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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:dasper.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings dasper_1.2.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.13-bioc/meat/dasper.Rcheck’
* using R version 4.1.1 (2021-08-10)
* using platform: x86_64-apple-darwin17.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘dasper/DESCRIPTION’ ... OK
* this is package ‘dasper’ 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 ... NOTE
Found the following hidden files and directories:
  .BBSoptions
  .git_fetch_output.txt
  .git_merge_output.txt
These were most likely included in error. See section ‘Package
structure’ in the ‘Writing R Extensions’ manual.
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘dasper’ can be installed ... NOTE
Found the following notes/warnings:
  Non-staged installation was used
See ‘/Users/biocbuild/bbs-3.13-bioc/meat/dasper.Rcheck/00install.out’ for details.
* 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 ... NOTE
Unexported object imported by a ':::' call: ‘grid:::calcControlPoints’
  See the note in ?`:::` about the use of this operator.
* 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 LazyData ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking line endings in shell scripts ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                    user system elapsed
coverage_process 107.605 14.873 118.664
junction_process  83.652  1.889  86.387
plot_sashimi      46.518  1.179  48.624
* 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: 3 NOTEs
See
  ‘/Users/biocbuild/bbs-3.13-bioc/meat/dasper.Rcheck/00check.log’
for details.

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL dasper
###
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* installing to library ‘/Library/Frameworks/R.framework/Versions/4.1/Resources/library’
* installing *source* package ‘dasper’ ...
** using non-staged installation via StagedInstall field
** R
** data
*** moving datasets to lazyload DB
** 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
* DONE (dasper)

R version 4.1.1 (2021-08-10) -- "Kick Things"
Copyright (C) 2021 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin17.0 (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(dasper)
> 
> test_check("dasper")
[1] "# Filtering junctions -----------------------------------------------------"
[1] "2021-10-14 18:13:13 - Filtering junctions..."
[1] "2021-10-14 18:13:13 - done!"
[1] "# Annotating junctions ----------------------------------------------------"
[1] "2021-10-14 18:13:13 - Obtaining co-ordinates of annotated exons and junctions from gtf/gff3..."
[1] "2021-10-14 18:13:43 - Getting junction annotation using overlapping exons..."
[1] "2021-10-14 18:13:45 - Tidying junction annotation..."
[1] "2021-10-14 18:13:46 - Deriving junction categories..."
[1] "2021-10-14 18:13:47 - done!"
[1] "# Normalise junctions -----------------------------------------------------"
[1] "2021-10-14 18:13:47 - Clustering junctions..."
[1] "2021-10-14 18:13:48 - Normalising junction counts..."
[1] "2021-10-14 18:13:49 - done!"
[1] "# Score junctions ---------------------------------------------------------"
[1] "2021-10-14 18:13:49 - Calculating the direction of change of junctions..."
[1] "2021-10-14 18:13:49 - Generating junction abnormality score..."
[1] "2021-10-14 18:13:50 - done!"
[1] "2021-10-14 18:14:22 - Loading junctions for sample 1/1..."
[1] "2021-10-14 18:14:22 - Adding control junctions..."
[1] "2021-10-14 18:14:22 - Tidying and storing junction data as a RangedSummarizedExperiment..."
[1] "2021-10-14 18:14:22 - done!"
[1] "2021-10-14 18:14:22 - Loading junctions for sample 1/2..."
[1] "2021-10-14 18:14:22 - Loading junctions for sample 2/2..."
[1] "2021-10-14 18:14:23 - Adding control junctions..."
[1] "2021-10-14 18:14:23 - Tidying and storing junction data as a RangedSummarizedExperiment..."
[1] "2021-10-14 18:14:23 - done!"
[1] "2021-10-14 18:14:23 - Loading junctions for sample 1/2..."
[1] "2021-10-14 18:14:23 - Loading junctions for sample 2/2..."
[1] "2021-10-14 18:14:23 - Adding control junctions..."
[1] "2021-10-14 18:14:23 - Downloading and importing fibroblasts junction data..."
[1] "2021-10-14 18:14:56 - Tidying and storing junction data as a RangedSummarizedExperiment..."
[1] "2021-10-14 18:14:59 - done!"
[1] "2021-10-14 18:14:59 - Loading junctions for sample 1/2..."
[1] "2021-10-14 18:14:59 - Loading junctions for sample 2/2..."
[1] "2021-10-14 18:14:59 - Adding control junctions..."
[1] "2021-10-14 18:14:59 - Loading junctions for sample 1/2..."
[1] "2021-10-14 18:14:59 - Loading junctions for sample 2/2..."
[1] "2021-10-14 18:14:59 - Adding control junctions..."
[1] "2021-10-14 18:14:59 - Loading junctions for sample 1/2..."
[1] "2021-10-14 18:14:59 - Loading junctions for sample 2/2..."
[1] "2021-10-14 18:14:59 - Adding control junctions..."
[1] "2021-10-14 18:15:13 - Obtaining co-ordinates of annotated exons and junctions from gtf/gff3..."
