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This page was generated on 2024-03-04 11:39:48 -0500 (Mon, 04 Mar 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 22.04.3 LTS)x86_64R Under development (unstable) (2024-01-16 r85808) -- "Unsuffered Consequences" 4676
palomino3Windows Server 2022 Datacenterx64R Under development (unstable) (2024-01-14 r85805 ucrt) -- "Unsuffered Consequences" 4414
merida1macOS 12.7.1 Montereyx86_64R Under development (unstable) (2024-01-16 r85808) -- "Unsuffered Consequences" 4441
kunpeng2Linux (openEuler 22.03 LTS-SP1)aarch64R Under development (unstable) (2024-01-16 r85812) -- "Unsuffered Consequences" 4417
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 1719/2251HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
RgnTX 1.5.0  (landing page)
Yue Wang
Snapshot Date: 2024-03-01 14:00:22 -0500 (Fri, 01 Mar 2024)
git_url: https://git.bioconductor.org/packages/RgnTX
git_branch: devel
git_last_commit: 839cec8
git_last_commit_date: 2023-10-24 11:42:27 -0500 (Tue, 24 Oct 2023)
nebbiolo1Linux (Ubuntu 22.04.3 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino3Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
merida1macOS 12.7.1 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kunpeng2Linux (openEuler 22.03 LTS-SP1) / 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: 1.5.0
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_1.5.0.tar.gz
StartedAt: 2024-03-02 09:24:45 -0500 (Sat, 02 Mar 2024)
EndedAt: 2024-03-02 09:45:40 -0500 (Sat, 02 Mar 2024)
EllapsedTime: 1254.8 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_1.5.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.19-bioc/meat/RgnTX.Rcheck’
* using R Under development (unstable) (2024-01-16 r85808)
* 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 12.7.1
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘RgnTX/DESCRIPTION’ ... OK
* this is package ‘RgnTX’ version ‘1.5.0’
* 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         83.025  1.477 109.199
permTestTxIA_customPick 50.139  0.724  59.794
permTestTxIA            48.125  0.657  54.618
permTestTx              41.723  0.642  49.397
permTestTx_customPick   35.974  0.472  44.673
permTestTx_customAll    33.353  0.437  40.142
overlapCountsTxIA       17.719  0.430  21.615
overlapWidthTx          15.511  0.260  18.332
distanceTx              15.278  0.254  18.061
randomizeFeaturesTx     13.536  0.178  17.164
getStopCodon            12.280  0.246  14.468
GRangesList2GRanges      9.997  0.666  12.710
randomizeFeaturesTxIA    9.388  0.190  11.730
randomizeTransByOrder    9.464  0.103  11.724
overlapCountsTx          9.296  0.226  11.193
getPermSpaceByFeatures   7.617  0.199   8.843
randomizeTx              7.112  0.116   9.180
getPermSpaceByTxID       5.382  0.083   6.111
extractRegions           5.140  0.122   5.823
calculateShift           5.030  0.202   6.125
shiftTx                  5.144  0.080   6.896
getPermSpaceByType       4.498  0.110   5.210
* 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/4.4-x86_64/Resources/library’
* installing *source* package ‘RgnTX’ ...
** 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 Under development (unstable) (2024-01-16 r85808) -- "Unsuffered Consequences"
Copyright (C) 2024 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

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, intersect, is.unsorted,
    lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin,
    pmin.int, rank, rbind, rownames, sapply, setdiff, table, tapply,
    union, 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 
104.311   3.319 134.472 

Example timings

RgnTX.Rcheck/RgnTX-Ex.timings

nameusersystemelapsed
GRanges2GRangesList0.4140.0340.506
GRangesList2GRanges 9.997 0.66612.710
calculateShift5.0300.2026.125
distanceTx15.278 0.25418.061
extractRegions5.1400.1225.823
getPermSpaceByFeatures7.6170.1998.843
getPermSpaceByTxID5.3820.0836.111
getPermSpaceByType4.4980.1105.210
getStopCodon12.280 0.24614.468
getTransInfo1.6400.1112.003
overlapCountsTx 9.296 0.22611.193
overlapCountsTxIA17.719 0.43021.615
overlapWidthTx15.511 0.26018.332
permTestTx41.723 0.64249.397
permTestTxIA48.125 0.65754.618
permTestTxIA_customPick50.139 0.72459.794
permTestTx_customAll33.353 0.43740.142
permTestTx_customPick35.974 0.47244.673
plotPermResults1.1940.0271.568
plotShiftedZScoreTx0.3430.0060.447
randomizeFeaturesTx13.536 0.17817.164
randomizeFeaturesTxIA 9.388 0.19011.730
randomizeTransByOrder 9.464 0.10311.724
randomizeTx7.1120.1169.180
shiftTx5.1440.0806.896
shiftedZScoreTx 83.025 1.477109.199