R Under development (unstable) (2026-02-03 r89375 ucrt) -- "Unsuffered Consequences"
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> library(testthat)
> library(lisat)
> testthat::test_check("lisat")
CIS_network calculates interactions between integration sites in a network view

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      <th class="gt_col_heading gt_columns_bottom_border gt_right" rowspan="1" colspan="1" scope="col" id="Locus">Locus</th>
      <th class="gt_col_heading gt_columns_bottom_border gt_left" rowspan="1" colspan="1" scope="col" id="Gene">Gene</th>
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    <tr><td headers="Chr" class="gt_row gt_left">chr14</td>
<td headers="Locus" class="gt_row gt_right">46622339</td>
<td headers="Gene" class="gt_row gt_left">RPL10L</td>
<td headers="Total_dots" class="gt_row gt_right">5</td>
<td headers="Central_connectivity" class="gt_row gt_right">3</td>
<td headers="Dimention" class="gt_row gt_right">23715</td>
<td headers="Order" class="gt_row gt_right">10</td>
<td headers="Gene_network" class="gt_row gt_left">RPL10L</td>
<td headers="Sample_A" class="gt_row gt_center" style="background-color: #999999; color: #FFFFFF;">FALSE</td>
<td headers="Sample_B" class="gt_row gt_center" style="background-color: #FF6B6B; color: #FFFFFF;">TRUE</td>
<td headers="Sample_C" class="gt_row gt_center" style="background-color: #FF6B6B; color: #FFFFFF;">TRUE</td></tr>
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<td headers="Locus" class="gt_row gt_right">119446557</td>
<td headers="Gene" class="gt_row gt_left">LOC105377975</td>
<td headers="Total_dots" class="gt_row gt_right">4</td>
<td headers="Central_connectivity" class="gt_row gt_right">3</td>
<td headers="Dimention" class="gt_row gt_right">29464</td>
<td headers="Order" class="gt_row gt_right">7</td>
<td headers="Gene_network" class="gt_row gt_left">LOC105377975</td>
<td headers="Sample_A" class="gt_row gt_center" style="background-color: #FF6B6B; color: #FFFFFF;">TRUE</td>
<td headers="Sample_B" class="gt_row gt_center" style="background-color: #FF6B6B; color: #FFFFFF;">TRUE</td>
<td headers="Sample_C" class="gt_row gt_center" style="background-color: #999999; color: #FFFFFF;">FALSE</td></tr>
    <tr><td headers="Chr" class="gt_row gt_left">chr7</td>
<td headers="Locus" class="gt_row gt_right">49323212</td>
<td headers="Gene" class="gt_row gt_left">LOC124901804</td>
<td headers="Total_dots" class="gt_row gt_right">4</td>
<td headers="Central_connectivity" class="gt_row gt_right">3</td>
<td headers="Dimention" class="gt_row gt_right">30996</td>
<td headers="Order" class="gt_row gt_right">7</td>
<td headers="Gene_network" class="gt_row gt_left">LOC124901804</td>
<td headers="Sample_A" class="gt_row gt_center" style="background-color: #FF6B6B; color: #FFFFFF;">TRUE</td>
<td headers="Sample_B" class="gt_row gt_center" style="background-color: #FF6B6B; color: #FFFFFF;">TRUE</td>
<td headers="Sample_C" class="gt_row gt_center" style="background-color: #FF6B6B; color: #FFFFFF;">TRUE</td></tr>
    <tr><td headers="Chr" class="gt_row gt_left">chr20</td>
<td headers="Locus" class="gt_row gt_right">38686365</td>
<td headers="Gene" class="gt_row gt_left">SLC32A1</td>
<td headers="Total_dots" class="gt_row gt_right">4</td>
<td headers="Central_connectivity" class="gt_row gt_right">3</td>
<td headers="Dimention" class="gt_row gt_right">33175</td>
<td headers="Order" class="gt_row gt_right">7</td>
<td headers="Gene_network" class="gt_row gt_left">SLC32A1; ARHGAP40</td>
<td headers="Sample_A" class="gt_row gt_center" style="background-color: #999999; color: #FFFFFF;">FALSE</td>
<td headers="Sample_B" class="gt_row gt_center" style="background-color: #FF6B6B; color: #FFFFFF;">TRUE</td>
<td headers="Sample_C" class="gt_row gt_center" style="background-color: #FF6B6B; color: #FFFFFF;">TRUE</td></tr>
    <tr><td headers="Chr" class="gt_row gt_left">chr11</td>
<td headers="Locus" class="gt_row gt_right">49305065</td>
<td headers="Gene" class="gt_row gt_left">FOLH1</td>
<td headers="Total_dots" class="gt_row gt_right">4</td>
<td headers="Central_connectivity" class="gt_row gt_right">2</td>
<td headers="Dimention" class="gt_row gt_right">32606</td>
<td headers="Order" class="gt_row gt_right">6</td>
<td headers="Gene_network" class="gt_row gt_left">FOLH1</td>
<td headers="Sample_A" class="gt_row gt_center" style="background-color: #FF6B6B; color: #FFFFFF;">TRUE</td>
