##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/R/R-4.3.1/bin/R CMD check --install=check:GA4GHshiny.install-out.txt --library=/home/biocbuild/R/R-4.3.1/site-library --no-vignettes --timings GA4GHshiny_1.24.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.18-bioc/meat/GA4GHshiny.Rcheck’
* using R version 4.3.1 (2023-06-16)
* using platform: aarch64-unknown-linux-gnu (64-bit)
* R was compiled by
    gcc (GCC) 10.3.1
    GNU Fortran (GCC) 10.3.1
* running under: openEuler 22.03 (LTS-SP1)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘GA4GHshiny/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘GA4GHshiny’ version ‘1.24.0’
* 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:
  .travis.yml
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 ‘GA4GHshiny’ 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 loading without being on the library search path ... 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 ... OK
* 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: 1 NOTE
See
  ‘/home/biocbuild/bbs-3.18-bioc/meat/GA4GHshiny.Rcheck/00check.log’
for details.

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/R/R-4.3.1/bin/R CMD INSTALL GA4GHshiny
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/R/R-4.3.1/site-library’
* installing *source* package ‘GA4GHshiny’ ...
** using staged installation
** R
** byte-compile and prepare package for lazy loading
No methods found in package ‘BiocGenerics’ for request: ‘lengths’ when loading ‘GA4GHclient’
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
No methods found in package ‘BiocGenerics’ for request: ‘lengths’ when loading ‘GA4GHclient’
** testing if installed package can be loaded from final location
No methods found in package ‘BiocGenerics’ for request: ‘lengths’ when loading ‘GA4GHclient’
** testing if installed package keeps a record of temporary installation path
* DONE (GA4GHshiny)

R version 4.3.1 (2023-06-16) -- "Beagle Scouts"
Copyright (C) 2023 The R Foundation for Statistical Computing
Platform: aarch64-unknown-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(GA4GHshiny)
Loading required package: GA4GHclient
Loading required package: S4Vectors
Loading required package: stats4
Loading required package: BiocGenerics

Attaching package: 'BiocGenerics'

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

    IQR, mad, sd, var, xtabs

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

    Filter, Find, Map, Position, Reduce, anyDuplicated, aperm, append,
    as.data.frame, basename, cbind, colnames, dirname, do.call,
    duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
    lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin,
    pmin.int, rank, rbind, rownames, sapply, setdiff, sort, table,
    tapply, union, unique, unsplit, which.max, which.min


Attaching package: 'S4Vectors'

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

    findMatches

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

    I, expand.grid, unname

No methods found in package 'BiocGenerics' for request: 'lengths' when loading 'GA4GHclient'
> 
> test_check("GA4GHshiny")
[ FAIL 0 | WARN 0 | SKIP 12 | PASS 4 ]

══ Skipped tests (12) ══════════════════════════════════════════════════════════
• On Bioconductor (12): 'test-app.R:4:5', 'test-initializeReferences.R:4:5',
  'test-initializeVariantSet.R:4:5', 'test-searchVariantsByGeneSymbol.R:7:5',
  'test-searchVariantsByGeneSymbol.R:20:5',
  'test-searchVariantsByGeneSymbol.R:33:5',
  'test-searchVariantsByGeneSymbol.R:46:5',
  'test-searchVariantsByGeneSymbol.R:58:5',
  'test-searchVariantsByGeneSymbol.R:70:5',
  'test-searchVariantsByGeneSymbol.R:83:5', 'test-tidyVariants.R:4:5',
  'test-tidyVariants.R:15:5'

[ FAIL 0 | WARN 0 | SKIP 12 | PASS 4 ]
> 
> proc.time()
   user  system elapsed 
 21.838   1.408  23.287