* using log directory ‘/Volumes/Builds/packages/big-sur-arm64/results/4.4/quhomology.Rcheck’ * using R version 4.4.0 alpha (2024-03-31 r86238) * using platform: aarch64-apple-darwin20 * R was compiled by Apple clang version 14.0.0 (clang-1400.0.29.202) GNU Fortran (GCC) 12.2.0 * running under: macOS Ventura 13.4 * using session charset: UTF-8 * checking for file ‘quhomology/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘quhomology’ version ‘1.1.1’ * 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 ‘quhomology’ can be installed ... [1s/1s] OK See 'https://www.r-project.org/nosvn/R.check/r-oldrel-macos-arm64/quhomology-00install.html' 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 ... [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 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 ... [1s/1s] OK * checking Rd files ... [0s/0s] NOTE checkRd: (-1) boundary_matrix.Rd:28: Lost braces; missing escapes or markup? 28 | This functions takes all words (or just the non-degenerate ones) of length $degree$ in the rack/biquandle (which are represented by $Z_k$) and then calculates their boundary via the following equation. For this, let $x=(x_i)_0^{degree-1}$ be an element of the rack/birack and let $n:=degree-1$. | ^ checkRd: (-1) boundary_matrix.Rd:29: Lost braces; missing escapes or markup? 29 | $$partial(x) = Sum_{i=0}^n (-1)^i ( (x_0...{(^x_i)}...x_n)-(x_0^{x_i}x_1^{x_i}...x_{i-1}^{x_i}{x_{i+1}}_{x_i}...{x_n}_{x_i}) )$$, where ^x_i means except x_i. | ^ checkRd: (-1) boundary_matrix.Rd:29: Lost braces; missing escapes or markup? 29 | $$partial(x) = Sum_{i=0}^n (-1)^i ( (x_0...{(^x_i)}...x_n)-(x_0^{x_i}x_1^{x_i}...x_{i-1}^{x_i}{x_{i+1}}_{x_i}...{x_n}_{x_i}) )$$, where ^x_i means except x_i. | ^ checkRd: (-1) boundary_matrix.Rd:29: Lost braces; missing escapes or markup? 29 | $$partial(x) = Sum_{i=0}^n (-1)^i ( (x_0...{(^x_i)}...x_n)-(x_0^{x_i}x_1^{x_i}...x_{i-1}^{x_i}{x_{i+1}}_{x_i}...{x_n}_{x_i}) )$$, where ^x_i means except x_i. | ^ checkRd: (-1) boundary_matrix.Rd:29: Lost braces; missing escapes or markup? 29 | $$partial(x) = Sum_{i=0}^n (-1)^i ( (x_0...{(^x_i)}...x_n)-(x_0^{x_i}x_1^{x_i}...x_{i-1}^{x_i}{x_{i+1}}_{x_i}...{x_n}_{x_i}) )$$, where ^x_i means except x_i. | ^ checkRd: (-1) boundary_matrix.Rd:29: Lost braces; missing escapes or markup? 29 | $$partial(x) = Sum_{i=0}^n (-1)^i ( (x_0...{(^x_i)}...x_n)-(x_0^{x_i}x_1^{x_i}...x_{i-1}^{x_i}{x_{i+1}}_{x_i}...{x_n}_{x_i}) )$$, where ^x_i means except x_i. | ^ checkRd: (-1) boundary_matrix.Rd:29: Lost braces; missing escapes or markup? 29 | $$partial(x) = Sum_{i=0}^n (-1)^i ( (x_0...{(^x_i)}...x_n)-(x_0^{x_i}x_1^{x_i}...x_{i-1}^{x_i}{x_{i+1}}_{x_i}...{x_n}_{x_i}) )$$, where ^x_i means except x_i. | ^ checkRd: (-1) boundary_matrix.Rd:29: Lost braces 29 | $$partial(x) = Sum_{i=0}^n (-1)^i ( (x_0...{(^x_i)}...x_n)-(x_0^{x_i}x_1^{x_i}...x_{i-1}^{x_i}{x_{i+1}}_{x_i}...{x_n}_{x_i}) )$$, where ^x_i means except x_i. | ^ checkRd: (-1) boundary_matrix.Rd:29: Lost braces; missing escapes or markup? 29 | $$partial(x) = Sum_{i=0}^n (-1)^i ( (x_0...{(^x_i)}...x_n)-(x_0^{x_i}x_1^{x_i}...x_{i-1}^{x_i}{x_{i+1}}_{x_i}...{x_n}_{x_i}) )$$, where ^x_i means except x_i. | ^ checkRd: (-1) boundary_matrix.Rd:29: Lost braces; missing escapes or markup? 