): test
resolutions(5): 1000 2000 4000 8000 16000

resolutions(5): 1000 2000 4000 8000 16000

HicFile object
.hic file: /Users/biocbuild/Library/Caches/org.R-project.R/R/ExperimentHub/c6001c69e56_7836 
resolution: 1000 
pairs file: 
metadata(0):

HicproFile object
HiC-Pro files:
  $ matrix:   /Users/biocbuild/Library/Caches/org.R-project.R/R/ExperimentHub/c60016c52103_7837 
  $ regions:  /Users/biocbuild/Library/Caches/org.R-project.R/R/ExperimentHub/c60067fa57a2_7838 
resolution: 1000 
pairs file: 
metadata(0):



Going through preflight checklist...
Parsing the entire contact matrice as a sparse matrix...
Modeling distance decay...
Filtering for contacts within provided targets...
`AggrHiCExperiment` object over 2 targets 
-------
fileName: "/Users/biocbuild/Library/Caches/org.R-project.R/R/ExperimentHub/c6006ad7b8a8_7752" 
focus: 2 targets 
resolutions(5): 1000 2000 4000 8000 16000
active resolution: 8000 
interactions: 10201 
scores(4): count balanced expected detrended 
slices(4): count balanced expected detrended 
topologicalFeatures: targets(2) 
pairsFile: N/A 
metadata(0):
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 168 ]
> 
> proc.time()
   user  system elapsed 
344.395  45.277 377.263