David Zhang
| Snapshot Date: 2021-10-14 04:50:12 -0400 (Thu, 14 Oct 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) |
| Back to Multiple platform build/check report for BioC 3.13 |
|
This page was generated on 2021-10-15 15:05:38 -0400 (Fri, 15 Oct 2021).
|
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. |
| Package 444/2041 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| dasper 1.2.0 (landing page) David Zhang
| nebbiolo1 | Linux (Ubuntu 20.04.2 LTS) / x86_64 | OK | OK | ERROR | |||||||||
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | OK | OK | | ||||||||
| machv2 | macOS 10.14.6 Mojave / x86_64 | OK | OK | OK | OK | | ||||||||
| 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: 2021-10-14 09:28:57 -0400 (Thu, 14 Oct 2021) |
| EndedAt: 2021-10-14 09:35:11 -0400 (Thu, 14 Oct 2021) |
| EllapsedTime: 374.6 seconds |
| RetCode: 1 |
| Status: ERROR |
| CheckDir: dasper.Rcheck |
| Warnings: NA |
##############################################################################
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###
### 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] "2021-10-14 09:31:26 - Filtering junctions..."
[1] "2021-10-14 09:31:26 - by count..."
[1] "2021-10-14 09:31:27 - done!"
[1] "# Annotating junctions ----------------------------------------------------"
[1] "2021-10-14 09:31:27 - Obtaining co-ordinates of annotated exons and junctions from gtf/gff3..."
[1] "2021-10-14 09:31:50 - Getting junction annotation using overlapping exons..."
[1] "2021-10-14 09:31:51 - Tidying junction annotation..."
[1] "2021-10-14 09:31:52 - Deriving junction categories..."
[1] "2021-10-14 09:31:52 - done!"
[1] "# Filtering junctions -----------------------------------------------------"
[1] "2021-10-14 09:31:52 - Filtering junctions..."
[1] "2021-10-14 09:31:52 - by type..."
[1] "2021-10-14 09:31:52 - done!"
[1] "# Normalise junctions -----------------------------------------------------"
[1] "2021-10-14 09:31:52 - Clustering junctions..."
[1] "2021-10-14 09:31:53 - Normalising junction counts..."
[1] "2021-10-14 09:31:53 - done!"
[1] "# Score junctions ---------------------------------------------------------"
[1] "2021-10-14 09:31:53 - Calculating the direction of change of junctions..."
[1] "2021-10-14 09:31:53 - Generating junction abnormality score..."
[1] "2021-10-14 09:31:53 - 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] "2021-10-14 09:31:53 - Obtaining exonic and intronic regions to load coverage from..."
[1] "2021-10-14 09:31:54 - Obtaining regions to use to normalise coverage..."
[1] "2021-10-14 09:32:00 - 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.
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)
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] "2021-10-14 09:32:23 - Filtering junctions..."
[1] "2021-10-14 09:32:23 - done!"
[1] "# Annotating junctions ----------------------------------------------------"
[1] "2021-10-14 09:32:23 - Obtaining co-ordinates of annotated exons and junctions from gtf/gff3..."
[1] "2021-10-14 09:32:45 - Getting junction annotation using overlapping exons..."
[1] "2021-10-14 09:32:47 - Tidying junction annotation..."
[1] "2021-10-14 09:32:47 - Deriving junction categories..."
[1] "2021-10-14 09:32:48 - done!"
[1] "# Normalise junctions -----------------------------------------------------"
[1] "2021-10-14 09:32:48 - Clustering junctions..."
[1] "2021-10-14 09:32:49 - Normalising junction counts..."
[1] "2021-10-14 09:32:49 - done!"
[1] "# Score junctions ---------------------------------------------------------"
[1] "2021-10-14 09:32:49 - Calculating the direction of change of junctions..."
[1] "2021-10-14 09:32:49 - Generating junction abnormality score..."
[1] "2021-10-14 09:32:49 - done!"
[1] "2021-10-14 09:33:12 - Loading junctions for sample 1/1..."
[1] "2021-10-14 09:33:12 - Adding control junctions..."
[1] "2021-10-14 09:33:12 - Tidying and storing junction data as a RangedSummarizedExperiment..."
[1] "2021-10-14 09:33:12 - done!"
