##############################################################################
##############################################################################
###
### Running command:
###
###   D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:restfulSE.install-out.txt --library=D:\biocbuild\bbs-3.15-bioc\R\library --no-vignettes --timings restfulSE_1.17.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'D:/biocbuild/bbs-3.15-bioc/meat/restfulSE.Rcheck'
* using R Under development (unstable) (2021-11-21 r81221)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'restfulSE/DESCRIPTION' ... OK
* this is package 'restfulSE' version '1.17.0'
* 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 whether package 'restfulSE' 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
BQ3_Source: no visible binding for global variable
  'SampleTypeLetterCode'
BQ3m2: no visible binding for global variable 'SampleTypeLetterCode'
Undefined global functions or variables:
  SampleTypeLetterCode
* 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 ... ERROR
Running examples in 'restfulSE-Ex.R' failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: RESTfulSummarizedExperiment
> ### Title: Construct RESTfulSummarizedExperiment
> ### Aliases: RESTfulSummarizedExperiment
> ###   RESTfulSummarizedExperiment,RangedSummarizedExperiment,H5S_dataset-method
> ###   .RESTfulSummarizedExperiment assay
> ###   assay,RESTfulSummarizedExperiment,missing-method
> 
> ### ** Examples
> 
> require("rhdf5client")
Loading required package: rhdf5client
> hsds = H5S_source(serverURL=URL_hsds())
Error in validObject(.Object) : 
  invalid class "H5S_source" object: 1: invalid object for slot "dsmeta" in class "H5S_source": got class "S4", should be or extend class "DataFrame"
invalid class "H5S_source" object: 2: invalid object for slot "dmains" in class "H5S_source": got class "S4", should be or extend class "DataFrame"
Calls: H5S_source -> new -> initialize -> initialize -> validObject
Execution halted
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
  Running 'testthat.R'
 ERROR
Running the tests in 'tests/testthat.R' failed.
Last 13 lines of output:
  == Failed tests ================================================================
  -- Error (test_reSE.R:9:2): H5S_source completes -------------------------------
  Error in `validObject(.Object)`: invalid class "H5S_source" object: 1: invalid object for slot "dsmeta" in class "H5S_source": got class "S4", should be or extend class "DataFrame"
  invalid class "H5S_source" object: 2: invalid object for slot "dmains" in class "H5S_source": got class "S4", should be or extend class "DataFrame"
  Backtrace:
      x
   1. \-rhdf5client::H5S_source(URL_hsds()) at test_reSE.R:9:1
   2.   \-methods::new("H5S_source", serverURL = serverURL, getReq = DataFrame())
   3.     +-methods::initialize(value, ...)
   4.     \-methods::initialize(value, ...)
   5.       \-methods::validObject(.Object)
  
  [ FAIL 1 | WARN 0 | SKIP 1 | PASS 3 ]
  Error: Test failures
  Execution halted
* 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 ERRORs, 1 NOTE
See
  'D:/biocbuild/bbs-3.15-bioc/meat/restfulSE.Rcheck/00check.log'
for details.