Back to Multiple platform build/check report for BioC 3.20: simplified long |
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This page was generated on 2024-06-21 13:22 -0400 (Fri, 21 Jun 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | 4.4.0 RC (2024-04-16 r86468) -- "Puppy Cup" | 4690 |
lconway | macOS 12.7.1 Monterey | x86_64 | 4.4.1 RC (2024-06-06 r86719) -- "Race for Your Life" | 4404 |
kjohnson3 | macOS 13.6.5 Ventura | arm64 | 4.4.1 RC (2024-06-06 r86719) -- "Race for Your Life" | 4353 |
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 1061/2242 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
KEGGlincs 1.31.0 (landing page) Shana White
| nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | OK | OK | ![]() | ||||||||
lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | OK | OK | ![]() | ||||||||
kjohnson3 | macOS 13.6.5 Ventura / arm64 | OK | OK | OK | OK | ![]() | ||||||||
To the developers/maintainers of the KEGGlincs package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/KEGGlincs.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: KEGGlincs |
Version: 1.31.0 |
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:KEGGlincs.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings KEGGlincs_1.31.0.tar.gz |
StartedAt: 2024-06-20 21:04:49 -0400 (Thu, 20 Jun 2024) |
EndedAt: 2024-06-20 21:09:29 -0400 (Thu, 20 Jun 2024) |
EllapsedTime: 279.3 seconds |
RetCode: 0 |
Status: OK |
CheckDir: KEGGlincs.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:KEGGlincs.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings KEGGlincs_1.31.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.20-bioc/meat/KEGGlincs.Rcheck’ * using R version 4.4.1 RC (2024-06-06 r86719) * 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 12.7.1 * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘KEGGlincs/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘KEGGlincs’ version ‘1.31.0’ * 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 ‘KEGGlincs’ 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 Namespace in Imports field not imported from: ‘XML’ 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 ... OK * 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 files in ‘vignettes’ ... OK * checking examples ... OK Examples with CPU (user + system) or elapsed time > 5s user system elapsed overlap_info 26.851 1.707 28.937 add_edge_data 25.344 1.607 28.269 path_genes_by_cell_type 19.579 0.743 20.630 edge_mapping_info 18.455 0.836 19.977 refine_mappings 17.944 0.739 18.987 get_graph_object 16.593 0.485 17.340 * 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: 1 NOTE See ‘/Users/biocbuild/bbs-3.20-bioc/meat/KEGGlincs.Rcheck/00check.log’ for details.
KEGGlincs.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL KEGGlincs ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library’ * installing *source* package ‘KEGGlincs’ ... ** using staged installation ** R ** 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 (KEGGlincs)
KEGGlincs.Rcheck/KEGGlincs-Ex.timings
name | user | system | elapsed | |
KEGG_lincs | 0.001 | 0.000 | 0.000 | |
KL_compare | 0 | 0 | 0 | |
add_edge_data | 25.344 | 1.607 | 28.269 | |
cyto_vis | 0.362 | 0.006 | 0.925 | |
edge_mapping_info | 18.455 | 0.836 | 19.977 | |
expand_KEGG_edges | 0.161 | 0.005 | 0.542 | |
expand_KEGG_mappings | 0.125 | 0.006 | 0.508 | |
generate_mappings | 0.001 | 0.000 | 0.001 | |
get_KGML | 0.230 | 0.005 | 1.185 | |
get_fisher_info | 0.004 | 0.000 | 0.004 | |
get_graph_object | 16.593 | 0.485 | 17.340 | |
keggerize_edges | 0.001 | 0.000 | 0.000 | |
node_mapping_info | 0.138 | 0.001 | 0.340 | |
overlap_info | 26.851 | 1.707 | 28.937 | |
path_genes_by_cell_type | 19.579 | 0.743 | 20.630 | |
refine_mappings | 17.944 | 0.739 | 18.987 | |
tidy_edge | 0.000 | 0.001 | 0.000 | |