29 | $$partial(x) = Sum_{i=0}^n (-1)^i ( (x_0...{(^x_i)}...x_n)-(x_0^{x_i}x_1^{x_i}...x_{i-1}^{x_i}{x_{i+1}}_{x_i}...{x_n}_{x_i}) )$$, where ^x_i means except x_i. | ^ checkRd: (-1) boundary_matrix.Rd:29: Lost braces; missing escapes or markup? 29 | $$partial(x) = Sum_{i=0}^n (-1)^i ( (x_0...{(^x_i)}...x_n)-(x_0^{x_i}x_1^{x_i}...x_{i-1}^{x_i}{x_{i+1}}_{x_i}...{x_n}_{x_i}) )$$, where ^x_i means except x_i. | ^ checkRd: (-1) boundary_matrix.Rd:29: Lost braces; missing escapes or markup? 29 | $$partial(x) = Sum_{i=0}^n (-1)^i ( (x_0...{(^x_i)}...x_n)-(x_0^{x_i}x_1^{x_i}...x_{i-1}^{x_i}{x_{i+1}}_{x_i}...{x_n}_{x_i}) )$$, where ^x_i means except x_i. | ^ checkRd: (-1) boundary_matrix_degenerate.Rd:25: Lost braces; missing escapes or markup? 25 | This functions takes all degenerate words of length $degree$ in the rack/biquandle (which are represented by ${Z}_k$) and then calculates their boundary via the followi ng equation. For this, let $x=(x_i)_0^{degree-1}$ be an element of the rack/birack and let $n:=degree-1$. | ^ checkRd: (-1) boundary_matrix_degenerate.Rd:25: Lost braces; missing escapes or markup? 25 | This functions takes all degenerate words of length $degree$ in the rack/biquandle (which are represented by ${Z}_k$) and then calculates their boundary via the followi ng equation. For this, let $x=(x_i)_0^{degree-1}$ be an element of the rack/birack and let $n:=degree-1$. | ^ checkRd: (-1) boundary_matrix_degenerate.Rd:26: Lost braces; missing escapes or markup? 26 | $$partial(x) = Sum_{i=0}^n (-1)^i ( (x_0...{(^x_i)}...x_n)-(x_0^{x_i}x_1^{x_i}...x_{i-1}^{x_i}{x_{i+1}}_{x_i}...{x_n}_{x_i}) )$$, where ^x_i means except x_i. | ^ checkRd: (-1) boundary_matrix_degenerate.Rd:26: Lost braces; missing escapes or markup? 26 | $$partial(x) = Sum_{i=0}^n (-1)^i ( (x_0...{(^x_i)}...x_n)-(x_0^{x_i}x_1^{x_i}...x_{i-1}^{x_i}{x_{i+1}}_{x_i}...{x_n}_{x_i}) )$$, where ^x_i means except x_i. | ^ checkRd: (-1) boundary_matrix_degenerate.Rd:26: Lost braces; missing escapes or markup? 26 | $$partial(x) = Sum_{i=0}^n (-1)^i ( (x_0...{(^x_i)}...x_n)-(x_0^{x_i}x_1^{x_i}...x_{i-1}^{x_i}{x_{i+1}}_{x_i}...{x_n}_{x_i}) )$$, where ^x_i means except x_i. | ^ checkRd: (-1) boundary_matrix_degenerate.Rd:26: Lost braces; missing escapes or markup? 26 | $$partial(x) = Sum_{i=0}^n (-1)^i ( (x_0...{(^x_i)}...x_n)-(x_0^{x_i}x_1^{x_i}...x_{i-1}^{x_i}{x_{i+1}}_{x_i}...{x_n}_{x_i}) )$$, where ^x_i means except x_i. | ^ checkRd: (-1) boundary_matrix_degenerate.Rd:26: Lost braces; missing escapes or markup? 26 | $$partial(x) = Sum_{i=0}^n (-1)^i ( (x_0...{(^x_i)}...x_n)-(x_0^{x_i}x_1^{x_i}...x_{i-1}^{x_i}{x_{i+1}}_{x_i}...{x_n}_{x_i}) )$$, where ^x_i means except x_i. | ^ checkRd: (-1) boundary_matrix_degenerate.Rd:26: Lost braces; missing escapes or markup? 26 | $$partial(x) = Sum_{i=0}^n (-1)^i ( (x_0...{(^x_i)}...x_n)-(x_0^{x_i}x_1^{x_i}...x_{i-1}^{x_i}{x_{i+1}}_{x_i}...{x_n}_{x_i}) )$$, where ^x_i means except x_i. | ^ checkRd: (-1) boundary_matrix_degenerate.Rd:26: Lost braces 26 | $$partial(x) = Sum_{i=0}^n (-1)^i ( (x_0...{(^x_i)}...x_n)-(x_0^{x_i}x_1^{x_i}...x_{i-1}^{x_i}{x_{i+1}}_{x_i}...{x_n}_{x_i}) )$$, where ^x_i means except x_i. | ^ checkRd: (-1) boundary_matrix_degenerate.Rd:26: Lost braces; missing escapes or markup? 26 | $$partial(x) = Sum_{i=0}^n (-1)^i ( (x_0...