- using R Under development (unstable) (2024-03-26 r86210)
- using platform: x86_64-pc-linux-gnu
- R was compiled by
gcc-13 (Debian 13.2.0-13) 13.2.0
GNU Fortran (Debian 13.2.0-13) 13.2.0
- running under: Debian GNU/Linux trixie/sid
- 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 serialization versions ... OK
- checking whether package ‘quhomology’ can be installed ... OK
See the install log 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/1s] OK
- checking loading without being on the library search path ... [0s/1s] 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 ... [5s/9s] OK
- checking Rd files ... [0s/1s] 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 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 ... 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 ... [2s/4s] OK
- checking for unstated dependencies in ‘tests’ ... OK
- checking tests ... [2s/5s] OK
Running ‘testthat.R’ [2s/4s]
- checking PDF version of manual ... [5s/11s] OK
- checking HTML version of manual ... [1s/2s] OK
- checking for non-standard things in the check directory ... OK
- DONE
Status: 2 NOTEs