| Back to Build/check report for BioC 3.18: simplified long |
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This page was generated on 2023-06-06 11:00:41 -0000 (Tue, 06 Jun 2023).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| kunpeng2 | Linux (openEuler 22.03 LTS-SP1) | aarch64 | 4.3.0 (2023-04-21) -- "Already Tomorrow" | 4366 |
| Click on any hostname to see more info about the system (e.g. compilers) (*) as reported by 'uname -p', except on Windows and Mac OS X | ||||
|
To the developers/maintainers of the scPCA package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/scPCA.git to reflect on this report. See Troubleshooting Build Report for more information. - Use the following Renviron settings to reproduce errors and warnings. Note: If "R CMD check" recently failed on the Linux builder over a missing dependency, add the missing dependency to "Suggests" in your DESCRIPTION file. See the Renviron.bioc for details. |
| Package 1826/2199 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| scPCA 1.15.0 (landing page) Philippe Boileau
| kunpeng2 | Linux (openEuler 22.03 LTS-SP1) / aarch64 | OK | OK | ERROR | |||||||||
| Package: scPCA |
| Version: 1.15.0 |
| Command: /home/biocbuild/R/R-4.3.0/bin/R CMD check --install=check:scPCA.install-out.txt --library=/home/biocbuild/R/R-4.3.0/site-library --timings scPCA_1.15.0.tar.gz |
| StartedAt: 2023-06-06 06:27:55 -0000 (Tue, 06 Jun 2023) |
| EndedAt: 2023-06-06 06:39:27 -0000 (Tue, 06 Jun 2023) |
| EllapsedTime: 691.9 seconds |
| RetCode: 1 |
| Status: ERROR |
| CheckDir: scPCA.Rcheck |
| Warnings: NA |
##############################################################################
##############################################################################
###
### Running command:
###
### /home/biocbuild/R/R-4.3.0/bin/R CMD check --install=check:scPCA.install-out.txt --library=/home/biocbuild/R/R-4.3.0/site-library --timings scPCA_1.15.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.18-bioc/meat/scPCA.Rcheck’
* using R version 4.3.0 (2023-04-21)
* using platform: aarch64-unknown-linux-gnu (64-bit)
* R was compiled by
gcc (GCC) 10.3.1
GNU Fortran (GCC) 10.3.1
* running under: openEuler 22.03 (LTS-SP1)
* using session charset: UTF-8
* checking for file ‘scPCA/DESCRIPTION’ ... OK
* this is package ‘scPCA’ version ‘1.15.0’
* 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 ‘scPCA’ 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 loading without being on the library search path ... OK
* checking dependencies in R code ... NOTE
Namespaces in Imports field not imported from:
‘DelayedArray’ ‘matrixStats’
All declared Imports should be used.
* 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 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.
Last 13 lines of output:
`bpFitGrid(...)` produced warnings.
── Failure ('test-fitGrid.R:556:3'): All cluster methods (kmeans, pam, hclust) run without errors ──
`bpFitGrid(...)` produced warnings.
── Failure ('test-fitGrid.R:563:3'): All cluster methods (kmeans, pam, hclust) run without errors ──
`bpFitGrid(...)` produced warnings.
── Failure ('test-fitGrid.R:570:3'): All cluster methods (kmeans, pam, hclust) run without errors ──
`bpFitGrid(...)` produced warnings.
── Failure ('test-fitGrid.R:649:3'): The grid can be fit using user-defined clusterings ──
`fitGrid(...)` produced warnings.
── Failure ('test-fitGrid.R:654:3'): The grid can be fit using user-defined clusterings ──
`bpFitGrid(...)` produced warnings.
[ FAIL 76 | WARN 65 | SKIP 0 | PASS 291 ]
Error: Test failures
Execution halted
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ...
‘scpca_intro.Rmd’ using ‘UTF-8’... OK
NONE
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE
Status: 1 ERROR, 1 NOTE
See
‘/home/biocbuild/bbs-3.18-bioc/meat/scPCA.Rcheck/00check.log’
for details.
scPCA.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/R/R-4.3.0/bin/R CMD INSTALL scPCA ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/R/R-4.3.0/site-library’ * installing *source* package ‘scPCA’ ... ** using staged installation ** R ** data *** moving datasets to lazyload DB ** inst ** byte-compile and prepare package for lazy loading ** help Loading required namespace: scPCA *** installing help indices *** copying figures ** 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 (scPCA)
scPCA.Rcheck/tests/testthat.Rout.fail
R version 4.3.0 (2023-04-21) -- "Already Tomorrow"
Copyright (C) 2023 The R Foundation for Statistical Computing
Platform: aarch64-unknown-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(scPCA)
>
> test_check("scPCA")
[ FAIL 76 | WARN 65 | SKIP 0 | PASS 291 ]
══ Failed tests ════════════════════════════════════════════════════════════════
── Failure ('test-contrastiveCov.R:17:3'): performs without issue when matrices are centered or scaled, and when using ScaledMatrix objects ──
`contrastiveCov(...)` produced warnings.
