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###
### Running command:
###
###   /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD check --install=check:HiCParser.install-out.txt --library=/home/biocbuild/bbs-3.22-bioc/R/site-library --timings HiCParser_1.1.1.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.22-bioc/meat/HiCParser.Rcheck’
* using R version 4.5.1 (2025-06-13)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
    GNU Fortran (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
* running under: Ubuntu 24.04.2 LTS
* using session charset: UTF-8
* checking for file ‘HiCParser/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘HiCParser’ version ‘1.1.1’
* 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 ‘HiCParser’ can be installed ... OK
* used C++ compiler: ‘g++ (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0’
* 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 loading without being on the library search path ... 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
.parseOneCool: no visible binding for global variable ‘start’
.parseOneCool: no visible binding for global variable ‘end’
.parseOneCool: no visible binding for global variable ‘chromosome’
.parseOneCool: no visible binding for global variable ‘index’
.parseOneCool: no visible binding for global variable ‘id1’
.parseOneCool: no visible binding for global variable ‘id2’
.parseOneHiCPro: no visible binding for global variable ‘chromosome’
.parseOneHiCPro: no visible binding for global variable ‘start’
.parseOneHiCPro: no visible binding for global variable ‘end’
.parseOneHiCPro: no visible binding for global variable ‘index’
.parseOneHiCPro: no visible binding for global variable ‘startIndex’
.parseOneHiCPro: no visible binding for global variable ‘stopIndex’
.setFromTabular: no visible binding for global variable ‘chromosome’
.setFromTabular: no visible binding for global variable ‘position 1’
.setFromTabular: no visible binding for global variable ‘position 2’
.setFromTabular: no visible global function definition for ‘.’
.setFromTabular: no visible binding for global variable ‘bin.1’
.setFromTabular: no visible binding for global variable ‘bin.2’
.setFromTabular: no visible binding for global variable ‘variable’
.setFromTabular: no visible binding for global variable ‘indexC’
.setFromTabular: no visible binding for global variable ‘index’
.setFromTabular: no visible binding for global variable ‘end’
.setFromTabular: no visible binding for global variable ‘start’
Undefined global functions or variables:
  . bin.1 bin.2 chromosome end id1 id2 index indexC position 1 position
  2 start startIndex stopIndex variable
Consider adding
  importFrom("stats", "end", "start")
to your NAMESPACE file.
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... NOTE
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  mergeInteractionSet.Rd: InteractionSet
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
* 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 line endings in C/C++/Fortran sources/headers ... OK
* checking line endings in Makefiles ... OK
* checking compilation flags in Makevars ... OK
* checking for GNU extensions in Makefiles ... OK
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking use of PKG_*FLAGS in Makefiles ... OK
* checking compiled code ... NOTE
Note: information on .o files is not available
* 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 ... OK
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: 3 NOTEs
See
  ‘/home/biocbuild/bbs-3.22-bioc/meat/HiCParser.Rcheck/00check.log’
for details.

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###
### Running command:
###
###   /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD INSTALL HiCParser
###
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* installing to library ‘/home/biocbuild/bbs-3.22-bioc/R/site-library’
* installing *source* package ‘HiCParser’ ...
** this is package ‘HiCParser’ version ‘1.1.1’
** using staged installation
** libs
using C++ compiler: ‘g++ (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0’
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/Rcpp/include' -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security  -c RcppExports.cpp -o RcppExports.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/Rcpp/include' -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security  -c parseHiCFile.cpp -o parseHiCFile.o
g++ -std=gnu++17 -shared -L/home/biocbuild/bbs-3.22-bioc/R/lib -L/usr/local/lib -o HiCParser.so RcppExports.o parseHiCFile.o -lz -L/home/biocbuild/bbs-3.22-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.22-bioc/R/site-library/00LOCK-HiCParser/00new/HiCParser/libs
** 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
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (HiCParser)

R version 4.5.1 (2025-06-13) -- "Great Square Root"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu

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(HiCParser)
> 
> test_check("HiCParser")
Loading required namespace: rhdf5
Parsing '/home/biocbuild/bbs-3.22-bioc/R/site-library/HiCParser/extdata/hicsample_21.tsv'.

Parsing '/home/biocbuild/bbs-3.22-bioc/R/site-library/HiCParser/extdata/hicsample_21.hic'.

Parsing '/home/biocbuild/bbs-3.22-bioc/R/site-library/HiCParser/extdata/hicsample_21.hic'.

Parsing '/home/biocbuild/bbs-3.22-bioc/R/site-library/HiCParser/extdata/hicsample_21.hic'.
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 48 ]
> 
> proc.time()
   user  system elapsed 
 10.417   0.571  10.977