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This page was generated on 2025-01-09 12:07 -0500 (Thu, 09 Jan 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 24.04.1 LTS)x86_644.4.2 (2024-10-31) -- "Pile of Leaves" 4744
palomino8Windows Server 2022 Datacenterx644.4.2 (2024-10-31 ucrt) -- "Pile of Leaves" 4487
merida1macOS 12.7.5 Montereyx86_644.4.2 (2024-10-31) -- "Pile of Leaves" 4515
kjohnson1macOS 13.6.6 Venturaarm644.4.2 (2024-10-31) -- "Pile of Leaves" 4467
taishanLinux (openEuler 24.03 LTS)aarch644.4.2 (2024-10-31) -- "Pile of Leaves" 4358
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 1735/2289HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
RgnTX 1.8.0  (landing page)
Yue Wang
Snapshot Date: 2025-01-02 13:00 -0500 (Thu, 02 Jan 2025)
git_url: https://git.bioconductor.org/packages/RgnTX
git_branch: RELEASE_3_20
git_last_commit: 6c2f504
git_last_commit_date: 2024-10-29 11:12:11 -0500 (Tue, 29 Oct 2024)
nebbiolo2Linux (Ubuntu 24.04.1 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino8Windows 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
taishanLinux (openEuler 24.03 LTS) / aarch64  OK    ERROR  skipped


CHECK results for RgnTX on palomino8

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: 1.8.0
Command: F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:RgnTX.install-out.txt --library=F:\biocbuild\bbs-3.20-bioc\R\library --no-vignettes --timings RgnTX_1.8.0.tar.gz
StartedAt: 2025-01-03 05:19:45 -0500 (Fri, 03 Jan 2025)
EndedAt: 2025-01-03 05:29:10 -0500 (Fri, 03 Jan 2025)
EllapsedTime: 564.9 seconds
RetCode: 0
Status:   OK  
CheckDir: RgnTX.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:RgnTX.install-out.txt --library=F:\biocbuild\bbs-3.20-bioc\R\library --no-vignettes --timings RgnTX_1.8.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'F:/biocbuild/bbs-3.20-bioc/meat/RgnTX.Rcheck'
* using R version 4.4.2 (2024-10-31 ucrt)
* using platform: x86_64-w64-mingw32
* R was compiled by
    gcc.exe (GCC) 13.3.0
    GNU Fortran (GCC) 13.3.0
* running under: Windows Server 2022 x64 (build 20348)
* using session charset: UTF-8
* using option '--no-vignettes'
* checking for file 'RgnTX/DESCRIPTION' ... OK
* this is package 'RgnTX' version '1.8.0'
* 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 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         43.58   1.35   44.93
permTestTxIA            21.44   0.53   21.99
permTestTxIA_customPick 20.41   0.52   20.92
permTestTx              19.18   0.28   19.48
permTestTx_customAll    17.93   0.30   18.23
permTestTx_customPick   17.09   0.43   17.53
overlapCountsTxIA        8.25   0.23    8.48
overlapWidthTx           7.99   0.11    8.13
distanceTx               7.20   0.13    7.33
randomizeFeaturesTx      6.30   0.16    6.47
GRangesList2GRanges      5.99   0.31    6.30
getStopCodon             5.89   0.03    5.93
* 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:
###
###   F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD INSTALL RgnTX
###
##############################################################################
##############################################################################


* installing to library 'F:/biocbuild/bbs-3.20-bioc/R/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 version 4.4.2 (2024-10-31 ucrt) -- "Pile of Leaves"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64

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, saveRDS, 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

Attaching package: 'IRanges'

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

    windows

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 
  58.15    1.90   60.68 

Example timings

RgnTX.Rcheck/RgnTX-Ex.timings

nameusersystemelapsed
GRanges2GRangesList0.270.030.29
GRangesList2GRanges5.990.316.30
calculateShift3.480.143.62
distanceTx7.200.137.33
extractRegions2.220.042.26
getPermSpaceByFeatures4.550.084.63
getPermSpaceByTxID2.870.133.00
getPermSpaceByType3.150.033.17
getStopCodon5.890.035.93
getTransInfo0.700.092.06
overlapCountsTx3.800.103.89
overlapCountsTxIA8.250.238.48
overlapWidthTx7.990.118.13
permTestTx19.18 0.2819.48
permTestTxIA21.44 0.5321.99
permTestTxIA_customPick20.41 0.5220.92
permTestTx_customAll17.93 0.3018.23
permTestTx_customPick17.09 0.4317.53
plotPermResults0.490.000.50
plotShiftedZScoreTx0.120.000.14
randomizeFeaturesTx6.300.166.47
randomizeFeaturesTxIA4.290.174.46
randomizeTransByOrder4.410.104.50
randomizeTx3.610.093.71
shiftTx2.970.063.03
shiftedZScoreTx43.58 1.3544.93