* using log directory ‘/home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/AntAngioCOOL.Rcheck’
* using R Under development (unstable) (2025-02-23 r87804)
* 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 ‘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 ... [6s/8s] OK
* checking whether the package can be loaded with stated dependencies ... [5s/6s] OK
* checking whether the package can be unloaded cleanly ... [5s/7s] OK
* checking whether the namespace can be loaded with stated dependencies ... [5s/6s] OK
* checking whether the namespace can be unloaded cleanly ... [6s/7s] OK
* checking loading without being on the library search path ... [6s/7s] 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 ... [53s/67s] OK
* checking Rd files ... [0s/0s] 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 ... [14s/17s] OK
Examples with CPU (user + system) or elapsed time > 5s
              user system elapsed
AntAngioCOOL 7.302  0.669   9.504
* checking PDF version of manual ... [4s/6s] OK
* checking HTML version of manual ... [0s/0s] OK
* checking for non-standard things in the check directory ... OK
* DONE
Status: 1 NOTE