Running examples in 'BIOM.utils-Ex.R' failed
The error most likely occurred in:

> ### Name: BIOM Examples
> ### Title: BIOM examples and related utilities
> ### Aliases: buildBiomExamples applyBiomMethods exampleBiomFile jtxt smat
> ###   dmat li1 li2 li3 li4
> 
> ### ** Examples
> 
> str(jtxt)
 chr "{\"generated_by\":\"MG-RAST revision 3.3.8.3\",\"matrix_type\":\"sparse\",\"date\":\"2014-08-27T21:52:33\",\"da"| __truncated__
> str(smat)
 num [1:774, 1:3] 0 0 0 0 1 1 1 2 2 2 ...
> str(dmat)
 int [1:20, 1:5] 101 102 103 104 105 106 107 108 109 110 ...
 - attr(*, "dimnames")=List of 2
  ..$ : chr [1:20] "a" "b" "c" "d" ...
  ..$ : chr [1:5] "A" "B" "C" "D" ...
> str(li1)
List of 2
 $ data: int [1:20, 1:5] 101 102 103 104 105 106 107 108 109 110 ...
  ..- attr(*, "dimnames")=List of 2
  .. ..$ : chr [1:20] "a" "b" "c" "d" ...
  .. ..$ : chr [1:5] "A" "B" "C" "D" ...
 $ type: chr "OTU"
> str(li2)
List of 4
 $ data   : int [1:20, 1:5] 101 102 103 104 105 106 107 108 109 110 ...
  ..- attr(*, "dimnames")=List of 2
  .. ..$ : chr [1:20] "a" "b" "c" "d" ...
  .. ..$ : chr [1:5] "A" "B" "C" "D" ...
 $ type   : chr "OTU table"
 $ rows   :List of 20
  ..$ : Named chr [1:2] "aaa" "metadata of aaa"
  .. ..- attr(*, "names")= chr [1:2] "id" "metadata"
  ..$ : Named chr [1:2] "bbb" "metadata of bbb"
  .. ..- attr(*, "names")= chr [1:2] "id" "metadata"
  ..$ : Named chr [1:2] "ccc" "metadata of ccc"
  .. ..- attr(*, "names")= chr [1:2] "id" "metadata"
  ..$ : Named chr [1:2] "ddd" "metadata of ddd"
  .. ..- attr(*, "names")= chr [1:2] "id" "metadata"
  ..$ : Named chr [1:2] "eee" "metadata of eee"
  .. ..- attr(*, "names")= chr [1:2] "id" "metadata"
  ..$ : Named chr [1:2] "fff" "metadata of fff"
  .. ..- attr(*, "names")= chr [1:2] "id" "metadata"
  ..$ : Named chr [1:2] "ggg" "metadata of ggg"
  .. ..- attr(*, "names")= chr [1:2] "id" "metadata"
  ..$ : Named chr [1:2] "hhh" "metadata of hhh"
  .. ..- attr(*, "names")= chr [1:2] "id" "metadata"
  ..$ : Named chr [1:2] "iii" "metadata of iii"
  .. ..- attr(*, "names")= chr [1:2] "id" "metadata"
  ..$ : Named chr [1:2] "jjj" "metadata of jjj"
  .. ..- attr(*, "names")= chr [1:2] "id" "metadata"
  ..$ : Named chr [1:2] "kkk" "metadata of kkk"
  .. ..- attr(*, "names")= chr [1:2] "id" "metadata"
  ..$ : Named chr [1:2] "lll" "metadata of lll"
  .. ..- attr(*, "names")= chr [1:2] "id" "metadata"
  ..$ : Named chr [1:2] "mmm" "metadata of mmm"
  .. ..- attr(*, "names")= chr [1:2] "id" "metadata"
  ..$ : Named chr [1:2] "nnn" "metadata of nnn"
  .. ..- attr(*, "names")= chr [1:2] "id" "metadata"
  ..$ : Named chr [1:2] "ooo" "metadata of ooo"
  .. ..- attr(*, "names")= chr [1:2] "id" "metadata"
  ..$ : Named chr [1:2] "ppp" "metadata of ppp"
  .. ..- attr(*, "names")= chr [1:2] "id" "metadata"
  ..$ : Named chr [1:2] "qqq" "metadata of qqq"
  .. ..- attr(*, "names")= chr [1:2] "id" "metadata"
  ..$ : Named chr [1:2] "rrr" "metadata of rrr"
  .. ..- attr(*, "names")= chr [1:2] "id" "metadata"
  ..$ : Named chr [1:2] "sss" "metadata of sss"
  .. ..- attr(*, "names")= chr [1:2] "id" "metadata"
  ..$ : Named chr [1:2] "ttt" "metadata of ttt"
  .. ..- attr(*, "names")= chr [1:2] "id" "metadata"
 $ columns:List of 5
  ..$ : Named chr [1:2] "AAA" "metadata of AAA"
  .. ..- attr(*, "names")= chr [1:2] "id" "metadata"
  ..$ : Named chr [1:2] "BBB" "metadata of BBB"
  .. ..- attr(*, "names")= chr [1:2] "id" "metadata"
  ..$ : Named chr [1:2] "CCC" "metadata of CCC"
  .. ..- attr(*, "names")= chr [1:2] "id" "metadata"
  ..$ : Named chr [1:2] "DDD" "metadata of DDD"
  .. ..- attr(*, "names")= chr [1:2] "id" "metadata"
  ..$ : Named chr [1:2] "EEE" "metadata of EEE"
  .. ..- attr(*, "names")= chr [1:2] "id" "metadata"
> str(li3)
List of 4
