##############################################################################
##############################################################################
###
### Running command:
###
###   D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:txcutr.install-out.txt --library=D:\biocbuild\bbs-3.15-bioc\R\library --no-vignettes --timings txcutr_1.1.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'D:/biocbuild/bbs-3.15-bioc/meat/txcutr.Rcheck'
* using R Under development (unstable) (2021-11-21 r81221)
* 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 '1.1.0'
* 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        11.58   0.47   53.92
generateMergeTable  7.91   0.21   70.81
truncateTxome       7.65   0.06   66.11
exportGTF           6.66   0.16   46.89
exportMergeTable    4.89   0.03   37.40
* 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

##############################################################################
##############################################################################
###
### Running command:
###
###   D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD INSTALL txcutr
###
##############################################################################
##############################################################################


* installing to library 'D:/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
  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
* DONE (txcutr)
Making 'packages.html' ...Warning in packageDescription(i, lib.loc = lib, fields = "Title", encoding = "UTF-8") :
  DESCRIPTION file of package 'Motif2Site' is missing or broken
 done

R Under development (unstable) (2021-11-21 r81221) -- "Unsuffered Consequences"
Copyright (C) 2021 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 
  69.20    0.89  594.90