Found the following problems:
carrierprob.Rd:109:1: Warning: inserting implicit <p>
carrierprob.Rd:109:1: Warning: trimming empty <p>
carrierprob.Rd:87:9: Warning: moved <style> tag to <head>! fix-style-tags: no to avoid.
carrierprob.Rd:93:9: Warning: <table> attribute "align" not allowed for HTML5
carrierprob.Rd:93:9: Warning: <table> attribute "align" not allowed for HTML5
carrierprob.Rd:93:9: Warning: <table> attribute "cellpadding" not allowed for HTML5
carrierprob.Rd:93:9: Warning: <table> attribute "cellspacing" not allowed for HTML5
carrierprob.Rd:95:9: Warning: <td> attribute "nowrap" not allowed for HTML5
carrierprob.Rd:98:9: Warning: <td> attribute "nowrap" not allowed for HTML5
penetrance.Rd:85:1: Warning: inserting implicit <p>
penetrance.Rd:85:1: Warning: trimming empty <p>
penetrance.Rd:83:1: Warning: <center> element removed from HTML5
penmodel.Rd:102:1: Warning: inserting implicit <p>
penmodel.Rd:102:1: Warning: trimming empty <p>
penmodel.Rd:100:2: Warning: <center> element removed from HTML5
penmodelem.Rd:123:1: Warning: inserting implicit <p>
penmodelem.Rd:126:1: Warning: inserting implicit <p>
penmodelem.Rd:123:1: Warning: trimming empty <p>
penmodelem.Rd:126:1: Warning: trimming empty <p>
penmodelem.Rd:121:1: Warning: <center> element removed from HTML5
penmodelem.Rd:125:1: Warning: <center> element removed from HTML5
penplot.Rd:155:1: Warning: inserting implicit <p>
penplot.Rd:159:1: Warning: inserting implicit <p>
penplot.Rd:166:1: Warning: inserting implicit <p>
penplot.Rd:169:1: Warning: inserting implicit <p>
penplot.Rd:176:1: Warning: inserting implicit <p>
penplot.Rd:155:1: Warning: trimming empty <p>
penplot.Rd:159:1: Warning: trimming empty <p>
penplot.Rd:166:1: Warning: trimming empty <p>
penplot.Rd:169:1: Warning: trimming empty <p>
penplot.Rd:176:1: Warning: trimming empty <p>
penplot.Rd:153:2: Warning: <center> element removed from HTML5
penplot.Rd:157:1: Warning: <center> element removed from HTML5
penplot.Rd:164:2: Warning: <center> element removed from HTML5
penplot.Rd:168:1: Warning: <center> element removed from HTML5
penplot.Rd:173:1: Warning: <center> element removed from HTML5
simfam.Rd:149:2: Warning: <center> element removed from HTML5
simfam.Rd:154:2: Warning: <center> element removed from HTML5
simfam.Rd:159:2: Warning: <center> element removed from HTML5