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This page was generated on 2021-09-17 15:06:33 -0400 (Fri, 17 Sep 2021).

CHECK results for dasper on machv2

To the developers/maintainers of the dasper package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/dasper.git to
reflect on this report. See How and When does the builder pull? When will my changes propagate? here 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 444/2041HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
dasper 1.2.0  (landing page)
David Zhang
Snapshot Date: 2021-09-16 04:50:11 -0400 (Thu, 16 Sep 2021)
git_url: https://git.bioconductor.org/packages/dasper
git_branch: RELEASE_3_13
git_last_commit: 9bf018b
git_last_commit_date: 2021-05-19 12:57:36 -0400 (Wed, 19 May 2021)
nebbiolo1Linux (Ubuntu 20.04.2 LTS) / x86_64  OK    OK    ERROR  
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: dasper
Version: 1.2.0
Command: /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
StartedAt: 2021-09-16 18:10:09 -0400 (Thu, 16 Sep 2021)
EndedAt: 2021-09-16 18:22:04 -0400 (Thu, 16 Sep 2021)
EllapsedTime: 715.7 seconds
RetCode: 0
Status:   OK  
CheckDir: dasper.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /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
###
##############################################################################
##############################################################################


* 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 109.185 14.990 120.510
junction_process  83.235  1.916  85.917
plot_sashimi      46.948  1.149  49.079
* 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.



Installation output

dasper.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL dasper
###
##############################################################################
##############################################################################


* 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)

Tests output

dasper.Rcheck/tests/testthat.Rout


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] "2021-09-16 18:18:02 - Filtering junctions..."
[1] "2021-09-16 18:18:02 - done!"
[1] "# Annotating junctions ----------------------------------------------------"
[1] "2021-09-16 18:18:02 - Obtaining co-ordinates of annotated exons and junctions from gtf/gff3..."
[1] "2021-09-16 18:18:33 - Getting junction annotation using overlapping exons..."
[1] "2021-09-16 18:18:35 - Tidying junction annotation..."
[1] "2021-09-16 18:18:36 - Deriving junction categories..."
[1] "2021-09-16 18:18:37 - done!"
[1] "# Normalise junctions -----------------------------------------------------"
[1] "2021-09-16 18:18:37 - Clustering junctions..."
[1] "2021-09-16 18:18:38 - Normalising junction counts..."
[1] "2021-09-16 18:18:39 - done!"
[1] "# Score junctions ---------------------------------------------------------"
[1] "2021-09-16 18:18:39 - Calculating the direction of change of junctions..."
[1] "2021-09-16 18:18:39 - Generating junction abnormality score..."
[1] "2021-09-16 18:18:39 - done!"
[1] "2021-09-16 18:19:12 - Loading junctions for sample 1/1..."
[1] "2021-09-16 18:19:12 - Adding control junctions..."
[1] "2021-09-16 18:19:12 - Tidying and storing junction data as a RangedSummarizedExperiment..."
[1] "2021-09-16 18:19:12 - done!"
[1] "2021-09-16 18:19:12 - Loading junctions for sample 1/2..."
[1] "2021-09-16 18:19:12 - Loading junctions for sample 2/2..."
[1] "2021-09-16 18:19:12 - Adding control junctions..."
[1] "2021-09-16 18:19:12 - Tidying and storing junction data as a RangedSummarizedExperiment..."
[1] "2021-09-16 18:19:12 - done!"
[1] "2021-09-16 18:19:12 - Loading junctions for sample 1/2..."
[1] "2021-09-16 18:19:12 - Loading junctions for sample 2/2..."
[1] "2021-09-16 18:19:12 - Adding control junctions..."
[1] "2021-09-16 18:19:12 - Downloading and importing fibroblasts junction data..."
[1] "2021-09-16 18:19:45 - Tidying and storing junction data as a RangedSummarizedExperiment..."
[1] "2021-09-16 18:19:47 - done!"
[1] "2021-09-16 18:19:47 - Loading junctions for sample 1/2..."
[1] "2021-09-16 18:19:48 - Loading junctions for sample 2/2..."
[1] "2021-09-16 18:19:48 - Adding control junctions..."
[1] "2021-09-16 18:19:48 - Loading junctions for sample 1/2..."
[1] "2021-09-16 18:19:48 - Loading junctions for sample 2/2..."
[1] "2021-09-16 18:19:48 - Adding control junctions..."
[1] "2021-09-16 18:19:48 - Loading junctions for sample 1/2..."
[1] "2021-09-16 18:19:48 - Loading junctions for sample 2/2..."
[1] "2021-09-16 18:19:48 - Adding control junctions..."
[1] "2021-09-16 18:20:01 - Obtaining co-ordinates of annotated exons and junctions from gtf/gff3..."
[1] "2021-09-16 18:20:56 - Filtering junctions..."
[1] "2021-09-16 18:20:56 - by count..."
[1] "2021-09-16 18:20:56 - done!"
[1] "2021-09-16 18:20:57 - Filtering junctions..."
[1] "2021-09-16 18:20:57 - by width..."
[1] "2021-09-16 18:20:57 - done!"
[1] "2021-09-16 18:20:57 - Filtering junctions..."
[1] "2021-09-16 18:20:57 - by type..."
[1] "2021-09-16 18:20:57 - done!"
[1] "2021-09-16 18:20:57 - Filtering junctions..."
[1] "2021-09-16 18:20:57 - by overlap with regions..."
[1] "2021-09-16 18:20:57 - done!"
[1] "2021-09-16 18:20:57 - Filtering junctions..."
[1] "2021-09-16 18:20:57 - by count..."
[1] "2021-09-16 18:20:57 - by width..."
[1] "2021-09-16 18:20:57 - by type..."
[1] "2021-09-16 18:20:57 - by overlap with regions..."
[1] "2021-09-16 18:20:57 - done!"
[1] "2021-09-16 18:21:06 - Clustering junctions..."
[1] "2021-09-16 18:21:06 - Filtering junctions..."
[1] "2021-09-16 18:21:06 - by count..."
[1] "2021-09-16 18:21:07 - done!"
[1] "2021-09-16 18:21:07 - Normalising junction counts..."
[1] "2021-09-16 18:21:07 - done!"
[1] "2021-09-16 18:21:07 - Calculating the direction of change of junctions..."
[1] "2021-09-16 18:21:07 - Generating junction abnormality score..."
[1] "2021-09-16 18:21:08 - done!"
[1] "2021-09-16 18:21:21 - generating outlier scores for sample 1/2"
[1] "2021-09-16 18:21:27 - 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] "2021-09-16 18:21:28 - 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] "2021-09-16 18:21:28 - generating outlier scores for sample 2/2"
[1] "2021-09-16 18:21:28 - 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] "2021-09-16 18:21:29 - 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] "2021-09-16 18:21:29 - done!"
[1] "2021-09-16 18:21:30 - 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] "2021-09-16 18:21:31 - 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] "2021-09-16 18:21:38 - Filtering junctions..."
[1] "2021-09-16 18:21:38 - by count..."
[1] "2021-09-16 18:21:38 - 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] "2021-09-16 18:21:55 - 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] "2021-09-16 18:21:56 - 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 
252.816  10.653 265.453 

Example timings

dasper.Rcheck/dasper-Ex.timings

nameusersystemelapsed
coverage_process109.185 14.990120.510
junction_load0.2620.0060.275
junction_process83.235 1.91685.917
outlier_process0.0000.0000.001
plot_sashimi46.948 1.14949.079