* using log directory ‘/home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/AntAngioCOOL.Rcheck’ * using R Under development (unstable) (2024-04-27 r86487) * using platform: x86_64-pc-linux-gnu * R was compiled by Debian clang version 18.1.4 (1) Debian flang-new version 18.1.4 (1) * running under: Debian GNU/Linux trixie/sid * using session charset: UTF-8 * checking for file ‘AntAngioCOOL/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘AntAngioCOOL’ version ‘1.2’ * 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 ‘AntAngioCOOL’ can be installed ... OK See 'https://www.r-project.org/nosvn/R.check/r-devel-linux-x86_64-debian-clang/AntAngioCOOL-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 ... [8s/9s] OK * checking whether the package can be loaded with stated dependencies ... [7s/8s] OK * checking whether the package can be unloaded cleanly ... [7s/8s] OK * checking whether the namespace can be loaded with stated dependencies ... [7s/7s] OK * checking whether the namespace can be unloaded cleanly ... [7s/9s] OK * checking loading without being on the library search path ... [8s/9s] 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 ... [65s/77s] OK * checking Rd files ... [0s/1s] NOTE checkRd: (-1) AntAngioCOOL.Rd:33: Lost braces; missing escapes or markup? 33 | 2- K-mer composition that shows the fraction of all possible subsequences with length k in the given peptide. To compute k-mer composition features, reduced amino acid alphabet that proposed by Zahiri et al (Zahiri et al., 2014) has been exploited: the 20 alphabet of amino acids have been reduced to a new alphabet with size 8 according to 544 physicochemical and biochemical indices that extracted from AAIndex database (Kawashima et al., 2008) (C1={A, E}, C2={I, L, F, M, V}, C3={N, D, T, S}, C4={G}, C5={P}, C6={R, K, Q, H}, C7={Y, W}, C8={C}). We have computed k-mer composition for k=2,3,4 for each peptide. | ^ checkRd: (-1) AntAngioCOOL.Rd:33: Lost braces; missing escapes or markup? 33 | 2- K-mer composition that shows the fraction of all possible subsequences with length k in the given peptide. To compute k-mer composition features, reduced amino acid alphabet that proposed by Zahiri et al (Zahiri et al., 2014) has been exploited: the 20 alphabet of amino acids have been reduced to a new alphabet with size 8 according to 544 physicochemical and biochemical indices that extracted from AAIndex database (Kawashima et al., 2008) (C1={A, E}, C2={I, L, F, M, V}, C3={N, D, T, S}, C4={G}, C5={P}, C6={R, K, Q, H}, C7={Y, W}, C8={C}). We have computed k-mer composition for k=2,3,4 for each peptide. | ^ checkRd: (-1) AntAngioCOOL.Rd:33: Lost braces; missing escapes or markup? 33 | 2- K-mer composition that shows the fraction of all possible subsequences with length k in the given peptide. To compute k-mer composition features, reduced amino acid alphabet that proposed by Zahiri et al (Zahiri et al., 2014) has been exploited: the 20 alphabet of amino acids have been reduced to a new alphabet with size 8 according to 544 physicochemical and biochemical indices that extracted from AAIndex database (Kawashima et al., 2008) (C1={A, E}, C2={I, L, F, M, V}, C3={N, D, T, S}, C4={G}, C5={P}, C6={R, K, Q, H}, C7={Y, W}, C8={C}). We have computed k-mer composition for k=2,3,4 for each peptide. | ^ checkRd: (-1) AntAngioCOOL.Rd:33: Lost braces; missing escapes or markup? 33 | 2- K-mer composition that shows the fraction of all possible subsequences with length k in the given peptide. To compute k-mer composition features, reduced amino acid alphabet that proposed by Zahiri et al (Zahiri et al., 2014) has been exploited: the 20 alphabet of amino acids have been reduced to a new alphabet with size 8 according to 544 physicochemical and biochemical indices that extracted from AAIndex database (Kawashima et al., 2008) (C1={A, E}, C2={I, L, F, M, V}, C3={N, D, T, S}, C4={G}, C5={P}, C6={R, K, Q, H}, C7={Y, W}, C8={C}). We have computed k-mer composition for k=2,3,4 for each peptide. | ^ checkRd: (-1) AntAngioCOOL.Rd:33: Lost braces; missing escapes or markup? 33 | 2- K-mer composition that shows the fraction of all possible subsequences with length k in the given peptide. To compute k-mer composition features, reduced amino acid alphabet that proposed by Zahiri et al (Zahiri et al., 2014) has been exploited: the 20 alphabet of amino acids have been reduced to a new alphabet with size 8 according to 544 physicochemical and biochemical indices that extracted from AAIndex database (Kawashima et al., 2008) (C1={A, E}, C2={I, L, F, M, V}, C3={N, D, T, S}, C4={G}, C5={P}, C6={R, K, Q, H}, C7={Y, W}, C8={C}). We have computed k-mer composition for k=2,3,4 for each peptide. | ^ checkRd: (-1) AntAngioCOOL.Rd:33: Lost braces; missing escapes or markup? 33 | 2- K-mer composition that shows the fraction of all possible subsequences with length k in the given peptide. To compute k-mer composition features, reduced amino acid alphabet that proposed by Zahiri et al (Zahiri et al., 2014) has been exploited: the 20 alphabet of amino acids have been reduced to a new alphabet with size 8 according to 544 physicochemical and biochemical indices that extracted from AAIndex database (Kawashima et al., 2008) (C1={A, E}, C2={I, L, F, M, V}, C3={N, D, T, S}, C4={G}, C5={P}, C6={R, K, Q, H}, C7={Y, W}, C8={C}). We have computed k-mer composition for k=2,3,4 for each peptide. | ^ checkRd: (-1) AntAngioCOOL.Rd:33: Lost braces; missing escapes or markup? 33 | 2- K-mer composition that shows the fraction of all possible subsequences with length k in the given peptide. To compute k-mer composition features, reduced amino acid alphabet that proposed by Zahiri et al (Zahiri et al., 2014) has been exploited: the 20 alphabet of amino acids have been reduced to a new alphabet with size 8 according to 544 physicochemical and biochemical indices that extracted from AAIndex database (Kawashima et al., 2008) (C1={A, E}, C2={I, L, F, M, V}, C3={N, D, T, S}, C4={G}, C5={P}, C6={R, K, Q, H}, C7={Y, W}, C8={C}). We have computed k-mer composition for k=2,3,4 for each peptide. | ^ checkRd: (-1) AntAngioCOOL.Rd:33: Lost braces; missing escapes or markup? 33 | 2- K-mer composition that shows the fraction of all possible subsequences with length k in the given peptide. To compute k-mer composition features, reduced amino acid alphabet that proposed by Zahiri et al (Zahiri et al., 2014) has been exploited: the 20 alphabet of amino acids have been reduced to a new alphabet with size 8 according to 544 physicochemical and biochemical indices that extracted from AAIndex database (Kawashima et al., 2008) (C1={A, E}, C2={I, L, F, M, V}, C3={N, D, T, S}, C4={G}, C5={P}, C6={R, K, Q, H}, C7={Y, W}, C8={C}). We have computed k-mer composition for k=2,3,4 for each peptide. | ^ * 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 R/sysdata.rda ... OK * checking examples ... [18s/22s] OK Examples with CPU (user + system) or elapsed time > 5s user system elapsed AntAngioCOOL 9.574 0.923 12.152 * checking PDF version of manual ... [5s/7s] OK * checking HTML version of manual ... [0s/0s] OK * checking for non-standard things in the check directory ... OK * DONE Status: 1 NOTE