Back to Multiple platform build/check report for BioC 3.20: simplified long |
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This page was generated on 2024-07-26 11:39 -0400 (Fri, 26 Jul 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4690 |
palomino8 | Windows Server 2022 Datacenter | x64 | 4.4.1 (2024-06-14 ucrt) -- "Race for Your Life" | 4384 |
lconway | macOS 12.7.1 Monterey | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4457 |
kjohnson3 | macOS 13.6.5 Ventura | arm64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4406 |
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 |
Package 1877/2248 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
scTensor 2.15.0 (landing page) Koki Tsuyuzaki
| nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | OK | ERROR | |||||||||
palomino8 | Windows Server 2022 Datacenter / x64 | OK | OK | WARNINGS | OK | ![]() | ||||||||
lconway | macOS 12.7.1 Monterey / x86_64 | OK | ERROR | skipped | skipped | |||||||||
kjohnson3 | macOS 13.6.5 Ventura / arm64 | OK | OK | WARNINGS | OK | ![]() | ||||||||
To the developers/maintainers of the scTensor package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/scTensor.git to reflect on this report. See Troubleshooting Build Report for more information. - Use the following Renviron settings to reproduce errors and warnings. - If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information. |
Package: scTensor |
Version: 2.15.0 |
Command: /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD check --install=check:scTensor.install-out.txt --library=/home/biocbuild/bbs-3.20-bioc/R/site-library --timings scTensor_2.15.0.tar.gz |
StartedAt: 2024-07-26 03:46:56 -0400 (Fri, 26 Jul 2024) |
EndedAt: 2024-07-26 03:55:06 -0400 (Fri, 26 Jul 2024) |
EllapsedTime: 489.9 seconds |
RetCode: 1 |
Status: ERROR |
CheckDir: scTensor.Rcheck |
Warnings: NA |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD check --install=check:scTensor.install-out.txt --library=/home/biocbuild/bbs-3.20-bioc/R/site-library --timings scTensor_2.15.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.20-bioc/meat/scTensor.Rcheck’ * using R version 4.4.1 (2024-06-14) * using platform: x86_64-pc-linux-gnu * R was compiled by gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 * running under: Ubuntu 22.04.4 LTS * using session charset: UTF-8 * checking for file ‘scTensor/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘scTensor’ version ‘2.15.0’ * 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 ‘scTensor’ can be installed ... OK * checking installed package size ... OK * checking package directory ... OK * checking ‘build’ directory ... OK * checking DESCRIPTION meta-information ... NOTE Package listed in more than one of Depends, Imports, Suggests, Enhances: ‘AnnotationHub’ A package should be listed in only one of these fields. * checking top-level files ... OK * checking for left-over files ... OK * checking index information ... OK * checking package subdirectories ... OK * checking code 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 ... OK * checking S3 generic/method consistency ... OK * checking replacement functions ... OK * checking foreign function calls ... OK * checking R code for possible problems ... NOTE .simulateDropoutCounts: no visible binding for global variable ‘v’ .simulateDropoutCounts: no visible binding for global variable ‘m’ Undefined global functions or variables: m v * checking Rd files ... WARNING checkRd: (5) newCCSParams.Rd:8: \item in \arguments must have non-empty label * 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’ OK * checking for unstated dependencies in vignettes ... OK * checking package vignettes ... OK * checking re-building of vignette outputs ... ERROR Error(s) in re-building vignettes: ... --- re-building ‘scTensor.Rmd’ using rmarkdown Quitting from lines 95-100 [Access] (scTensor.Rmd) Error: processing vignette 'scTensor.Rmd' failed with diagnostics: file is not a database --- failed re-building ‘scTensor.Rmd’ --- re-building ‘scTensor_1_Data_format_ID_Conversion.Rmd’ using rmarkdown --- finished re-building ‘scTensor_1_Data_format_ID_Conversion.Rmd’ --- re-building ‘scTensor_2_Report_Interpretation.Rmd’ using rmarkdown --- finished re-building ‘scTensor_2_Report_Interpretation.Rmd’ --- re-building ‘scTensor_3_CCI_Simulation.Rmd’ using rmarkdown --- finished re-building ‘scTensor_3_CCI_Simulation.Rmd’ --- re-building ‘scTensor_4_Reanalysis.Rmd’ using rmarkdown --- finished re-building ‘scTensor_4_Reanalysis.Rmd’ SUMMARY: processing the following file failed: ‘scTensor.Rmd’ Error: Vignette re-building failed. Execution halted * checking PDF version of manual ... OK * DONE Status: 1 ERROR, 1 WARNING, 2 NOTEs See ‘/home/biocbuild/bbs-3.20-bioc/meat/scTensor.Rcheck/00check.log’ for details.