<td headers="Sample_B" class="gt_row gt_center" style="background-color: #FF6B6B; color: #FFFFFF;">TRUE</td>
<td headers="Sample_C" class="gt_row gt_center" style="background-color: #FF6B6B; color: #FFFFFF;">TRUE</td></tr>
    <tr><td headers="Chr" class="gt_row gt_left">chr17</td>
<td headers="Locus" class="gt_row gt_right">96254683</td>
<td headers="Gene" class="gt_row gt_left">RPL23AP87</td>
<td headers="Total_dots" class="gt_row gt_right">4</td>
<td headers="Central_connectivity" class="gt_row gt_right">2</td>
<td headers="Dimention" class="gt_row gt_right">32661</td>
<td headers="Order" class="gt_row gt_right">6</td>
<td headers="Gene_network" class="gt_row gt_left">RPL23AP87</td>
<td headers="Sample_A" class="gt_row gt_center" style="background-color: #999999; color: #FFFFFF;">FALSE</td>
<td headers="Sample_B" class="gt_row gt_center" style="background-color: #FF6B6B; color: #FFFFFF;">TRUE</td>
<td headers="Sample_C" class="gt_row gt_center" style="background-color: #FF6B6B; color: #FFFFFF;">TRUE</td></tr>
    <tr><td headers="Chr" class="gt_row gt_left">chr12</td>
<td headers="Locus" class="gt_row gt_right">136321446</td>
<td headers="Gene" class="gt_row gt_left">ANHX</td>
<td headers="Total_dots" class="gt_row gt_right">4</td>
<td headers="Central_connectivity" class="gt_row gt_right">1</td>
<td headers="Dimention" class="gt_row gt_right">51276</td>
<td headers="Order" class="gt_row gt_right">5</td>
<td headers="Gene_network" class="gt_row gt_left">ANHX</td>
<td headers="Sample_A" class="gt_row gt_center" style="background-color: #999999; color: #FFFFFF;">FALSE</td>
<td headers="Sample_B" class="gt_row gt_center" style="background-color: #FF6B6B; color: #FFFFFF;">TRUE</td>
<td headers="Sample_C" class="gt_row gt_center" style="background-color: #FF6B6B; color: #FFFFFF;">TRUE</td></tr>
    <tr><td headers="Chr" class="gt_row gt_left">chr8</td>
<td headers="Locus" class="gt_row gt_right">4382729</td>
<td headers="Gene" class="gt_row gt_left">CSMD1</td>
<td headers="Total_dots" class="gt_row gt_right">4</td>
<td headers="Central_connectivity" class="gt_row gt_right">2</td>
<td headers="Dimention" class="gt_row gt_right">34476</td>
<td headers="Order" class="gt_row gt_right">5</td>
<td headers="Gene_network" class="gt_row gt_left">CSMD1</td>
<td headers="Sample_A" class="gt_row gt_center" style="background-color: #FF6B6B; color: #FFFFFF;">TRUE</td>
<td headers="Sample_B" class="gt_row gt_center" style="background-color: #999999; color: #FFFFFF;">FALSE</td>
<td headers="Sample_C" class="gt_row gt_center" style="background-color: #FF6B6B; color: #FFFFFF;">TRUE</td></tr>
    <tr><td headers="Chr" class="gt_row gt_left">chr4</td>
<td headers="Locus" class="gt_row gt_right">102665076</td>
<td headers="Gene" class="gt_row gt_left">MANBA</td>
<td headers="Total_dots" class="gt_row gt_right">4</td>
<td headers="Central_connectivity" class="gt_row gt_right">2</td>
<td headers="Dimention" class="gt_row gt_right">41393</td>
<td headers="Order" class="gt_row gt_right">5</td>
<td headers="Gene_network" class="gt_row gt_left">MANBA</td>
<td headers="Sample_A" class="gt_row gt_center" style="background-color: #FF6B6B; color: #FFFFFF;">TRUE</td>
<td headers="Sample_B" class="gt_row gt_center" style="background-color: #FF6B6B; color: #FFFFFF;">TRUE</td>
<td headers="Sample_C" class="gt_row gt_center" style="background-color: #FF6B6B; color: #FFFFFF;">TRUE</td></tr>
    <tr><td headers="Chr" class="gt_row gt_left">chr19</td>
<td headers="Locus" class="gt_row gt_right">117947388</td>
<td headers="Gene" class="gt_row gt_left">CENPBD2P</td>
<td headers="Total_dots" class="gt_row gt_right">3</td>
<td headers="Central_connectivity" class="gt_row gt_right">2</td>
<td headers="Dimention" class="gt_row gt_right">2379</td>
<td headers="Order" class="gt_row gt_right">4</td>
<td headers="Gene_network" class="gt_row gt_left">CENPBD2P</td>
<td headers="Sample_A" class="gt_row gt_center" style="background-color: #FF6B6B; color: #FFFFFF;">TRUE</td>
<td headers="Sample_B" class="gt_row gt_center" style="background-color: #FF6B6B; color: #FFFFFF;">TRUE</td>
<td headers="Sample_C" class="gt_row gt_center" style="background-color: #FF6B6B; color: #FFFFFF;">TRUE</td></tr>
  </tbody>
  
</table>
</div>
[ FAIL 0 | WARN 6 | SKIP 1 | PASS 0 ]

══ Skipped tests (1) ═══════════════════════════════════════════════════════════
• empty test (1):

[ FAIL 0 | WARN 6 | SKIP 1 | PASS 0 ]
> 
> proc.time()
   user  system elapsed 
  65.71    2.09   68.26