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This page was generated on 2023-10-16 11:36:46 -0400 (Mon, 16 Oct 2023).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 22.04.2 LTS)x86_644.3.1 (2023-06-16) -- "Beagle Scouts" 4626
palomino3Windows Server 2022 Datacenterx644.3.1 (2023-06-16 ucrt) -- "Beagle Scouts" 4379
merida1macOS 12.6.4 Montereyx86_644.3.1 (2023-06-16) -- "Beagle Scouts" 4395
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 2161/2230HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
txcutr 1.6.0  (landing page)
Mervin Fansler
Snapshot Date: 2023-10-15 14:00:13 -0400 (Sun, 15 Oct 2023)
git_url: https://git.bioconductor.org/packages/txcutr
git_branch: RELEASE_3_17
git_last_commit: fd0e085
git_last_commit_date: 2023-04-25 11:34:30 -0400 (Tue, 25 Apr 2023)
nebbiolo1Linux (Ubuntu 22.04.2 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 12.6.4 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kjohnson2macOS 12.6.1 Monterey / arm64see weekly results here

CHECK results for txcutr on palomino3


To the developers/maintainers of the txcutr package:
- 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 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: txcutr
Version: 1.6.0
Command: F:\biocbuild\bbs-3.17-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:txcutr.install-out.txt --library=F:\biocbuild\bbs-3.17-bioc\R\library --no-vignettes --timings txcutr_1.6.0.tar.gz
StartedAt: 2023-10-16 07:53:19 -0400 (Mon, 16 Oct 2023)
EndedAt: 2023-10-16 08:17:55 -0400 (Mon, 16 Oct 2023)
EllapsedTime: 1476.1 seconds
RetCode: 0
Status:   OK  
CheckDir: txcutr.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   F:\biocbuild\bbs-3.17-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:txcutr.install-out.txt --library=F:\biocbuild\bbs-3.17-bioc\R\library --no-vignettes --timings txcutr_1.6.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'F:/biocbuild/bbs-3.17-bioc/meat/txcutr.Rcheck'
* using R version 4.3.1 (2023-06-16 ucrt)
* using platform: x86_64-w64-mingw32 (64-bit)
* R was compiled by
    gcc.exe (GCC) 12.2.0
    GNU Fortran (GCC) 12.2.0
* running under: Windows Server 2022 x64 (build 20348)
* using session charset: UTF-8
* using option '--no-vignettes'
* checking for file 'txcutr/DESCRIPTION' ... OK
* this is package 'txcutr' version '1.6.0'
* 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 '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
exportFASTA        16.12   0.41   62.28
generateMergeTable 13.02   0.27  105.75
truncateTxome      12.32   0.18  104.80
exportGTF           8.73   0.17   55.11
exportMergeTable    6.59   0.14   52.72
* 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:
###
###   F:\biocbuild\bbs-3.17-bioc\R\bin\R.exe CMD INSTALL txcutr
###
##############################################################################
##############################################################################


* installing to library 'F:/biocbuild/bbs-3.17-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 4.3.1 (2023-06-16 ucrt) -- "Beagle Scouts"
Copyright (C) 2023 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64 (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, 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, sort, table,
    tapply, union, unique, unsplit, which.max, which.min

Loading required package: S4Vectors

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: 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 
 109.43    2.71  883.00 

Example timings

txcutr.Rcheck/txcutr-Ex.timings

nameusersystemelapsed
exportFASTA16.12 0.4162.28
exportGTF 8.73 0.1755.11
exportMergeTable 6.59 0.1452.72
generateMergeTable 13.02 0.27105.75
truncateTxome 12.32 0.18104.80
txdbToGRangesList1.000.051.04