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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_1.6.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.19-bioc/meat/RgnTX.Rcheck’
* using R version 4.4.1 (2024-06-14)
* 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 ‘1.6.0’
* 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         84.858  1.036 105.750
permTestTxIA_customPick 53.317  0.857  63.148
permTestTxIA            51.248  0.686  60.036
permTestTx              42.532  0.639  50.283
permTestTx_customPick   37.074  0.463  44.685
permTestTx_customAll    33.161  0.388  39.244
overlapCountsTxIA       17.893  0.417  21.440
overlapWidthTx          15.865  0.310  18.145
randomizeFeaturesTx     14.807  0.224  18.569
distanceTx              13.610  0.234  15.744
getStopCodon            12.583  0.245  14.713
randomizeTransByOrder   10.566  0.146  13.021
GRangesList2GRanges      9.914  0.602  11.786
randomizeFeaturesTxIA    9.267  0.151  11.733
overlapCountsTx          9.122  0.226  11.004
randomizeTx              6.988  0.116   9.215
getPermSpaceByFeatures   6.636  0.151   7.597
extractRegions           6.069  0.117   7.049
calculateShift           5.927  0.219   7.193
getPermSpaceByTxID       5.483  0.112   6.168
shiftTx                  5.047  0.052   6.196
getPermSpaceByType       4.435  0.069   5.051
* 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