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This page was generated on 2025-08-14 11:45 -0400 (Thu, 14 Aug 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 24.04.3 LTS)x86_644.5.1 (2025-06-13) -- "Great Square Root" 4824
palomino7Windows Server 2022 Datacenterx644.5.1 (2025-06-13 ucrt) -- "Great Square Root" 4566
merida1macOS 12.7.5 Montereyx86_644.5.1 RC (2025-06-05 r88288) -- "Great Square Root" 4604
kjohnson1macOS 13.6.6 Venturaarm644.5.1 Patched (2025-06-14 r88325) -- "Great Square Root" 4545
kunpeng2Linux (openEuler 24.03 LTS)aarch64R Under development (unstable) (2025-02-19 r87757) -- "Unsuffered Consequences" 4579
Click on any hostname to see more info about the system (e.g. compilers)      (*) as reported by 'uname -p', except on Windows and Mac OS X

Package 1767/2341HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
RgnTX 1.10.0  (landing page)
Yue Wang
Snapshot Date: 2025-08-11 13:40 -0400 (Mon, 11 Aug 2025)
git_url: https://git.bioconductor.org/packages/RgnTX
git_branch: RELEASE_3_21
git_last_commit: 682feeb
git_last_commit_date: 2025-04-15 12:52:17 -0400 (Tue, 15 Apr 2025)
nebbiolo1Linux (Ubuntu 24.04.3 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino7Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
merida1macOS 12.7.5 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kjohnson1macOS 13.6.6 Ventura / arm64  OK    OK    OK    OK  UNNEEDED, same version is already published
kunpeng2Linux (openEuler 24.03 LTS) / aarch64  OK    OK    OK  


CHECK results for RgnTX on merida1

To the developers/maintainers of the RgnTX package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/RgnTX.git to reflect on this report. See Troubleshooting Build Report for more information.
- Use the following Renviron settings to reproduce errors and warnings.
- If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information.

raw results


Summary

Package: RgnTX
Version: 1.10.0
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_1.10.0.tar.gz
StartedAt: 2025-08-12 08:57:23 -0400 (Tue, 12 Aug 2025)
EndedAt: 2025-08-12 09:14:49 -0400 (Tue, 12 Aug 2025)
EllapsedTime: 1046.0 seconds
RetCode: 0
Status:   OK  
CheckDir: RgnTX.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### 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_1.10.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.21-bioc/meat/RgnTX.Rcheck’
* using R version 4.5.1 RC (2025-06-05 r88288)
* using platform: x86_64-apple-darwin20
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    GNU Fortran (GCC) 14.2.0
* 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 ‘1.10.0’
* 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         84.388  1.164  87.882
permTestTxIA_customPick 49.079  0.463  50.184
permTestTxIA            47.709  0.559  48.723
permTestTx              41.351  0.407  42.431
permTestTx_customPick   35.661  0.359  36.658
permTestTx_customAll    31.283  0.276  32.137
overlapCountsTxIA       16.533  0.239  17.107
overlapWidthTx          14.495  0.172  14.899
randomizeFeaturesTx     13.921  0.146  14.283
getStopCodon            12.879  0.191  13.298
distanceTx              10.318  0.214  10.605
randomizeTransByOrder    9.700  0.098  10.075
randomizeFeaturesTxIA    9.296  0.116   9.707
GRangesList2GRanges      8.355  0.414   8.855
overlapCountsTx          7.627  0.096   7.816
randomizeTx              7.320  0.073   7.564
getPermSpaceByTxID       5.874  0.130   6.093
shiftTx                  5.236  0.053   5.536
getPermSpaceByFeatures   5.108  0.118   5.336
* 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


Installation output

RgnTX.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL RgnTX
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library’
* installing *source* package ‘RgnTX’ ...
** this is package ‘RgnTX’ version ‘1.10.0’
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (RgnTX)

Tests output

RgnTX.Rcheck/tests/testthat.Rout


R version 4.5.1 RC (2025-06-05 r88288) -- "Great Square Root"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin20

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> library(testthat)
> library(RgnTX)
> 
> test_check("RgnTX")
Loading required package: GenomicFeatures
Loading required package: BiocGenerics
Loading required package: generics

Attaching package: 'generics'

The following objects are masked from 'package:base':

    as.difftime, as.factor, as.ordered, intersect, is.element, setdiff,
    setequal, union


Attaching package: 'BiocGenerics'

The following objects are masked from 'package:stats':

    IQR, mad, sd, var, xtabs

The following objects are masked from 'package:base':

    Filter, Find, Map, Position, Reduce, anyDuplicated, aperm, append,
    as.data.frame, basename, cbind, colnames, dirname, do.call,
    duplicated, eval, evalq, get, grep, grepl, is.unsorted, lapply,
    mapply, match, mget, order, paste, pmax, pmax.int, pmin, pmin.int,
    rank, rbind, rownames, sapply, saveRDS, table, tapply, unique,
    unsplit, which.max, which.min

Loading required package: S4Vectors
Loading required package: stats4

Attaching package: 'S4Vectors'

The following object is masked from 'package:utils':

    findMatches

The following objects are masked from 'package:base':

    I, expand.grid, unname

Loading required package: IRanges
Loading required package: GenomeInfoDb
Loading required package: GenomicRanges
Loading required package: AnnotationDbi
Loading required package: Biobase
Welcome to Bioconductor

    Vignettes contain introductory material; view with
    'browseVignettes()'. To cite Bioconductor, see
    'citation("Biobase")', and for packages 'citation("pkgname")'.

[ FAIL 0 | WARN 0 | SKIP 0 | PASS 42 ]
> 
> proc.time()
   user  system elapsed 
104.711   2.970 110.039 

Example timings

RgnTX.Rcheck/RgnTX-Ex.timings

nameusersystemelapsed
GRanges2GRangesList0.3120.0130.326
GRangesList2GRanges8.3550.4148.855
calculateShift3.5140.1283.656
distanceTx10.318 0.21410.605
extractRegions4.7040.1094.855
getPermSpaceByFeatures5.1080.1185.336
getPermSpaceByTxID5.8740.1306.093
getPermSpaceByType4.3100.0934.582
getStopCodon12.879 0.19113.298
getTransInfo1.3180.1161.438
overlapCountsTx7.6270.0967.816
overlapCountsTxIA16.533 0.23917.107
overlapWidthTx14.495 0.17214.899
permTestTx41.351 0.40742.431
permTestTxIA47.709 0.55948.723
permTestTxIA_customPick49.079 0.46350.184
permTestTx_customAll31.283 0.27632.137
permTestTx_customPick35.661 0.35936.658
plotPermResults1.2070.0131.309
plotShiftedZScoreTx0.4120.0210.480
randomizeFeaturesTx13.921 0.14614.283
randomizeFeaturesTxIA9.2960.1169.707
randomizeTransByOrder 9.700 0.09810.075
randomizeTx7.3200.0737.564
shiftTx5.2360.0535.536
shiftedZScoreTx84.388 1.16487.882