Back to Multiple platform build/check report for BioC 3.13
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This page was generated on 2021-09-20 15:05:10 -0400 (Mon, 20 Sep 2021).

CHECK results for dasper on tokay2

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: 2021-09-19 04:50:10 -0400 (Sun, 19 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: C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe --arch x64 CMD check --no-multiarch --install=check:dasper.install-out.txt --library=C:\Users\biocbuild\bbs-3.13-bioc\R\library --no-vignettes --timings dasper_1.2.0.tar.gz
StartedAt: 2021-09-19 21:15:09 -0400 (Sun, 19 Sep 2021)
EndedAt: 2021-09-19 21:29:05 -0400 (Sun, 19 Sep 2021)
EllapsedTime: 835.5 seconds
RetCode: 0
Status:   OK  
CheckDir: dasper.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe --arch x64 CMD check --no-multiarch --install=check:dasper.install-out.txt --library=C:\Users\biocbuild\bbs-3.13-bioc\R\library --no-vignettes --timings dasper_1.2.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.13-bioc/meat/dasper.Rcheck'
* using R version 4.1.1 (2021-08-10)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* 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
These were most likely included in error. See section 'Package
structure' in the 'Writing R Extensions' manual.
* checking for portable file names ... OK
* checking whether package 'dasper' can be installed ... NOTE
Found the following notes/warnings:
  Non-staged installation was used
See 'C:/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 142.81  25.69  296.84
junction_process  63.52   1.39   65.86
plot_sashimi      36.91   0.87   38.56
* 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
  'C:/Users/biocbuild/bbs-3.13-bioc/meat/dasper.Rcheck/00check.log'
for details.



Installation output

dasper.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe --arch x64 CMD INSTALL --no-multiarch dasper
###
##############################################################################
##############################################################################


* installing to library 'C:/Users/biocbuild/bbs-3.13-bioc/R/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
  converting help for package 'dasper'
    finding HTML links ... done
    coverage_process                        html  
    dasper                                  html  
    junction_load                           html  
    junction_process                        html  
    junctions_example                       html  
    finding level-2 HTML links ... done

    outlier_process                         html  
    plot_sashimi                            html  
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (dasper)
Making 'packages.html' ... done

