Found the following HTML validation problems:
CV_.html:101:1 (CV_.Rd:58): Warning: <h5> anchor "Usage" already defined
CV_.html:137:1 (CV_.Rd:78): Warning: <h5> anchor "Usage" already defined
CV_.html:143:1 (CV_.Rd:82): Warning: <h5> anchor "Arguments" already defined
CV_.html:166:1 (CV_.Rd:95): Warning: <h5> anchor "Usage" already defined
CV_.html:182:1 (CV_.Rd:105): Warning: <h5> anchor "Usage" already defined
MzQCDateTime.html:115:1 (MzQCDateTime.Rd:65): Warning: <h5> anchor "Usage" already defined
MzQCDateTime.html:121:1 (MzQCDateTime.Rd:69): Warning: <h5> anchor "Arguments" already defined
MzQCDateTime.html:144:1 (MzQCDateTime.Rd:82): Warning: <h5> anchor "Usage" already defined
MzQCDateTime.html:150:1 (MzQCDateTime.Rd:86): Warning: <h5> anchor "Arguments" already defined
MzQCDateTime.html:173:1 (MzQCDateTime.Rd:99): Warning: <h5> anchor "Usage" already defined
MzQCDateTime.html:179:1 (MzQCDateTime.Rd:103): Warning: <h5> anchor "Arguments" already defined
MzQCDateTime.html:202:1 (MzQCDateTime.Rd:116): Warning: <h5> anchor "Usage" already defined
MzQCDateTime.html:208:1 (MzQCDateTime.Rd:120): Warning: <h5> anchor "Arguments" already defined
MzQCDateTime.html:233:1 (MzQCDateTime.Rd:135): Warning: <h5> anchor "Usage" already defined
MzQCDateTime.html:239:1 (MzQCDateTime.Rd:139): Warning: <h5> anchor "Arguments" already defined
MzQCanalysisSoftware.html:245:1 (MzQCanalysisSoftware.Rd:142): Warning: missing </ul> before </div>
MzQCanalysisSoftware.html:133:1 (MzQCanalysisSoftware.Rd:78): Warning: <h5> anchor "Usage" already defined
MzQCanalysisSoftware.html:139:1 (MzQCanalysisSoftware.Rd:82): Warning: <h5> anchor "Arguments" already defined
MzQCanalysisSoftware.html:162:1 (MzQCanalysisSoftware.Rd:95): Warning: <h5> anchor "Usage" already defined
MzQCanalysisSoftware.html:168:1 (MzQCanalysisSoftware.Rd:99): Warning: <h5> anchor "Arguments" already defined
MzQCanalysisSoftware.html:191:1 (MzQCanalysisSoftware.Rd:112): Warning: <h5> anchor "Usage" already defined
MzQCanalysisSoftware.html:197:1 (MzQCanalysisSoftware.Rd:116): Warning: <h5> anchor "Arguments" already defined
MzQCanalysisSoftware.html:222:1 (MzQCanalysisSoftware.Rd:131): Warning: <h5> anchor "Usage" already defined
MzQCanalysisSoftware.html:228:1 (MzQCanalysisSoftware.Rd:135): Warning: <h5> anchor "Arguments" already defined
MzQCbaseQuality.html:256:1 (MzQCbaseQuality.Rd:139): Warning: missing </ul> before </div>
MzQCbaseQuality.html:113:1 (MzQCbaseQuality.Rd:56): Warning: <h5> anchor "Usage" already defined
MzQCbaseQuality.html:119:1 (MzQCbaseQuality.Rd:60): Warning: <h5> anchor "Arguments" already defined
MzQCbaseQuality.html:142:1 (MzQCbaseQuality.Rd:73): Warning: <h5> anchor "Usage" already defined
MzQCbaseQuality.html:148:1 (MzQCbaseQuality.Rd:77): Warning: <h5> anchor "Arguments" already defined
MzQCbaseQuality.html:173:1 (MzQCbaseQuality.Rd:92): Warning: <h5> anchor "Usage" already defined
