##############################################################################
##############################################################################
###
### Running command:
###
###   /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
###
##############################################################################
##############################################################################


* 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 12.7.5
* 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         86.554  1.185 108.819
permTestTxIA_customPick 54.010  0.848  64.645
permTestTxIA            51.940  0.631  62.378
permTestTx              43.029  0.563  50.950
permTestTx_customPick   37.503  0.461  46.887
permTestTx_customAll    33.601  0.450  42.664
overlapCountsTxIA       18.199  0.388  20.799
overlapWidthTx          15.989  0.312  19.253
randomizeFeaturesTx     14.976  0.216  18.154
distanceTx              13.503  0.310  14.187
getStopCodon            12.696  0.251  14.858
randomizeTransByOrder   10.858  0.166  13.173
GRangesList2GRanges     10.121  0.662  11.429
overlapCountsTx          9.420  0.225  10.744
randomizeFeaturesTxIA    9.393  0.148  11.392
randomizeTx              7.068  0.100   8.798
getPermSpaceByFeatures   6.867  0.174   8.348
extractRegions           6.353  0.162   7.182
calculateShift           6.045  0.266   6.586
getPermSpaceByTxID       5.565  0.135   6.624
shiftTx                  5.096  0.054   6.351
getPermSpaceByType       4.461  0.071   5.412
* 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