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### Running command:
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###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:RgnTX.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings RgnTX_1.8.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.20-bioc/meat/RgnTX.Rcheck’
* using R version 4.4.2 (2024-10-31)
* 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 12.7.6
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘RgnTX/DESCRIPTION’ ... OK
* this is package ‘RgnTX’ version ‘1.8.0’
* 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 ‘RgnTX’ 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 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 files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                          user system elapsed
shiftedZScoreTx         84.957  1.167  97.978
permTestTxIA            51.274  0.696  54.032
permTestTxIA_customPick 50.869  0.569  55.035
permTestTx              42.853  0.480  45.189
permTestTx_customPick   36.909  0.389  42.590
permTestTx_customAll    33.722  0.366  37.031
overlapCountsTxIA       17.854  0.420  18.660
randomizeFeaturesTx     14.894  0.201  17.198
distanceTx              14.708  0.222  15.272
overlapWidthTx          14.552  0.177  14.890
getStopCodon            12.312  0.173  12.736
GRangesList2GRanges      9.877  0.573  10.750
randomizeTransByOrder    9.719  0.082  10.951
randomizeFeaturesTxIA    9.324  0.131  10.724
overlapCountsTx          8.934  0.160   9.181
randomizeTx              8.159  0.116   9.029
getPermSpaceByFeatures   6.911  0.166   7.299
getPermSpaceByTxID       6.677  0.095   6.957
calculateShift           6.085  0.219   6.618
getPermSpaceByType       5.513  0.082   5.688
extractRegions           5.208  0.086   5.519
shiftTx                  5.157  0.067   5.479
* 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: OK