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This page was generated on 2021-10-15 15:06:02 -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: 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: 2021-10-14 21:54:49 -0400 (Thu, 14 Oct 2021) |
EndedAt: 2021-10-14 22:08:56 -0400 (Thu, 14 Oct 2021) |
EllapsedTime: 847.1 seconds |
RetCode: 0 |
Status: OK |
CheckDir: dasper.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### 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 139.09 23.88 299.80 junction_process 69.09 1.12 71.05 plot_sashimi 34.83 0.86 36.50 * 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.
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
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] "2021-10-14 22:04:35 - Filtering junctions..." [1] "2021-10-14 22:04:35 - done!" [1] "# Annotating junctions ----------------------------------------------------" [1] "2021-10-14 22:04:35 - Obtaining co-ordinates of annotated exons and junctions from gtf/gff3..." [1] "2021-10-14 22:04:57 - Getting junction annotation using overlapping exons..." [1] "2021-10-14 22:04:58 - Tidying junction annotation..." [1] "2021-10-14 22:04:59 - Deriving junction categories..." [1] "2021-10-14 22:05:00 - done!" [1] "# Normalise junctions -----------------------------------------------------" [1] "2021-10-14 22:05:00 - Clustering junctions..." [1] "2021-10-14 22:05:01 - Normalising junction counts..." [1] "2021-10-14 22:05:01 - done!" [1] "# Score junctions ---------------------------------------------------------" [1] "2021-10-14 22:05:01 - Calculating the direction of change of junctions..." [1] "2021-10-14 22:05:01 - Generating junction abnormality score..." [1] "2021-10-14 22:05:01 - done!" [1] "2021-10-14 22:05:24 - Loading junctions for sample 1/1..." [1] "2021-10-14 22:05:24 - Adding control junctions..." [1] "2021-10-14 22:05:24 - Tidying and storing junction data as a RangedSummarizedExperiment..." [1] "2021-10-14 22:05:24 - done!" [1] "2021-10-14 22:05:24 - Loading junctions for sample 1/2..." [1] "2021-10-14 22:05:24 - Loading junctions for sample 2/2..." [1] "2021-10-14 22:05:25 - Adding control junctions..." [1] "2021-10-14 22:05:25 - Tidying and storing junction data as a RangedSummarizedExperiment..." [1] "2021-10-14 22:05:25 - done!" [1] "2021-10-14 22:05:25 - Loading junctions for sample 1/2..." [1] "2021-10-14 22:05:25 - Loading junctions for sample 2/2..." [1] "2021-10-14 22:05:25 - Adding control junctions..." [1] "2021-10-14 22:05:25 - Downloading and importing fibroblasts junction data..." [1] "2021-10-14 22:05:57 - Tidying and storing junction data as a RangedSummarizedExperiment..." [1] "2021-10-14 22:05:59 - done!" [1] "2021-10-14 22:06:00 - Loading junctions for sample 1/2..." [1] "2021-10-14 22:06:00 - Loading junctions for sample 2/2..." [1] "2021-10-14 22:06:00 - Adding control junctions..." [1] "2021-10-14 22:06:00 - Loading junctions for sample 1/2..." [1] "2021-10-14 22:06:00 - Loading junctions for sample 2/2..." [1] "2021-10-14 22:06:00 - Adding control junctions..." [1] "2021-10-14 22:06:00 - Loading junctions for sample 1/2..." [1] "2021-10-14 22:06:00 - Loading junctions for sample 2/2..." [1] "2021-10-14 22:06:00 - Adding control junctions..." [1] "2021-10-14 22:06:15 - Obtaining co-ordinates of annotated exons and junctions from gtf/gff3..." [1] "2021-10-14 22:06:55 - Filtering junctions..." [1] "2021-10-14 22:06:55 - by count..." [1] "2021-10-14 22:06:55 - done!" [1] "2021-10-14 22:06:55 - Filtering junctions..." [1] "2021-10-14 22:06:55 - by width..." [1] "2021-10-14 22:06:55 - done!" [1] "2021-10-14 22:06:55 - Filtering junctions..." [1] "2021-10-14 22:06:55 - by type..." [1] "2021-10-14 22:06:55 - done!" [1] "2021-10-14 22:06:55 - Filtering junctions..." [1] "2021-10-14 22:06:55 - by overlap with regions..." [1] "2021-10-14 22:06:55 - done!" [1] "2021-10-14 22:06:55 - Filtering junctions..." [1] "2021-10-14 22:06:55 - by count..." [1] "2021-10-14 22:06:55 - by width..." [1] "2021-10-14 22:06:55 - by type..." [1] "2021-10-14 22:06:55 - by overlap with regions..." [1] "2021-10-14 22:06:55 - done!" [1] "2021-10-14 22:07:02 - Clustering junctions..." [1] "2021-10-14 22:07:02 - Filtering junctions..." [1] "2021-10-14 22:07:02 - by count..." [1] "2021-10-14 22:07:02 - done!" [1] "2021-10-14 22:07:02 - Normalising junction counts..." [1] "2021-10-14 22:07:02 - done!" [1] "2021-10-14 22:07:02 - Calculating the direction of change of junctions..." [1] "2021-10-14 22:07:03 - Generating junction abnormality score..." [1] "2021-10-14 22:07:03 - done!" [1] "2021-10-14 22:07:17 - generating outlier scores for sample 1/2" [1] "2021-10-14 22:07:38 - 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 22:07:39 - 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 22:07:39 - generating outlier scores for sample 2/2" [1] "2021-10-14 22:07:39 - 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 22:07:40 - 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 22:07:40 - done!" [1] "2021-10-14 22:07:41 - 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 22:07:42 - 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 22:08:11 - Filtering junctions..." [1] "2021-10-14 22:08:11 - by count..." [1] "2021-10-14 22:08:11 - 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] "2021-10-14 22:08:48 - 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 22:08:48 - 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 205.70 8.64 282.76
dasper.Rcheck/dasper-Ex.timings
name | user | system | elapsed | |
coverage_process | 139.09 | 23.88 | 299.80 | |
junction_load | 0.39 | 0.00 | 0.57 | |
junction_process | 69.09 | 1.12 | 71.05 | |
outlier_process | 0 | 0 | 0 | |
plot_sashimi | 34.83 | 0.86 | 36.50 | |