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This page was generated on 2025-08-20 12:04 -0400 (Wed, 20 Aug 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 24.04.3 LTS)x86_644.5.1 (2025-06-13) -- "Great Square Root" 4818
lconwaymacOS 12.7.1 Montereyx86_644.5.1 (2025-06-13) -- "Great Square Root" 4596
kjohnson3macOS 13.7.7 Venturaarm644.5.1 Patched (2025-06-14 r88325) -- "Great Square Root" 4538
taishanLinux (openEuler 24.03 LTS)aarch644.5.0 (2025-04-11) -- "How About a Twenty-Six" 4536
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 2305/2317HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
XINA 1.27.0  (landing page)
Lang Ho Lee
Snapshot Date: 2025-08-19 13:45 -0400 (Tue, 19 Aug 2025)
git_url: https://git.bioconductor.org/packages/XINA
git_branch: devel
git_last_commit: f21a8fd
git_last_commit_date: 2025-04-15 11:36:47 -0400 (Tue, 15 Apr 2025)
nebbiolo2Linux (Ubuntu 24.04.3 LTS) / x86_64  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
kjohnson3macOS 13.7.7 Ventura / arm64  OK    OK    OK    OK  UNNEEDED, same version is already published
taishanLinux (openEuler 24.03 LTS) / aarch64  OK    OK    OK  


CHECK results for XINA on nebbiolo2

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: 1.27.0
Command: /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD check --install=check:XINA.install-out.txt --library=/home/biocbuild/bbs-3.22-bioc/R/site-library --timings XINA_1.27.0.tar.gz
StartedAt: 2025-08-20 03:58:24 -0400 (Wed, 20 Aug 2025)
EndedAt: 2025-08-20 04:00:36 -0400 (Wed, 20 Aug 2025)
EllapsedTime: 132.1 seconds
RetCode: 0
Status:   OK  
CheckDir: XINA.Rcheck
Warnings: 0

Command output

##############################################################################
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### Running command:
###
###   /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD check --install=check:XINA.install-out.txt --library=/home/biocbuild/bbs-3.22-bioc/R/site-library --timings XINA_1.27.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.22-bioc/meat/XINA.Rcheck’
* using R version 4.5.1 (2025-06-13)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
    GNU Fortran (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
* running under: Ubuntu 24.04.3 LTS
* using session charset: UTF-8
* checking for file ‘XINA/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘XINA’ version ‘1.27.0’
* 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 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 ... 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 ... NOTE
Non-topic package-anchored link(s) in Rd file 'xina_enrichment.Rd':
  ‘[STRINGdb]{get_enrichment}’

Non-topic package-anchored link(s) in Rd file 'xina_plot_single.Rd':
  ‘[base]{Round}’

See section 'Cross-references' in the 'Writing R Extensions' manual.
* 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             19.580  0.108  19.715
plot_condition_compositions 13.174  0.076  13.250
mutate_colors                8.108  0.045   8.153
plot_clusters                7.045  0.063   7.108
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: 1 NOTE
See
  ‘/home/biocbuild/bbs-3.22-bioc/meat/XINA.Rcheck/00check.log’
for details.


Installation output

XINA.Rcheck/00install.out

##############################################################################
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###
### Running command:
###
###   /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD INSTALL XINA
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.22-bioc/R/site-library’
* installing *source* package ‘XINA’ ...
** this is package ‘XINA’ version ‘1.27.0’
** 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_enriched2.1660.0302.197
draw_alluvial_plot0.0510.0010.052
get_comigrations_by_name0.0410.0010.042
get_condition_biased_comigrations4.6880.0684.757
get_unknown_ppi_nodes0.0960.0040.100
load_previous_results0.8360.0320.868
make_random_xina_data0.1490.0140.163
mutate_colors8.1080.0458.153
plot_clusters7.0450.0637.108
plot_clusters_all1.4920.0051.497
plot_condition_compositions13.174 0.07613.250
plot_enrichment_results000
xina_analysis000
xina_clustering19.580 0.10819.715
xina_enrichment000
xina_plot_all4.3790.0914.464
xina_plot_bycluster0.2030.0040.208
xina_plot_single0.1400.0010.142