* using log directory ‘/srv/hornik/tmp/CRAN/ddtlcm.Rcheck’ * using R Under development (unstable) (2024-03-28 r86217) * using platform: x86_64-pc-linux-gnu * R was compiled by Debian clang version 17.0.6 (5) Debian flang-new version 17.0.6 (5) * running under: Debian GNU/Linux trixie/sid * using session charset: UTF-8 * checking for file ‘ddtlcm/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘ddtlcm’ version ‘0.2.1’ * package encoding: UTF-8 * checking CRAN incoming feasibility ... [4s/5s] NOTE Maintainer: ‘Mengbing Li ’ Found the following (possibly) invalid file URI: URI: inst/ddtlcm_workflow_example.pdf From: README.md * 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 ‘ddtlcm’ can be installed ... [9s/9s] OK * 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 code files for non-ASCII characters ... OK * checking R files for syntax errors ... OK * checking whether the package can be loaded ... [2s/2s] OK * checking whether the package can be loaded with stated dependencies ... [2s/2s] OK * checking whether the package can be unloaded cleanly ... [2s/2s] OK * checking whether the namespace can be loaded with stated dependencies ... [2s/2s] OK * checking whether the namespace can be unloaded cleanly ... [2s/2s] OK * checking loading without being on the library search path ... [2s/2s] 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 ... [12s/12s] OK * checking Rd files ... [0s/0s] NOTE checkRd: (-1) ddtlcm_fit.Rd:34: Lost braces 34 | 1 singleton root node (labeled as "u1"), and K-1 internal nodes (labeled as "u1" through "u{K-1}"). | ^ checkRd: (-1) ddtlcm_fit.Rd:42: Lost braces; missing escapes or markup? 42 | \item{\code{class_assignments}}{a N-vector with integer entries from {1, ..., K}. The initial values for | ^ checkRd: (-1) draw_mnorm.Rd:6: Lost braces; missing escapes or markup? 6 | from x ~ N(Q^{-1}a, Q^{-1}), where Q^{-1} is the precision matrix} | ^ checkRd: (-1) draw_mnorm.Rd:6: Lost braces; missing escapes or markup? 6 | from x ~ N(Q^{-1}a, Q^{-1}), where Q^{-1} is the precision matrix} | ^ checkRd: (-1) draw_mnorm.Rd:6: Lost braces; missing escapes or markup? 6 | from x ~ N(Q^{-1}a, Q^{-1}), where Q^{-1} is the precision matrix} | ^ checkRd: (-1) draw_mnorm.Rd:18: Lost braces; missing escapes or markup? 18 | from x ~ N(Q^{-1}a, Q^{-1}), where Q^{-1} is the precision matrix | ^ checkRd: (-1) draw_mnorm.Rd:18: Lost braces; missing escapes or markup? 18 | from x ~ N(Q^{-1}a, Q^{-1}), where Q^{-1} is the precision matrix | ^ checkRd: (-1) draw_mnorm.Rd:18: Lost braces; missing escapes or markup? 18 | from x ~ N(Q^{-1}a, Q^{-1}), where Q^{-1} is the precision matrix | ^ checkRd: (-1) draw_mnorm.Rd:14: Lost braces; missing escapes or markup? 14 | Q^{-1}a} | ^ checkRd: (-1) initialize_hclust.Rd:20: Lost braces; missing escapes or markup? 20 | \item{leaf_data}{a K by J matrix of logit(theta_{kj})} | ^ checkRd: (-1) logllk_ddt_lcm.Rd:43: Lost braces; missing escapes or markup? 43 | \item{leaf_data}{a K by J matrix of logit(theta_{kj})} | ^ checkRd: (-1) logllk_lcm.Rd:20: Lost braces; missing escapes or markup? 20 | \item{leaf_data}{a K by J matrix of logit(theta_{kj})} | ^ checkRd: (-1) predict.ddt_lcm.Rd:23: Lost braces; missing escapes or markup? 23 | taking values in {1, ..., K}} | ^ checkRd: (-1) predict.summary.ddt_lcm.Rd:21: Lost braces; missing escapes or markup? 21 | taking values in {1, ..., K}} | ^ checkRd: (-1) reattach_point.Rd:28: Lost braces; missing escapes or markup? 28 | \item{\code{div_dist_to_root_child}}{a N-vector with integer entries from {1, ..., K}. The initial values for | ^ checkRd: (-1) sample_class_assignment.Rd:19: Lost braces; missing escapes or markup? 19 | \item{leaf_data}{a K by J matrix of logit(theta_{kj})} | ^ checkRd: (-1) sample_leaf_locations_pg.Rd:38: Lost braces; missing escapes or markup? 38 | Each element takes value in {1, ..., K}.} | ^ checkRd: (-1) simulate_lcm_given_tree.Rd:63: Lost braces; missing escapes or markup? 63 | Y_{ij} | Z_i = k ~ Binomial(class_item_probability_{kj}) | ^ checkRd: (-1) simulate_lcm_given_tree.Rd:63: Lost braces; missing escapes or markup? 63 | Y_{ij} | Z_i = k ~ Binomial(class_item_probability_{kj}) | ^ checkRd: (-1) simulate_lcm_given_tree.Rd:49: Lost braces; missing escapes or markup? 49 | \item{\code{class_assignments}}{a N-vector with integer entries from {1, ..., K}. The initial values for | ^ checkRd: (-1) simulate_lcm_response.Rd:32: Lost braces; missing escapes or markup? 32 | Y_{ij} | Z_i = k ~ Binomial(class_item_probability_{kj}) | ^ checkRd: (-1) simulate_lcm_response.Rd:32: Lost braces; missing escapes or markup? 32 | Y_{ij} | Z_i = k ~ Binomial(class_item_probability_{kj}) | ^ * checking Rd metadata ... NOTE Invalid package aliases in Rd file 'ddtlcm.Rd': ‘-package’ * checking Rd line widths ... NOTE Rd file 'plot.ddt_lcm.Rd': \examples lines wider than 100 characters: # we will plot: "responseprob_1,1,1" for the class 1 response probability of item 3 in major group 2; # "classprob_1" for the probability of being assigned to class 1; "c" for the divergence function parameter; plot(x = result_diet_1000iters, parameter_names = c("responseprob_1,1,1", "classprob_1", "c", "diffusionvar_1"), burnin = 500) These lines will be truncated in the PDF manual. * 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 contents of ‘data’ directory ... OK * checking data for non-ASCII characters ... [2s/2s] OK * checking LazyData ... OK * checking data for ASCII and uncompressed saves ... OK * checking installed files from ‘inst/doc’ ... OK * checking files in ‘vignettes’ ... OK * checking examples ... [24s/24s] NOTE Examples with CPU (user + system) or elapsed time > 5s user system elapsed compute_IC 5.184 0.116 5.3 * checking for unstated dependencies in ‘tests’ ... OK * checking tests ... [9s/9s] OK Running ‘testthat.R’ [8s/8s] * checking for unstated dependencies in vignettes ... OK * checking package vignettes ... OK * checking re-building of vignette outputs ... [25s/25s] OK * checking PDF version of manual ... [3s/3s] OK * checking HTML version of manual ... [1s/1s] OK * checking for non-standard things in the check directory ... OK * checking for detritus in the temp directory ... OK * DONE Status: 5 NOTEs