Back to Multiple platform build/check report for BioC 3.19: simplified long |
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This page was generated on 2024-03-28 11:41:17 -0400 (Thu, 28 Mar 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | R Under development (unstable) (2024-03-18 r86148) -- "Unsuffered Consequences" | 4708 |
palomino3 | Windows Server 2022 Datacenter | x64 | R Under development (unstable) (2024-03-16 r86144 ucrt) -- "Unsuffered Consequences" | 4446 |
lconway | macOS 12.7.1 Monterey | x86_64 | R Under development (unstable) (2024-03-18 r86148) -- "Unsuffered Consequences" | 4471 |
kunpeng2 | Linux (openEuler 22.03 LTS-SP1) | aarch64 | R Under development (unstable) (2024-03-19 r86153) -- "Unsuffered Consequences" | 4426 |
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 1871/2270 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
scFeatures 1.3.4 (landing page) Yue Cao
| nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | OK | OK | |||||||||
palomino3 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | |||||||||
lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | OK | OK | |||||||||
kunpeng2 | Linux (openEuler 22.03 LTS-SP1) / 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. - See Martin Grigorov's blog post for how to debug Linux ARM64 related issues on a x86_64 host. |
Package: scFeatures |
Version: 1.3.4 |
Command: /home/biocbuild/R/R-4.4-devel-2024.03.20/bin/R CMD check --install=check:scFeatures.install-out.txt --library=/home/biocbuild/R/R-4.4-devel-2024.03.20/site-library --no-vignettes --timings scFeatures_1.3.4.tar.gz |
StartedAt: 2024-03-28 09:22:49 -0000 (Thu, 28 Mar 2024) |
EndedAt: 2024-03-28 09:31:03 -0000 (Thu, 28 Mar 2024) |
EllapsedTime: 493.8 seconds |
RetCode: 0 |
Status: OK |
CheckDir: scFeatures.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/R/R-4.4-devel-2024.03.20/bin/R CMD check --install=check:scFeatures.install-out.txt --library=/home/biocbuild/R/R-4.4-devel-2024.03.20/site-library --no-vignettes --timings scFeatures_1.3.4.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.19-bioc/meat/scFeatures.Rcheck’ * using R Under development (unstable) (2024-03-19 r86153) * using platform: aarch64-unknown-linux-gnu * 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 * using option ‘--no-vignettes’ * checking for file ‘scFeatures/DESCRIPTION’ ... OK * this is package ‘scFeatures’ version ‘1.3.4’ * 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 ‘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 6.66 0.195 7.212 run_pathway_prop 4.97 0.032 5.012 * checking for unstated dependencies in vignettes ... OK * checking package vignettes ... OK * checking running R code from vignettes ... SKIPPED * checking re-building of vignette outputs ... SKIPPED * checking PDF version of manual ... OK * DONE Status: 2 NOTEs See ‘/home/biocbuild/bbs-3.19-bioc/meat/scFeatures.Rcheck/00check.log’ for details.
scFeatures.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/R/R-4.4-devel-2024.03.20/bin/R CMD INSTALL scFeatures ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/R/R-4.4-devel-2024.03.20/site-library’ * installing *source* package ‘scFeatures’ ... ** 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 | 0.138 | 0.024 | 0.163 | |
remove_mito_ribo | 2.861 | 0.606 | 2.204 | |
run_CCI | 3.567 | 0.053 | 3.629 | |
run_L_function | 0.444 | 0.035 | 0.481 | |
run_Morans_I | 0.415 | 0.040 | 0.456 | |
run_association_study_report | 0 | 0 | 0 | |
run_celltype_interaction | 0.279 | 0.016 | 0.296 | |
run_gene_cor | 0.431 | 0.029 | 0.414 | |
run_gene_cor_celltype | 0.359 | 0.012 | 0.367 | |
run_gene_mean | 0.477 | 0.004 | 0.482 | |
run_gene_mean_celltype | 0.584 | 0.012 | 0.596 | |
run_gene_prop | 0.382 | 0.000 | 0.382 | |
run_gene_prop_celltype | 0.378 | 0.004 | 0.383 | |
run_nn_correlation | 0.297 | 0.012 | 0.309 | |
run_pathway_gsva | 6.660 | 0.195 | 7.212 | |
run_pathway_mean | 2.303 | 0.052 | 2.360 | |
run_pathway_prop | 4.970 | 0.032 | 5.012 | |
run_proportion_logit | 0.218 | 0.004 | 0.223 | |
run_proportion_ratio | 0.261 | 0.028 | 0.290 | |
run_proportion_raw | 0.206 | 0.004 | 0.212 | |
scFeatures | 1.310 | 0.362 | 0.611 | |