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This page was generated on 2021-09-17 15:05:38 -0400 (Fri, 17 Sep 2021).

CHECK results for dasper on nebbiolo1

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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: /home/biocbuild/bbs-3.13-bioc/R/bin/R CMD check --install=check:dasper.install-out.txt --library=/home/biocbuild/bbs-3.13-bioc/R/library --no-vignettes --timings dasper_1.2.0.tar.gz
StartedAt: 2021-09-16 09:28:13 -0400 (Thu, 16 Sep 2021)
EndedAt: 2021-09-16 09:34:35 -0400 (Thu, 16 Sep 2021)
EllapsedTime: 382.5 seconds
RetCode: 1
Status:   ERROR  
CheckDir: dasper.Rcheck
Warnings: NA

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.13-bioc/R/bin/R CMD check --install=check:dasper.install-out.txt --library=/home/biocbuild/bbs-3.13-bioc/R/library --no-vignettes --timings dasper_1.2.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.13-bioc/meat/dasper.Rcheck’
* using R version 4.1.1 (2021-08-10)
* using platform: x86_64-pc-linux-gnu (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
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 ‘/home/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 ... ERROR
Running examples in ‘dasper-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: coverage_norm
> ### Title: Processing coverage
> ### Aliases: coverage_norm coverage_process coverage_score
> 
> ### ** Examples
> 
> 
> ##### Set up txdb #####
> 
> # use GenomicState to load txdb (GENCODE v31)
> ref <- GenomicState::GenomicStateHub(
+     version = "31",
+     genome = "hg38",
+     filetype = "TxDb"
+ )[[1]]
snapshotDate(): 2021-05-18
loading from cache
Loading required package: GenomicFeatures
Loading required package: BiocGenerics
Loading required package: parallel

Attaching package: ‘BiocGenerics’

The following objects are masked from ‘package:parallel’:

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
    clusterExport, clusterMap, parApply, parCapply, parLapply,
    parLapplyLB, parRapply, parSapply, parSapplyLB

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
Loading required package: stats4

Attaching package: ‘S4Vectors’

The following objects are masked from ‘package:base’:

    I, expand.grid, unname

Loading required package: IRanges
Loading required package: GenomeInfoDb
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")'.

> 
> ##### Set up BigWig #####
> 
> # obtain path to example bw on recount2
> bw_path <- recount::download_study(
+     project = "SRP012682",
+     type = "samples",
+     download = FALSE
+ )[[1]]
Setting options('download.file.method.GEOquery'='auto')
Setting options('GEOquery.inmemory.gpl'=FALSE)
> ## Don't show: 
> # cache the bw for speed in later
> # examples/testing during R CMD Check
> bw_path <- dasper:::.file_cache(bw_path)
> ## End(Don't show)
> 
> ##### junction_process #####
> 
> junctions_processed <- junction_process(
+     junctions_example,
+     ref,
+     types = c("ambig_gene", "unannotated"),
+ )
[1] "# Filtering junctions -----------------------------------------------------"
[1] "2021-09-16 09:30:51 - Filtering junctions..."
[1] "2021-09-16 09:30:51 - by count..."
[1] "2021-09-16 09:30:51 - done!"
[1] "# Annotating junctions ----------------------------------------------------"
[1] "2021-09-16 09:30:51 - Obtaining co-ordinates of annotated exons and junctions from gtf/gff3..."
[1] "2021-09-16 09:31:14 - Getting junction annotation using overlapping exons..."
[1] "2021-09-16 09:31:15 - Tidying junction annotation..."
[1] "2021-09-16 09:31:15 - Deriving junction categories..."
[1] "2021-09-16 09:31:16 - done!"
[1] "# Filtering junctions -----------------------------------------------------"
[1] "2021-09-16 09:31:16 - Filtering junctions..."
[1] "2021-09-16 09:31:16 - by type..."
[1] "2021-09-16 09:31:16 - done!"
[1] "# Normalise junctions -----------------------------------------------------"
[1] "2021-09-16 09:31:16 - Clustering junctions..."
[1] "2021-09-16 09:31:16 - Normalising junction counts..."
[1] "2021-09-16 09:31:17 - done!"
[1] "# Score junctions ---------------------------------------------------------"
[1] "2021-09-16 09:31:17 - Calculating the direction of change of junctions..."
[1] "2021-09-16 09:31:17 - Generating junction abnormality score..."
[1] "2021-09-16 09:31:17 - done!"
> 
> ##### coverage_norm #####
> 
> coverage_normed <- coverage_norm(
+     junctions_processed,
+     ref,
+     unannot_width = 20,
+     coverage_paths_case = rep(bw_path, 2),
+     coverage_paths_control = rep(bw_path, 2)
+ )
[1] "2021-09-16 09:31:17 - Obtaining exonic and intronic regions to load coverage from..."
[1] "2021-09-16 09:31:17 - Obtaining regions to use to normalise coverage..."
[1] "2021-09-16 09:31:24 - Loading coverage..."
Error: BiocParallel errors
  element index: 1, 2
  first error: megadepth not found. You can install it via megadepth::install_megadepth()
Execution halted
* 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: 1 ERROR, 3 NOTEs
See
  ‘/home/biocbuild/bbs-3.13-bioc/meat/dasper.Rcheck/00check.log’
for details.


