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This page was generated on 2024-03-28 11:40:53 -0400 (Thu, 28 Mar 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 22.04.3 LTS)x86_64R Under development (unstable) (2024-03-18 r86148) -- "Unsuffered Consequences" 4708
palomino3Windows Server 2022 Datacenterx64R Under development (unstable) (2024-03-16 r86144 ucrt) -- "Unsuffered Consequences" 4446
lconwaymacOS 12.7.1 Montereyx86_64R Under development (unstable) (2024-03-18 r86148) -- "Unsuffered Consequences" 4471
kunpeng2Linux (openEuler 22.03 LTS-SP1)aarch64R Under development (unstable) (2024-03-19 r86153) -- "Unsuffered Consequences" 4426
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 1079/2270HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
KEGGlincs 1.29.0  (landing page)
Shana White , Mario Medvedovic
Snapshot Date: 2024-03-27 14:00:18 -0400 (Wed, 27 Mar 2024)
git_url: https://git.bioconductor.org/packages/KEGGlincs
git_branch: devel
git_last_commit: 90ee3d5
git_last_commit_date: 2023-10-24 10:53:15 -0400 (Tue, 24 Oct 2023)
nebbiolo1Linux (Ubuntu 22.04.3 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino3Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
lconwaymacOS 12.7.1 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kunpeng2Linux (openEuler 22.03 LTS-SP1) / aarch64  OK    OK    OK  

CHECK results for KEGGlincs on kunpeng2


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.
- See Martin Grigorov's blog post for how to debug Linux ARM64 related issues on a x86_64 host.

raw results


Summary

Package: KEGGlincs
Version: 1.29.0
Command: /home/biocbuild/R/R-4.4-devel-2024.03.20/bin/R CMD check --install=check:KEGGlincs.install-out.txt --library=/home/biocbuild/R/R-4.4-devel-2024.03.20/site-library --no-vignettes --timings KEGGlincs_1.29.0.tar.gz
StartedAt: 2024-03-28 06:36:14 -0000 (Thu, 28 Mar 2024)
EndedAt: 2024-03-28 06:41:12 -0000 (Thu, 28 Mar 2024)
EllapsedTime: 297.6 seconds
RetCode: 0
Status:   OK  
CheckDir: KEGGlincs.Rcheck
Warnings: 0

Command output

##############################################################################
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###
### Running command:
###
###   /home/biocbuild/R/R-4.4-devel-2024.03.20/bin/R CMD check --install=check:KEGGlincs.install-out.txt --library=/home/biocbuild/R/R-4.4-devel-2024.03.20/site-library --no-vignettes --timings KEGGlincs_1.29.0.tar.gz
###
##############################################################################
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* using log directory ‘/home/biocbuild/bbs-3.19-bioc/meat/KEGGlincs.Rcheck’
* using R Under development (unstable) (2024-03-19 r86153)
* using platform: aarch64-unknown-linux-gnu
* R was compiled by
    gcc (GCC) 10.3.1
    GNU Fortran (GCC) 10.3.1
* running under: openEuler 22.03 (LTS-SP1)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘KEGGlincs/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘KEGGlincs’ version ‘1.29.0’
* 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 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
add_edge_data           30.400  0.815  31.796
overlap_info            30.180  0.539  30.876
edge_mapping_info       19.991  0.279  20.412
path_genes_by_cell_type 19.245  0.578  19.961
refine_mappings         19.261  0.080  19.487
get_graph_object        17.671  0.216  18.026
* 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
  ‘/home/biocbuild/bbs-3.19-bioc/meat/KEGGlincs.Rcheck/00check.log’
for details.


Installation output

KEGGlincs.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/R/R-4.4-devel-2024.03.20/bin/R CMD INSTALL KEGGlincs
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/R/R-4.4-devel-2024.03.20/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_lincs0.0010.0000.000
KL_compare000
add_edge_data30.400 0.81531.796
cyto_vis0.5090.0000.610
edge_mapping_info19.991 0.27920.412
expand_KEGG_edges0.20.00.3
expand_KEGG_mappings0.1510.0040.256
generate_mappings0.0010.0000.001
get_KGML0.3540.0080.664
get_fisher_info0.0040.0000.004
get_graph_object17.671 0.21618.026
keggerize_edges000
node_mapping_info0.1680.0040.274
overlap_info30.180 0.53930.876
path_genes_by_cell_type19.245 0.57819.961
refine_mappings19.261 0.08019.487
tidy_edge000