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-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(dasper)
> 
> test_check("dasper")
[1] "# Filtering junctions -----------------------------------------------------"
[1] "2021-09-19 21:24:46 - Filtering junctions..."
[1] "2021-09-19 21:24:46 - done!"
[1] "# Annotating junctions ----------------------------------------------------"
[1] "2021-09-19 21:24:46 - Obtaining co-ordinates of annotated exons and junctions from gtf/gff3..."
[1] "2021-09-19 21:25:10 - Getting junction annotation using overlapping exons..."
[1] "2021-09-19 21:25:11 - Tidying junction annotation..."
[1] "2021-09-19 21:25:12 - Deriving junction categories..."
[1] "2021-09-19 21:25:13 - done!"
[1] "# Normalise junctions -----------------------------------------------------"
[1] "2021-09-19 21:25:13 - Clustering junctions..."
[1] "2021-09-19 21:25:13 - Normalising junction counts..."
[1] "2021-09-19 21:25:14 - done!"
[1] "# Score junctions ---------------------------------------------------------"
[1] "2021-09-19 21:25:14 - Calculating the direction of change of junctions..."
[1] "2021-09-19 21:25:14 - Generating junction abnormality score..."
[1] "2021-09-19 21:25:14 - done!"
[1] "2021-09-19 21:25:38 - Loading junctions for sample 1/1..."
[1] "2021-09-19 21:25:38 - Adding control junctions..."
[1] "2021-09-19 21:25:38 - Tidying and storing junction data as a RangedSummarizedExperiment..."
[1] "2021-09-19 21:25:38 - done!"
[1] "2021-09-19 21:25:38 - Loading junctions for sample 1/2..."
[1] "2021-09-19 21:25:38 - Loading junctions for sample 2/2..."
[1] "2021-09-19 21:25:38 - Adding control junctions..."
[1] "2021-09-19 21:25:38 - Tidying and storing junction data as a RangedSummarizedExperiment..."
[1] "2021-09-19 21:25:38 - done!"
[1] "2021-09-19 21:25:38 - Loading junctions for sample 1/2..."
[1] "2021-09-19 21:25:38 - Loading junctions for sample 2/2..."
[1] "2021-09-19 21:25:39 - Adding control junctions..."
[1] "2021-09-19 21:25:39 - Downloading and importing fibroblasts junction data..."
[1] "2021-09-19 21:26:10 - Tidying and storing junction data as a RangedSummarizedExperiment..."
[1] "2021-09-19 21:26:13 - done!"
[1] "2021-09-19 21:26:13 - Loading junctions for sample 1/2..."
[1] "2021-09-19 21:26:13 - Loading junctions for sample 2/2..."
[1] "2021-09-19 21:26:13 - Adding control junctions..."
[1] "2021-09-19 21:26:13 - Loading junctions for sample 1/2..."
[1] "2021-09-19 21:26:13 - Loading junctions for sample 2/2..."
[1] "2021-09-19 21:26:13 - Adding control junctions..."
[1] "2021-09-19 21:26:13 - Loading junctions for sample 1/2..."
[1] "2021-09-19 21:26:13 - Loading junctions for sample 2/2..."
[1] "2021-09-19 21:26:13 - Adding control junctions..."
[1] "2021-09-19 21:26:27 - Obtaining co-ordinates of annotated exons and junctions from gtf/gff3..."
[1] "2021-09-19 21:27:08 - Filtering junctions..."
[1] "2021-09-19 21:27:08 - by count..."
[1] "2021-09-19 21:27:08 - done!"
[1] "2021-09-19 21:27:08 - Filtering junctions..."
[1] "2021-09-19 21:27:08 - by width..."
[1] "2021-09-19 21:27:08 - done!"
[1] "2021-09-19 21:27:08 - Filtering junctions..."
[1] "2021-09-19 21:27:08 - by type..."
[1] "2021-09-19 21:27:08 - done!"
[1] "2021-09-19 21:27:08 - Filtering junctions..."
[1] "2021-09-19 21:27:09 - by overlap with regions..."
[1] "2021-09-19 21:27:09 - done!"
[1] "2021-09-19 21:27:09 - Filtering junctions..."
[1] "2021-09-19 21:27:09 - by count..."
[1] "2021-09-19 21:27:09 - by width..."
[1] "2021-09-19 21:27:09 - by type..."
[1] "2021-09-19 21:27:09 - by overlap with regions..."
[1] "2021-09-19 21:27:09 - done!"
[1] "2021-09-19 21:27:15 - Clustering junctions..."
[1] "2021-09-19 21:27:15 - Filtering junctions..."
[1] "2021-09-19 21:27:15 - by count..."
[1] "2021-09-19 21:27:16 - done!"
[1] "2021-09-19 21:27:16 - Normalising junction counts..."
[1] "2021-09-19 21:27:16 - done!"
[1] "2021-09-19 21:27:16 - Calculating the direction of change of junctions..."
[1] "2021-09-19 21:27:17 - Generating junction abnormality score..."
[1] "2021-09-19 21:27:17 - done!"
[1] "2021-09-19 21:27:32 - generating outlier scores for sample 1/2"
[1] "2021-09-19 21:27:50 - 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] "2021-09-19 21:27:51 - 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] "2021-09-19 21:27:51 - generating outlier scores for sample 2/2"
[1] "2021-09-19 21:27:52 - 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] "2021-09-19 21:27:53 - 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] "2021-09-19 21:27:53 - done!"
[1] "2021-09-19 21:27:53 - 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] "2021-09-19 21:27:54 - 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] "2021-09-19 21:28:23 - Filtering junctions..."
[1] "2021-09-19 21:28:23 - by count..."
[1] "2021-09-19 21:28:23 - done!"
building whole annotation region map done
2 chromosomes for annotated regions read
Processing C:\Users\biocbuild\AppData\Local/R/cache/R/BiocFileCache/4264484562df_SRR660824_SRS389722_SRX222703_male_lung.bw
building whole annotation region map done
2 chromosomes for annotated regions read
Processing C:\Users\biocbuild\AppData\Local/R/cache/R/BiocFileCache/4264484562df_SRR660824_SRS389722_SRX222703_male_lung.bw
[1] "2021-09-19 21:28:57 - 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] "2021-09-19 21:28:57 - 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 
 208.34    8.17  281.07 

Example timings

dasper.Rcheck/dasper-Ex.timings

nameusersystemelapsed
coverage_process142.81 25.69296.84
junction_load0.390.000.52
junction_process63.52 1.3965.86
outlier_process000
plot_sashimi36.91 0.8738.56