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CHECK report for XINA on machv2

This page was generated on 2020-10-17 11:59:54 -0400 (Sat, 17 Oct 2020).

TO THE DEVELOPERS/MAINTAINERS OF THE XINA PACKAGE: Please make sure to use the following settings in order to reproduce any error or warning you see on this page.
Package 1895/1905HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
XINA 1.6.0
Lang Ho Lee
Snapshot Date: 2020-10-16 14:40:19 -0400 (Fri, 16 Oct 2020)
URL: https://git.bioconductor.org/packages/XINA
Branch: RELEASE_3_11
Last Commit: b9fd1a6
Last Changed Date: 2020-04-27 15:19:09 -0400 (Mon, 27 Apr 2020)
malbec2 Linux (Ubuntu 18.04.4 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  OK  OK  OK  NA 
machv2 macOS 10.14.6 Mojave / x86_64  OK  OK [ OK ] OK UNNEEDED, same version exists in internal repository

Summary

Package: XINA
Version: 1.6.0
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_1.6.0.tar.gz
StartedAt: 2020-10-17 06:19:53 -0400 (Sat, 17 Oct 2020)
EndedAt: 2020-10-17 06:23:01 -0400 (Sat, 17 Oct 2020)
EllapsedTime: 188.0 seconds
RetCode: 0
Status:  OK 
CheckDir: XINA.Rcheck
Warnings: 0

Command output

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### Running command:
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###   /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_1.6.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.11-bioc/meat/XINA.Rcheck’
* using R version 4.0.3 (2020-10-10)
* 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 ‘1.6.0’
* 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                   39.708  0.291  40.018
plot_condition_compositions       19.013  0.079  19.106
mutate_colors                     11.596  0.064  11.764
plot_clusters                     11.606  0.039  11.659
get_condition_biased_comigrations  6.778  0.023   6.813
xina_plot_all                      6.386  0.202   6.805
* 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

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL XINA
###
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* installing to library ‘/Library/Frameworks/R.framework/Versions/4.0/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_enriched4.2660.1184.392
draw_alluvial_plot0.0970.0080.106
get_comigrations_by_name0.0590.0020.063
get_condition_biased_comigrations6.7780.0236.813
get_unknown_ppi_nodes0.0930.0070.100
load_previous_results1.9820.0282.014
make_random_xina_data0.3450.0320.381
mutate_colors11.596 0.06411.764
plot_clusters11.606 0.03911.659
plot_clusters_all4.1460.0304.181
plot_condition_compositions19.013 0.07919.106
plot_enrichment_results0.0010.0010.001
xina_analysis000
xina_clustering39.708 0.29140.018
xina_enrichment0.0010.0000.001
xina_plot_all6.3860.2026.805
xina_plot_bycluster0.2400.0180.258
xina_plot_single0.1600.0160.178