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This page was generated on 2022-08-08 13:20:00 -0400 (Mon, 08 Aug 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 20.04.4 LTS)x86_644.2.1 (2022-06-23) -- "Funny-Looking Kid" 4362
merida1macOS 10.14.6 Mojavex86_644.2.1 (2022-06-23) -- "Funny-Looking Kid" 4180
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

CHECK results for txcutr on nebbiolo1


To the developers/maintainers of the txcutr package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/txcutr.git to
reflect on this report. See How and When does the builder pull? When will my changes propagate? for more information.
- Make sure to use the following settings in order to reproduce any error or warning you see on this page.

raw results

Package 2075/2140HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
txcutr 1.2.0  (landing page)
Mervin Fansler
Snapshot Date: 2022-08-07 13:55:12 -0400 (Sun, 07 Aug 2022)
git_url: https://git.bioconductor.org/packages/txcutr
git_branch: RELEASE_3_15
git_last_commit: 52c0f97
git_last_commit_date: 2022-04-26 12:19:46 -0400 (Tue, 26 Apr 2022)
nebbiolo1Linux (Ubuntu 20.04.4 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
merida1macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: txcutr
Version: 1.2.0
Command: /home/biocbuild/bbs-3.15-bioc/R/bin/R CMD check --install=check:txcutr.install-out.txt --library=/home/biocbuild/bbs-3.15-bioc/R/library --no-vignettes --timings txcutr_1.2.0.tar.gz
StartedAt: 2022-08-07 22:30:05 -0400 (Sun, 07 Aug 2022)
EndedAt: 2022-08-07 22:38:14 -0400 (Sun, 07 Aug 2022)
EllapsedTime: 489.5 seconds
RetCode: 0
Status:   OK  
CheckDir: txcutr.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.15-bioc/R/bin/R CMD check --install=check:txcutr.install-out.txt --library=/home/biocbuild/bbs-3.15-bioc/R/library --no-vignettes --timings txcutr_1.2.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.15-bioc/meat/txcutr.Rcheck’
* using R version 4.2.1 (2022-06-23)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘txcutr/DESCRIPTION’ ... OK
* this is package ‘txcutr’ version ‘1.2.0’
* 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 ‘txcutr’ 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
truncateTxome      177.137 10.336  55.470
generateMergeTable 166.901 10.134  50.773
exportGTF           84.922  6.666  29.035
exportMergeTable    79.827  4.428  24.510
exportFASTA         40.563  3.792  24.719
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’
 OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... 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

txcutr.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.15-bioc/R/bin/R CMD INSTALL txcutr
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.15-bioc/R/library’
* installing *source* package ‘txcutr’ ...
** using staged installation
** R
** 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 (txcutr)

Tests output

txcutr.Rcheck/tests/testthat.Rout


R version 4.2.1 (2022-06-23) -- "Funny-Looking Kid"
Copyright (C) 2022 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)

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(txcutr)
> 
> test_check("txcutr")
Loading required package: stats4
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, 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, sort, table,
    tapply, union, unique, unsplit, which.max, which.min

Loading required package: S4Vectors

Attaching package: 'S4Vectors'

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

    I, expand.grid, unname

Loading required package: IRanges
Loading required package: GenomeInfoDb
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")'.