[1] "2021-10-14 18:16:08 - Filtering junctions..."
[1] "2021-10-14 18:16:08 - by count..."
[1] "2021-10-14 18:16:08 - done!"
[1] "2021-10-14 18:16:08 - Filtering junctions..."
[1] "2021-10-14 18:16:08 - by width..."
[1] "2021-10-14 18:16:08 - done!"
[1] "2021-10-14 18:16:08 - Filtering junctions..."
[1] "2021-10-14 18:16:08 - by type..."
[1] "2021-10-14 18:16:08 - done!"
[1] "2021-10-14 18:16:08 - Filtering junctions..."
[1] "2021-10-14 18:16:08 - by overlap with regions..."
[1] "2021-10-14 18:16:08 - done!"
[1] "2021-10-14 18:16:09 - Filtering junctions..."
[1] "2021-10-14 18:16:09 - by count..."
[1] "2021-10-14 18:16:09 - by width..."
[1] "2021-10-14 18:16:09 - by type..."
[1] "2021-10-14 18:16:09 - by overlap with regions..."
[1] "2021-10-14 18:16:09 - done!"
[1] "2021-10-14 18:16:18 - Clustering junctions..."
[1] "2021-10-14 18:16:18 - Filtering junctions..."
[1] "2021-10-14 18:16:18 - by count..."
[1] "2021-10-14 18:16:18 - done!"
[1] "2021-10-14 18:16:19 - Normalising junction counts..."
[1] "2021-10-14 18:16:19 - done!"
[1] "2021-10-14 18:16:19 - Calculating the direction of change of junctions..."
[1] "2021-10-14 18:16:19 - Generating junction abnormality score..."
[1] "2021-10-14 18:16:19 - done!"
[1] "2021-10-14 18:16:33 - generating outlier scores for sample 1/2"
[1] "2021-10-14 18:16:38 - fitting outlier detection model with parameters: behaviour=deprecated, bootstrap=FALSE, contamination=auto, max_features=1, max_samples=auto, n_estimators=100, n_jobs=NULL, random_state=32, verbose=0, warm_start=FALSE"
[1] "2021-10-14 18:16:39 - fitting outlier detection model with parameters: behaviour=deprecated, bootstrap=FALSE, contamination=auto, max_features=1, max_samples=auto, n_estimators=100, n_jobs=NULL, random_state=32, verbose=0, warm_start=FALSE"
[1] "2021-10-14 18:16:39 - generating outlier scores for sample 2/2"
[1] "2021-10-14 18:16:40 - fitting outlier detection model with parameters: behaviour=deprecated, bootstrap=FALSE, contamination=auto, max_features=1, max_samples=auto, n_estimators=100, n_jobs=NULL, random_state=32, verbose=0, warm_start=FALSE"
[1] "2021-10-14 18:16:41 - fitting outlier detection model with parameters: behaviour=deprecated, bootstrap=FALSE, contamination=auto, max_features=1, max_samples=auto, n_estimators=100, n_jobs=NULL, random_state=32, verbose=0, warm_start=FALSE"
[1] "2021-10-14 18:16:41 - done!"
[1] "2021-10-14 18:16:42 - fitting outlier detection model with parameters: behaviour=deprecated, bootstrap=FALSE, contamination=auto, max_features=1, max_samples=auto, n_estimators=100, n_jobs=NULL, random_state=32, verbose=0, warm_start=FALSE"
[1] "2021-10-14 18:16:43 - fitting outlier detection model with parameters: behaviour=deprecated, bootstrap=FALSE, contamination=auto, max_features=1, max_samples=auto, n_estimators=100, n_jobs=NULL, random_state=32, verbose=0, warm_start=FALSE"
[1] "2021-10-14 18:16:50 - Filtering junctions..."
[1] "2021-10-14 18:16:50 - by count..."
[1] "2021-10-14 18:16:50 - done!"
building whole annotation region map done
2 chromosomes for annotated regions read
Processing /Users/biocbuild/Library/Caches/BiocFileCache/53351b4dc4ee_SRR660824_SRS389722_SRX222703_male_lung.bw
building whole annotation region map done
2 chromosomes for annotated regions read
Processing /Users/biocbuild/Library/Caches/BiocFileCache/53351b4dc4ee_SRR660824_SRS389722_SRX222703_male_lung.bw
[1] "2021-10-14 18:17:08 - fitting outlier detection model with parameters: behaviour=deprecated, bootstrap=FALSE, contamination=auto, max_features=1, max_samples=auto, n_estimators=100, n_jobs=NULL, random_state=32, verbose=0, warm_start=FALSE"
[1] "2021-10-14 18:17:08 - fitting outlier detection model with parameters: behaviour=deprecated, bootstrap=FALSE, contamination=auto, max_features=1, max_samples=auto, n_estimators=100, n_jobs=NULL, random_state=32, verbose=0, warm_start=FALSE"
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 212 ]
> 
> proc.time()
   user  system elapsed 
253.752  10.643 266.918