Package: XINA

Version: 1.5.0

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_1.5.0.tar.gz

StartedAt: 2020-01-10 09:38:55 -0500 (Fri, 10 Jan 2020)

EndedAt: 2020-01-10 09:42:44 -0500 (Fri, 10 Jan 2020)

EllapsedTime: 228.9 seconds

RetCode: 0

Status:  OK

CheckDir: XINA.Rcheck

Warnings: 0

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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_1.5.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.11-bioc/meat/XINA.Rcheck’
* using R Under development (unstable) (2019-12-14 r77572)
* 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 ‘1.5.0’
* 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 (user + system) or elapsed time > 5s
                                    user system elapsed
xina_clustering                   39.154  0.809  39.967
plot_condition_compositions       26.362  0.117  26.482
plot_clusters                     15.642  0.075  15.718
mutate_colors                     14.596  0.075  14.673
get_condition_biased_comigrations  9.220  0.068   9.291
xina_plot_all                      6.536  0.848   6.773
* 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-3.11-bioc/meat/XINA.Rcheck/00check.log’
for details.

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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
** 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)

name	user	system	elapsed
alluvial_enriched	4.130	0.184	4.317
draw_alluvial_plot	0.089	0.014	0.104
get_comigrations_by_name	0.057	0.014	0.071
get_condition_biased_comigrations	9.220	0.068	9.291
get_unknown_ppi_nodes	0.104	0.029	0.133
load_previous_results	1.837	0.171	2.007
make_random_xina_data	0.352	0.052	0.403
mutate_colors	14.596	0.075	14.673
plot_clusters	15.642	0.075	15.718
plot_clusters_all	1.893	0.079	1.975
plot_condition_compositions	26.362	0.117	26.482
plot_enrichment_results	0.001	0.000	0.001
xina_analysis	0	0	0
xina_clustering	39.154	0.809	39.967
xina_enrichment	0.001	0.001	0.001
xina_plot_all	6.536	0.848	6.773
xina_plot_bycluster	0.190	0.095	0.284
xina_plot_single	0.169	0.102	0.271