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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_1.4.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.18-bioc/meat/RgnTX.Rcheck’
* using R version 4.3.3 (2024-02-29)
* using platform: x86_64-apple-darwin20 (64-bit)
* 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 ‘RgnTX/DESCRIPTION’ ... OK
* this is package ‘RgnTX’ 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 ... 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 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 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         82.521  1.634  99.089
permTestTxIA_customPick 50.305  0.497  53.966
permTestTxIA            48.621  0.654  52.067
permTestTx              43.132  0.500  46.116
permTestTx_customPick   35.318  0.323  38.826
permTestTx_customAll    32.226  0.305  35.788
overlapCountsTxIA       18.697  0.340  19.652
overlapWidthTx          14.929  0.253  15.914
distanceTx              14.623  0.245  15.697
getStopCodon            13.586  0.215  14.072
randomizeFeaturesTx     13.634  0.164  15.151
GRangesList2GRanges     10.196  0.609  11.176
randomizeTransByOrder    9.381  0.096  10.323
randomizeFeaturesTxIA    9.189  0.134  10.234
randomizeTx              8.110  0.131   8.719
overlapCountsTx          7.967  0.122   8.181
getPermSpaceByFeatures   7.147  0.153   7.610
getPermSpaceByTxID       6.848  0.124   7.150
calculateShift           5.128  0.206   5.594
extractRegions           5.140  0.097   5.898
shiftTx                  5.096  0.095   5.937
* 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 ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: OK