── Failure ('test-contrastiveCov.R:20:3'): performs without issue when matrices are centered or scaled, and when using ScaledMatrix objects ──
`contrastiveCov(...)` produced warnings.
── Failure ('test-contrastiveCov.R:46:3'): performs without issue when matrices are centered or scaled, and when using ScaledMatrix objects ──
`contrastiveCov(...)` produced warnings.
── Failure ('test-contrastiveCov.R:50:3'): performs without issue when matrices are centered or scaled, and when using ScaledMatrix objects ──
`contrastiveCov(dm_toy, dm_back, c(0, 1, 2), center = FALSE, scale = TRUE)` produced warnings.
── Failure ('test-covMat.R:34:3'): Routine can center, scale, center and scale, or neither ──
`covMat(background_df, center = TRUE, scale = TRUE)` produced warnings.
── Failure ('test-covMat.R:36:3'): Routine can center, scale, center and scale, or neither ──
`covMat(background_df, center = FALSE, scale = TRUE)` produced warnings.
── Failure ('test-covMat.R:39:3'): Routine can center, scale, center and scale, or neither ──
`covMat(as_tibble(background_df), center = TRUE, scale = TRUE)` produced warnings.
── Failure ('test-covMat.R:41:3'): Routine can center, scale, center and scale, or neither ──
`covMat(as_tibble(background_df), center = FALSE, scale = TRUE)` produced warnings.
── Failure ('test-covMat.R:44:3'): Routine can center, scale, center and scale, or neither ──
`covMat(as.matrix(background_df), center = TRUE, scale = TRUE)` produced warnings.
── Failure ('test-covMat.R:46:3'): Routine can center, scale, center and scale, or neither ──
`covMat(as.matrix(background_df), center = FALSE, scale = TRUE)` produced warnings.
── Failure ('test-covMat.R:58:3'): Routine can center, scale, center and scale, or neither ──
`covMat(DelayedArray(background_df), center = TRUE, scale = TRUE)` produced warnings.
── Failure ('test-covMat.R:62:3'): Routine can center, scale, center and scale, or neither ──
`covMat(DelayedArray(background_df), center = FALSE, scale = TRUE)` produced warnings.
── Failure ('test-covMat.R:68:3'): Routine can center, scale, center and scale, or neither ──
`covMat(background_df, center = TRUE, scale = TRUE, scaled_matrix = TRUE)` produced warnings.
── Failure ('test-covMat.R:75:3'): Routine can center, scale, center and scale, or neither ──
`covMat(background_df, center = FALSE, scale = TRUE, scaled_matrix = TRUE)` produced warnings.
── Failure ('test-covMat.R:82:3'): Routine can center, scale, center and scale, or neither ──
`covMat(...)` produced warnings.
── Failure ('test-covMat.R:88:3'): Routine can center, scale, center and scale, or neither ──
`covMat(...)` produced warnings.
── Failure ('test-covMat.R:107:3'): Routine can center, scale, center and scale, or neither ──
`covMat(...)` produced warnings.
── Failure ('test-covMat.R:119:3'): Routine can center, scale, center and scale, or neither ──
`covMat(...)` produced warnings.
── Failure ('test-covMat.R:157:3'): Routine can center, scale, center and scale, or neither ──
`covMat(...)` produced warnings.
── Failure ('test-covMat.R:169:3'): Routine can center, scale, center and scale, or neither ──
`covMat(...)` produced warnings.
── Failure ('test-fitGrid.R:198:3'): All cluster methods (kmeans, pam, hclust) run without errors ──
`fitGrid(...)` produced warnings.
── Failure ('test-fitGrid.R:205:3'): All cluster methods (kmeans, pam, hclust) run without errors ──
`fitGrid(...)` produced warnings.
── Failure ('test-fitGrid.R:212:3'): All cluster methods (kmeans, pam, hclust) run without errors ──
`fitGrid(...)` produced warnings.
