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 15:06:02 -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 |
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###
### 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
###
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* 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
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###
### Running command:
###
### C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe --arch x64 CMD INSTALL --no-multiarch dasper
###
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* 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 | |