Back to Build/check report for BioC 3.17: simplified long |
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This page was generated on 2023-03-01 07:38:50 -0000 (Wed, 01 Mar 2023).
Hostname | OS | Arch (*) | R version | Installed pkgs |
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kunpeng1 | Linux (Ubuntu 22.04.1 LTS) | aarch64 | R Under development (unstable) (2023-01-14 r83615) -- "Unsuffered Consequences" | 4266 |
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To the developers/maintainers of the scFeatures package: - Please 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 How and When does the builder pull? When will my changes propagate? for more information. - Make sure to use the following settings in order to reproduce any error or warning you see on this page. |
Package 1789/2171 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
scFeatures 0.99.25 (landing page) Yue Cao
| kunpeng1 | Linux (Ubuntu 22.04.1 LTS) / aarch64 | OK | OK | OK | |||||||||
Package: scFeatures |
Version: 0.99.25 |
Command: /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:scFeatures.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/library --timings scFeatures_0.99.25.tar.gz |
StartedAt: 2023-02-28 14:30:58 -0000 (Tue, 28 Feb 2023) |
EndedAt: 2023-02-28 14:42:31 -0000 (Tue, 28 Feb 2023) |
EllapsedTime: 692.8 seconds |
RetCode: 0 |
Status: OK |
CheckDir: scFeatures.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:scFeatures.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/library --timings scFeatures_0.99.25.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.17-bioc/meat/scFeatures.Rcheck’ * using R Under development (unstable) (2023-01-14 r83615) * using platform: aarch64-unknown-linux-gnu (64-bit) * R was compiled by gcc (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0 GNU Fortran (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0 * running under: Ubuntu 22.04.1 LTS * using session charset: UTF-8 * checking for file ‘scFeatures/DESCRIPTION’ ... OK * this is package ‘scFeatures’ version ‘0.99.25’ * 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 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 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 helper_CCI: no visible binding for global variable 'LRdb' helper_CCI: 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 Consider adding importFrom("utils", "capture.output") 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 22.657 0.571 23.229 run_pathway_gsva 10.568 0.692 11.260 run_pathway_mean 10.674 0.468 11.143 run_association_study_report 6.246 0.626 6.892 run_gene_mean_celltype 5.450 0.164 5.614 run_gene_prop_celltype 5.392 0.168 5.560 * checking for unstated dependencies in vignettes ... OK * checking package vignettes in ‘inst/doc’ ... OK * checking running R code from vignettes ... ‘scFeatures_overview.Rmd’ using ‘UTF-8’... OK NONE * checking re-building of vignette outputs ... OK * checking PDF version of manual ... OK * DONE Status: 1 NOTE See ‘/home/biocbuild/bbs-3.17-bioc/meat/scFeatures.Rcheck/00check.log’ for details.
scFeatures.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD INSTALL scFeatures ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.17-bioc/R/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 | 0.179 | 0.028 | 0.207 | |
makeSeurat | 1.419 | 0.012 | 1.431 | |
process_data | 0.514 | 0.024 | 0.539 | |
remove_mito_ribo | 1.408 | 0.669 | 0.823 | |
run_CCI | 3.054 | 0.264 | 3.319 | |
run_L_function | 1.213 | 0.152 | 1.367 | |
run_Morans_I | 1.808 | 0.152 | 1.960 | |
run_association_study_report | 6.246 | 0.626 | 6.892 | |
run_celltype_interaction | 0.900 | 0.028 | 0.927 | |
run_gene_cor | 3.124 | 0.031 | 3.118 | |
run_gene_cor_celltype | 4.513 | 0.144 | 4.646 | |
run_gene_mean | 4.433 | 0.152 | 4.585 | |
run_gene_mean_celltype | 5.450 | 0.164 | 5.614 | |
run_gene_prop | 3.089 | 0.048 | 3.137 | |
run_gene_prop_celltype | 5.392 | 0.168 | 5.560 | |
run_nn_correlation | 1.126 | 0.012 | 1.138 | |
run_pathway_gsva | 10.568 | 0.692 | 11.260 | |
run_pathway_mean | 10.674 | 0.468 | 11.143 | |
run_pathway_prop | 22.657 | 0.571 | 23.229 | |
run_proportion_logit | 0.358 | 0.031 | 0.390 | |
run_proportion_ratio | 0.480 | 0.036 | 0.515 | |
run_proportion_raw | 0.367 | 0.008 | 0.376 | |
scFeatures | 1.551 | 0.101 | 0.576 | |