* using log directory ‘/home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/ftrCOOL.Rcheck’
* using R Under development (unstable) (2025-02-26 r87830)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    Debian clang version 19.1.7 (1+b1)
    Debian flang-new version 19.1.7 (1+b1)
* running under: Debian GNU/Linux trixie/sid
* using session charset: UTF-8
* checking for file ‘ftrCOOL/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘ftrCOOL’ version ‘2.0.0’
* 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 serialization versions ... OK
* checking whether package ‘ftrCOOL’ can be installed ... OK
See 'https://www.r-project.org/nosvn/R.check/r-devel-linux-x86_64-debian-clang/ftrCOOL-00install.html' for details.
* 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 ... [0s/0s] OK
* checking whether the package can be loaded with stated dependencies ... [0s/0s] OK
* checking whether the package can be unloaded cleanly ... [0s/0s] OK
* checking whether the namespace can be loaded with stated dependencies ... [0s/0s] OK
* checking whether the namespace can be unloaded cleanly ... [0s/0s] OK
* checking loading without being on the library search path ... [0s/0s] 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 ... [62s/76s] OK
* checking Rd files ... [1s/2s] NOTE
checkRd: (-1) MMI_DNA.Rd:20: Lost braces; missing escapes or markup?
    20 | MMI computes mutual information based on 2-mers T2 = { AA, AC, AG, AT, CC, CG, CT, GG, GT, TT}
       |                                                      ^
checkRd: (-1) MMI_DNA.Rd:21: Lost braces; missing escapes or markup?
    21 | and 3-mers T3 = {AAA, AAC, AAG, AAT, ACC, ACG, ACT, AGG, AGT, ATT, CCC, CCG, CCT, CGG, CGT, CTT, GGG, GGT, GTT and TTT}
       |                 ^
checkRd: (-1) MMI_RNA.Rd:20: Lost braces; missing escapes or markup?
    20 | MMI computes mutual information based on 2-mers T2 = { AA, AC, AG, AU, CC, CG, CU, GG, GU, U}
       |                                                      ^
checkRd: (-1) MMI_RNA.Rd:21: Lost braces; missing escapes or markup?
    21 | and 3-mers T3 = {AAA, AAC, AAG, AAU, ACC, ACG, ACU, AGG, AGU, AUU, CCC, CCG, CCU, CGG, CGU, CUU, GGG, GGU, GUU and UUU}
       |                 ^
checkRd: (-1) binary_5bit_T1.Rd:40: Lost braces; missing escapes or markup?
    40 | Then represent group of amino acids by a 5 dimentional vector i.e.{e1, e2, e3, e4, e5}.
       |                                                                   ^
checkRd: (-1) binary_5bit_T1.Rd:41: Lost braces; missing escapes or markup?
    41 | e1={G, A, V, L, M, I}, e2={F, Y, W}, e3={K, R, H}, e4={D, E}, e5={S, T, C, P, N, Q}. e1 is ecoded by 10000
       |    ^
checkRd: (-1) binary_5bit_T1.Rd:41: Lost braces; missing escapes or markup?
    41 | e1={G, A, V, L, M, I}, e2={F, Y, W}, e3={K, R, H}, e4={D, E}, e5={S, T, C, P, N, Q}. e1 is ecoded by 10000
       |                           ^
checkRd: (-1) binary_5bit_T1.Rd:41: Lost braces; missing escapes or markup?
    41 | e1={G, A, V, L, M, I}, e2={F, Y, W}, e3={K, R, H}, e4={D, E}, e5={S, T, C, P, N, Q}. e1 is ecoded by 10000
       |                                         ^
checkRd: (-1) binary_5bit_T1.Rd:41: Lost braces; missing escapes or markup?
    41 | e1={G, A, V, L, M, I}, e2={F, Y, W}, e3={K, R, H}, e4={D, E}, e5={S, T, C, P, N, Q}. e1 is ecoded by 10000
       |                                                       ^
checkRd: (-1) binary_5bit_T1.Rd:41: Lost braces; missing escapes or markup?
    41 | e1={G, A, V, L, M, I}, e2={F, Y, W}, e3={K, R, H}, e4={D, E}, e5={S, T, C, P, N, Q}. e1 is ecoded by 10000
       |                                                                  ^
checkRd: (-1) binary_6bit.Rd:40: Lost braces; missing escapes or markup?
    40 | Then represent group of amino acids by a 6 dimentional vector i.e.{e1, e2, e3, e4, e5, e6}.
       |                                                                   ^
checkRd: (-1) binary_6bit.Rd:41: Lost braces; missing escapes or markup?
    41 | e1={H, R, K}, e2={D, E, N, D}, e3={C}, e4={S, T, P, A, G}, e5={M, I, L, V}, e6={F, Y, W}.
       |    ^
checkRd: (-1) binary_6bit.Rd:41: Lost braces; missing escapes or markup?
    41 | e1={H, R, K}, e2={D, E, N, D}, e3={C}, e4={S, T, P, A, G}, e5={M, I, L, V}, e6={F, Y, W}.
       |                  ^
checkRd: (-1) binary_6bit.Rd:41: Lost braces; missing escapes or markup?
    41 | e1={H, R, K}, e2={D, E, N, D}, e3={C}, e4={S, T, P, A, G}, e5={M, I, L, V}, e6={F, Y, W}.
       |                                   ^
checkRd: (-1) binary_6bit.Rd:41: Lost braces; missing escapes or markup?
    41 | e1={H, R, K}, e2={D, E, N, D}, e3={C}, e4={S, T, P, A, G}, e5={M, I, L, V}, e6={F, Y, W}.
       |                                           ^
checkRd: (-1) binary_6bit.Rd:41: Lost braces; missing escapes or markup?
    41 | e1={H, R, K}, e2={D, E, N, D}, e3={C}, e4={S, T, P, A, G}, e5={M, I, L, V}, e6={F, Y, W}.
       |                                                               ^
checkRd: (-1) binary_6bit.Rd:41: Lost braces; missing escapes or markup?
    41 | e1={H, R, K}, e2={D, E, N, D}, e3={C}, e4={S, T, P, A, G}, e5={M, I, L, V}, e6={F, Y, W}.
       |                                                                                ^
* 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 examples ... [42s/52s] OK
Examples with CPU (user + system) or elapsed time > 5s
                  user system elapsed
AutoCorDiNUC_DNA 4.854   0.01   6.408
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ... [1s/1s] OK
  Running ‘testthat.R’ [1s/1s]
* checking PDF version of manual ... [11s/14s] OK
* checking HTML version of manual ... [5s/10s] OK
* checking for non-standard things in the check directory ... OK
* DONE
Status: 1 NOTE