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This page was generated on 2021-10-15 15:06:58 -0400 (Fri, 15 Oct 2021).

CHECK results for XINA on machv2

To the developers/maintainers of the XINA package:
- Please 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 How and When does the builder pull? When will my changes propagate? here 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 2030/2041HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
XINA 1.10.0  (landing page)
Lang Ho Lee
Snapshot Date: 2021-10-14 04:50:12 -0400 (Thu, 14 Oct 2021)
git_url: https://git.bioconductor.org/packages/XINA
git_branch: RELEASE_3_13
git_last_commit: 1ddc683
git_last_commit_date: 2021-05-19 12:37:43 -0400 (Wed, 19 May 2021)
nebbiolo1Linux (Ubuntu 20.04.2 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
tokay2Windows Server 2012 R2 Standard / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
machv2macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: XINA
Version: 1.10.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:XINA.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings XINA_1.10.0.tar.gz
StartedAt: 2021-10-15 01:16:46 -0400 (Fri, 15 Oct 2021)
EndedAt: 2021-10-15 01:19:58 -0400 (Fri, 15 Oct 2021)
EllapsedTime: 191.2 seconds
RetCode: 0
Status:   OK  
CheckDir: XINA.Rcheck
Warnings: 0

Command output

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### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:XINA.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings XINA_1.10.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.13-bioc/meat/XINA.Rcheck’
* using R version 4.1.1 (2021-08-10)
* using platform: x86_64-apple-darwin17.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘XINA/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘XINA’ version ‘1.10.0’
* 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 ... NOTE
Found the following hidden files and directories:
  .git_fetch_output.txt
  .git_merge_output.txt
These were most likely included in error. See section ‘Package
structure’ in the ‘Writing R Extensions’ manual.
* 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                   41.805  0.332  42.201
plot_condition_compositions       21.225  0.108  21.388
plot_clusters                     12.787  0.048  12.848
mutate_colors                     12.195  0.046  12.251
get_condition_biased_comigrations  6.611  0.029   6.646
xina_plot_all                      6.096  0.148   6.258
* 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
  ‘/Users/biocbuild/bbs-3.13-bioc/meat/XINA.Rcheck/00check.log’
for details.



Installation output

XINA.Rcheck/00install.out

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


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.1/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_enriched4.1260.1344.266
draw_alluvial_plot0.0690.0080.076
get_comigrations_by_name0.0470.0030.050
get_condition_biased_comigrations6.6110.0296.646
get_unknown_ppi_nodes0.0890.0070.096
load_previous_results1.7190.0231.742
make_random_xina_data0.2830.0250.308
mutate_colors12.195 0.04612.251
plot_clusters12.787 0.04812.848
plot_clusters_all4.2910.0344.331
plot_condition_compositions21.225 0.10821.388
plot_enrichment_results0.0000.0000.001
xina_analysis0.0000.0010.000
xina_clustering41.805 0.33242.201
xina_enrichment0.0000.0010.000
xina_plot_all6.0960.1486.258
xina_plot_bycluster0.2460.0070.254
xina_plot_single0.1860.0070.194