── Failure ('test-fitGrid.R:219:3'): All cluster methods (kmeans, pam, hclust) run without errors ──
`fitGrid(...)` produced warnings.
── Failure ('test-fitGrid.R:226:3'): All cluster methods (kmeans, pam, hclust) run without errors ──
`fitGrid(...)` produced warnings.
── Failure ('test-fitGrid.R:233:3'): All cluster methods (kmeans, pam, hclust) run without errors ──
`fitGrid(...)` produced warnings.
── Failure ('test-fitGrid.R:240:3'): All cluster methods (kmeans, pam, hclust) run without errors ──
`fitGrid(...)` produced warnings.
── Failure ('test-fitGrid.R:247:3'): All cluster methods (kmeans, pam, hclust) run without errors ──
`fitGrid(...)` produced warnings.
── Failure ('test-fitGrid.R:254:3'): All cluster methods (kmeans, pam, hclust) run without errors ──
`fitGrid(...)` produced warnings.
── Failure ('test-fitGrid.R:261:3'): All cluster methods (kmeans, pam, hclust) run without errors ──
`fitGrid(...)` produced warnings.
── Failure ('test-fitGrid.R:268:3'): All cluster methods (kmeans, pam, hclust) run without errors ──
`fitGrid(...)` produced warnings.
── Failure ('test-fitGrid.R:275:3'): All cluster methods (kmeans, pam, hclust) run without errors ──
`fitGrid(...)` produced warnings.
── Failure ('test-fitGrid.R:282:3'): All cluster methods (kmeans, pam, hclust) run without errors ──
`fitGrid(...)` produced warnings.
── Failure ('test-fitGrid.R:289:3'): All cluster methods (kmeans, pam, hclust) run without errors ──
`fitGrid(...)` produced warnings.
── Failure ('test-fitGrid.R:296:3'): All cluster methods (kmeans, pam, hclust) run without errors ──
`fitGrid(...)` produced warnings.
── Failure ('test-fitGrid.R:303:3'): All cluster methods (kmeans, pam, hclust) run without errors ──
`fitGrid(...)` produced warnings.
── Failure ('test-fitGrid.R:310:3'): All cluster methods (kmeans, pam, hclust) run without errors ──
`fitGrid(...)` produced warnings.
── Failure ('test-fitGrid.R:317:3'): All cluster methods (kmeans, pam, hclust) run without errors ──
`fitGrid(...)` produced warnings.
── Failure ('test-fitGrid.R:324:3'): All cluster methods (kmeans, pam, hclust) run without errors ──
`fitGrid(...)` produced warnings.
── Failure ('test-fitGrid.R:331:3'): All cluster methods (kmeans, pam, hclust) run without errors ──
`fitGrid(...)` produced warnings.
── Failure ('test-fitGrid.R:338:3'): All cluster methods (kmeans, pam, hclust) run without errors ──
`fitGrid(...)` produced warnings.
── Failure ('test-fitGrid.R:345:3'): All cluster methods (kmeans, pam, hclust) run without errors ──
`fitGrid(...)` produced warnings.
── Failure ('test-fitGrid.R:352:3'): All cluster methods (kmeans, pam, hclust) run without errors ──
`fitGrid(...)` produced warnings.
── Failure ('test-fitGrid.R:359:3'): All cluster methods (kmeans, pam, hclust) run without errors ──
`fitGrid(...)` produced warnings.
── Failure ('test-fitGrid.R:366:3'): All cluster methods (kmeans, pam, hclust) run without errors ──
`fitGrid(...)` produced warnings.
── Failure ('test-fitGrid.R:373:3'): All cluster methods (kmeans, pam, hclust) run without errors ──
`fitGrid(...)` produced warnings.
── Failure ('test-fitGrid.R:380:3'): All cluster methods (kmeans, pam, hclust) run without errors ──
`fitGrid(...)` produced warnings.
── Failure ('test-fitGrid.R:388:3'): All cluster methods (kmeans, pam, hclust) run without errors ──
`bpFitGrid(...)` produced warnings.
── Failure ('test-fitGrid.R:395:3'): All cluster methods (kmeans, pam, hclust) run without errors ──
`bpFitGrid(...)` produced warnings.
── Failure ('test-fitGrid.R:402:3'): All cluster methods (kmeans, pam, hclust) run without errors ──
`bpFitGrid(...)` produced warnings.
── Failure ('test-fitGrid.R:409:3'): All cluster methods (kmeans, pam, hclust) run without errors ──
`bpFitGrid(...)` produced warnings.
