Package: XINA

Version: 1.2.0

Command: /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD check --install=check:XINA.install-out.txt --library=/home/biocbuild/bbs-3.9-bioc/R/library --no-vignettes --timings XINA_1.2.0.tar.gz

StartedAt: 2019-10-16 05:46:14 -0400 (Wed, 16 Oct 2019)

EndedAt: 2019-10-16 05:48:45 -0400 (Wed, 16 Oct 2019)

EllapsedTime: 150.4 seconds

RetCode: 0

Status:  OK

CheckDir: XINA.Rcheck

Warnings: 0

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### Running command:
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###   /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD check --install=check:XINA.install-out.txt --library=/home/biocbuild/bbs-3.9-bioc/R/library --no-vignettes --timings XINA_1.2.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.9-bioc/meat/XINA.Rcheck’
* using R version 3.6.1 (2019-07-05)
* using platform: x86_64-pc-linux-gnu (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             35.388  0.028  35.428
plot_condition_compositions 18.640  0.004  18.646
mutate_colors               13.047  0.019  13.066
plot_clusters               11.023  0.012  11.036
* 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
  ‘/home/biocbuild/bbs-3.9-bioc/meat/XINA.Rcheck/00check.log’
for details.

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### Running command:
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###   /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD INSTALL XINA
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* installing to library ‘/home/biocbuild/bbs-3.9-bioc/R/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	2.322	0.028	2.349
draw_alluvial_plot	0.065	0.000	0.066
get_comigrations_by_name	0.034	0.000	0.034
get_condition_biased_comigrations	4.997	0.000	4.997
get_unknown_ppi_nodes	0.063	0.000	0.064
load_previous_results	1.170	0.008	1.178
make_random_xina_data	0.294	0.004	0.298
mutate_colors	13.047	0.019	13.066
plot_clusters	11.023	0.012	11.036
plot_clusters_all	1.071	0.004	1.075
plot_condition_compositions	18.640	0.004	18.646
plot_enrichment_results	0	0	0
xina_analysis	0	0	0
xina_clustering	35.388	0.028	35.428
xina_enrichment	0	0	0
xina_plot_all	4.449	0.068	4.518
xina_plot_bycluster	0.169	0.012	0.181
xina_plot_single	0.138	0.004	0.142