[1] "2021-10-14 09:33:12 - Loading junctions for sample 1/2..."
[1] "2021-10-14 09:33:12 - Loading junctions for sample 2/2..."
[1] "2021-10-14 09:33:12 - Adding control junctions..."
[1] "2021-10-14 09:33:12 - Tidying and storing junction data as a RangedSummarizedExperiment..."
[1] "2021-10-14 09:33:12 - done!"
[1] "2021-10-14 09:33:12 - Loading junctions for sample 1/2..."
[1] "2021-10-14 09:33:12 - Loading junctions for sample 2/2..."
[1] "2021-10-14 09:33:12 - Adding control junctions..."
[1] "2021-10-14 09:33:12 - Downloading and importing fibroblasts junction data..."
[1] "2021-10-14 09:33:39 - Tidying and storing junction data as a RangedSummarizedExperiment..."
[1] "2021-10-14 09:33:41 - done!"
[1] "2021-10-14 09:33:41 - Loading junctions for sample 1/2..."
[1] "2021-10-14 09:33:41 - Loading junctions for sample 2/2..."
[1] "2021-10-14 09:33:41 - Adding control junctions..."
[1] "2021-10-14 09:33:41 - Loading junctions for sample 1/2..."
[1] "2021-10-14 09:33:41 - Loading junctions for sample 2/2..."
[1] "2021-10-14 09:33:41 - Adding control junctions..."
[1] "2021-10-14 09:33:41 - Loading junctions for sample 1/2..."
[1] "2021-10-14 09:33:41 - Loading junctions for sample 2/2..."
[1] "2021-10-14 09:33:41 - Adding control junctions..."
[1] "2021-10-14 09:33:49 - Obtaining co-ordinates of annotated exons and junctions from gtf/gff3..."
[1] "2021-10-14 09:34:24 - Filtering junctions..."
[1] "2021-10-14 09:34:24 - by count..."
[1] "2021-10-14 09:34:24 - done!"
[1] "2021-10-14 09:34:24 - Filtering junctions..."
[1] "2021-10-14 09:34:24 - by width..."
[1] "2021-10-14 09:34:24 - done!"
[1] "2021-10-14 09:34:24 - Filtering junctions..."
[1] "2021-10-14 09:34:24 - by type..."
[1] "2021-10-14 09:34:24 - done!"
[1] "2021-10-14 09:34:25 - Filtering junctions..."
[1] "2021-10-14 09:34:25 - by overlap with regions..."
[1] "2021-10-14 09:34:25 - done!"
[1] "2021-10-14 09:34:25 - Filtering junctions..."
[1] "2021-10-14 09:34:25 - by count..."
[1] "2021-10-14 09:34:25 - by width..."
[1] "2021-10-14 09:34:25 - by type..."
[1] "2021-10-14 09:34:25 - by overlap with regions..."
[1] "2021-10-14 09:34:25 - done!"
[1] "2021-10-14 09:34:31 - Clustering junctions..."
[1] "2021-10-14 09:34:31 - Filtering junctions..."
[1] "2021-10-14 09:34:31 - by count..."
[1] "2021-10-14 09:34:31 - done!"
[1] "2021-10-14 09:34:31 - Normalising junction counts..."
[1] "2021-10-14 09:34:32 - done!"
[1] "2021-10-14 09:34:32 - Calculating the direction of change of junctions..."
[1] "2021-10-14 09:34:32 - Generating junction abnormality score..."
[1] "2021-10-14 09:34:32 - done!"
[1] "2021-10-14 09:34:41 - generating outlier scores for sample 1/2"
[1] "2021-10-14 09:34:43 - 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 09:34:44 - 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 09:34:44 - generating outlier scores for sample 2/2"
[1] "2021-10-14 09:34:44 - 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 09:34:45 - 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 09:34:45 - done!"
[1] "2021-10-14 09:34:45 - 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 09:34:46 - 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 09:34:51 - Filtering junctions..."
[1] "2021-10-14 09:34:51 - by count..."
[1] "2021-10-14 09:34:51 - 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] "2021-10-14 09:35:08 - 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 09:35:08 - 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
171.023 10.963 186.698
dasper.Rcheck/dasper-Ex.timings
| name | user | system | elapsed |