* using log directory 'd:/RCompile/CRANincoming/R-devel/sffdr.Rcheck'
* using R Under development (unstable) (2024-11-19 r87348 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 'sffdr/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'sffdr' version '1.0.0'
* package encoding: UTF-8
* checking CRAN incoming feasibility ... [17s] NOTE
Maintainer: 'Andrew Bass <ab3105@cam.ac.uk>'

New submission

Possibly misspelled words in DESCRIPTION:
  GWAS (9:236, 9:591)
  Pleiotropy (9:14)
  colocalization (9:629)
  fFDR (9:180)
  sfFDR (9:140, 9:152, 9:335)

Found the following \keyword or \concept entries
which likely give several index terms:
  File 'bmi.Rd':
    \keyword{dataset,}
* 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 'sffdr' can be installed ... OK
* 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 '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 ... 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 ... NOTE
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  fpi0est.Rd: gam.control, gam
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
* 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 pragmas in C/C++ headers and code ... OK
* checking compilation flags used ... OK
* checking compiled code ... OK
* checking installed files from 'inst/doc' ... OK
* checking files in 'vignettes' ... OK
* checking examples ... [208s] NOTE
Examples with CPU (user + system) or elapsed time > 10s
            user system elapsed
plot.sffdr 43.69   8.43   52.19
bmi        44.61   7.39   52.03
fpi0est    42.08   9.48   51.60
sffdr      41.72   7.73   49.54
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking re-building of vignette outputs ... [86s] OK
* checking PDF version of manual ... [20s] OK
* checking HTML version of manual ... OK
* DONE
Status: 3 NOTEs