Benjamin Schuster-Boeckler
| Snapshot Date: 2019-10-15 17:01:26 -0400 (Tue, 15 Oct 2019) |
| URL: https://git.bioconductor.org/packages/BEARscc |
| Branch: RELEASE_3_9 |
| Last Commit: 0db2b02 |
| Last Changed Date: 2019-05-02 11:54:10 -0400 (Thu, 02 May 2019) |
| Back to Multiple platform build/check report for BioC 3.9 |
|
This page was generated on 2019-10-16 12:13:09 -0400 (Wed, 16 Oct 2019).
| Package 124/1741 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| BEARscc 1.4.0 Benjamin Schuster-Boeckler
| malbec2 | Linux (Ubuntu 18.04.2 LTS) / x86_64 | OK | OK | [ WARNINGS ] | | ||||||
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | WARNINGS | OK | | ||||||
| celaya2 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | WARNINGS | OK | |
| Package: BEARscc |
| Version: 1.4.0 |
| Command: /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD check --install=check:BEARscc.install-out.txt --library=/home/biocbuild/bbs-3.9-bioc/R/library --no-vignettes --timings BEARscc_1.4.0.tar.gz |
| StartedAt: 2019-10-16 00:00:45 -0400 (Wed, 16 Oct 2019) |
| EndedAt: 2019-10-16 00:06:34 -0400 (Wed, 16 Oct 2019) |
| EllapsedTime: 349.6 seconds |
| RetCode: 0 |
| Status: WARNINGS |
| CheckDir: BEARscc.Rcheck |
| Warnings: 1 |
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### Running command:
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### /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD check --install=check:BEARscc.install-out.txt --library=/home/biocbuild/bbs-3.9-bioc/R/library --no-vignettes --timings BEARscc_1.4.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.9-bioc/meat/BEARscc.Rcheck’
* using R version 3.6.1 (2019-07-05)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘BEARscc/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘BEARscc’ version ‘1.4.0’
* 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 ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘BEARscc’ can be installed ... OK
* 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 ... OK
* 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 ... WARNING
Object named ‘.Random.seed’ found in datasets:
‘BEARscc_examples’ ‘analysis_examples’
Please remove it.
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
user system elapsed
estimate_noiseparameters 470.192 2.293 92.586
simulate_replicates 41.845 0.136 11.175
report_cell_metrics 25.492 0.080 5.558
* 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 WARNING
See
‘/home/biocbuild/bbs-3.9-bioc/meat/BEARscc.Rcheck/00check.log’
for details.
BEARscc.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD INSTALL BEARscc ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.9-bioc/R/library’ * installing *source* package ‘BEARscc’ ... ** using staged installation ** R ** data ** 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 from temporary location ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (BEARscc)
BEARscc.Rcheck/tests/testthat.Rout
R version 3.6.1 (2019-07-05) -- "Action of the Toes"
Copyright (C) 2019 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(BEARscc)
>
> test_check("BEARscc")
[1] "Running BEARscc on example data to test for correct installation."
[1] "Fitting parameter alpha to establish spike-in derived noise model."
[1] "Estimating error for spike-ins with alpha = 0"
[1] "Estimating error for spike-ins with alpha = 0.25"
[1] "Estimating error for spike-ins with alpha = 0.5"
[1] "Estimating error for spike-ins with alpha = 0.75"
[1] "Estimating error for spike-ins with alpha = 1"
[1] "There are adequate spike-in drop-outs to build the drop-out model. Estimating the drop-out model now."
[1] "Injecting noise for testing..."
[1] "Creating a simulated replicated counts matrix: 1."
[1] "Creating a simulated replicated counts matrix: 2."
[1] "Creating a simulated replicated counts matrix: 3."
[1] "Creating consensus matrix for testing..."
[1] "Computing cluster and cell metrics for testing..."
══ testthat results ═══════════════════════════════════════════════════════════
[ OK: 25 | SKIPPED: 0 | WARNINGS: 13 | FAILED: 0 ]
>
> proc.time()
user system elapsed
304.592 1.459 56.007
BEARscc.Rcheck/BEARscc-Ex.timings
| name | user | system | elapsed | |
| BEARscc_examples | 0.013 | 0.000 | 0.013 | |
| analysis_examples | 0.015 | 0.000 | 0.015 | |
| cluster_consensus | 0.024 | 0.000 | 0.024 | |
| compute_consensus | 0.075 | 0.008 | 0.083 | |
| estimate_noiseparameters | 470.192 | 2.293 | 92.586 | |
| report_cell_metrics | 25.492 | 0.080 | 5.558 | |
| report_cluster_metrics | 3.179 | 0.017 | 1.073 | |
| simulate_replicates | 41.845 | 0.136 | 11.175 | |