Package: gemini

Version: 1.1.0

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_1.1.0.tar.gz

StartedAt: 2020-01-16 04:42:46 -0500 (Thu, 16 Jan 2020)

EndedAt: 2020-01-16 04:46:42 -0500 (Thu, 16 Jan 2020)

EllapsedTime: 235.9 seconds

RetCode: 0

Status:  OK

CheckDir: gemini.Rcheck

Warnings: 0

##############################################################################
##############################################################################
###
### Running 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_1.1.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.11-bioc/meat/gemini.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 ‘gemini/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘gemini’ version ‘1.1.0’
* 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 (user + system) or elapsed time > 5s
                    user system elapsed
gemini_inference  36.036  6.073  42.121
update_tau_pb     16.207  2.877  19.085
update_x_pb       14.449  2.115  16.567
gemini_initialize 10.821  0.175  10.997
initialize_x       6.174  0.041   6.217
update_y_pb        5.006  0.267   5.273
* 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-3.11-bioc/meat/gemini.Rcheck/00check.log’
for details.

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL gemini
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.0/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 Under development (unstable) (2019-12-14 r77572) -- "Unsuffered Consequences"
Copyright (C) 2019 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 
  9.818   0.752  10.525 

name	user	system	elapsed
Sgene2Pguides_hash	0.001	0.000	0.001
Sguide2Pguides_hash	0	0	0
compound	0.002	0.001	0.003
dot-median_normalize	0.000	0.000	0.001
gemini_boxplot	3.110	0.136	3.246
gemini_calculate_lfc	0.572	0.052	0.625
gemini_create_input	0.504	0.013	0.517
gemini_inference	36.036	6.073	42.121
gemini_initialize	10.821	0.175	10.997
gemini_plot_mae	1.150	0.022	1.172
gemini_prepare_input	0.595	0.012	0.606
gemini_score	1.122	0.017	1.140
initialize_s	2.352	0.084	2.437
initialize_tau	3.869	0.042	3.912
initialize_x	6.174	0.041	6.217
initialize_y	1.044	0.025	1.069
pipe	0.001	0.000	0.001
update_mae	2.440	0.028	2.467
update_s_pb	2.640	0.460	3.107
update_tau_pb	16.207	2.877	19.085
update_x_pb	14.449	2.115	16.567
update_y_pb	5.006	0.267	5.273