| Back to Long Tests report for BioC 3.13 |
This page was generated on 2021-12-11 17:30:01 -0500 (Sat, 11 Dec 2021).
|
To the developers/maintainers of the zellkonverter package: Please make sure to use the following settings in order to reproduce any error or warning you see on this page. |
| Package 20/20 | Hostname | OS / Arch | CHECK | |||||||
| zellkonverter 1.5.0 (landing page) Luke Zappia
| rex3 | Linux (Ubuntu 20.04.2 LTS) / x86_64 | ERROR | |||||||
| Package: zellkonverter |
| Version: 1.5.0 |
| Command: /home/biocbuild/bbs-3.13-bioc/R/bin/R CMD check --test-dir=longtests --no-stop-on-test-error --no-codoc --no-examples --no-manual --ignore-vignettes --check-subdirs=no zellkonverter_1.5.0.tar.gz |
| StartedAt: 2021-12-11 09:32:51 -0500 (Sat, 11 Dec 2021) |
| EndedAt: 2021-12-11 09:34:18 -0500 (Sat, 11 Dec 2021) |
| EllapsedTime: 86.5 seconds |
| RetCode: 1 |
| Status: ERROR |
| CheckDir: zellkonverter.Rcheck |
| Warnings: NA |
zellkonverter.Rcheck/tests/testthat.Rout.fail
R Under development (unstable) (2021-02-10 r79979) -- "Unsuffered Consequences"
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(zellkonverter)
>
> test_check("zellkonverter")
══ Failed tests ════════════════════════════════════════════════════════════════
── Error (test-cellrank_pancreas.R:4:1): (code run outside of `test_that()`) ───
Error in `BiocFileCache(ask = FALSE)`: DEFUNCT: As of BiocFileCache (>1.15.1), default caching location has changed.
Problematic cache: /home/biocbuild/.cache/BiocFileCache
See https://www.bioconductor.org/packages/devel/bioc/vignettes/BiocFileCache/inst/doc/BiocFileCache.html#default-caching-location-update
Backtrace:
█
1. └─BiocFileCache::BiocFileCache(ask = FALSE) test-cellrank_pancreas.R:4:0
── Error (test-pegasus_marrow.R:4:1): (code run outside of `test_that()`) ──────
Error in `BiocFileCache(ask = FALSE)`: DEFUNCT: As of BiocFileCache (>1.15.1), default caching location has changed.
Problematic cache: /home/biocbuild/.cache/BiocFileCache
See https://www.bioconductor.org/packages/devel/bioc/vignettes/BiocFileCache/inst/doc/BiocFileCache.html#default-caching-location-update
Backtrace:
█
1. └─BiocFileCache::BiocFileCache(ask = FALSE) test-pegasus_marrow.R:4:0
── Error (test-scIB_pancreas.R:4:1): (code run outside of `test_that()`) ───────
Error in `BiocFileCache(ask = FALSE)`: DEFUNCT: As of BiocFileCache (>1.15.1), default caching location has changed.
Problematic cache: /home/biocbuild/.cache/BiocFileCache
See https://www.bioconductor.org/packages/devel/bioc/vignettes/BiocFileCache/inst/doc/BiocFileCache.html#default-caching-location-update
Backtrace:
█
1. └─BiocFileCache::BiocFileCache(ask = FALSE) test-scIB_pancreas.R:4:0
── Error (test-scanpy_pbmc3k.R:4:1): (code run outside of `test_that()`) ───────
Error in `BiocFileCache(ask = FALSE)`: DEFUNCT: As of BiocFileCache (>1.15.1), default caching location has changed.
Problematic cache: /home/biocbuild/.cache/BiocFileCache
See https://www.bioconductor.org/packages/devel/bioc/vignettes/BiocFileCache/inst/doc/BiocFileCache.html#default-caching-location-update
Backtrace:
█
1. └─BiocFileCache::BiocFileCache(ask = FALSE) test-scanpy_pbmc3k.R:4:0
── Error (test-scanpy_trajectory.R:4:1): (code run outside of `test_that()`) ───
Error in `BiocFileCache(ask = FALSE)`: DEFUNCT: As of BiocFileCache (>1.15.1), default caching location has changed.
Problematic cache: /home/biocbuild/.cache/BiocFileCache
See https://www.bioconductor.org/packages/devel/bioc/vignettes/BiocFileCache/inst/doc/BiocFileCache.html#default-caching-location-update
Backtrace:
█
1. └─BiocFileCache::BiocFileCache(ask = FALSE) test-scanpy_trajectory.R:4:0
── Error (test-scvelo_pancreas.R:4:1): (code run outside of `test_that()`) ─────
Error in `BiocFileCache(ask = FALSE)`: DEFUNCT: As of BiocFileCache (>1.15.1), default caching location has changed.
