Back to Multiple platform build/check report for BioC 3.14
ABCDEFGHIJ[K]LMNOPQRSTUVWXYZ

This page was generated on 2022-01-21 13:07:58 -0500 (Fri, 21 Jan 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 20.04.4 LTS)x86_644.1.2 (2021-11-01) -- "Bird Hippie" 4329
tokay2Windows Server 2012 R2 Standardx644.1.2 (2021-11-01) -- "Bird Hippie" 4079
machv2macOS 10.14.6 Mojavex86_644.1.2 (2021-11-01) -- "Bird Hippie" 4140
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

CHECK results for KEGGlincs on machv2


To the developers/maintainers of the KEGGlincs package:
- Please 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 How and When does the builder pull? When will my changes propagate? here for more information.
- Make sure to use the following settings in order to reproduce any error or warning you see on this page.

raw results

Package 980/2083HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
KEGGlincs 1.20.0  (landing page)
Shana White , Mario Medvedovic
Snapshot Date: 2022-01-20 01:55:04 -0500 (Thu, 20 Jan 2022)
git_url: https://git.bioconductor.org/packages/KEGGlincs
git_branch: RELEASE_3_14
git_last_commit: 65205d4
git_last_commit_date: 2021-10-26 12:30:32 -0500 (Tue, 26 Oct 2021)
nebbiolo2Linux (Ubuntu 20.04.4 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
tokay2Windows Server 2012 R2 Standard / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
machv2macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: KEGGlincs
Version: 1.20.0
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_1.20.0.tar.gz
StartedAt: 2022-01-20 14:22:29 -0500 (Thu, 20 Jan 2022)
EndedAt: 2022-01-20 14:27:04 -0500 (Thu, 20 Jan 2022)
EllapsedTime: 275.1 seconds
RetCode: 0
Status:   OK  
CheckDir: KEGGlincs.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### 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_1.20.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.14-bioc/meat/KEGGlincs.Rcheck’
* using R version 4.1.2 (2021-11-01)
* using platform: x86_64-apple-darwin17.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘KEGGlincs/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘KEGGlincs’ version ‘1.20.0’
* 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 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 ... 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            23.473  2.159  25.879
add_edge_data           22.066  1.457  24.176
edge_mapping_info       12.796  0.459  13.486
path_genes_by_cell_type 12.011  0.218  12.952
refine_mappings         10.975  0.348  11.554
get_graph_object         9.646  0.151  10.023
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... 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-3.14-bioc/meat/KEGGlincs.Rcheck/00check.log’
for details.



Installation output

KEGGlincs.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL KEGGlincs
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.1/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)

Tests output


Example timings

KEGGlincs.Rcheck/KEGGlincs-Ex.timings

nameusersystemelapsed
KEGG_lincs0.0000.0000.001
KL_compare000
add_edge_data22.066 1.45724.176
cyto_vis0.6030.0070.829
edge_mapping_info12.796 0.45913.486
expand_KEGG_edges0.2910.0110.522
expand_KEGG_mappings0.3950.0570.693
generate_mappings0.0020.0000.001
get_KGML0.2990.0020.957
get_fisher_info0.0060.0000.007
get_graph_object 9.646 0.15110.023
keggerize_edges000
node_mapping_info0.2770.0150.513
overlap_info23.473 2.15925.879
path_genes_by_cell_type12.011 0.21812.952
refine_mappings10.975 0.34811.554
tidy_edge0.0000.0010.001