• using R Under development (unstable) (2025-10-19 r88945)
• using platform: x86_64-pc-linux-gnu
• R was compiled by     Debian clang version 19.1.7 (7)     Debian flang-new version 19.1.7 (7)
• running under: Debian GNU/Linux forky/sid
• using session charset: UTF-8
• checking for file ‘rmzqc/DESCRIPTION’ ... OK
• this is package ‘rmzqc’ version ‘0.7.0’
• package encoding: UTF-8
• checking CRAN incoming feasibility ... [1s/2s] OK
• 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 executable files ... OK
• checking for hidden files and directories ... OK
• checking for portable file names ... OK
• checking for sufficient/correct file permissions ... OK
• checking serialization versions ... OK
• checking whether package ‘rmzqc’ can be installed ... OK See the install log for details.
• checking package directory ... OK
• checking for future file timestamps ... 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 code files for non-ASCII characters ... OK
• checking R files for syntax errors ... OK
• checking whether the package can be loaded ... [1s/1s] OK
• checking whether the package can be loaded with stated dependencies ... [1s/1s] OK
• checking whether the package can be unloaded cleanly ... [1s/1s] OK
• checking whether the namespace can be loaded with stated dependencies ... [0s/1s] OK
• checking whether the namespace can be unloaded cleanly ... [1s/1s] OK
• checking loading without being on the library search path ... [1s/1s] OK
• checking use of S3 registration ... 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 ... [6s/9s] OK
• checking Rd files ... [1s/1s] OK
• checking Rd metadata ... OK
• checking Rd line widths ... 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 installed files from ‘inst/doc’ ... OK
• checking files in ‘vignettes’ ... OK
• checking examples ... [5s/9s] OK Examples with CPU (user + system) or elapsed time > 5s                     user system elapsed toAnalysisSoftware 3.891 0.223 7.41
• checking for unstated dependencies in ‘tests’ ... OK
• checking tests ... [16s/21s] OK   Running ‘testthat.R’ [16s/20s]
• checking for unstated dependencies in vignettes ... OK
• checking package vignettes ... OK
• checking re-building of vignette outputs ... [22s/28s] OK
• checking PDF version of manual ... [7s/10s] OK
• checking HTML version of manual ... [3s/4s] NOTE 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>
• checking for non-standard things in the check directory ... OK
• DONE

Status: 1 NOTE