Back to Multiple platform build/check report for BioC 3.22: simplified long |
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This page was generated on 2025-09-23 12:04 -0400 (Tue, 23 Sep 2025).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo2 | Linux (Ubuntu 24.04.3 LTS) | x86_64 | 4.5.1 Patched (2025-08-23 r88802) -- "Great Square Root" | 4816 |
lconway | macOS 12.7.1 Monterey | x86_64 | 4.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" | 4605 |
kjohnson3 | macOS 13.7.7 Ventura | arm64 | 4.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" | 4549 |
taishan | Linux (openEuler 24.03 LTS) | aarch64 | 4.5.0 (2025-04-11) -- "How About a Twenty-Six" | 4560 |
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 1903/2334 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
scFeatures 1.9.0 (landing page) Yue Cao
| nebbiolo2 | Linux (Ubuntu 24.04.3 LTS) / x86_64 | OK | OK | OK | ![]() | ||||||||
lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | OK | OK | ![]() | ||||||||
kjohnson3 | macOS 13.7.7 Ventura / arm64 | OK | OK | OK | OK | ![]() | ||||||||
taishan | Linux (openEuler 24.03 LTS) / aarch64 | OK | OK | OK | ||||||||||
To the developers/maintainers of the scFeatures package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/scFeatures.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: scFeatures |
Version: 1.9.0 |
Command: /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD check --install=check:scFeatures.install-out.txt --library=/home/biocbuild/bbs-3.22-bioc/R/site-library --timings scFeatures_1.9.0.tar.gz |
StartedAt: 2025-09-23 03:55:16 -0400 (Tue, 23 Sep 2025) |
EndedAt: 2025-09-23 04:03:42 -0400 (Tue, 23 Sep 2025) |
EllapsedTime: 506.4 seconds |
RetCode: 0 |
Status: OK |
CheckDir: scFeatures.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD check --install=check:scFeatures.install-out.txt --library=/home/biocbuild/bbs-3.22-bioc/R/site-library --timings scFeatures_1.9.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.22-bioc/meat/scFeatures.Rcheck’ * using R version 4.5.1 Patched (2025-08-23 r88802) * using platform: x86_64-pc-linux-gnu * R was compiled by gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0 GNU Fortran (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0 * running under: Ubuntu 24.04.3 LTS * using session charset: UTF-8 * checking for file ‘scFeatures/DESCRIPTION’ ... OK * this is package ‘scFeatures’ version ‘1.9.0’ * package encoding: UTF-8 * checking package namespace information ... OK * checking package dependencies ... INFO Imports includes 24 non-default packages. Importing from so many packages makes the package vulnerable to any of them becoming unavailable. Move as many as possible to Suggests and use conditionally. * 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 ‘scFeatures’ 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 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 ... NOTE Namespaces in Imports field not imported from: 'DT' 'Seurat' 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 ... NOTE helper_CCI: no visible global function definition for 'data' helper_CCI: no visible binding for global variable 'LRdb' helper_CCI: no visible global function definition for 'capture.output' helper_pathway_gsva: no visible global function definition for 'capture.output' run_pathway_gsva: no visible global function definition for 'capture.output' Undefined global functions or variables: LRdb capture.output data Consider adding importFrom("utils", "capture.output", "data") to your NAMESPACE file. * 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 Examples with CPU (user + system) or elapsed time > 5s user system elapsed run_pathway_gsva 47.415 0.877 48.293 * checking for unstated dependencies in vignettes ... OK * checking package vignettes ... OK * checking re-building of vignette outputs ... OK * checking PDF version of manual ... OK * DONE Status: 2 NOTEs See ‘/home/biocbuild/bbs-3.22-bioc/meat/scFeatures.Rcheck/00check.log’ for details.
scFeatures.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD INSTALL scFeatures ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.22-bioc/R/site-library’ * installing *source* package ‘scFeatures’ ... ** this is package ‘scFeatures’ version ‘1.9.0’ ** 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 (scFeatures)
scFeatures.Rcheck/scFeatures-Ex.timings
name | user | system | elapsed | |
get_num_cell_per_spot | 0.162 | 0.017 | 0.180 | |
remove_mito_ribo | 1.63 | 0.09 | 1.72 | |
run_CCI | 2.811 | 0.160 | 2.972 | |
run_L_function | 0.356 | 0.037 | 0.393 | |
run_Morans_I | 0.353 | 0.010 | 0.363 | |
run_association_study_report | 0 | 0 | 0 | |
run_celltype_interaction | 0.22 | 0.01 | 0.23 | |
run_gene_cor | 0.387 | 0.026 | 0.413 | |
run_gene_cor_celltype | 0.316 | 0.022 | 0.338 | |
run_gene_mean | 0.366 | 0.024 | 0.390 | |
run_gene_mean_celltype | 0.427 | 0.014 | 0.442 | |
run_gene_prop | 0.324 | 0.015 | 0.340 | |
run_gene_prop_celltype | 0.365 | 0.021 | 0.386 | |
run_nn_correlation | 0.268 | 0.015 | 0.283 | |
run_pathway_gsva | 47.415 | 0.877 | 48.293 | |
run_pathway_mean | 3.290 | 0.181 | 3.471 | |
run_pathway_prop | 3.329 | 0.228 | 3.568 | |
run_proportion_logit | 0.202 | 0.008 | 0.210 | |
run_proportion_ratio | 0.246 | 0.010 | 0.256 | |
run_proportion_raw | 0.201 | 0.007 | 0.209 | |
scFeatures | 0.512 | 0.039 | 0.551 | |