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###
### Running command:
###
###   /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:RLSeq.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/site-library --timings RLSeq_1.5.2.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.17-bioc/meat/RLSeq.Rcheck’
* using R version 4.3.0 alpha (2023-04-03 r84154)
* using platform: x86_64-pc-linux-gnu (64-bit)
* R was compiled by
    gcc (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0
    GNU Fortran (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0
* running under: Ubuntu 22.04.2 LTS
* using session charset: UTF-8
* checking for file ‘RLSeq/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘RLSeq’ version ‘1.5.2’
* 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 ‘RLSeq’ 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 loading without being on the library search path ... OK
* checking startup messages can be suppressed ... 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 contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                       user system elapsed
report               54.232  4.146  59.986
RLSeq                33.043  2.733  38.245
predictCondition     15.417  1.948  17.825
plotEnrichment       14.105  1.400  15.722
txFeatureOverlap     10.484  1.175  11.760
geneAnnotation        9.210  1.315  11.218
plotRLRegionOverlap   8.501  1.004  10.234
featureEnrich         8.902  0.564   9.669
corrHeatmap           7.180  0.909   8.190
plotTxFeatureOverlap  6.337  1.084   7.938
corrAnalyze           4.787  0.628   6.410
* 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 ...
  ‘RLSeq.Rmd’ using ‘UTF-8’... OK
 NONE
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: OK

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###
### Running command:
###
###   /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD INSTALL RLSeq
###
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* installing to library ‘/home/biocbuild/bbs-3.17-bioc/R/site-library’
* installing *source* package ‘RLSeq’ ...
** using staged installation
** R
** data
** 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 (RLSeq)

R version 4.3.0 alpha (2023-04-03 r84154)
Copyright (C) 2023 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(RLSeq)
> 
> test_check("RLSeq")
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
Loading required package: stats4

Attaching package: 'S4Vectors'

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

    I, expand.grid, unname

see ?RLHub and browseVignettes('RLHub') for documentation
see ?RLHub and browseVignettes('RLHub') for documentation
see ?RLHub and browseVignettes('RLHub') for documentation
see ?RLHub and browseVignettes('RLHub') for documentation
[1] "Note: The minimum p-value with only 30 permutations is 0.032258064516129. You should consider increasing the number of permutations."
see ?RLHub and browseVignettes('RLHub') for documentation
see ?RLHub and browseVignettes('RLHub') for documentation
see ?RLHub and browseVignettes('RLHub') for documentation
see ?RLHub and browseVignettes('RLHub') for documentation
see ?RLHub and browseVignettes('RLHub') for documentation
Loading required package: GenomicFeatures
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")'.

  1690 genes were dropped because they have exons located on both strands
  of the same reference sequence or on more than one reference sequence,
  so cannot be represented by a single genomic range.
  Use 'single.strand.genes.only=FALSE' to get all the genes in a
  GRangesList object, or use suppressMessages() to suppress this message.
see ?RLHub and browseVignettes('RLHub') for documentation
[1] "Note: The minimum p-value with only 30 permutations is 0.032258064516129. You should consider increasing the number of permutations."
see ?RLHub and browseVignettes('RLHub') for documentation
see ?RLHub and browseVignettes('RLHub') for documentation
see ?RLHub and browseVignettes('RLHub') for documentation
see ?RLHub and browseVignettes('RLHub') for documentation
see ?RLHub and browseVignettes('RLHub') for documentation
  1690 genes were dropped because they have exons located on both strands
  of the same reference sequence or on more than one reference sequence,
  so cannot be represented by a single genomic range.
  Use 'single.strand.genes.only=FALSE' to get all the genes in a
  GRangesList object, or use suppressMessages() to suppress this message.
see ?RLHub and browseVignettes('RLHub') for documentation
[ FAIL 0 | WARN 134 | SKIP 0 | PASS 8 ]

[ FAIL 0 | WARN 134 | SKIP 0 | PASS 8 ]
> 
> proc.time()
   user  system elapsed 
262.340  19.368 298.238