• using R Under development (unstable) (2025-10-19 r88945)
• using platform: x86_64-pc-linux-gnu
• R was compiled by     gcc-15 (Debian 15.2.0-4) 15.2.0     GNU Fortran (Debian 15.2.0-4) 15.2.0
• running under: Debian GNU/Linux forky/sid
• using session charset: UTF-8
• checking for file ‘pagoda2/DESCRIPTION’ ... OK
• this is package ‘pagoda2’ version ‘1.0.13’
• 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 whether package ‘pagoda2’ can be installed ... OK See the install log for details.
• used C++ compiler: ‘g++-15 (Debian 15.2.0-4) 15.2.0’
• checking package directory ... OK
• checking for future file timestamps ... 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 ... [3s/3s] OK
• checking whether the package can be loaded with stated dependencies ... [3s/3s] OK
• checking whether the package can be unloaded cleanly ... [3s/4s] OK
• checking whether the namespace can be loaded with stated dependencies ... [2s/3s] OK
• checking whether the namespace can be unloaded cleanly ... [3s/3s] OK
• checking loading without being on the library search path ... [3s/3s] 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 ... [19s/25s] 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 line endings in C/C++/Fortran sources/headers ... OK
• checking line endings in Makefiles ... OK
• checking compilation flags in Makevars ... OK
• checking for GNU extensions in Makefiles ... OK
• checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
• checking use of PKG_*FLAGS in Makefiles ... OK
• checking use of SHLIB_OPENMP_*FLAGS in Makefiles ... OK
• checking pragmas in C/C++ headers and code ... OK
• checking compilation flags used ... OK
• checking compiled code ... OK
• checking examples ... [3s/3s] OK
• checking for unstated dependencies in ‘tests’ ... OK
• checking tests ... [3s/4s] OK   Running ‘testthat.R’ [3s/4s]
• checking PDF version of manual ... [7s/9s] OK
• checking HTML version of manual ... [3s/4s] NOTE Found the following HTML validation problems: Pagoda2.html:237:1 (Pagoda2.Rd:199): Warning: <h5> anchor "Usage" already defined Pagoda2.html:253:1 (Pagoda2.Rd:213): Warning: <h5> anchor "Arguments" already defined Pagoda2.html:282:1 (Pagoda2.Rd:236): Warning: <h5> anchor "Returns" already defined Pagoda2.html:300:1 (Pagoda2.Rd:246): Warning: <h5> anchor "Usage" already defined Pagoda2.html:320:1 (Pagoda2.Rd:264): Warning: <h5> anchor "Arguments" already defined Pagoda2.html:357:1 (Pagoda2.Rd:295): Warning: <h5> anchor "Returns" already defined Pagoda2.html:364:1 (Pagoda2.Rd:298): Warning: <h5> anchor "Examples" already defined Pagoda2.html:394:1 (Pagoda2.Rd:323): Warning: <h5> anchor "Usage" already defined Pagoda2.html:413:1 (Pagoda2.Rd:340): Warning: <h5> anchor "Arguments" already defined Pagoda2.html:448:1 (Pagoda2.Rd:369): Warning: <h5> anchor "Returns" already defined Pagoda2.html:455:1 (Pagoda2.Rd:372): Warning: <h5> anchor "Examples" already defined Pagoda2.html:487:1 (Pagoda2.Rd:399): Warning: <h5> anchor "Usage" already defined Pagoda2.html:502:1 (Pagoda2.Rd:412): Warning: <h5> anchor "Arguments" already defined Pagoda2.html:530:1 (Pagoda2.Rd:434): Warning: <h5> anchor "Returns" already defined Pagoda2.html:547:1 (Pagoda2.Rd:443): Warning: <h5> anchor "Usage" already defined Pagoda2.html:563:1 (Pagoda2.Rd:453): Warning: <h5> anchor "Usage" already defined Pagoda2.html:580:1 (Pagoda2.Rd:468): Warning: <h5> anchor "Arguments" already defined Pagoda2.html:611:1 (Pagoda2.Rd:493): Warning: <h5> anchor "Returns" already defined Pagoda2.html:628:1 (Pagoda2.Rd:502): Warning: <h5> anchor "Usage" already defined Pagoda2.html:642:1 (Pagoda2.Rd:514): Warning: <h5> anchor "Arguments" already defined Pagoda2.html:667:1 (Pagoda2.Rd:533): Warning: <h5> anchor "Returns" already defined Pagoda2.html:684:1 (Pagoda2.Rd:542): Warning: <h5> anchor "Usage" already defined Pagoda2.html:699:1 (Pagoda2.Rd:555): Warning: <h5> anchor "Arguments" already defined Pagoda2.html:726:1 (Pagoda2.Rd:576): Warning: <h5> anchor "Returns" already defined Pagoda2.html:743:1 (Pagoda2.Rd:585): Warning: <h5> anchor "Usage" already defined Pagoda2.html:759:1 (Pagoda2.Rd:599): Warning: <h5> anchor "Arguments" already defined Pagoda2.html:788:1 (Pagoda2.Rd:622): Warning: <h5> anchor "Returns" already defined Pagoda2.html:810:1 (Pagoda2.Rd:636): Warning: <h5> anchor "Usage" already defined Pagoda2.html:830:1 (Pagoda2.Rd:654): Warning: <h5> anchor "Arguments" already defined Pagoda2.html:867:1 (Pagoda2.Rd:685): Warning: <h5> anchor "Returns" already defined Pagoda2.html:884:1 (Pagoda2.Rd:694): Warning: <h5> anchor "Usage" already defined Pagoda2.html:895:1 (Pagoda2.Rd:703): Warning: <h5> anchor "Arguments" already defined Pagoda2.html:914:1 (Pagoda2.Rd:716): Warning: <h5> anchor "Returns" already defined Pagoda2.html:931:1 (Pagoda2.Rd:725): Warning: <h5> anchor "Usage" already defined Pagoda2.html:953:1 (Pagoda2.Rd:745): Warning: <h5> anchor "Arguments" already defined Pagoda2.html:994:1 (Pagoda2.Rd:780): Warning: <h5> anchor "Returns" already defined Pagoda2.html:1011:1 (Pagoda2.Rd:789): Warning: <h5> anchor "Usage" already defined Pagoda2.html:1026:1 (Pagoda2.Rd:802): Warning: <h5> anchor "Arguments" already defined Pagoda2.html:1053:1 (Pagoda2.Rd:823): Warning: <h5> anchor "Returns" already defined Pagoda2.html:1070:1 (Pagoda2.Rd:832): Warning: <h5> anchor "Usage" already defined Pagoda2.html:1080:1 (Pagoda2.Rd:840): Warning: <h5> anchor "Arguments" already defined Pagoda2.html:1097:1 (Pagoda2.Rd:851): Warning: <h5> anchor "Returns" already defined Pagoda2.html:1114:1 (Pagoda2.Rd:860): Warning: <h5> anchor "Usage" already defined Pagoda2.html:1120:1 (Pagoda2.Rd:864): Warning: <h5> anchor "Arguments" already defined Pagoda2.html:1135:1 (Pagoda2.Rd:873): Warning: <h5> anchor "Returns" already defined Pagoda2.html:1152:1 (Pagoda2.Rd:882): Warning: <h5> anchor "Usage" already defined Pagoda2.html:1172:1 (Pagoda2.Rd:900): Warning: <h5> anchor "Arguments" already defined Pagoda2.html:1209:1 (Pagoda2.Rd:931): Warning: <h5> anchor "Returns" already defined Pagoda2.html:1227:1 (Pagoda2.Rd:941): Warning: <h5> anchor "Usage" already defined Pagoda2.html:1249:1 (Pagoda2.Rd:961): Warning: <h5> anchor "Arguments" already defined Pagoda2.html:1290:1 (Pagoda2.Rd:996): Warning: <h5> anchor "Returns" already defined Pagoda2.html:1307:1 (Pagoda2.Rd:1005): Warning: <h5> anchor "Usage" already defined Pagoda2.html:1335:1 (Pagoda2.Rd:1031): Warning: <h5> anchor "Arguments" already defined Pagoda2.html:1388:1 (Pagoda2.Rd:1078): Warning: <h5> anchor "Returns" already defined Pagoda2.html:1406:1 (Pagoda2.Rd:1088): Warning: <h5> anchor "Usage" already defined Pagoda2.html:1433:1 (Pagoda2.Rd:1113): Warning: <h5> anchor "Arguments" already defined Pagoda2.html:1484:1 (Pagoda2.Rd:1158): Warning: <h5> anchor "Returns" already defined Pagoda2.html:1501:1 (Pagoda2.Rd:1167): Warning: <h5> anchor "Usage" already defined Pagoda2.html:1523:1 (Pagoda2.Rd:1187): Warning: <h5> anchor "Arguments" already defined Pagoda2.html:1565:1 (Pagoda2.Rd:1223): Warning: <h5> anchor "Returns" already defined Pagoda2.html:1582:1 (Pagoda2.Rd:1232): Warning: <h5> anchor "Usage" already defined Pagoda2.html:1588:1 (Pagoda2.Rd:1236): Warning: <h5> anchor "Arguments" already defined diffExprOnP2FromWebSelection.html:60:1 (diffExprOnP2FromWebSelection.Rd:17): Warning: missing </ul> before </div> diffExprOnP2FromWebSelectionOneGroup.html:56:1 (diffExprOnP2FromWebSelectionOneGroup.Rd:15): Warning: missing </ul> before </div> dot-onUnload.html:46:1 (dot-onUnload.Rd:10): Warning: missing </ul> before </div> p2.generate.dr.go.web.html:50:1 (p2.generate.dr.go.web.Rd:12): Warning: missing </ul> before </div> p2.generate.go.html:69:1 (p2.generate.go.Rd:25): Warning: missing </ul> before </div> p2.generate.go.web.html:63:1 (p2.generate.go.web.Rd:21): Warning: missing </ul> before </div> p2.generate.go.web.fromGOEnv.html:46:1 (p2.generate.go.web.fromGOEnv.Rd:10): Warning: missing </ul> before </div> p2.generate.human.go.web.html:50:1 (p2.generate.human.go.web.Rd:12): Warning: missing </ul> before </div> p2.generate.mouse.go.web.html:50:1 (p2.generate.mouse.go.web.Rd:12): Warning: missing </ul> before </div> p2ViewPagodaApp.html:257:1 (p2ViewPagodaApp.Rd:155): Warning: missing </ul> before </div> p2ViewPagodaApp.html:158:1 (p2ViewPagodaApp.Rd:100): Warning: <h5> anchor "Usage" already defined p2ViewPagodaApp.html:164:1 (p2ViewPagodaApp.Rd:104): Warning: <h5> anchor "Arguments" already defined p2ViewPagodaApp.html:181:1 (p2ViewPagodaApp.Rd:115): Warning: <h5> anchor "Returns" already defined p2ViewPagodaApp.html:198:1 (p2ViewPagodaApp.Rd:124): Warning: <h5> anchor "Usage" already defined p2ViewPagodaApp.html:204:1 (p2ViewPagodaApp.Rd:128): Warning: <h5> anchor "Arguments" already defined p2ViewPagodaApp.html:217:1 (p2ViewPagodaApp.Rd:135): Warning: <h5> anchor "Returns" already defined p2ViewPagodaApp.html:234:1 (p2ViewPagodaApp.Rd:144): Warning: <h5> anchor "Usage" already defined p2ViewPagodaApp.html:240:1 (p2ViewPagodaApp.Rd:148): Warning: <h5> anchor "Arguments" already defined pagoda2WebApp_call.html:40:1 (pagoda2WebApp_call.Rd:7): Warning: missing </ul> before </div> readPagoda2SelectionFile.html:50:1 (readPagoda2SelectionFile.Rd:12): Warning: missing </ul> before </div>
• checking for non-standard things in the check directory ... OK
• DONE

Status: 1 NOTE