##############################################################################
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###
### 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.

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###
### Running command:
###
###   D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD INSTALL restfulSE
###
##############################################################################
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* installing to library 'D:/biocbuild/bbs-3.15-bioc/R/library'
* installing *source* package 'restfulSE' ...
** using staged installation
** R
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'restfulSE'
    finding HTML links ... done
    BQ3_Array-class                         html  
    BQ3_Array                               html  
    BQ3_ArraySeed-class                     html  
    BQ3_Matrix-class                        html  
    BQ3_Source-class                        html  
    BQ3_Source                              html  
    BQM_Array-class                         html  
    BQM_Array                               html  
    BQM_ArraySeed-class                     html  
    BQM_Matrix-class                        html  
    BQM_Source-class                        html  
    BQM_Source                              html  
    BQSummarizedExperiment                  html  
    DelayedArray-BQ3_ArraySeed-method       html  
    RESTfulSummarizedExperiment-class       html  
    RESTfulSummarizedExperiment             html  
    assay-BQSummarizedExperiment-missing-method
                                            html  
    assayNames-BQSummarizedExperiment-method
                                            html  
    basic_clinvars                          html  
    bqConn                                  html  
    cgcConn                                 html  
    dim-BQ3_ArraySeed-method                html  
    dim-BQM_ArraySeed-method                html  
    dim-RESTfulSummarizedExperiment-method
                                            html  
    dimnames-BQ3_ArraySeed-method           html  
    dimnames-BQM_ArraySeed-method           html  
    goPatt                                  html  
    gtexTiss                                html  
    isbCgcDatasets                          html  
    isbCgcTables                            html  
    newDA                                   html  
    pancan_SE                               html  
    se1.3M                                  html  
    seByTumor                               html  
    seByTumor_2016                          html  
    tasicCortex                             html  
** 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 (restfulSE)
Making 'packages.html' ... done

R Under development (unstable) (2021-11-21 r81221) -- "Unsuffered Consequences"
Copyright (C) 2021 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64 (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(restfulSE)
Loading required package: SummarizedExperiment
Loading required package: MatrixGenerics
Loading required package: matrixStats

Attaching package: 'MatrixGenerics'

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

    colAlls, colAnyNAs, colAnys, colAvgsPerRowSet, colCollapse,
    colCounts, colCummaxs, colCummins, colCumprods, colCumsums,
    colDiffs, colIQRDiffs, colIQRs, colLogSumExps, colMadDiffs,
    colMads, colMaxs, colMeans2, colMedians, colMins, colOrderStats,
    colProds, colQuantiles, colRanges, colRanks, colSdDiffs, colSds,
    colSums2, colTabulates, colVarDiffs, colVars, colWeightedMads,
    colWeightedMeans, colWeightedMedians, colWeightedSds,
    colWeightedVars, rowAlls, rowAnyNAs, rowAnys, rowAvgsPerColSet,
    rowCollapse, rowCounts, rowCummaxs, rowCummins, rowCumprods,
    rowCumsums, rowDiffs, rowIQRDiffs, rowIQRs, rowLogSumExps,
    rowMadDiffs, rowMads, rowMaxs, rowMeans2, rowMedians, rowMins,
    rowOrderStats, rowProds, rowQuantiles, rowRanges, rowRanks,
    rowSdDiffs, rowSds, rowSums2, rowTabulates, rowVarDiffs, rowVars,
    rowWeightedMads, rowWeightedMeans, rowWeightedMedians,
    rowWeightedSds, rowWeightedVars

Loading required package: GenomicRanges
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, 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

Loading required package: S4Vectors

Attaching package: 'S4Vectors'

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

    I, expand.grid, unname

Loading required package: IRanges

Attaching package: 'IRanges'

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

    windows

Loading required package: GenomeInfoDb
Loading required package: Biobase
Welcome to Bioconductor

    Vignettes contain introductory material; view with
    'browseVignettes()'. To cite Bioconductor, see
    'citation("Biobase")', and for packages 'citation("pkgname")'.


Attaching package: 'Biobase'

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

    rowMedians

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

    anyMissing, rowMedians

Loading required package: DelayedArray
Loading required package: Matrix

Attaching package: 'Matrix'

The following object is masked from 'package:S4Vectors':

    expand


Attaching package: 'DelayedArray'

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

    aperm, apply, rowsum, scale, sweep


> library(rhdf5client)
> 
> test_check("restfulSE")
[ FAIL 1 | WARN 0 | SKIP 1 | PASS 3 ]

== Skipped tests ===============================================================
* CGC_BILLING not set (1)

== 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