* using log directory ‘/srv/hornik/tmp/CRAN_pretest/pagoda2.Rcheck’
* using R Under development (unstable) (2025-08-17 r88631)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    Debian clang version 19.1.7 (3+b1)
    Debian flang-new version 19.1.7 (3+b1)
* 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 ... [5s/5s] 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 ... [53s/53s] OK
* used C++ compiler: ‘Debian clang version 19.1.7 (3+b1)’
* 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 ... [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 ... [1s/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 ... [11s/11s] OK
* checking Rd files ... [0s/0s] 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 ... [2s/2s] OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ... [2s/2s] OK
  Running ‘testthat.R’ [2s/2s]
* checking PDF version of manual ... [4s/4s] OK
* checking HTML version of manual ... [2s/2s] NOTE
Found the following HTML validation problems:
p2ViewPagodaApp.html:83:1 (p2ViewPagodaApp.Rd:47): Warning: <a> attribute "id" has invalid value "method-p2ViewPagodaApp -new"
p2ViewPagodaApp.html:148:1 (p2ViewPagodaApp.Rd:96): Warning: <a> attribute "id" has invalid value "method-p2ViewPagodaApp -getgenecldata"
p2ViewPagodaApp.html:188:1 (p2ViewPagodaApp.Rd:120): Warning: <a> attribute "id" has invalid value "method-p2ViewPagodaApp -call"
p2ViewPagodaApp.html:224:1 (p2ViewPagodaApp.Rd:140): Warning: <a> attribute "id" has invalid value "method-p2ViewPagodaApp -clone"
* checking for non-standard things in the check directory ... OK
* checking for detritus in the temp directory ... OK
* DONE
Status: 1 NOTE