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### Running command:
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###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:HiCool.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings HiCool_1.4.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.19-bioc/meat/HiCool.Rcheck’
* using R version 4.4.0 (2024-04-24)
* 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 12.7.1
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘HiCool/DESCRIPTION’ ... OK
* this is package ‘HiCool’ version ‘1.4.0’
* 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 ... NOTE
Found the following hidden files and directories:
  .BBSoptions
These were most likely included in error. See section ‘Package
structure’ in the ‘Writing R Extensions’ manual.
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘HiCool’ can be installed ... NOTE
Found the following notes/warnings:
  Non-staged installation was used
See ‘/Users/biocbuild/bbs-3.19-bioc/meat/HiCool.Rcheck/00install.out’ for details.
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Package listed in more than one of Depends, Imports, Suggests, Enhances:
  ‘rmarkdown’
A package should be listed in only one of these fields.
* 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 ... OK
* 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 line endings in shell scripts ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
            user system elapsed
HiCool    54.513  6.355  61.257
HiCReport 30.540  4.380  37.712
getLoops   6.354  0.672   7.440
* 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: 3 NOTEs
See
  ‘/Users/biocbuild/bbs-3.19-bioc/meat/HiCool.Rcheck/00check.log’
for details.

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### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL HiCool
###
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* installing to library ‘/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library’
* installing *source* package ‘HiCool’ ...
** using non-staged installation via StagedInstall field
** R
** 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
* DONE (HiCool)

R version 4.4.0 (2024-04-24) -- "Puppy Cup"
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.

> library(testthat)
> library(HiCool)
Loading required package: 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("HiCool")
see ?HiContactsData and browseVignettes('HiContactsData') for documentation
loading from cache
see ?HiContactsData and browseVignettes('HiContactsData') for documentation
loading from cache
HiCool :: Recovering bowtie2 genome index from AWS iGenomes...
HiCool :: Initiating processing of fastq files [tmp folder: /tmp/Rtmpz8ewU6/Y0JTRY]...
HiCool :: Mapping fastq files...
[E::idx_find_and_load] Could not retrieve index file for '/tmp/Rtmpz8ewU6/Y0JTRY/tmp/8448c221/temp_alignment.bam'
[E::idx_find_and_load] Could not retrieve index file for '/tmp/Rtmpz8ewU6/Y0JTRY/tmp/8448c221/temp_alignment.bam'
[E::idx_find_and_load] Could not retrieve index file for '/tmp/Rtmpz8ewU6/Y0JTRY/tmp/8448c221/temp_alignment.bam'
[E::idx_find_and_load] Could not retrieve index file for '/tmp/Rtmpz8ewU6/Y0JTRY/tmp/c2853e49/temp_alignment.bam'
[E::idx_find_and_load] Could not retrieve index file for '/tmp/Rtmpz8ewU6/Y0JTRY/tmp/c2853e49/temp_alignment.bam'
[E::idx_find_and_load] Could not retrieve index file for '/tmp/Rtmpz8ewU6/Y0JTRY/tmp/c2853e49/temp_alignment.bam'
[E::idx_find_and_load] Could not retrieve index file for '/tmp/Rtmpz8ewU6/Y0JTRY/tmp/dea0400645f7_7833^mapped-R64-1-1^Y0JTRY.for.bam'
[E::idx_find_and_load] Could not retrieve index file for '/tmp/Rtmpz8ewU6/Y0JTRY/tmp/dea0400645f7_7833^mapped-R64-1-1^Y0JTRY.rev.bam'
INFO:cooler.create:Writing chunk 0: /tmp/Rtmpz8ewU6/Y0JTRY/tmp8_jz9sic.multi.cool::0
INFO:cooler.create:Creating cooler at "/tmp/Rtmpz8ewU6/Y0JTRY/tmp8_jz9sic.multi.cool::/0"
INFO:cooler.create:Writing chroms
INFO:cooler.create:Writing bins
INFO:cooler.create:Writing pixels
INFO:cooler.create:Writing indexes
INFO:cooler.create:Writing info
INFO:cooler.create:Merging into /tmp/Rtmpz8ewU6/Y0JTRY/dea0400645f7_7833^mapped-R64-1-1^Y0JTRY.cool
INFO:cooler.create:Creating cooler at "/tmp/Rtmpz8ewU6/Y0JTRY/dea0400645f7_7833^mapped-R64-1-1^Y0JTRY.cool::/"
INFO:cooler.create:Writing chroms
INFO:cooler.create:Writing bins
INFO:cooler.create:Writing pixels
INFO:cooler.reduce:nnzs: [60531]
INFO:cooler.reduce:current: [60531]
INFO:cooler.create:Writing indexes
INFO:cooler.create:Writing info
HiCool :: Best-suited minimum resolution automatically inferred: 1000
HiCool :: Removing unwanted chromosomes...
HiCool :: Parsing pairs into .cool file...
HiCool :: Generating multi-resolution .mcool file...
HiCool :: Balancing .mcool file...
HiCool :: Tidying up everything for you...
HiCool :: .fastq to .mcool processing done!
HiCool :: Check ./HiCool/folder to find the generated files
HiCool :: Generating HiCool report. This might take a while.
HiCool :: Report generated and available @ /Users/biocbuild/bbs-3.19-bioc/meat/HiCool.Rcheck/tests/testthat/HiCool/dea0400645f7_7833^mapped-R64-1-1^Y0JTRY.html
HiCool :: All processing successfully achieved. Congrats!
see ?HiContactsData and browseVignettes('HiContactsData') for documentation
loading from cache
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 3 ]
> 
> proc.time()
   user  system elapsed 
 73.300   8.237  79.078