CRAN submission needs work

[scharlton2]

* using log directory 'd:/RCompile/CRANincoming/R-devel/phreeqc.Rcheck'
* using R Under development (unstable) (2024-11-21 r87360 ucrt)
* using platform: x86_64-w64-mingw32
* R was compiled by
    gcc.exe (GCC) 13.3.0
    GNU Fortran (GCC) 13.3.0
* running under: Windows Server 2022 x64 (build 20348)
* using session charset: UTF-8
* checking for file 'phreeqc/DESCRIPTION' ... OK
* this is package 'phreeqc' version '3.8.5'
* package encoding: UTF-8
* checking CRAN incoming feasibility ... [11s] NOTE
Maintainer: 'S.R. Charlton <[email protected]>'

Found the following (possibly) invalid URLs:
  URL: https://water.usgs.gov/water-resources/software/PHREEQC/IPhreeqc.pdf
    From: man/phrAccumulateLine.Rd
          man/phrClearAccumulatedLines.Rd
          man/phrGetAccumulatedLines.Rd
          man/phrGetComponentList.Rd
          man/phrGetDumpFileName.Rd
          man/phrGetDumpFileOn.Rd
          man/phrGetDumpStrings.Rd
          man/phrGetDumpStringsOn.Rd
          man/phrGetErrorFileName.Rd
          man/phrGetErrorFileOn.Rd
          man/phrGetErrorStrings.Rd
          man/phrGetErrorStringsOn.Rd
          man/phrGetLogFileName.Rd
          man/phrGetLogFileOn.Rd
          man/phrGetLogStrings.Rd
          man/phrGetOutputFileName.Rd
          man/phrGetOutputFileOn.Rd
          man/phrGetOutputStrings.Rd
          man/phrGetOutputStringsOn.Rd
          man/phrGetSelectedOutput.Rd
          man/phrGetSelectedOutputFileName.Rd
          man/phrGetWarningStrings.Rd
          man/phrLoadDatabase.Rd
          man/phrLoadDatabaseString.Rd
          man/phrRunAccumulated.Rd
          man/phrRunFile.Rd
          man/phrRunString.Rd
          man/phrSetDumpFileName.Rd
          man/phrSetDumpFileOn.Rd
          man/phrSetDumpStringsOn.Rd
          man/phrSetErrorFileName.Rd
          man/phrSetErrorFileOn.Rd
          man/phrSetErrorStringsOn.Rd
          man/phrSetLogFileName.Rd
          man/phrSetLogFileOn.Rd
          man/phrSetLogStringsOn.Rd
          man/phrSetOutputFileName.Rd
          man/phrSetOutputFileOn.Rd
          man/phrSetOutputStringsOn.Rd
          man/phrSetSelectedOutputFileName.Rd
          man/phrSetSelectedOutputFileOn.Rd
          man/phreeqc-package.Rd
    Status: 404
    Message: Not Found
  URL: https://wwwbrr.cr.usgs.gov/projects/GWC_coupled/phreeqc
    From: man/Amm.dat.Rd
          man/ColdChem.dat.Rd
          man/Kinec.v2.dat.Rd
          man/Kinec_v3.dat.Rd
          man/PHREEQC_ThermoddemV1.10_15Dec2020.dat.Rd
          man/ex1.Rd
          man/ex10.Rd
          man/ex11.Rd
          man/ex12.Rd
          man/ex13.Rd
          man/ex14.Rd
          man/ex15.Rd
          man/ex15.dat.Rd
          man/ex16.Rd
          man/ex17.Rd
          man/ex18.Rd
          man/ex19.Rd
          man/ex2.Rd
          man/ex20.Rd
          man/ex21.Rd
          man/ex22.Rd
          man/ex3.Rd
          man/ex4.Rd
          man/ex5.Rd
          man/ex6.Rd
          man/ex7.Rd
          man/ex8.Rd
          man/ex9.Rd
          man/iso.dat.Rd
          man/minteq.dat.Rd
          man/minteq.v4.dat.Rd
          man/phrGetLogStringsOn.Rd
          man/phreeqc.dat.Rd
          man/phreeqc_rates.dat.Rd
          man/pitzer.dat.Rd
          man/sit.dat.Rd
          man/wateq4f.dat.Rd
    Status: 404
    Message: Not Found
* 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 hidden files and directories ... OK
* checking for portable file names ... OK
* checking whether package 'phreeqc' can be installed ... OK
* used C compiler: 'gcc.exe (GCC) 13.3.0'
* used C++ compiler: 'g++.exe (GCC) 13.3.0'
* checking installed package size ... OK
* checking package directory ... OK
* checking for future file timestamps ... OK
* checking DESCRIPTION meta-information ... NOTE
Author field differs from that derived from Authors@R
  Author:    'S.R. Charlton [aut, cre], D.L. Parkhurst [aut], and C.A.J. Appelo [aut], with contributions from D. Gillespie [ctb] for Chipmunk BASIC and S.D. Cohen [ctb], A.C. Hindmarsh [ctb], R. Serban [ctb], D. Shumaker [ctb], and A.G. Taylor [ctb] for CVODE/SUNDIALS'
  Authors@R: 'S.R. Charlton [aut, cre]'

* 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 ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking loading without being on the library search path ... 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 ... OK
* checking Rd files ... 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 contents of 'data' directory ... OK
* checking data for non-ASCII characters ... OK
* checking LazyData ... OK
* checking data for ASCII and uncompressed saves ... 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 ... OK
* checking PDF version of manual ... [21s] OK
* checking HTML version of manual ... [12s] OK
* DONE
Status: 2 NOTEs