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This page was generated on 2023-01-02 09:00:35 -0500 (Mon, 02 Jan 2023).

HostnameOSArch (*)R versionInstalled pkgs
palomino5Windows Server 2022 Datacenterx64R Under development (unstable) (2022-12-25 r83502 ucrt) -- "Unsuffered Consequences" 4165
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 palomino5


To the developers/maintainers of the KEGGlincs package:
Make sure to use the following settings in order to reproduce any error or warning you see on this page.

raw results

Package 1008/2158HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
KEGGlincs 1.25.0  (landing page)
Shana White , Mario Medvedovic
Snapshot Date: 2022-12-28 11:00:06 -0500 (Wed, 28 Dec 2022)
git_url: https://git.bioconductor.org/packages/KEGGlincs
git_branch: master
git_last_commit: b36adf1
git_last_commit_date: 2022-11-01 11:14:35 -0500 (Tue, 01 Nov 2022)
palomino5Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  

Summary

Package: KEGGlincs
Version: 1.25.0
Command: F:\biocbuild\bbs-3.17-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:KEGGlincs.install-out.txt --library=F:\biocbuild\bbs-3.17-bioc\R\library --no-vignettes --timings KEGGlincs_1.25.0.tar.gz
StartedAt: 2022-12-29 00:50:42 -0500 (Thu, 29 Dec 2022)
EndedAt: 2022-12-29 00:53:28 -0500 (Thu, 29 Dec 2022)
EllapsedTime: 166.2 seconds
RetCode: 0
Status:   OK  
CheckDir: KEGGlincs.Rcheck
Warnings: 0

Command output

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###
### Running command:
###
###   F:\biocbuild\bbs-3.17-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:KEGGlincs.install-out.txt --library=F:\biocbuild\bbs-3.17-bioc\R\library --no-vignettes --timings KEGGlincs_1.25.0.tar.gz
###
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* using log directory 'F:/biocbuild/bbs-3.17-bioc-rtools43/meat/KEGGlincs.Rcheck'
* using R Under development (unstable) (2022-12-25 r83502 ucrt)
* using platform: x86_64-w64-mingw32 (64-bit)
* R was compiled by
    gcc.exe (GCC) 10.4.0
    GNU Fortran (GCC) 10.4.0
* running under: Windows Server x64 (build 20348)
* using session charset: UTF-8
* using option '--no-vignettes'
* checking for file 'KEGGlincs/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'KEGGlincs' version '1.25.0'
* 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 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            13.18   1.49   14.86
add_edge_data           12.10   1.58   15.91
edge_mapping_info        8.01   0.50    8.71
path_genes_by_cell_type  7.52   0.33    8.02
refine_mappings          6.75   0.20    7.15
get_graph_object         5.92   0.33    6.44
* 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
  'F:/biocbuild/bbs-3.17-bioc-rtools43/meat/KEGGlincs.Rcheck/00check.log'
for details.



Installation output

KEGGlincs.Rcheck/00install.out

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###
### Running command:
###
###   F:\biocbuild\bbs-3.17-bioc\R\bin\R.exe CMD INSTALL KEGGlincs
###
##############################################################################
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* installing to library 'F:/biocbuild/bbs-3.17-bioc/R/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_lincs0.000.020.02
KL_compare000
add_edge_data12.10 1.5815.91
cyto_vis0.220.000.57
edge_mapping_info8.010.508.71
expand_KEGG_edges0.130.000.31
expand_KEGG_mappings0.090.000.28
generate_mappings000
get_KGML0.270.010.86
get_fisher_info000
get_graph_object5.920.336.44
keggerize_edges000
node_mapping_info0.110.010.31
overlap_info13.18 1.4914.86
path_genes_by_cell_type7.520.338.02
refine_mappings6.750.207.15
tidy_edge000