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CHECK report for XINA on celaya2

This page was generated on 2019-10-16 13:03:14 -0400 (Wed, 16 Oct 2019).

Package 1731/1741HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
XINA 1.2.0
Lang Ho Lee and Sasha A. Singh
Snapshot Date: 2019-10-15 17:01:26 -0400 (Tue, 15 Oct 2019)
URL: https://git.bioconductor.org/packages/XINA
Branch: RELEASE_3_9
Last Commit: 78cf6c7
Last Changed Date: 2019-05-02 11:54:13 -0400 (Thu, 02 May 2019)
malbec2 Linux (Ubuntu 18.04.2 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository
celaya2 OS X 10.11.6 El Capitan / x86_64  OK  OK [ OK ] OK UNNEEDED, same version exists in internal repository

Summary

Package: XINA
Version: 1.2.0
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_1.2.0.tar.gz
StartedAt: 2019-10-16 07:47:40 -0400 (Wed, 16 Oct 2019)
EndedAt: 2019-10-16 07:51:11 -0400 (Wed, 16 Oct 2019)
EllapsedTime: 211.7 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_1.2.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.9-bioc/meat/XINA.Rcheck’
* using R version 3.6.1 (2019-07-05)
* using platform: x86_64-apple-darwin15.6.0 (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 ‘1.2.0’
* 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 ... NOTE
Package in Depends field not imported from: ‘Biobase’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
* 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 or elapsed time > 5s
                                    user system elapsed
xina_clustering                   37.537  0.705  38.246
plot_condition_compositions       27.111  0.098  27.213
plot_clusters                     15.417  0.073  15.492
mutate_colors                     14.776  0.076  14.854
get_condition_biased_comigrations  8.982  0.050   9.035
xina_plot_all                      6.011  0.910   6.234
* 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-3.9-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
###
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* installing to library ‘/Library/Frameworks/R.framework/Versions/3.6/Resources/library’
* installing *source* package ‘XINA’ ...
** using staged installation
** R
** data
** 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_enriched4.5700.3104.883
draw_alluvial_plot0.0960.0100.108
get_comigrations_by_name0.0550.0060.060
get_condition_biased_comigrations8.9820.0509.035
get_unknown_ppi_nodes0.0870.0150.103
load_previous_results2.0510.0802.131
make_random_xina_data0.3630.0680.432
mutate_colors14.776 0.07614.854
plot_clusters15.417 0.07315.492
plot_clusters_all1.6740.0601.736
plot_condition_compositions27.111 0.09827.213
plot_enrichment_results0.0000.0000.001
xina_analysis0.0000.0010.001
xina_clustering37.537 0.70538.246
xina_enrichment0.0010.0010.001
xina_plot_all6.0110.9106.234
xina_plot_bycluster0.2000.1100.311
xina_plot_single0.1400.0970.237