- 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
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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
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Pagoda2.html:1290:1 (Pagoda2.Rd:996): Warning: <h5> anchor "Returns" already defined
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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
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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