• using R Under development (unstable) (2024-12-10 r87437)
• using platform: x86_64-pc-linux-gnu
• R was compiled by     clang version 19.1.5     flang-new version 19.1.5
• running under: Fedora Linux 36 (Workstation Edition)
• using session charset: UTF-8
• using option ‘--no-stop-on-test-error’
• 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 whether package ‘ftrCOOL’ can be installed ... [35s/39s] OK See the install log for details.
• checking installed package size ... OK
• checking package 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 ... [99s/114s] OK
• checking Rd files ... 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 ... [67s/74s] OK
• checking for unstated dependencies in ‘tests’ ... OK
• checking tests ... OK   Running ‘testthat.R’
• checking PDF version of manual ... [16s/22s] OK
• checking HTML version of manual ... [9s/16s] OK
• checking for non-standard things in the check directory ... OK
• checking for detritus in the temp directory ... OK
• DONE

Status: 1 NOTE