• using R Under development (unstable) (2023-11-26 r85638)
• using platform: x86_64-pc-linux-gnu
• R was compiled by     Debian clang version 17.0.5 (1)     Debian flang-new version 17.0.5 (1)
• running under: Debian GNU/Linux trixie/sid
• using session charset: UTF-8
• checking for file ‘spmoran/DESCRIPTION’ ... OK
• checking extension type ... Package
• this is package ‘spmoran’ version ‘0.2.2.9’
• 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 serialization versions ... OK
• checking whether package ‘spmoran’ can be installed ... OK See the install log for details.
• checking package directory ... OK
• checking for future file timestamps ... OK
• checking ‘build’ 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 R 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/6s] 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/6s] 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 ... [78s/94s] OK
• checking Rd files ... [1s/1s] NOTE checkRd: (-1) besf_vc.Rd:18: Lost braces; missing escapes or markup?     18 | \item{xconst}{Matrix of explanatory variables with constant coefficients (N x K_{c}). Default is NULL}        | ^ checkRd: (-1) besf_vc.Rd:42: Lost braces; missing escapes or markup?     42 | \item{c}{Matrix with columns for the estimated coefficients on xconst, their standard errors, z-values, and p-values (K_{c} x 4). Effective if xconst_nvc = FALSE}        | ^ checkRd: (-1) besf_vc.Rd:43: Lost braces; missing escapes or markup?     43 | \item{c_vc}{Matrix of estimated NVCs on xconst (N x K_{c}). Effective if xconst_nvc = TRUE}        | ^ checkRd: (-1) besf_vc.Rd:44: Lost braces; missing escapes or markup?     44 | \item{cse_vc}{Matrix of standard errors for the NVCs on xconst (N x k_{c}). Effective if xconst_nvc = TRUE}        | ^ checkRd: (-1) besf_vc.Rd:45: Lost braces; missing escapes or markup?     45 | \item{cz_vc}{Matrix of z-values for the NVCs on xconst (N x K_{c}). Effective if xconst_nvc = TRUE}        | ^ checkRd: (-1) besf_vc.Rd:46: Lost braces; missing escapes or markup?     46 | \item{cp_vc}{Matrix of p-values for the NVCs on xconst (N x K_{c}). Effective if xconst_nvc = TRUE}        | ^ checkRd: (-1) nongauss_y.Rd:17: Lost braces; missing escapes or markup?     17 | If tr_num >0, the SAL transformation is iterated tr_num times to Gaussianize y. The SAL transformation is defined as SAL(y)=a+b*sinh(c*arcsinh(y)-d) where {a,b,c,d} are parameters. Based on Rios and Tobar (2019), the iteration of the SAL transformation approximates a wide variety of non-Gaussian distributions without explicitly assuming data distribution. The resf and resf_vc functions return tr_par, which is a list whose k-th element includes the {a,b,c,d} parameters used for the k-th SAL transformation.        | ^ checkRd: (-1) nongauss_y.Rd:17: Lost braces; missing escapes or markup?     17 | If tr_num >0, the SAL transformation is iterated tr_num times to Gaussianize y. The SAL transformation is defined as SAL(y)=a+b*sinh(c*arcsinh(y)-d) where {a,b,c,d} are parameters. Based on Rios and Tobar (2019), the iteration of the SAL transformation approximates a wide variety of non-Gaussian distributions without explicitly assuming data distribution. The resf and resf_vc functions return tr_par, which is a list whose k-th element includes the {a,b,c,d} parameters used for the k-th SAL transformation.        | ^ checkRd: (-1) predict0.Rd:15: Lost braces; missing escapes or markup?     15 | \item{xgroup0}{Matrix of group IDs that may be group IDs (integers) or group names (N_0 x K_{group}). Default is NULL}        | ^ checkRd: (-1) predict0_vc.Rd:15: Lost braces; missing escapes or markup?     15 | \item{xgroup0}{Matrix of group indeces that may be group IDs (integers) or group names (N_0 x K_{group}). Default is NULL}        | ^ checkRd: (-1) resf.Rd:15: Lost braces; missing escapes or markup?     15 | \item{xgroup}{Matrix of group IDs. The IDs may be group numbers or group names (N x K_{group}). Default is NULL}        | ^ checkRd: (-1) resf.Rd:31: Lost braces; missing escapes or markup?     31 | \item{b_g}{List of K_{group} matrices with columns for the estimated group effects, their standard errors, and t-values}        | ^ checkRd: (-1) resf_vc.Rd:19: Lost braces; missing escapes or markup?     19 | \item{xconst}{Matrix of explanatory variables with constant coefficients (N x K_{c}). Default is NULL}        | ^ checkRd: (-1) resf_vc.Rd:20: Lost braces; missing escapes or markup?     20 | \item{xgroup}{Matrix of group IDs. The IDs may be group numbers or group names (N x K_{g}). Default is NULL}        | ^ checkRd: (-1) resf_vc.Rd:46: Lost braces; missing escapes or markup?     46 | \item{c}{Matrix with columns for the estimated coefficients on xconst, their standard errors, t-values, and p-values (K_{c} x 4). Effective if xconst_nvc = FALSE}        | ^ checkRd: (-1) resf_vc.Rd:47: Lost braces; missing escapes or markup?     47 | \item{c_vc}{Matrix of estimated NVCs on xconst (N x K_{c}). Effective if xconst_nvc = TRUE}        | ^ checkRd: (-1) resf_vc.Rd:48: Lost braces; missing escapes or markup?     48 | \item{cse_vc}{Matrix of standard errors for the NVCs on xconst (N x k_{c}). Effective if xconst_nvc = TRUE}        | ^ checkRd: (-1) resf_vc.Rd:49: Lost braces; missing escapes or markup?     49 | \item{ct_vc}{Matrix of t-values for the NVCs on xconst (N x K_{c}). Effective if xconst_nvc = TRUE}        | ^ checkRd: (-1) resf_vc.Rd:50: Lost braces; missing escapes or markup?     50 | \item{cp_vc}{Matrix of p-values for the NVCs on xconst (N x K_{c}). Effective if xconst_nvc = TRUE}        | ^ checkRd: (-1) resf_vc.Rd:51: Lost braces; missing escapes or markup?     51 | \item{b_g}{List of K_{g} matrices with columns for the estimated group effects, their standard errors, and t-values}        | ^
• checking Rd metadata ... OK
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• checking for unstated dependencies in examples ... OK
• checking sizes of PDF files under ‘inst/doc’ ... OK
• checking installed files from ‘inst/doc’ ... OK
• checking files in ‘vignettes’ ... OK
• checking examples ... [25s/30s] OK
• checking for unstated dependencies in vignettes ... OK
• checking package vignettes in ‘inst/doc’ ... OK
• checking re-building of vignette outputs ... [2s/2s] OK
• checking PDF version of manual ... [6s/9s] OK
• checking HTML version of manual ... [2s/2s] OK
• checking for non-standard things in the check directory ... OK
• DONE

Status: 1 NOTE