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This page was generated on 2022-08-11 11:06:51 -0400 (Thu, 11 Aug 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 20.04.4 LTS)x86_644.2.1 (2022-06-23) -- "Funny-Looking Kid" 4375
palomino4Windows Server 2022 Datacenterx644.2.1 (2022-06-23 ucrt) -- "Funny-Looking Kid" 4159
lconwaymacOS 12.2.1 Montereyx86_644.2.1 Patched (2022-07-09 r82577) -- "Funny-Looking Kid" 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 palomino4


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? 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 1004/2139HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
KEGGlincs 1.23.0  (landing page)
Shana White , Mario Medvedovic
Snapshot Date: 2022-08-10 14:00:02 -0400 (Wed, 10 Aug 2022)
git_url: https://git.bioconductor.org/packages/KEGGlincs
git_branch: master
git_last_commit: e4eee38
git_last_commit_date: 2022-04-26 11:36:19 -0400 (Tue, 26 Apr 2022)
nebbiolo2Linux (Ubuntu 20.04.4 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino4Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
lconwaymacOS 12.2.1 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: KEGGlincs
Version: 1.23.0
Command: F:\biocbuild\bbs-3.16-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:KEGGlincs.install-out.txt --library=F:\biocbuild\bbs-3.16-bioc\R\library --no-vignettes --timings KEGGlincs_1.23.0.tar.gz
StartedAt: 2022-08-11 02:57:05 -0400 (Thu, 11 Aug 2022)
EndedAt: 2022-08-11 03:00:18 -0400 (Thu, 11 Aug 2022)
EllapsedTime: 192.4 seconds
RetCode: 0
Status:   OK  
CheckDir: KEGGlincs.Rcheck
Warnings: 0

Command output

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###
### Running command:
###
###   F:\biocbuild\bbs-3.16-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:KEGGlincs.install-out.txt --library=F:\biocbuild\bbs-3.16-bioc\R\library --no-vignettes --timings KEGGlincs_1.23.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'F:/biocbuild/bbs-3.16-bioc/meat/KEGGlincs.Rcheck'
* using R version 4.2.1 (2022-06-23 ucrt)
* using platform: x86_64-w64-mingw32 (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 '1.23.0'
* 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            16.65   1.15   18.00
add_edge_data           15.05   1.43   18.62
edge_mapping_info        9.19   0.63   10.00
path_genes_by_cell_type  8.80   0.25    9.25
get_graph_object         7.49   0.24    7.91
refine_mappings          6.19   0.43    6.80
* 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-3.16-bioc/meat/KEGGlincs.Rcheck/00check.log'
for details.



Installation output

KEGGlincs.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O http://155.52.207.166/BBS/3.16/bioc/src/contrib/KEGGlincs_1.23.0.tar.gz && rm -rf KEGGlincs.buildbin-libdir && mkdir KEGGlincs.buildbin-libdir && F:\biocbuild\bbs-3.16-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=KEGGlincs.buildbin-libdir KEGGlincs_1.23.0.tar.gz && F:\biocbuild\bbs-3.16-bioc\R\bin\R.exe CMD INSTALL KEGGlincs_1.23.0.zip && rm KEGGlincs_1.23.0.tar.gz KEGGlincs_1.23.0.zip
###
##############################################################################
##############################################################################


  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed

  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
 44 2149k   44  955k    0     0  7488k      0 --:--:-- --:--:-- --:--:-- 7520k
100 2149k  100 2149k    0     0  11.4M      0 --:--:-- --:--:-- --:--:-- 11.4M
only one architecture so ignoring '--merge-multiarch'
* 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
* MD5 sums
packaged installation of 'KEGGlincs' as KEGGlincs_1.23.0.zip
* DONE (KEGGlincs)
* installing to library 'F:/biocbuild/bbs-3.16-bioc/R/library'
package 'KEGGlincs' successfully unpacked and MD5 sums checked

Tests output


Example timings

KEGGlincs.Rcheck/KEGGlincs-Ex.timings

nameusersystemelapsed
KEGG_lincs000
KL_compare000
add_edge_data15.05 1.4318.62
cyto_vis0.310.000.50
edge_mapping_info 9.19 0.6310.00
expand_KEGG_edges0.150.000.34
expand_KEGG_mappings0.270.010.47
generate_mappings000
get_KGML0.150.000.72
get_fisher_info000
get_graph_object7.490.247.91
keggerize_edges000
node_mapping_info0.160.000.34
overlap_info16.65 1.1518.00
path_genes_by_cell_type8.800.259.25
refine_mappings6.190.436.80
tidy_edge000