Installation output

dasper.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.13-bioc/R/bin/R CMD INSTALL dasper
###
##############################################################################
##############################################################################


* installing to library ‘/home/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
** 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-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(dasper)
> 
> test_check("dasper")
[1] "# Filtering junctions -----------------------------------------------------"
[1] "2021-09-16 09:31:46 - Filtering junctions..."
[1] "2021-09-16 09:31:46 - done!"
[1] "# Annotating junctions ----------------------------------------------------"
[1] "2021-09-16 09:31:46 - Obtaining co-ordinates of annotated exons and junctions from gtf/gff3..."
[1] "2021-09-16 09:32:09 - Getting junction annotation using overlapping exons..."
[1] "2021-09-16 09:32:10 - Tidying junction annotation..."
[1] "2021-09-16 09:32:11 - Deriving junction categories..."
[1] "2021-09-16 09:32:12 - done!"
[1] "# Normalise junctions -----------------------------------------------------"
[1] "2021-09-16 09:32:12 - Clustering junctions..."
[1] "2021-09-16 09:32:12 - Normalising junction counts..."
[1] "2021-09-16 09:32:13 - done!"
[1] "# Score junctions ---------------------------------------------------------"
[1] "2021-09-16 09:32:13 - Calculating the direction of change of junctions..."
[1] "2021-09-16 09:32:13 - Generating junction abnormality score..."
[1] "2021-09-16 09:32:13 - done!"
[1] "2021-09-16 09:32:36 - Loading junctions for sample 1/1..."
[1] "2021-09-16 09:32:36 - Adding control junctions..."
[1] "2021-09-16 09:32:36 - Tidying and storing junction data as a RangedSummarizedExperiment..."
[1] "2021-09-16 09:32:36 - done!"
[1] "2021-09-16 09:32:36 - Loading junctions for sample 1/2..."
[1] "2021-09-16 09:32:36 - Loading junctions for sample 2/2..."
[1] "2021-09-16 09:32:36 - Adding control junctions..."
[1] "2021-09-16 09:32:36 - Tidying and storing junction data as a RangedSummarizedExperiment..."
[1] "2021-09-16 09:32:36 - done!"
[1] "2021-09-16 09:32:36 - Loading junctions for sample 1/2..."
[1] "2021-09-16 09:32:36 - Loading junctions for sample 2/2..."
[1] "2021-09-16 09:32:36 - Adding control junctions..."
[1] "2021-09-16 09:32:36 - Downloading and importing fibroblasts junction data..."
[1] "2021-09-16 09:33:05 - Tidying and storing junction data as a RangedSummarizedExperiment..."
[1] "2021-09-16 09:33:07 - done!"
[1] "2021-09-16 09:33:07 - Loading junctions for sample 1/2..."
[1] "2021-09-16 09:33:07 - Loading junctions for sample 2/2..."
[1] "2021-09-16 09:33:07 - Adding control junctions..."
[1] "2021-09-16 09:33:07 - Loading junctions for sample 1/2..."
[1] "2021-09-16 09:33:07 - Loading junctions for sample 2/2..."
[1] "2021-09-16 09:33:07 - Adding control junctions..."