Problematic cache: /home/biocbuild/.cache/BiocFileCache
See https://www.bioconductor.org/packages/devel/bioc/vignettes/BiocFileCache/inst/doc/BiocFileCache.html#default-caching-location-update
Backtrace:
█
1. └─BiocFileCache::BiocFileCache(ask = FALSE) test-scvelo_pancreas.R:4:0
── Error (test-scvi_citeseq.R:4:1): (code run outside of `test_that()`) ────────
Error in `BiocFileCache(ask = FALSE)`: DEFUNCT: As of BiocFileCache (>1.15.1), default caching location has changed.
Problematic cache: /home/biocbuild/.cache/BiocFileCache
See https://www.bioconductor.org/packages/devel/bioc/vignettes/BiocFileCache/inst/doc/BiocFileCache.html#default-caching-location-update
Backtrace:
█
1. └─BiocFileCache::BiocFileCache(ask = FALSE) test-scvi_citeseq.R:4:0
── Error (test-squidpy_visium.R:4:1): (code run outside of `test_that()`) ──────
Error in `BiocFileCache(ask = FALSE)`: DEFUNCT: As of BiocFileCache (>1.15.1), default caching location has changed.
Problematic cache: /home/biocbuild/.cache/BiocFileCache
See https://www.bioconductor.org/packages/devel/bioc/vignettes/BiocFileCache/inst/doc/BiocFileCache.html#default-caching-location-update
Backtrace:
█
1. └─BiocFileCache::BiocFileCache(ask = FALSE) test-squidpy_visium.R:4:0
[ FAIL 8 | WARN 0 | SKIP 0 | PASS 21 ]
Error: Test failures
Execution halted
##############################################################################
##############################################################################
###
### Running command:
###
### /home/biocbuild/bbs-3.13-bioc/R/bin/R CMD check --test-dir=longtests --no-stop-on-test-error --no-codoc --no-examples --no-manual --ignore-vignettes --check-subdirs=no zellkonverter_1.5.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.13-bioc-longtests/meat/zellkonverter.Rcheck’
* using R Under development (unstable) (2021-02-10 r79979)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using options ‘--no-codoc --no-examples --no-manual --ignore-vignettes --no-stop-on-test-error’
* checking for file ‘zellkonverter/DESCRIPTION’ ... OK
* this is package ‘zellkonverter’ version ‘1.5.0’
* 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 ‘zellkonverter’ can be installed ... NOTE
Found the following notes/warnings:
Non-staged installation was used
See ‘/home/biocbuild/bbs-3.13-bioc-longtests/meat/zellkonverter.Rcheck/00install.out’ for details.
* checking installed package size ... OK
* checking package 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 ... SKIPPED
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking line endings in shell scripts ... OK
* checking files in ‘vignettes’ ... SKIPPED
* checking examples ... SKIPPED
* checking for unstated dependencies in ‘longtests’ ... OK
* checking tests in ‘longtests’ ...
Running ‘testthat.R’
ERROR
Running the tests in ‘longtests/testthat.R’ failed.
Last 13 lines of output:
Backtrace:
█
1. └─BiocFileCache::BiocFileCache(ask = FALSE) test-scvi_citeseq.R:4:0
── Error (test-squidpy_visium.R:4:1): (code run outside of `test_that()`) ──────
Error in `BiocFileCache(ask = FALSE)`: DEFUNCT: As of BiocFileCache (>1.15.1), default caching location has changed.
Problematic cache: /home/biocbuild/.cache/BiocFileCache
See https://www.bioconductor.org/packages/devel/bioc/vignettes/BiocFileCache/inst/doc/BiocFileCache.html#default-caching-location-update
Backtrace:
█
1. └─BiocFileCache::BiocFileCache(ask = FALSE) test-squidpy_visium.R:4:0
[ FAIL 8 | WARN 0 | SKIP 0 | PASS 21 ]
Error: Test failures
Execution halted
* DONE
Status: 1 ERROR, 1 NOTE
See
‘/home/biocbuild/bbs-3.13-bioc-longtests/meat/zellkonverter.Rcheck/00check.log’
for details.
zellkonverter.Rcheck/00install.out
* installing *source* package ‘zellkonverter’ ... ** using non-staged installation via StagedInstall field ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices *** copying figures ** building package indices ** installing vignettes ** testing if installed package can be loaded * DONE (zellkonverter)