Package: gemini

Version: 1.0.0

Command: /home/biocbuild/bbs-3.10-bioc/R/bin/R CMD check --install=check:gemini.install-out.txt --library=/home/biocbuild/bbs-3.10-bioc/R/library --no-vignettes --timings gemini_1.0.0.tar.gz

StartedAt: 2020-04-15 06:41:17 -0400 (Wed, 15 Apr 2020)

EndedAt: 2020-04-15 06:44:07 -0400 (Wed, 15 Apr 2020)

EllapsedTime: 169.6 seconds

RetCode: 0

Status:  OK

CheckDir: gemini.Rcheck

Warnings: 0

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### Running command:
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###   /home/biocbuild/bbs-3.10-bioc/R/bin/R CMD check --install=check:gemini.install-out.txt --library=/home/biocbuild/bbs-3.10-bioc/R/library --no-vignettes --timings gemini_1.0.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.10-bioc/meat/gemini.Rcheck’
* using R version 3.6.3 (2020-02-29)
* using platform: x86_64-pc-linux-gnu (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  27.356  0.032  27.528
update_tau_pb     11.420  0.012  11.471
update_x_pb       10.520  0.016  10.564
gemini_initialize  6.888  0.064   6.967
* 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
  ‘/home/biocbuild/bbs-3.10-bioc/meat/gemini.Rcheck/00check.log’
for details.

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### Running command:
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###   /home/biocbuild/bbs-3.10-bioc/R/bin/R CMD INSTALL gemini
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* installing to library ‘/home/biocbuild/bbs-3.10-bioc/R/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-pc-linux-gnu (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 
  7.144   0.304   7.592 

name	user	system	elapsed
Sgene2Pguides_hash	0	0	0
Sguide2Pguides_hash	0.000	0.000	0.001
compound	0.000	0.000	0.001
dot-median_normalize	0	0	0
gemini_boxplot	2.052	0.028	2.086
gemini_calculate_lfc	0.488	0.032	0.520
gemini_create_input	0.360	0.040	0.404
gemini_inference	27.356	0.032	27.528
gemini_initialize	6.888	0.064	6.967
gemini_plot_mae	0.872	0.008	0.883
gemini_prepare_input	0.48	0.00	0.48
gemini_score	0.972	0.020	0.993
initialize_s	1.944	0.020	1.992
initialize_tau	2.500	0.044	2.556
initialize_x	3.452	0.020	3.511
initialize_y	0.780	0.020	0.803
pipe	0	0	0
update_mae	1.620	0.024	1.645
update_s_pb	2.588	0.020	2.614
update_tau_pb	11.420	0.012	11.471
update_x_pb	10.520	0.016	10.564
update_y_pb	3.896	0.020	3.985