{(^x_i)}...x_n)-(x_0^{x_i}x_1^{x_i}...x_{i-1}^{x_i}{x_{i+1}}_{x_i}...{x_n}_{x_i}) )$$, where ^x_i means except x_i. | ^ checkRd: (-1) boundary_matrix_degenerate.Rd:26: Lost braces; missing escapes or markup? 26 | $$partial(x) = Sum_{i=0}^n (-1)^i ( (x_0...{(^x_i)}...x_n)-(x_0^{x_i}x_1^{x_i}...x_{i-1}^{x_i}{x_{i+1}}_{x_i}...{x_n}_{x_i}) )$$, where ^x_i means except x_i. | ^ checkRd: (-1) boundary_matrix_degenerate.Rd:26: Lost braces; missing escapes or markup? 26 | $$partial(x) = Sum_{i=0}^n (-1)^i ( (x_0...{(^x_i)}...x_n)-(x_0^{x_i}x_1^{x_i}...x_{i-1}^{x_i}{x_{i+1}}_{x_i}...{x_n}_{x_i}) )$$, where ^x_i means except x_i. | ^ checkRd: (-1) boundary_matrix_degenerate.Rd:26: Lost braces; missing escapes or markup? 26 | $$partial(x) = Sum_{i=0}^n (-1)^i ( (x_0...{(^x_i)}...x_n)-(x_0^{x_i}x_1^{x_i}...x_{i-1}^{x_i}{x_{i+1}}_{x_i}...{x_n}_{x_i}) )$$, where ^x_i means except x_i. | ^ checkRd: (-1) boundary_names.Rd:26: Lost braces; missing escapes or markup? 26 | This calculates all possible permutations of elements in $Z_k$ of length $degree$. If degenerate is true, it loops through all of them, removing the degenerate ones (that is, those where $x_i=x_{i+1}$, for an element $x=(x_i)_0^{degree})$). | ^ checkRd: (-1) boundary_names.Rd:26: Lost braces; missing escapes or markup? 26 | This calculates all possible permutations of elements in $Z_k$ of length $degree$. If degenerate is true, it loops through all of them, removing the degenerate ones (that is, those where $x_i=x_{i+1}$, for an element $x=(x_i)_0^{degree})$). | ^ checkRd: (-1) boundary_names_degenerate.Rd:23: Lost braces; missing escapes or markup? 23 | This calculates all possible permutations of elements in ${Z}_k$ of length $degree$. If degenerate is true, it loops through all of them, removing the non-degenerate ones (that is, those where $x_i =/= x_{i+1}$ for all $i=0,...,degree-1$, for an element $x=(x_i)_0^{degree})$). | ^ checkRd: (-1) boundary_names_degenerate.Rd:23: Lost braces; missing escapes or markup? 23 | This calculates all possible permutations of elements in ${Z}_k$ of length $degree$. If degenerate is true, it loops through all of them, removing the non-degenerate ones (that is, those where $x_i =/= x_{i+1}$ for all $i=0,...,degree-1$, for an element $x=(x_i)_0^{degree})$). | ^ checkRd: (-1) boundary_names_degenerate.Rd:23: Lost braces; missing escapes or markup? 23 | This calculates all possible permutations of elements in ${Z}_k$ of length $degree$. If degenerate is true, it loops through all of them, removing the non-degenerate ones (that is, those where $x_i =/= x_{i+1}$ for all $i=0,...,degree-1$, for an element $x=(x_i)_0^{degree})$). | ^ * checking Rd metadata ... 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 ... NOTE Auto-generated content requiring editing in Rd file 'quhomology-package.Rd': \details: ‘...o use the package, including the most important functions ~~’ * checking for unstated dependencies in examples ... OK * checking examples ... [1s/1s] OK * checking for unstated dependencies in ‘tests’ ... OK * checking tests ... [1s/1s] OK Running ‘testthat.R’ [1s/1s] * checking PDF version of manual ... [4s/4s] OK * DONE Status: 2 NOTEs * using check arguments '--no-clean-on-error ' * elapsed time (check, wall clock): 0:18