'select()' returned 1:1 mapping between keys and columns
Truncating transcripts...
Done.
Checking for duplicate transcripts...
Removed 1 duplicates.
Creating exon ranges...
Done.
Creating tx ranges...
Done.
Creating gene ranges...
Done.
'select()' returned 1:1 mapping between keys and columns
Truncating transcripts...
Done.
Checking for duplicate transcripts...
Removed 1 duplicates.
Creating exon ranges...
Done.
Creating tx ranges...
Done.
Creating gene ranges...
Done.
'select()' returned 1:1 mapping between keys and columns
Truncating transcripts...
Done.
Checking for duplicate transcripts...
Removed 1 duplicates.
Creating exon ranges...
Done.
Creating tx ranges...
Done.
Creating gene ranges...
Done.
'select()' returned 1:1 mapping between keys and columns
Truncating transcripts...
Done.
Checking for duplicate transcripts...
Removed 1 duplicates.
Creating exon ranges...
Done.
Creating tx ranges...
Done.
Creating gene ranges...
Done.
'select()' returned 1:1 mapping between keys and columns
Truncating transcripts...
Done.
Checking for duplicate transcripts...
Removed 0 duplicates.
Creating exon ranges...
Done.
Creating tx ranges...
Done.
Creating gene ranges...
Done.
'select()' returned 1:1 mapping between keys and columns
Truncating transcripts...
Done.
Checking for duplicate transcripts...
Removed 0 duplicates.
Creating exon ranges...
Done.
Creating tx ranges...
Done.
Creating gene ranges...
Done.
'select()' returned 1:1 mapping between keys and columns
Truncating transcripts...
Done.
Checking for duplicate transcripts...
Removed 0 duplicates.
Creating exon ranges...
Done.
Creating tx ranges...
Done.
Creating gene ranges...
Done.
'select()' returned 1:1 mapping between keys and columns
Truncating transcripts...
Done.
Checking for duplicate transcripts...
Removed 0 duplicates.
Creating exon ranges...
Done.
Creating tx ranges...
Done.
Creating gene ranges...
Done.
'select()' returned 1:1 mapping between keys and columns
Truncating transcripts...
Done.
Checking for duplicate transcripts...
Removed 0 duplicates.
Creating exon ranges...
Done.
Creating tx ranges...
Done.
Creating gene ranges...
Done.
'select()' returned 1:1 mapping between keys and columns
Truncating transcripts...
Done.
Checking for duplicate transcripts...
Removed 0 duplicates.
Creating exon ranges...
Done.
Creating tx ranges...
Done.
Creating gene ranges...
Done.
'select()' returned 1:1 mapping between keys and columns
Truncating transcripts...
Done.
Checking for duplicate transcripts...
Removed 0 duplicates.
Creating exon ranges...
Done.
Creating tx ranges...
Done.
Creating gene ranges...
Done.
'select()' returned 1:1 mapping between keys and columns
Truncating transcripts...
Done.
Checking for duplicate transcripts...
Removed 0 duplicates.
Creating exon ranges...
Done.
Creating tx ranges...
Done.
Creating gene ranges...
Done.
'select()' returned 1:1 mapping between keys and columns
Truncating transcripts...
Done.
Checking for duplicate transcripts...
Removed 0 duplicates.
Creating exon ranges...
Done.
Creating tx ranges...
Done.
Creating gene ranges...
Done.
'select()' returned 1:1 mapping between keys and columns
Truncating transcripts...
Done.
Checking for duplicate transcripts...
Removed 0 duplicates.
Creating exon ranges...
Done.
Creating tx ranges...
Done.
Creating gene ranges...
Done.
'select()' returned 1:1 mapping between keys and columns
Truncating transcripts...
Done.
Checking for duplicate transcripts...
Removed 0 duplicates.
Creating exon ranges...
Done.
Creating tx ranges...
Done.
Creating gene ranges...
Done.
'select()' returned 1:1 mapping between keys and columns
Truncating transcripts...
Done.
Checking for duplicate transcripts...
Removed 0 duplicates.
Creating exon ranges...
Done.
Creating tx ranges...
Done.
Creating gene ranges...
Done.
'select()' returned 1:1 mapping between keys and columns
Truncating transcripts...
Done.
Checking for duplicate transcripts...
Removed 0 duplicates.
Creating exon ranges...
Done.
Creating tx ranges...
Done.
Creating gene ranges...
Done.
'select()' returned 1:1 mapping between keys and columns
Truncating transcripts...
Done.
Checking for duplicate transcripts...
Removed 0 duplicates.
Creating exon ranges...
Done.
Creating tx ranges...
Done.
Creating gene ranges...
Done.
'select()' returned 1:1 mapping between keys and columns
Truncating transcripts...
Done.
Checking for duplicate transcripts...
Removed 0 duplicates.
Creating exon ranges...
Done.
Creating tx ranges...
Done.
Creating gene ranges...
Done.
'select()' returned 1:1 mapping between keys and columns
Truncating transcripts...
Done.
Checking for duplicate transcripts...
Removed 0 duplicates.
Creating exon ranges...
Done.
Creating tx ranges...
Done.
Creating gene ranges...
Done.
'select()' returned 1:1 mapping between keys and columns
Truncating transcripts...
Done.
Checking for duplicate transcripts...
Removed 0 duplicates.
Creating exon ranges...
Done.
Creating tx ranges...
Done.
Creating gene ranges...
Done.
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 117 ]
> 
> proc.time()
   user  system elapsed 
 80.311  15.441  87.973 

Example timings

txcutr.Rcheck/txcutr-Ex.timings

nameusersystemelapsed
exportFASTA40.563 3.79224.719
exportGTF84.922 6.66629.035
exportMergeTable79.827 4.42824.510
generateMergeTable166.901 10.134 50.773
truncateTxome177.137 10.336 55.470
txdbToGRangesList0.9980.1311.130