Package: ImmuneSpaceR

Version: 1.10.5

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:ImmuneSpaceR.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings ImmuneSpaceR_1.10.5.tar.gz

StartedAt: 2019-04-16 00:40:52 -0400 (Tue, 16 Apr 2019)

EndedAt: 2019-04-16 00:42:38 -0400 (Tue, 16 Apr 2019)

EllapsedTime: 105.8 seconds

RetCode: 0

Status:  OK

CheckDir: ImmuneSpaceR.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:ImmuneSpaceR.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings ImmuneSpaceR_1.10.5.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.8-bioc/meat/ImmuneSpaceR.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 ‘ImmuneSpaceR/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘ImmuneSpaceR’ version ‘1.10.5’
* 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 ‘ImmuneSpaceR’ 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
Unexported objects imported by ':::' calls:
  ‘Rlabkey:::.lkdefaults’ ‘Rlabkey:::labkey.getRequestOptions’
  See the note in ?`:::` about the use of this operator.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
.getDataToPlot: no visible binding for global variable ‘value_reported’
Undefined global functions or variables:
  value_reported
* 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 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: 2 NOTEs
See
  ‘/Users/biocbuild/bbs-3.8-bioc/meat/ImmuneSpaceR.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 ImmuneSpaceR
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* installing to library ‘/Library/Frameworks/R.framework/Versions/3.5/Resources/library’
* installing *source* package ‘ImmuneSpaceR’ ...
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
*** copying figures
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (ImmuneSpaceR)

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(ImmuneSpaceR)
A .netrc file is required to connect to ImmuneSpace. For more information on how to create one, refer to the Configuration section of the introduction vignette.
> 
> if (Sys.info()["user"] != "biocbuild") test_check("ImmuneSpaceR")
> 
> proc.time()
   user  system elapsed 
  4.491   0.326   4.848 

name	user	system	elapsed
CreateConnection	0.052	0.012	0.303
ISpalette	0.003	0.000	0.003
ImmuneSpaceConnection	0.013	0.001	0.049
check_netrc	0.001	0.001	0.000
interactive_netrc	0.001	0.000	0.001
loadConnection	0.056	0.001	0.057
template_IS	0.025	0.023	0.063
theme_IS	0.534	0.009	0.549
write_netrc	0.001	0.001	0.001