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

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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_1.2.0.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.

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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/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)

name	user	system	elapsed
alluvial_enriched	4.570	0.310	4.883
draw_alluvial_plot	0.096	0.010	0.108
get_comigrations_by_name	0.055	0.006	0.060
get_condition_biased_comigrations	8.982	0.050	9.035
get_unknown_ppi_nodes	0.087	0.015	0.103
load_previous_results	2.051	0.080	2.131
make_random_xina_data	0.363	0.068	0.432
mutate_colors	14.776	0.076	14.854
plot_clusters	15.417	0.073	15.492
plot_clusters_all	1.674	0.060	1.736
plot_condition_compositions	27.111	0.098	27.213
plot_enrichment_results	0.000	0.000	0.001
xina_analysis	0.000	0.001	0.001
xina_clustering	37.537	0.705	38.246
xina_enrichment	0.001	0.001	0.001
xina_plot_all	6.011	0.910	6.234
xina_plot_bycluster	0.200	0.110	0.311
xina_plot_single	0.140	0.097	0.237