Package: pogos

Version: 1.2.1

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:pogos.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings pogos_1.2.1.tar.gz

StartedAt: 2019-04-16 01:57:58 -0400 (Tue, 16 Apr 2019)

EndedAt: 2019-04-16 01:59:35 -0400 (Tue, 16 Apr 2019)

EllapsedTime: 97.6 seconds

RetCode: 0

Status:  OK

CheckDir: pogos.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:pogos.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings pogos_1.2.1.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.8-bioc/meat/pogos.Rcheck’
* using R version 3.5.3 (2019-03-11)
* using platform: x86_64-apple-darwin15.6.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘pogos/DESCRIPTION’ ... OK
* this is package ‘pogos’ version ‘1.2.1’
* 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 ‘pogos’ 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
compoundsByCell: no visible binding for global variable ‘cell_lines_v1’
compoundsByCell: no visible binding for global variable ‘compounds_v1’
compoundsByCell: no visible binding for global variable ‘datasets_v1’
lkc: no visible binding for global variable ‘cell_lines_v1’
lkc: no visible binding for global variable ‘compounds_v1’
lkc: no visible binding for global variable ‘datasets_v1’
plot,DRProfSet-missing: no visible binding for global variable ‘dose’
plot,DRProfSet-missing: no visible binding for global variable
  ‘response’
plot,DRProfSet-missing: no visible binding for global variable ‘drug’
plot,DRTraceSet-missing: no visible binding for global variable ‘dose’
plot,DRTraceSet-missing: no visible binding for global variable
  ‘response’
plot,DRTraceSet-missing: no visible binding for global variable
  ‘cell_line’
Undefined global functions or variables:
  cell_line cell_lines_v1 compounds_v1 datasets_v1 dose drug response
* 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
* 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: 1 NOTE
See
  ‘/Users/biocbuild/bbs-3.8-bioc/meat/pogos.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 pogos
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* installing to library ‘/Library/Frameworks/R.framework/Versions/3.5/Resources/library’
* installing *source* package ‘pogos’ ...
** R
** data
*** moving datasets to lazyload DB
** 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
* DONE (pogos)

R version 3.5.3 (2019-03-11) -- "Great Truth"
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(pogos)
Loading required package: rjson
Loading required package: httr
> 
> test_check("pogos")
══ testthat results  ═══════════════════════════════════════════════════════════
OK: 5 SKIPPED: 0 FAILED: 0
> 
> proc.time()
   user  system elapsed 
  4.411   0.282   5.123 

name	user	system	elapsed
DRProfSet	0.001	0.001	0.003
DRTraceSet	1.143	0.040	1.790
basicDecoder	0.008	0.002	0.045
compoundsByCell	0.001	0.000	0.001
compounds_v1	0.038	0.008	0.047
iriCCLE	0.473	0.051	0.526
rxdbQuery_v1	0.009	0.001	0.046
topEndpoints_v1	0.001	0.000	0.001
traces	0.014	0.001	0.016