[1] "2021-09-16 09:33:07 - Loading junctions for sample 1/2..."
[1] "2021-09-16 09:33:07 - Loading junctions for sample 2/2..."
[1] "2021-09-16 09:33:07 - Adding control junctions..."
[1] "2021-09-16 09:33:15 - Obtaining co-ordinates of annotated exons and junctions from gtf/gff3..."
[1] "2021-09-16 09:33:51 - Filtering junctions..."
[1] "2021-09-16 09:33:51 - by count..."
[1] "2021-09-16 09:33:51 - done!"
[1] "2021-09-16 09:33:51 - Filtering junctions..."
[1] "2021-09-16 09:33:51 - by width..."
[1] "2021-09-16 09:33:51 - done!"
[1] "2021-09-16 09:33:51 - Filtering junctions..."
[1] "2021-09-16 09:33:51 - by type..."
[1] "2021-09-16 09:33:51 - done!"
[1] "2021-09-16 09:33:51 - Filtering junctions..."
[1] "2021-09-16 09:33:51 - by overlap with regions..."
[1] "2021-09-16 09:33:51 - done!"
[1] "2021-09-16 09:33:51 - Filtering junctions..."
[1] "2021-09-16 09:33:51 - by count..."
[1] "2021-09-16 09:33:51 - by width..."
[1] "2021-09-16 09:33:51 - by type..."
[1] "2021-09-16 09:33:51 - by overlap with regions..."
[1] "2021-09-16 09:33:51 - done!"
[1] "2021-09-16 09:33:57 - Clustering junctions..."
[1] "2021-09-16 09:33:57 - Filtering junctions..."
[1] "2021-09-16 09:33:57 - by count..."
[1] "2021-09-16 09:33:58 - done!"
[1] "2021-09-16 09:33:58 - Normalising junction counts..."
[1] "2021-09-16 09:33:58 - done!"
[1] "2021-09-16 09:33:58 - Calculating the direction of change of junctions..."
[1] "2021-09-16 09:33:58 - Generating junction abnormality score..."
[1] "2021-09-16 09:33:58 - done!"
[1] "2021-09-16 09:34:07 - generating outlier scores for sample 1/2"
[1] "2021-09-16 09:34:09 - 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 09:34:10 - 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 09:34:10 - generating outlier scores for sample 2/2"
[1] "2021-09-16 09:34:10 - 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 09:34:11 - 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 09:34:11 - done!"
[1] "2021-09-16 09:34:11 - 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 09:34:12 - 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 09:34:17 - Filtering junctions..."
[1] "2021-09-16 09:34:17 - by count..."
[1] "2021-09-16 09:34:17 - done!"
building whole annotation region map done
2 chromosomes for annotated regions read
Processing /home/biocbuild/.cache/R/BiocFileCache/f164bf9d4c75_SRR660824_SRS389722_SRX222703_male_lung.bw
building whole annotation region map done
2 chromosomes for annotated regions read
Processing /home/biocbuild/.cache/R/BiocFileCache/f164bf9d4c75_SRR660824_SRS389722_SRX222703_male_lung.bw
[1] "2021-09-16 09:34:30 - 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 09:34:31 - 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"
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 212 ]
> 
> proc.time()
   user  system elapsed 
175.343   7.859 185.256 

Example timings

dasper.Rcheck/dasper-Ex.timings

nameusersystemelapsed