MzQCbaseQuality.html:179:1 (MzQCbaseQuality.Rd:96): Warning: <h5> anchor "Arguments" already defined
MzQCbaseQuality.html:202:1 (MzQCbaseQuality.Rd:109): Warning: <h5> anchor "Usage" already defined
MzQCbaseQuality.html:208:1 (MzQCbaseQuality.Rd:113): Warning: <h5> anchor "Arguments" already defined
MzQCbaseQuality.html:233:1 (MzQCbaseQuality.Rd:128): Warning: <h5> anchor "Usage" already defined
MzQCbaseQuality.html:239:1 (MzQCbaseQuality.Rd:132): Warning: <h5> anchor "Arguments" already defined
MzQCcontrolledVocabulary.html:118:1 (MzQCcontrolledVocabulary.Rd:70): Warning: <h5> anchor "Usage" already defined
MzQCcontrolledVocabulary.html:124:1 (MzQCcontrolledVocabulary.Rd:74): Warning: <h5> anchor "Arguments" already defined
MzQCcontrolledVocabulary.html:147:1 (MzQCcontrolledVocabulary.Rd:87): Warning: <h5> anchor "Usage" already defined
MzQCcontrolledVocabulary.html:153:1 (MzQCcontrolledVocabulary.Rd:91): Warning: <h5> anchor "Arguments" already defined
MzQCcontrolledVocabulary.html:176:1 (MzQCcontrolledVocabulary.Rd:104): Warning: <h5> anchor "Usage" already defined
MzQCcontrolledVocabulary.html:182:1 (MzQCcontrolledVocabulary.Rd:108): Warning: <h5> anchor "Arguments" already defined
MzQCcontrolledVocabulary.html:207:1 (MzQCcontrolledVocabulary.Rd:123): Warning: <h5> anchor "Usage" already defined
MzQCcontrolledVocabulary.html:213:1 (MzQCcontrolledVocabulary.Rd:127): Warning: <h5> anchor "Arguments" already defined
MzQCcvParameter.html:123:1 (MzQCcvParameter.Rd:75): Warning: <h5> anchor "Usage" already defined
MzQCcvParameter.html:129:1 (MzQCcvParameter.Rd:79): Warning: <h5> anchor "Arguments" already defined
MzQCcvParameter.html:152:1 (MzQCcvParameter.Rd:92): Warning: <h5> anchor "Usage" already defined
MzQCcvParameter.html:158:1 (MzQCcvParameter.Rd:96): Warning: <h5> anchor "Arguments" already defined
MzQCcvParameter.html:181:1 (MzQCcvParameter.Rd:109): Warning: <h5> anchor "Usage" already defined
MzQCcvParameter.html:187:1 (MzQCcvParameter.Rd:113): Warning: <h5> anchor "Arguments" already defined
MzQCcvParameter.html:212:1 (MzQCcvParameter.Rd:128): Warning: <h5> anchor "Usage" already defined
MzQCcvParameter.html:218:1 (MzQCcvParameter.Rd:132): Warning: <h5> anchor "Arguments" already defined
MzQCinputFile.html:236:1 (MzQCinputFile.Rd:133): Warning: missing </ul> before </div>
MzQCinputFile.html:124:1 (MzQCinputFile.Rd:69): Warning: <h5> anchor "Usage" already defined
MzQCinputFile.html:130:1 (MzQCinputFile.Rd:73): Warning: <h5> anchor "Arguments" already defined
MzQCinputFile.html:153:1 (MzQCinputFile.Rd:86): Warning: <h5> anchor "Usage" already defined
MzQCinputFile.html:159:1 (MzQCinputFile.Rd:90): Warning: <h5> anchor "Arguments" already defined
MzQCinputFile.html:182:1 (MzQCinputFile.Rd:103): Warning: <h5> anchor "Usage" already defined
MzQCinputFile.html:188:1 (MzQCinputFile.Rd:107): Warning: <h5> anchor "Arguments" already defined
