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### Running command:
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###   /home/biocbuild/R/R-4.3.1/bin/R CMD check --install=check:HiCExperiment.install-out.txt --library=/home/biocbuild/R/R-4.3.1/site-library --timings HiCExperiment_1.2.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.18-bioc/meat/HiCExperiment.Rcheck’
* using R version 4.3.1 (2023-06-16)
* using platform: aarch64-unknown-linux-gnu (64-bit)
* R was compiled by
    gcc (GCC) 10.3.1
    GNU Fortran (GCC) 10.3.1
* running under: openEuler 22.03 (LTS-SP1)
* using session charset: UTF-8
* checking for file ‘HiCExperiment/DESCRIPTION’ ... OK
* this is package ‘HiCExperiment’ 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 ‘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 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 loading without being on the library search path ... OK
* checking 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'.
* 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    152.075  3.957 164.560
HiCExperiment      22.318  2.626  34.212
AggrHiCExperiment  14.053  1.306  19.226
HicproFile-class    5.319  0.832  13.595
export-methods      4.904  0.498   8.429
data                3.700  0.256   6.329
CoolFile-class      3.538  0.407   9.104
HicFile-class       3.579  0.260   9.111
as                  2.928  0.383   5.662
* 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 ...
  ‘HiCExperiment.Rmd’ using ‘UTF-8’... OK
 NONE
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: 2 NOTEs
See
  ‘/home/biocbuild/bbs-3.18-bioc/meat/HiCExperiment.Rcheck/00check.log’
for details.