scTensor.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD INSTALL scTensor ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.20-bioc/R/site-library’ * installing *source* package ‘scTensor’ ... ** using staged installation ** R ** data ** inst ** byte-compile and prepare package for lazy loading Creating a new generic function for ‘show’ in package ‘scTensor’ ** 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 (scTensor)
scTensor.Rcheck/tests/testthat.Rout
R version 4.4.1 (2024-06-14) -- "Race for Your Life" Copyright (C) 2024 The R Foundation for Statistical Computing Platform: x86_64-pc-linux-gnu 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("scTensor") > > options(testthat.use_colours = FALSE) > > test_file("testthat/test_GermMale.R") ══ Testing test_GermMale.R ═════════════════════════════════════════════════════ [ FAIL 0 | WARN 0 | SKIP 0 | PASS 0 ] [ FAIL 0 | WARN 0 | SKIP 0 | PASS 0 ] [ FAIL 1 | WARN 0 | SKIP 0 | PASS 0 ] ── Failure ('test_GermMale.R:5:1'): (code run outside of `test_that()`) ──────── dim(GermMale) not equivalent to c(2547, 852). 1/2 mismatches [1] 242 - 2547 == -2305 [ FAIL 1 | WARN 0 | SKIP 0 | PASS 0 ] > test_file("testthat/test_tsneGermMale.R") ══ Testing test_tsneGermMale.R ═════════════════════════════════════════════════ [ FAIL 0 | WARN 0 | SKIP 0 | PASS 0 ] [ FAIL 0 | WARN 0 | SKIP 0 | PASS 0 ] [ FAIL 0 | WARN 0 | SKIP 0 | PASS 1 ] Done! > test_file("testthat/test_labelGermMale.R") ══ Testing test_labelGermMale.R ════════════════════════════════════════════════ [ FAIL 0 | WARN 0 | SKIP 0 | PASS 0 ] [ FAIL 0 | WARN 0 | SKIP 0 | PASS 0 ] [ FAIL 0 | WARN 0 | SKIP 0 | PASS 1 ] Done! > test_file("testthat/test_cellCellFunctions.R") ══ Testing test_cellCellFunctions.R ════════════════════════════════════════════ [ FAIL 0 | WARN 0 | SKIP 0 | PASS 0 ] [ FAIL 0 | WARN 0 | SKIP 0 | PASS 0 ] [ FAIL 1 | WARN 0 | SKIP 0 | PASS 0 ] ── Error ('test_cellCellFunctions.R:4:1'): (code run outside of `test_that()`) ── <packageNotFoundError/error/condition> Error in `library(LRBase.Hsa.eg.db)`: there is no package called 'LRBase.Hsa.eg.db' Backtrace: ▆ 1. └─base::library(LRBase.Hsa.eg.db) at test_cellCellFunctions.R:4:1 [ FAIL 1 | WARN 0 | SKIP 0 | PASS 0 ] > test_file("testthat/test_CCSParamsFunctions.R") ══ Testing test_CCSParamsFunctions.R ═══════════════════════════════════════════ [ FAIL 0 | WARN 0 | SKIP 0 | PASS 0 ] [ FAIL 0 | WARN 0 | SKIP 0 | PASS 0 ] [ FAIL 0 | WARN 0 | SKIP 0 | PASS 1 ] [ FAIL 0 | WARN 0 | SKIP 0 | PASS 2 ] [ FAIL 0 | WARN 0 | SKIP 0 | PASS 3 ] [ FAIL 0 | WARN 0 | SKIP 0 | PASS 4 ] [ FAIL 0 | WARN 0 | SKIP 0 | PASS 5 ] [ FAIL 0 | WARN 0 | SKIP 0 | PASS 6 ] [ FAIL 0 | WARN 0 | SKIP 0 | PASS 7 ] [ FAIL 0 | WARN 0 | SKIP 0 | PASS 8 ] [ FAIL 0 | WARN 0 | SKIP 0 | PASS 9 ] [ FAIL 0 | WARN 0 | SKIP 0 | PASS 10 ] [ FAIL 0 | WARN 0 | SKIP 0 | PASS 11 ] Done! > > proc.time() user system elapsed 15.342 1.270 16.628
scTensor.Rcheck/scTensor-Ex.timings
name | user | system | elapsed | |
GermMale | 0.958 | 0.109 | 1.066 | |
cellCellDecomp | 0.003 | 0.000 | 0.003 | |
cellCellRanks | 0.001 | 0.001 | 0.001 | |
cellCellReport | 0.003 | 0.000 | 0.003 | |
cellCellSetting | 0.001 | 0.000 | 0.001 | |
cellCellSimulate | 0.001 | 0.000 | 0.001 | |
getParam | 0.001 | 0.000 | 0.001 | |
labelGermMale | 0.001 | 0.000 | 0.001 | |
m | 0.002 | 0.000 | 0.002 | |
newCCSParams | 0.000 | 0.000 | 0.001 | |
scTensor-package | 0 | 0 | 0 | |
setParam | 0.002 | 0.000 | 0.002 | |
tsneGermMale | 0.001 | 0.000 | 0.001 | |
v | 0.002 | 0.000 | 0.001 | |