Back to Multiple platform build/check report for BioC 3.19: simplified long |
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This page was generated on 2024-07-24 09:06 -0400 (Wed, 24 Jul 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4747 |
palomino7 | Windows Server 2022 Datacenter | x64 | 4.4.1 (2024-06-14 ucrt) -- "Race for Your Life" | 4489 |
merida1 | macOS 12.7.5 Monterey | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4518 |
kjohnson1 | macOS 13.6.6 Ventura | arm64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4467 |
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 1893/2300 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
scFeatures 1.4.0 (landing page) Yue Cao
| nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | OK | OK | |||||||||
palomino7 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | |||||||||
merida1 | macOS 12.7.5 Monterey / x86_64 | OK | OK | OK | OK | |||||||||
kjohnson1 | macOS 13.6.6 Ventura / arm64 | OK | 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: 1.4.0 |
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:scFeatures.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings scFeatures_1.4.0.tar.gz |
StartedAt: 2024-07-22 12:05:23 -0400 (Mon, 22 Jul 2024) |
EndedAt: 2024-07-22 12:22:17 -0400 (Mon, 22 Jul 2024) |
EllapsedTime: 1014.1 seconds |
RetCode: 0 |
Status: OK |
CheckDir: scFeatures.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:scFeatures.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings scFeatures_1.4.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.19-bioc/meat/scFeatures.Rcheck’ * using R version 4.4.1 (2024-06-14) * using platform: x86_64-apple-darwin20 * R was compiled by Apple clang version 14.0.0 (clang-1400.0.29.202) GNU Fortran (GCC) 12.2.0 * running under: macOS Monterey 12.7.5 * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘scFeatures/DESCRIPTION’ ... OK * this is package ‘scFeatures’ version ‘1.4.0’ * 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 ‘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 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_prop 8.287 0.122 10.629 run_pathway_gsva 7.292 0.476 10.252 run_CCI 3.825 0.288 5.213 * 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 ‘/Users/biocbuild/bbs-3.19-bioc/meat/scFeatures.Rcheck/00check.log’ for details.
scFeatures.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL scFeatures ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/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 | 0.278 | 0.031 | 0.386 | |
remove_mito_ribo | 2.499 | 0.102 | 3.272 | |
run_CCI | 3.825 | 0.288 | 5.213 | |
run_L_function | 2.066 | 0.043 | 2.650 | |
run_Morans_I | 0.673 | 0.015 | 0.976 | |
run_association_study_report | 0.000 | 0.001 | 0.001 | |
run_celltype_interaction | 0.392 | 0.015 | 0.589 | |
run_gene_cor | 0.695 | 0.027 | 0.942 | |
run_gene_cor_celltype | 0.641 | 0.035 | 0.850 | |
run_gene_mean | 0.708 | 0.032 | 0.941 | |
run_gene_mean_celltype | 0.974 | 0.022 | 1.259 | |
run_gene_prop | 0.630 | 0.010 | 0.813 | |
run_gene_prop_celltype | 0.654 | 0.019 | 0.850 | |
run_nn_correlation | 0.556 | 0.026 | 0.739 | |
run_pathway_gsva | 7.292 | 0.476 | 10.252 | |
run_pathway_mean | 3.657 | 0.169 | 4.881 | |
run_pathway_prop | 8.287 | 0.122 | 10.629 | |
run_proportion_logit | 0.343 | 0.010 | 0.449 | |
run_proportion_ratio | 0.480 | 0.015 | 0.634 | |
run_proportion_raw | 0.347 | 0.011 | 0.457 | |
scFeatures | 1.176 | 0.089 | 1.612 | |