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### Running command:
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###   F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:ISAnalytics.install-out.txt --library=F:\biocbuild\bbs-3.20-bioc\R\library --no-vignettes --timings ISAnalytics_1.16.1.tar.gz
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* using log directory 'F:/biocbuild/bbs-3.20-bioc/meat/ISAnalytics.Rcheck'
* using R version 4.4.2 (2024-10-31 ucrt)
* using platform: x86_64-w64-mingw32
* R was compiled by
    gcc.exe (GCC) 13.3.0
    GNU Fortran (GCC) 13.3.0
* running under: Windows Server 2022 x64 (build 20348)
* using session charset: UTF-8
* using option '--no-vignettes'
* checking for file 'ISAnalytics/DESCRIPTION' ... OK
* this is package 'ISAnalytics' version '1.16.1'
* 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 whether package 'ISAnalytics' 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 ... OK
* checking R code for possible problems ... OK
* checking Rd files ... NOTE
checkRd: (-1) refGenes_hg19.Rd:21: Lost braces; missing escapes or markup?
    21 | \item Download from {http://hgdownload.soe.ucsc.edu/goldenPath/hg19/database/}
       |                     ^
* 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
integration_alluvial_plot      4.05   0.06   10.06
import_parallel_Vispa2Matrices 2.47   0.29   22.07
import_Vispa2_stats            1.84   0.28    7.35
top_cis_overtime_heatmap       1.46   0.15   13.67
sharing_heatmap                1.30   0.02    9.40
CIS_grubbs_overtime            1.17   0.12    7.49
sharing_venn                   1.09   0.09   38.22
realign_after_collisions       0.80   0.08    6.55
HSC_population_plot            0.81   0.06    6.97
iss_source                     0.81   0.05    7.91
is_sharing                     0.80   0.03    8.94
remove_collisions              0.76   0.04    6.45
compute_near_integrations      0.72   0.03   11.39
HSC_population_size_estimate   0.54   0.03    6.34
* 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: 1 NOTE
See
  'F:/biocbuild/bbs-3.20-bioc/meat/ISAnalytics.Rcheck/00check.log'
for details.