Package: gemini

Version: 1.0.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:gemini.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings gemini_1.0.0.tar.gz

StartedAt: 2020-04-15 02:30:43 -0400 (Wed, 15 Apr 2020)

EndedAt: 2020-04-15 02:33:44 -0400 (Wed, 15 Apr 2020)

EllapsedTime: 180.8 seconds

RetCode: 0

Status:  OK

CheckDir: gemini.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:gemini.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings gemini_1.0.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.10-bioc/meat/gemini.Rcheck’
* using R version 3.6.3 (2020-02-29)
* using platform: x86_64-apple-darwin15.6.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘gemini/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘gemini’ version ‘1.0.0’
* 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 ... NOTE
Found the following hidden files and directories:
  .github
These were most likely included in error. See section ‘Package
structure’ in the ‘Writing R Extensions’ manual.
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘gemini’ 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 ... NOTE
gemini_boxplot : <anonymous>: no visible binding for global variable
  ‘.’
gemini_boxplot: no visible binding for global variable ‘.’
gemini_boxplot : <anonymous>: no visible binding for global variable
  ‘gi’
gemini_boxplot : <anonymous>: no visible binding for global variable
  ‘hj’
gemini_boxplot: no visible binding for global variable ‘label’
gemini_boxplot: no visible binding for global variable ‘y’
gemini_calculate_lfc: no visible binding for global variable ‘.’
update_s_pb: no visible binding for global variable ‘.’
update_tau_pb: no visible binding for global variable ‘.’
Undefined global functions or variables:
  . gi hj label y
* 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
gemini_inference  27.473  2.712  30.402
update_tau_pb     12.443  1.168  13.664
update_x_pb       10.561  0.948  11.565
gemini_initialize  7.641  0.087   7.751
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’
 OK
* 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: 2 NOTEs
See
  ‘/Users/biocbuild/bbs-3.10-bioc/meat/gemini.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 gemini
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* installing to library ‘/Library/Frameworks/R.framework/Versions/3.6/Resources/library’
* installing *source* package ‘gemini’ ...
** 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 (gemini)

R version 3.6.3 (2020-02-29) -- "Holding the Windsock"
Copyright (C) 2020 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin15.6.0 (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> library(testthat)
> library(gemini)
> 
> test_check("gemini")
══ testthat results  ═══════════════════════════════════════════════════════════
[ OK: 7 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 0 ]
> 
> proc.time()
   user  system elapsed 
  7.708   0.378   8.113 

name	user	system	elapsed
Sgene2Pguides_hash	0.000	0.000	0.001
Sguide2Pguides_hash	0.001	0.000	0.001
compound	0.002	0.000	0.002
dot-median_normalize	0.000	0.001	0.000
gemini_boxplot	1.933	0.079	2.031
gemini_calculate_lfc	0.427	0.022	0.455
gemini_create_input	0.301	0.011	0.312
gemini_inference	27.473	2.712	30.402
gemini_initialize	7.641	0.087	7.751
gemini_plot_mae	1.006	0.011	1.021
gemini_prepare_input	0.509	0.008	0.519
gemini_score	1.088	0.012	1.103
initialize_s	1.972	0.054	2.033
initialize_tau	2.681	0.038	2.734
initialize_x	4.565	0.025	4.613
initialize_y	0.851	0.012	0.865
pipe	0	0	0
update_mae	1.588	0.012	1.606
update_s_pb	2.468	0.230	2.706
update_tau_pb	12.443	1.168	13.664
update_x_pb	10.561	0.948	11.565
update_y_pb	3.670	0.123	3.815