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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_1.7.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.20-bioc/meat/RgnTX.Rcheck’
* using R version 4.4.0 Patched (2024-04-24 r86482)
* 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 12.7.4
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘RgnTX/DESCRIPTION’ ... OK
* this is package ‘RgnTX’ version ‘1.7.0’
* 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         88.070  1.332 110.997
permTestTxIA_customPick 53.673  0.738  63.216
permTestTxIA            52.064  0.600  59.825
permTestTx              43.248  0.500  49.782
permTestTx_customPick   37.241  0.468  46.035
permTestTx_customAll    34.337  0.404  40.095
overlapCountsTxIA       18.251  0.434  21.559
overlapWidthTx          16.117  0.253  18.297
distanceTx              15.030  0.262  17.750
randomizeFeaturesTx     14.922  0.203  19.317
getStopCodon            14.785  0.217  16.781
GRangesList2GRanges     10.343  0.607  12.360
randomizeTransByOrder   10.688  0.184  13.645
overlapCountsTx          9.363  0.204  10.858
randomizeFeaturesTxIA    9.276  0.139  12.361
getPermSpaceByFeatures   8.055  0.190   9.342
randomizeTx              7.023  0.105   8.691
getPermSpaceByTxID       5.612  0.097   6.564
extractRegions           5.350  0.087   6.080
calculateShift           5.027  0.197   6.011
shiftTx                  5.052  0.055   6.139
getPermSpaceByType       4.683  0.099   5.553
* 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