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This page was generated on 2022-04-13 12:07:32 -0400 (Wed, 13 Apr 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 20.04.4 LTS)x86_644.1.3 (2022-03-10) -- "One Push-Up" 4324
tokay2Windows Server 2012 R2 Standardx644.1.3 (2022-03-10) -- "One Push-Up" 4077
machv2macOS 10.14.6 Mojavex86_644.1.3 (2022-03-10) -- "One Push-Up" 4137
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CHECK results for txcutr on tokay2


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 2021/2083HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
txcutr 1.0.0  (landing page)
Mervin Fansler
Snapshot Date: 2022-04-12 01:55:07 -0400 (Tue, 12 Apr 2022)
git_url: https://git.bioconductor.org/packages/txcutr
git_branch: RELEASE_3_14
git_last_commit: 21b6a51
git_last_commit_date: 2021-10-26 13:14:01 -0400 (Tue, 26 Oct 2021)
nebbiolo2Linux (Ubuntu 20.04.4 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
tokay2Windows Server 2012 R2 Standard / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
machv2macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: txcutr
Version: 1.0.0
Command: C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:txcutr.install-out.txt --library=C:\Users\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings txcutr_1.0.0.tar.gz
StartedAt: 2022-04-13 04:32:15 -0400 (Wed, 13 Apr 2022)
EndedAt: 2022-04-13 05:26:34 -0400 (Wed, 13 Apr 2022)
EllapsedTime: 3259.0 seconds
RetCode: 0
Status:   OK  
CheckDir: txcutr.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:txcutr.install-out.txt --library=C:\Users\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings txcutr_1.0.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.14-bioc/meat/txcutr.Rcheck'
* using R version 4.1.3 (2022-03-10)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'txcutr/DESCRIPTION' ... OK
* this is package 'txcutr' version '1.0.0'
* 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
* loading checks for arch 'i386'
** 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
* loading checks for arch 'x64'
** 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 ...
** running examples for arch 'i386' ... OK
Examples with CPU (user + system) or elapsed time > 5s
                    user system elapsed
exportFASTA        21.15   1.85   76.42
generateMergeTable 14.36   0.21  120.82
truncateTxome      14.25   0.15  113.85
exportGTF          11.41   1.04   68.39
exportMergeTable    8.29   0.07   59.11
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
                    user system elapsed
exportFASTA        17.01   0.42   69.57
generateMergeTable 16.42   0.05  128.52
truncateTxome      15.70   0.07  121.98
exportGTF          11.02   0.06   61.25
exportMergeTable    8.66   0.05   59.37
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
  Running 'testthat.R'
 OK
** running tests for arch 'x64' ...
  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:
###
###   C:\cygwin\bin\curl.exe -O http://155.52.207.166/BBS/3.14/bioc/src/contrib/txcutr_1.0.0.tar.gz && rm -rf txcutr.buildbin-libdir && mkdir txcutr.buildbin-libdir && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=txcutr.buildbin-libdir txcutr_1.0.0.tar.gz && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL txcutr_1.0.0.zip && rm txcutr_1.0.0.tar.gz txcutr_1.0.0.zip
###
##############################################################################
##############################################################################


  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed

  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
100 18854  100 18854    0     0   156k      0 --:--:-- --:--:-- --:--:--  157k

install for i386

* installing *source* package 'txcutr' ...
** using staged installation
** R
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'txcutr'
    finding HTML links ... done
    dot-clipTranscript                      html  
    dot-fillReduce                          html  
    dot-mutateEach-CompressedGRangesList-method
                                            html  
    dot-propagateMap                        html  
    exportFASTA                             html  
    exportGTF                               html  
    exportMergeTable                        html  
    generateMergeTable                      html  
    truncateTxome                           html  
    finding level-2 HTML links ... done

    txdbToGRangesList                       html  
** 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

install for x64

* installing *source* package 'txcutr' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'txcutr' as txcutr_1.0.0.zip
* DONE (txcutr)
* installing to library 'C:/Users/biocbuild/bbs-3.14-bioc/R/library'
package 'txcutr' successfully unpacked and MD5 sums checked

Tests output

txcutr.Rcheck/tests_i386/testthat.Rout


R version 4.1.3 (2022-03-10) -- "One Push-Up"
Copyright (C) 2022 The R Foundation for Statistical Computing
Platform: i386-w64-mingw32/i386 (32-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

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 
 123.71    2.28 1084.87

txcutr.Rcheck/tests_x64/testthat.Rout


R version 4.1.3 (2022-03-10) -- "One Push-Up"
Copyright (C) 2022 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, 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

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 
 122.79    1.57  997.79

Example timings

txcutr.Rcheck/examples_i386/txcutr-Ex.timings

nameusersystemelapsed
exportFASTA21.15 1.8576.42
exportGTF11.41 1.0468.39
exportMergeTable 8.29 0.0759.11
generateMergeTable 14.36 0.21120.82
truncateTxome 14.25 0.15113.85
txdbToGRangesList1.220.031.25

txcutr.Rcheck/examples_x64/txcutr-Ex.timings

nameusersystemelapsed
exportFASTA17.01 0.4269.57
exportGTF11.02 0.0661.25
exportMergeTable 8.66 0.0559.37
generateMergeTable 16.42 0.05128.52
truncateTxome 15.70 0.07121.98
txdbToGRangesList1.300.031.33