── Failure ('test-fitGrid.R:416:3'): All cluster methods (kmeans, pam, hclust) run without errors ──
`bpFitGrid(...)` produced warnings.
── Failure ('test-fitGrid.R:423:3'): All cluster methods (kmeans, pam, hclust) run without errors ──
`bpFitGrid(...)` produced warnings.
── Failure ('test-fitGrid.R:430:3'): All cluster methods (kmeans, pam, hclust) run without errors ──
`bpFitGrid(...)` produced warnings.
── Failure ('test-fitGrid.R:437:3'): All cluster methods (kmeans, pam, hclust) run without errors ──
`bpFitGrid(...)` produced warnings.
── Failure ('test-fitGrid.R:444:3'): All cluster methods (kmeans, pam, hclust) run without errors ──
`bpFitGrid(...)` produced warnings.
── Failure ('test-fitGrid.R:451:3'): All cluster methods (kmeans, pam, hclust) run without errors ──
`bpFitGrid(...)` produced warnings.
── Failure ('test-fitGrid.R:458:3'): All cluster methods (kmeans, pam, hclust) run without errors ──
`bpFitGrid(...)` produced warnings.
── Failure ('test-fitGrid.R:465:3'): All cluster methods (kmeans, pam, hclust) run without errors ──
`bpFitGrid(...)` produced warnings.
── Failure ('test-fitGrid.R:472:3'): All cluster methods (kmeans, pam, hclust) run without errors ──
`bpFitGrid(...)` produced warnings.
── Failure ('test-fitGrid.R:479:3'): All cluster methods (kmeans, pam, hclust) run without errors ──
`bpFitGrid(...)` produced warnings.
── Failure ('test-fitGrid.R:486:3'): All cluster methods (kmeans, pam, hclust) run without errors ──
`bpFitGrid(...)` produced warnings.
── Failure ('test-fitGrid.R:493:3'): All cluster methods (kmeans, pam, hclust) run without errors ──
`bpFitGrid(...)` produced warnings.
── Failure ('test-fitGrid.R:500:3'): All cluster methods (kmeans, pam, hclust) run without errors ──
`bpFitGrid(...)` produced warnings.
── Failure ('test-fitGrid.R:507:3'): All cluster methods (kmeans, pam, hclust) run without errors ──
`bpFitGrid(...)` produced warnings.
── Failure ('test-fitGrid.R:514:3'): All cluster methods (kmeans, pam, hclust) run without errors ──
`bpFitGrid(...)` produced warnings.
── Failure ('test-fitGrid.R:521:3'): All cluster methods (kmeans, pam, hclust) run without errors ──
`bpFitGrid(...)` produced warnings.
── Failure ('test-fitGrid.R:528:3'): All cluster methods (kmeans, pam, hclust) run without errors ──
`bpFitGrid(...)` produced warnings.
── Failure ('test-fitGrid.R:535:3'): All cluster methods (kmeans, pam, hclust) run without errors ──
`bpFitGrid(...)` produced warnings.
── Failure ('test-fitGrid.R:542:3'): All cluster methods (kmeans, pam, hclust) run without errors ──
`bpFitGrid(...)` produced warnings.
── Failure ('test-fitGrid.R:549:3'): All cluster methods (kmeans, pam, hclust) run without errors ──
`bpFitGrid(...)` produced warnings.
── Failure ('test-fitGrid.R:556:3'): All cluster methods (kmeans, pam, hclust) run without errors ──
`bpFitGrid(...)` produced warnings.
── Failure ('test-fitGrid.R:563:3'): All cluster methods (kmeans, pam, hclust) run without errors ──
`bpFitGrid(...)` produced warnings.
── Failure ('test-fitGrid.R:570:3'): All cluster methods (kmeans, pam, hclust) run without errors ──
`bpFitGrid(...)` produced warnings.
── Failure ('test-fitGrid.R:649:3'): The grid can be fit using user-defined clusterings ──
`fitGrid(...)` produced warnings.
── Failure ('test-fitGrid.R:654:3'): The grid can be fit using user-defined clusterings ──
`bpFitGrid(...)` produced warnings.
[ FAIL 76 | WARN 65 | SKIP 0 | PASS 291 ]
Error: Test failures
Execution halted
scPCA.Rcheck/scPCA-Ex.timings
| name | user | system | elapsed | |
| background_df | 0.002 | 0.000 | 0.003 | |
| scPCA | 2.954 | 0.088 | 3.044 | |
| toy_df | 0.001 | 0.000 | 0.001 | |