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This page was generated on 2024-12-23 12:04 -0500 (Mon, 23 Dec 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 24.04.1 LTS)x86_644.4.2 (2024-10-31) -- "Pile of Leaves" 4744
palomino8Windows Server 2022 Datacenterx644.4.2 (2024-10-31 ucrt) -- "Pile of Leaves" 4487
merida1macOS 12.7.5 Montereyx86_644.4.2 (2024-10-31) -- "Pile of Leaves" 4515
kjohnson1macOS 13.6.6 Venturaarm644.4.2 (2024-10-31) -- "Pile of Leaves" 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 1082/2289HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
KEGGlincs 1.32.0  (landing page)
Shana White , Mario Medvedovic
Snapshot Date: 2024-12-19 13:00 -0500 (Thu, 19 Dec 2024)
git_url: https://git.bioconductor.org/packages/KEGGlincs
git_branch: RELEASE_3_20
git_last_commit: 73da76c
git_last_commit_date: 2024-10-29 10:14:43 -0500 (Tue, 29 Oct 2024)
nebbiolo2Linux (Ubuntu 24.04.1 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino8Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
merida1macOS 12.7.5 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kjohnson1macOS 13.6.6 Ventura / arm64  OK    OK    OK    OK  UNNEEDED, same version is already published


CHECK results for KEGGlincs on nebbiolo2

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.

raw results


Summary

Package: KEGGlincs
Version: 1.32.0
Command: /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD check --install=check:KEGGlincs.install-out.txt --library=/home/biocbuild/bbs-3.20-bioc/R/site-library --timings KEGGlincs_1.32.0.tar.gz
StartedAt: 2024-12-20 01:43:58 -0500 (Fri, 20 Dec 2024)
EndedAt: 2024-12-20 01:50:59 -0500 (Fri, 20 Dec 2024)
EllapsedTime: 420.3 seconds
RetCode: 0
Status:   OK  
CheckDir: KEGGlincs.Rcheck
Warnings: 0

Command output

##############################################################################
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###
### Running command:
###
###   /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD check --install=check:KEGGlincs.install-out.txt --library=/home/biocbuild/bbs-3.20-bioc/R/site-library --timings KEGGlincs_1.32.0.tar.gz
###
##############################################################################
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* using log directory ‘/home/biocbuild/bbs-3.20-bioc/meat/KEGGlincs.Rcheck’
* using R version 4.4.2 (2024-10-31)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 13.2.0-23ubuntu4) 13.2.0
    GNU Fortran (Ubuntu 13.2.0-23ubuntu4) 13.2.0
* running under: Ubuntu 24.04.1 LTS
* using session charset: UTF-8
* checking for file ‘KEGGlincs/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘KEGGlincs’ version ‘1.32.0’
* checking package namespace information ... OK
* checking package dependencies ...Warning: unable to access index for repository https://CRAN.R-project.org/src/contrib:
  cannot open URL 'https://CRAN.R-project.org/src/contrib/PACKAGES'
 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 loading without being on the library search path ... 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            19.364  0.843  20.401
add_edge_data           18.507  0.701  20.257
path_genes_by_cell_type 12.571  0.701  13.469
edge_mapping_info       12.043  0.418  13.004
refine_mappings         11.911  0.246  12.361
get_graph_object        11.197  0.160  11.552
* 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: 1 NOTE
See
  ‘/home/biocbuild/bbs-3.20-bioc/meat/KEGGlincs.Rcheck/00check.log’
for details.


Installation output

KEGGlincs.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD INSTALL KEGGlincs
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.20-bioc/R/site-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)

Tests output


Example timings

KEGGlincs.Rcheck/KEGGlincs-Ex.timings

nameusersystemelapsed
KEGG_lincs000
KL_compare000
add_edge_data18.507 0.70120.257
cyto_vis0.3190.0010.866
edge_mapping_info12.043 0.41813.004
expand_KEGG_edges0.1330.0000.502
expand_KEGG_mappings0.1180.0000.488
generate_mappings000
get_KGML0.2720.0151.219
get_fisher_info0.0030.0000.003
get_graph_object11.197 0.16011.552
keggerize_edges000
node_mapping_info0.1040.0000.299
overlap_info19.364 0.84320.401
path_genes_by_cell_type12.571 0.70113.469
refine_mappings11.911 0.24612.361
tidy_edge000