* using log directory ‘/data/gannet/ripley/R/packages/tests-clang/pould.Rcheck’
* using R Under development (unstable) (2025-02-17 r87732)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    clang version 20.1.0-rc2
    flang version 20.1.0-rc2
* running under: Fedora Linux 40 (Workstation Edition)
* using session charset: UTF-8
* using option ‘--no-stop-on-test-error’
* checking for file ‘pould/DESCRIPTION’ ... OK
* this is package ‘pould’ version ‘1.0.1’
* package encoding: UTF-8
* 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 ‘pould’ can be installed ... [22s/33s] OK
See 'https://www.r-project.org/nosvn/R.check/r-devel-linux-x86_64-fedora-clang/pould-00install.html' for details.
* checking installed package size ... OK
* checking package directory ... 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 ... [6s/11s] 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 ... [30s/46s] OK
* checking Rd files ... NOTE
checkRd: (-1) LD.heat.map.Rd:5: Lost braces; missing escapes or markup?
     5 | \title{Generates heat-maps for four linkage disequilibrium (LD) values ({D'}, {Wn}, {WLoc1/Loc2} and {WLoc2/Loc1}) generated for all pairs of phased and unphased two-locus haplotypes by LDWrap().}
       |                                                                         ^
checkRd: (-1) LD.heat.map.Rd:5: Lost braces; missing escapes or markup?
     5 | \title{Generates heat-maps for four linkage disequilibrium (LD) values ({D'}, {Wn}, {WLoc1/Loc2} and {WLoc2/Loc1}) generated for all pairs of phased and unphased two-locus haplotypes by LDWrap().}
       |                                                                               ^
checkRd: (-1) LD.heat.map.Rd:5: Lost braces; missing escapes or markup?
     5 | \title{Generates heat-maps for four linkage disequilibrium (LD) values ({D'}, {Wn}, {WLoc1/Loc2} and {WLoc2/Loc1}) generated for all pairs of phased and unphased two-locus haplotypes by LDWrap().}
       |                                                                                     ^
checkRd: (-1) LD.heat.map.Rd:5: Lost braces; missing escapes or markup?
     5 | \title{Generates heat-maps for four linkage disequilibrium (LD) values ({D'}, {Wn}, {WLoc1/Loc2} and {WLoc2/Loc1}) generated for all pairs of phased and unphased two-locus haplotypes by LDWrap().}
       |                                                                                                      ^
checkRd: (-1) LD.sign.test.Rd:27: Lost braces; missing escapes or markup?
    27 | Applies binom.test() to pairs of {D'}, {Wn}, {WLoc1/Loc2}, {WLoc2/Loc1} and number of haplotypes values in the *_LD_results.csv files generated by LDWrap().
       |                                  ^
checkRd: (-1) LD.sign.test.Rd:27: Lost braces; missing escapes or markup?
    27 | Applies binom.test() to pairs of {D'}, {Wn}, {WLoc1/Loc2}, {WLoc2/Loc1} and number of haplotypes values in the *_LD_results.csv files generated by LDWrap().
       |                                        ^
checkRd: (-1) LD.sign.test.Rd:27: Lost braces; missing escapes or markup?
    27 | Applies binom.test() to pairs of {D'}, {Wn}, {WLoc1/Loc2}, {WLoc2/Loc1} and number of haplotypes values in the *_LD_results.csv files generated by LDWrap().
       |                                              ^
checkRd: (-1) LD.sign.test.Rd:27: Lost braces; missing escapes or markup?
    27 | Applies binom.test() to pairs of {D'}, {Wn}, {WLoc1/Loc2}, {WLoc2/Loc1} and number of haplotypes values in the *_LD_results.csv files generated by LDWrap().
       |                                                            ^
checkRd: (-1) LD.sign.test.Rd:24: Lost braces; missing escapes or markup?
    24 | A data frame of five columns ({D'}, {Wn}, {WLoc1/Loc2}, {WLoc2/Loc1} and N_Haplotypes) and four rows (#unphased > phased, #unphased = phased, #locus pairs and p-values).
       |                               ^
checkRd: (-1) LD.sign.test.Rd:24: Lost braces; missing escapes or markup?
    24 | A data frame of five columns ({D'}, {Wn}, {WLoc1/Loc2}, {WLoc2/Loc1} and N_Haplotypes) and four rows (#unphased > phased, #unphased = phased, #locus pairs and p-values).
       |                                     ^
checkRd: (-1) LD.sign.test.Rd:24: Lost braces; missing escapes or markup?
    24 | A data frame of five columns ({D'}, {Wn}, {WLoc1/Loc2}, {WLoc2/Loc1} and N_Haplotypes) and four rows (#unphased > phased, #unphased = phased, #locus pairs and p-values).
       |                                           ^
checkRd: (-1) LD.sign.test.Rd:24: Lost braces; missing escapes or markup?
    24 | A data frame of five columns ({D'}, {Wn}, {WLoc1/Loc2}, {WLoc2/Loc1} and N_Haplotypes) and four rows (#unphased > phased, #unphased = phased, #locus pairs and p-values).
       |                                                         ^
checkRd: (-1) cALD.Rd:33: Lost braces; missing escapes or markup?
    33 | A vector of {D'}, {Wn}, {WLocus2/Locus1}, {WLocus1/Locus2} values, and the number of haplotypes evaluated
       |             ^
checkRd: (-1) cALD.Rd:33: Lost braces; missing escapes or markup?
    33 | A vector of {D'}, {Wn}, {WLocus2/Locus1}, {WLocus1/Locus2} values, and the number of haplotypes evaluated
       |                   ^
checkRd: (-1) cALD.Rd:33: Lost braces; missing escapes or markup?
    33 | A vector of {D'}, {Wn}, {WLocus2/Locus1}, {WLocus1/Locus2} values, and the number of haplotypes evaluated
       |                         ^
checkRd: (-1) cALD.Rd:33: Lost braces; missing escapes or markup?
    33 | A vector of {D'}, {Wn}, {WLocus2/Locus1}, {WLocus1/Locus2} values, and the number of haplotypes evaluated
       |                                           ^
* 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 installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [12s/19s] OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... [7s/12s] OK
* checking HTML version of manual ... OK
* checking for non-standard things in the check directory ... OK
* checking for detritus in the temp directory ... OK
* DONE
Status: 1 NOTE