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This page was generated on 2024-04-17 11:38:23 -0400 (Wed, 17 Apr 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 22.04.3 LTS)x86_644.3.3 (2024-02-29) -- "Angel Food Cake" 4676
palomino4Windows Server 2022 Datacenterx644.3.3 (2024-02-29 ucrt) -- "Angel Food Cake" 4414
merida1macOS 12.7.1 Montereyx86_644.3.3 (2024-02-29) -- "Angel Food Cake" 4437
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 2254/2266HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
XINA 1.20.0  (landing page)
Lang Ho Lee
Snapshot Date: 2024-04-15 14:05:01 -0400 (Mon, 15 Apr 2024)
git_url: https://git.bioconductor.org/packages/XINA
git_branch: RELEASE_3_18
git_last_commit: 8ca83bc
git_last_commit_date: 2023-10-24 11:07:35 -0400 (Tue, 24 Oct 2023)
nebbiolo2Linux (Ubuntu 22.04.3 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
merida1macOS 12.7.1 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kjohnson1macOS 13.6.1 Ventura / arm64see weekly results here

CHECK results for XINA on merida1


To the developers/maintainers of the XINA package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/XINA.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.

raw results


Summary

Package: XINA
Version: 1.20.0
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:XINA.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings XINA_1.20.0.tar.gz
StartedAt: 2024-04-16 10:32:34 -0400 (Tue, 16 Apr 2024)
EndedAt: 2024-04-16 10:36:33 -0400 (Tue, 16 Apr 2024)
EllapsedTime: 238.3 seconds
RetCode: 0
Status:   OK  
CheckDir: XINA.Rcheck
Warnings: 0

Command output

##############################################################################
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### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:XINA.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings XINA_1.20.0.tar.gz
###
##############################################################################
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* using log directory ‘/Users/biocbuild/bbs-3.18-bioc/meat/XINA.Rcheck’
* using R version 4.3.3 (2024-02-29)
* using platform: x86_64-apple-darwin20 (64-bit)
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    GNU Fortran (GCC) 12.2.0
* running under: macOS Monterey 12.7.1
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘XINA/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘XINA’ version ‘1.20.0’
* package encoding: UTF-8
* 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 ‘XINA’ 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 ... OK
* 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 contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                                    user system elapsed
xina_clustering                   44.024  0.438  47.059
plot_condition_compositions       28.461  0.162  30.020
mutate_colors                     16.943  0.072  17.461
plot_clusters                     16.236  0.083  17.121
get_condition_biased_comigrations 10.075  0.097  10.340
xina_plot_all                      5.300  0.396   6.330
alluvial_enriched                  5.179  0.102   5.337
* 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: OK


Installation output

XINA.Rcheck/00install.out

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


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library’
* installing *source* package ‘XINA’ ...
** using staged installation
** R
** data
** 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 (XINA)

Tests output


Example timings

XINA.Rcheck/XINA-Ex.timings

nameusersystemelapsed
alluvial_enriched5.1790.1025.337
draw_alluvial_plot0.1040.0120.118
get_comigrations_by_name0.0620.0040.067
get_condition_biased_comigrations10.075 0.09710.340
get_unknown_ppi_nodes0.1040.0110.115
load_previous_results2.3370.0482.389
make_random_xina_data0.5020.0330.537
mutate_colors16.943 0.07217.461
plot_clusters16.236 0.08317.121
plot_clusters_all3.3290.0393.520
plot_condition_compositions28.461 0.16230.020
plot_enrichment_results0.0000.0010.001
xina_analysis0.0010.0000.001
xina_clustering44.024 0.43847.059
xina_enrichment0.0010.0010.002
xina_plot_all5.3000.3966.330
xina_plot_bycluster0.3040.0160.353
xina_plot_single0.2200.0130.255