 $ data   :List of 20
  ..$ : int [1:5] 101 121 141 161 181
  ..$ : int [1:5] 102 122 142 162 182
  ..$ : int [1:5] 103 123 143 163 183
  ..$ : int [1:5] 104 124 144 164 184
  ..$ : int [1:5] 105 125 145 165 185
  ..$ : int [1:5] 106 126 146 166 186
  ..$ : int [1:5] 107 127 147 167 187
  ..$ : int [1:5] 108 128 148 168 188
  ..$ : int [1:5] 109 129 149 169 189
  ..$ : int [1:5] 110 130 150 170 190
  ..$ : int [1:5] 111 131 151 171 191
  ..$ : int [1:5] 112 132 152 172 192
  ..$ : int [1:5] 113 133 153 173 193
  ..$ : int [1:5] 114 134 154 174 194
  ..$ : int [1:5] 115 135 155 175 195
  ..$ : int [1:5] 116 136 156 176 196
  ..$ : int [1:5] 117 137 157 177 197
  ..$ : int [1:5] 118 138 158 178 198
  ..$ : int [1:5] 119 139 159 179 199
  ..$ : int [1:5] 120 140 160 180 200
 $ type   : chr "OTU table"
 $ rows   :List of 20
  ..$ : Named chr [1:2] "aaa" "metadata of aaa"
  .. ..- attr(*, "names")= chr [1:2] "id" "metadata"
  ..$ : Named chr [1:2] "bbb" "metadata of bbb"
  .. ..- attr(*, "names")= chr [1:2] "id" "metadata"
  ..$ : Named chr [1:2] "ccc" "metadata of ccc"
  .. ..- attr(*, "names")= chr [1:2] "id" "metadata"
  ..$ : Named chr [1:2] "ddd" "metadata of ddd"
  .. ..- attr(*, "names")= chr [1:2] "id" "metadata"
  ..$ : Named chr [1:2] "eee" "metadata of eee"
  .. ..- attr(*, "names")= chr [1:2] "id" "metadata"
  ..$ : Named chr [1:2] "fff" "metadata of fff"
  .. ..- attr(*, "names")= chr [1:2] "id" "metadata"
  ..$ : Named chr [1:2] "ggg" "metadata of ggg"
  .. ..- attr(*, "names")= chr [1:2] "id" "metadata"
  ..$ : Named chr [1:2] "hhh" "metadata of hhh"
  .. ..- attr(*, "names")= chr [1:2] "id" "metadata"
  ..$ : Named chr [1:2] "iii" "metadata of iii"
  .. ..- attr(*, "names")= chr [1:2] "id" "metadata"
  ..$ : Named chr [1:2] "jjj" "metadata of jjj"
  .. ..- attr(*, "names")= chr [1:2] "id" "metadata"
  ..$ : Named chr [1:2] "kkk" "metadata of kkk"
  .. ..- attr(*, "names")= chr [1:2] "id" "metadata"
  ..$ : Named chr [1:2] "lll" "metadata of lll"
  .. ..- attr(*, "names")= chr [1:2] "id" "metadata"
  ..$ : Named chr [1:2] "mmm" "metadata of mmm"
  .. ..- attr(*, "names")= chr [1:2] "id" "metadata"
  ..$ : Named chr [1:2] "nnn" "metadata of nnn"
  .. ..- attr(*, "names")= chr [1:2] "id" "metadata"
  ..$ : Named chr [1:2] "ooo" "metadata of ooo"
  .. ..- attr(*, "names")= chr [1:2] "id" "metadata"
  ..$ : Named chr [1:2] "ppp" "metadata of ppp"
  .. ..- attr(*, "names")= chr [1:2] "id" "metadata"
  ..$ : Named chr [1:2] "qqq" "metadata of qqq"
  .. ..- attr(*, "names")= chr [1:2] "id" "metadata"
  ..$ : Named chr [1:2] "rrr" "metadata of rrr"
  .. ..- attr(*, "names")= chr [1:2] "id" "metadata"
  ..$ : Named chr [1:2] "sss" "metadata of sss"
  .. ..- attr(*, "names")= chr [1:2] "id" "metadata"
  ..$ : Named chr [1:2] "ttt" "metadata of ttt"
  .. ..- attr(*, "names")= chr [1:2] "id" "metadata"
 $ columns:List of 5
  ..$ : Named chr [1:2] "AAA" "metadata of AAA"
  .. ..- attr(*, "names")= chr [1:2] "id" "metadata"
  ..$ : Named chr [1:2] "BBB" "metadata of BBB"
  .. ..- attr(*, "names")= chr [1:2] "id" "metadata"
  ..$ : Named chr [1:2] "CCC" "metadata of CCC"
  .. ..- attr(*, "names")= chr [1:2] "id" "metadata"
  ..$ : Named chr [1:2] "DDD" "metadata of DDD"
  .. ..- attr(*, "names")= chr [1:2] "id" "metadata"
  ..$ : Named chr [1:2] "EEE" "metadata of EEE"
  .. ..- attr(*, "names")= chr [1:2] "id" "metadata"
> exampleBiomFile()
[1] "C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/BIOM.utils/BIOM.utils.Rcheck/BIOM.utils/extdata/example-json.txt"
> 
> xx <- biom (file=exampleBiomFile())
Error in loadNamespace(x) : there is no package called 'RJSONIO'
Calls: biom ... loadNamespace -> withRestarts -> withOneRestart -> doWithOneRestart
Execution halted