MzQCinputFile.html:213:1 (MzQCinputFile.Rd:122): Warning: <h5> anchor "Usage" already defined
MzQCinputFile.html:219:1 (MzQCinputFile.Rd:126): Warning: <h5> anchor "Arguments" already defined
MzQCmetadata.html:235:1 (MzQCmetadata.Rd:132): Warning: missing </ul> before </div>
MzQCmetadata.html:123:1 (MzQCmetadata.Rd:68): Warning: <h5> anchor "Usage" already defined
MzQCmetadata.html:129:1 (MzQCmetadata.Rd:72): Warning: <h5> anchor "Arguments" already defined
MzQCmetadata.html:152:1 (MzQCmetadata.Rd:85): Warning: <h5> anchor "Usage" already defined
MzQCmetadata.html:158:1 (MzQCmetadata.Rd:89): Warning: <h5> anchor "Arguments" already defined
MzQCmetadata.html:181:1 (MzQCmetadata.Rd:102): Warning: <h5> anchor "Usage" already defined
MzQCmetadata.html:187:1 (MzQCmetadata.Rd:106): Warning: <h5> anchor "Arguments" already defined
MzQCmetadata.html:212:1 (MzQCmetadata.Rd:121): Warning: <h5> anchor "Usage" already defined
MzQCmetadata.html:218:1 (MzQCmetadata.Rd:125): Warning: <h5> anchor "Arguments" already defined
MzQCmzQC.html:261:1 (MzQCmzQC.Rd:155): Warning: missing </ul> before </div>
MzQCmzQC.html:149:1 (MzQCmzQC.Rd:91): Warning: <h5> anchor "Usage" already defined
MzQCmzQC.html:155:1 (MzQCmzQC.Rd:95): Warning: <h5> anchor "Arguments" already defined
MzQCmzQC.html:178:1 (MzQCmzQC.Rd:108): Warning: <h5> anchor "Usage" already defined
MzQCmzQC.html:184:1 (MzQCmzQC.Rd:112): Warning: <h5> anchor "Arguments" already defined
MzQCmzQC.html:207:1 (MzQCmzQC.Rd:125): Warning: <h5> anchor "Usage" already defined
MzQCmzQC.html:213:1 (MzQCmzQC.Rd:129): Warning: <h5> anchor "Arguments" already defined
MzQCmzQC.html:238:1 (MzQCmzQC.Rd:144): Warning: <h5> anchor "Usage" already defined
MzQCmzQC.html:244:1 (MzQCmzQC.Rd:148): Warning: <h5> anchor "Arguments" already defined
MzQCqualityMetric.html:241:1 (MzQCqualityMetric.Rd:138): Warning: missing </ul> before </div>
MzQCqualityMetric.html:129:1 (MzQCqualityMetric.Rd:74): Warning: <h5> anchor "Usage" already defined
MzQCqualityMetric.html:135:1 (MzQCqualityMetric.Rd:78): Warning: <h5> anchor "Arguments" already defined
MzQCqualityMetric.html:158:1 (MzQCqualityMetric.Rd:91): Warning: <h5> anchor "Usage" already defined
MzQCqualityMetric.html:164:1 (MzQCqualityMetric.Rd:95): Warning: <h5> anchor "Arguments" already defined
MzQCqualityMetric.html:187:1 (MzQCqualityMetric.Rd:108): Warning: <h5> anchor "Usage" already defined
MzQCqualityMetric.html:193:1 (MzQCqualityMetric.Rd:112): Warning: <h5> anchor "Arguments" already defined
MzQCqualityMetric.html:218:1 (MzQCqualityMetric.Rd:127): Warning: <h5> anchor "Usage" already defined
MzQCqualityMetric.html:224:1 (MzQCqualityMetric.Rd:131): Warning: <h5> anchor "Arguments" already defined
MzQCrunQuality.html:91:1 (MzQCrunQuality.Rd:46): Warning: missing </ul> before </div>
MzQCsetQuality.html:92:1 (MzQCsetQuality.Rd:47): Warning: missing </ul> before </div>