| Back to Multiple platform build/check report for BioC 3.12 |
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This page was generated on 2021-05-06 12:36:51 -0400 (Thu, 06 May 2021).
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To the developers/maintainers of the slingshot package: Please make sure to use the following settings in order to reproduce any error or warning you see on this page. |
| Package 1734/1974 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| slingshot 1.8.0 (landing page) Kelly Street
| malbec1 | Linux (Ubuntu 18.04.5 LTS) / x86_64 | OK | OK | OK | |||||||||
| tokay1 | Windows Server 2012 R2 Standard / x64 | OK | OK | OK | OK | |||||||||
| merida1 | macOS 10.14.6 Mojave / x86_64 | OK | OK | ERROR | OK | |||||||||
| Package: slingshot |
| Version: 1.8.0 |
| Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:slingshot.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings slingshot_1.8.0.tar.gz |
| StartedAt: 2021-05-06 06:22:09 -0400 (Thu, 06 May 2021) |
| EndedAt: 2021-05-06 06:25:47 -0400 (Thu, 06 May 2021) |
| EllapsedTime: 218.3 seconds |
| RetCode: 1 |
| Status: ERROR |
| CheckDir: slingshot.Rcheck |
| Warnings: NA |
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### Running command:
###
### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:slingshot.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings slingshot_1.8.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.12-bioc/meat/slingshot.Rcheck’
* using R version 4.0.5 (2021-03-31)
* using platform: x86_64-apple-darwin17.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘slingshot/DESCRIPTION’ ... OK
* this is package ‘slingshot’ version ‘1.8.0’
* 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 ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘slingshot’ 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 ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘testthat.R’
ERROR
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
> library(testthat)
> library(slingshot)
Loading required package: princurve
>
> test_check("slingshot")
* 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
See
‘/Users/biocbuild/bbs-3.12-bioc/meat/slingshot.Rcheck/00check.log’
for details.
slingshot.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL slingshot ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.0/Resources/library’ * installing *source* package ‘slingshot’ ... ** using staged installation ** R ** data ** inst ** byte-compile and prepare package for lazy loading in method for ‘slingshot’ with signature ‘data="ClusterExperiment"’: no definition for class “ClusterExperiment” ** 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 (slingshot)
slingshot.Rcheck/tests/testthat.Rout.fail
R version 4.0.5 (2021-03-31) -- "Shake and Throw"
Copyright (C) 2021 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin17.0 (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(slingshot)
Loading required package: princurve
>
> test_check("slingshot")
slingshot.Rcheck/slingshot-Ex.timings
| name | user | system | elapsed | |
| SlingshotDataSet | 0.977 | 0.089 | 1.066 | |
| embedCurves | 1.173 | 0.054 | 1.228 | |
| getCurves | 0.345 | 0.012 | 0.357 | |
| getLineages | 0.028 | 0.003 | 0.032 | |
| newSlingshotDataSet | 0.003 | 0.001 | 0.003 | |
| pairs-SlingshotDataSet | 0.274 | 0.010 | 0.284 | |
| plot-SlingshotDataSet | 0.279 | 0.009 | 0.290 | |
| plot3d-SlingshotDataSet | 0.000 | 0.000 | 0.001 | |
| plotGenePseudotime | 0.288 | 0.007 | 0.296 | |
| predict.SlingshotDataSet | 0.304 | 0.012 | 0.317 | |
| slingAdjacency | 0.029 | 0.002 | 0.032 | |
| slingBranchGraph | 0.256 | 0.004 | 0.260 | |
| slingBranchID | 0.269 | 0.010 | 0.279 | |
| slingClusterLabels | 0.034 | 0.008 | 0.043 | |
| slingCurves | 0.216 | 0.017 | 0.233 | |
| slingLineages | 0.022 | 0.001 | 0.023 | |
| slingParams | 0.106 | 0.002 | 0.109 | |
| slingPseudotime | 0.495 | 0.017 | 0.513 | |
| slingshot | 0.271 | 0.005 | 0.278 | |
| slingshotExample | 0.262 | 0.005 | 0.267 | |