Package: HCAExplorer

Version: 1.0.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:HCAExplorer.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings HCAExplorer_1.0.0.tar.gz

StartedAt: 2020-04-15 02:59:12 -0400 (Wed, 15 Apr 2020)

EndedAt: 2020-04-15 03:01:51 -0400 (Wed, 15 Apr 2020)

EllapsedTime: 159.1 seconds

RetCode: 0

Status:  WARNINGS

CheckDir: HCAExplorer.Rcheck

Warnings: 1

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:HCAExplorer.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings HCAExplorer_1.0.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.10-bioc/meat/HCAExplorer.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 ‘HCAExplorer/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘HCAExplorer’ 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 ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘HCAExplorer’ 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 object imported by a ':::' call: ‘utils:::format.object_size’
  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
.getManifest: no visible binding for global variable ‘projectId’
.getManifestFileFormats: no visible binding for global variable
  ‘projectId’
.subset.HCAExplorer: no visible binding for global variable ‘projectId’
[,HCAExplorer: no visible binding for global variable ‘projectId’
getManifest,HCAExplorer: no visible binding for global variable
  ‘projectId’
getManifestFileFormats,HCAExplorer: no visible binding for global
  variable ‘projectId’
Undefined global functions or variables:
  projectId
* 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 ... WARNING
Documented arguments not in \usage in documentation object 'values,HCAExplorer-method':
  ‘...’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
                      user system elapsed
getManifest          1.284  0.088  26.070
activate.HCAExplorer 0.700  0.019   8.917
filter.HCAExplorer   0.607  0.008   6.130
resetQuery           0.502  0.006   5.935
* 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 WARNING, 2 NOTEs
See
  ‘/Users/biocbuild/bbs-3.10-bioc/meat/HCAExplorer.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 HCAExplorer
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* installing to library ‘/Library/Frameworks/R.framework/Versions/3.6/Resources/library’
* installing *source* package ‘HCAExplorer’ ...
** using staged installation
** R
** byte-compile and prepare package for lazy loading
Creating a generic function for ‘fields’ from package ‘vctrs’ in package ‘HCAExplorer’
** 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 (HCAExplorer)

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(HCAExplorer)
Loading required package: dplyr

Attaching package: 'dplyr'

The following object is masked from 'package:testthat':

    matches

The following objects are masked from 'package:stats':

    filter, lag

The following objects are masked from 'package:base':

    intersect, setdiff, setequal, union

> 
> test_check("HCAExplorer")
══ testthat results  ═══════════════════════════════════════════════════════════
[ OK: 1 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 0 ]
> 
> proc.time()
   user  system elapsed 
  3.887   0.260   4.172 

name	user	system	elapsed
HCAExplorer	0.418	0.036	2.497
activate.HCAExplorer	0.700	0.019	8.917
fields-HCAExplorer-method	0.172	0.002	2.369
filter.HCAExplorer	0.607	0.008	6.130
getManifest	1.284	0.088	26.070
getManifestFileFormats	0.293	0.005	3.050
nextResults	0.423	0.005	2.937
resetQuery	0.502	0.006	5.935
resetSelect	0.453	0.005	4.733
results	0.255	0.002	2.288
select.HCAExplorer	0.510	0.005	4.686
show-HCAExplorer-method	0.192	0.002	2.263
sub-HCAExplorer-method	0.317	0.003	2.810
undoQuery	0.571	0.005	4.951
values-HCAExplorer-method	0.289	0.007	2.324
viewProjects	0.609	0.094	4.476