Back to Multiple platform build/check report for BioC 3.15
ABCDEFGHIJ[K]LMNOPQRSTUVWXYZ

This page was generated on 2022-01-17 11:11:22 -0500 (Mon, 17 Jan 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 20.04.4 LTS)x86_64R Under development (unstable) (2022-01-05 r81451) -- "Unsuffered Consequences" 4161
riesling1Windows Server 2019 Standardx64R Under development (unstable) (2021-11-21 r81221) -- "Unsuffered Consequences" 4056
palomino3Windows Server 2022 Datacenterx64R Under development (unstable) (2021-12-21 r81400 ucrt) -- "Unsuffered Consequences" 3998
merida1macOS 10.14.6 Mojavex86_64R Under development (unstable) (2022-01-05 r81451) -- "Unsuffered Consequences" 4115
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 merida1


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 978/2074HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
KEGGlincs 1.21.0  (landing page)
Shana White , Mario Medvedovic
Snapshot Date: 2022-01-16 13:55:18 -0500 (Sun, 16 Jan 2022)
git_url: https://git.bioconductor.org/packages/KEGGlincs
git_branch: master
git_last_commit: cf1a185
git_last_commit_date: 2021-10-26 12:30:32 -0500 (Tue, 26 Oct 2021)
nebbiolo1Linux (Ubuntu 20.04.4 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
riesling1Windows Server 2019 Standard / x64  OK    OK    OK    OK  
palomino3Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  NO, package depends on 'AnnotationDbi' which is not available
merida1macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: KEGGlincs
Version: 1.21.0
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_1.21.0.tar.gz
StartedAt: 2022-01-17 02:09:35 -0500 (Mon, 17 Jan 2022)
EndedAt: 2022-01-17 02:14:40 -0500 (Mon, 17 Jan 2022)
EllapsedTime: 305.3 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_1.21.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.15-bioc/meat/KEGGlincs.Rcheck’
* using R Under development (unstable) (2022-01-05 r81451)
* 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 ‘1.21.0’
* 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 ... NOTE
Found the following hidden files and directories:
  .git_fetch_output.txt
  .git_merge_output.txt
These were most likely included in error. See section ‘Package
structure’ in the ‘Writing R Extensions’ manual.
* 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            26.699  1.535  28.460
add_edge_data           25.293  1.560  27.381
edge_mapping_info       14.819  0.426  15.446
path_genes_by_cell_type 12.842  0.207  13.258
refine_mappings         12.574  0.376  13.154
get_graph_object        11.374  0.173  12.339
* 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: 2 NOTEs
See
  ‘/Users/biocbuild/bbs-3.15-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/4.2/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_data25.293 1.56027.381
cyto_vis0.6230.0050.815
edge_mapping_info14.819 0.42615.446
expand_KEGG_edges0.3030.0080.500
expand_KEGG_mappings0.3890.0440.614
generate_mappings0.0010.0000.001
get_KGML0.3100.0020.859
get_fisher_info0.0070.0010.007
get_graph_object11.374 0.17312.339
keggerize_edges0.0000.0000.001
node_mapping_info0.2580.0120.459
overlap_info26.699 1.53528.460
path_genes_by_cell_type12.842 0.20713.258
refine_mappings12.574 0.37613.154
tidy_edge000