* using log directory ‘/srv/hornik/tmp/CRAN/multilevelcoda.Rcheck’ * using R Under development (unstable) (2024-03-10 r86083) * 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 ‘multilevelcoda/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘multilevelcoda’ version ‘1.2.3’ * package encoding: UTF-8 * checking CRAN incoming feasibility ... [4s/7s] NOTE Maintainer: ‘Flora Le <13florale@gmail.com>’ New submission Package was archived on CRAN Possibly misspelled words in DESCRIPTION: ILR (22:35) isotemporal (24:48) CRAN repository db overrides: X-CRAN-Comment: Archived on 2024-02-29 as issues were not corrected in time. Suggests or Enhances not in mainstream repositories: cmdstanr Availability using Additional_repositories specification: cmdstanr yes https://mc-stan.org/r-packages/ * checking package namespace information ... OK * checking package dependencies ... NOTE Package suggested but not available for checking: ‘cmdstanr’ * 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 ‘multilevelcoda’ can be installed ... [17s/17s] 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 R files for non-ASCII characters ... OK * checking R files for syntax errors ... OK * checking whether the package can be loaded ... [4s/3s] OK * checking whether the package can be loaded with stated dependencies ... [3s/3s] OK * checking whether the package can be unloaded cleanly ... [3s/3s] OK * checking whether the namespace can be loaded with stated dependencies ... [3s/3s] OK * checking whether the namespace can be unloaded cleanly ... [4s/3s] OK * checking loading without being on the library search path ... [5s/5s] 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 ... [18s/16s] OK * checking Rd files ... [0s/0s] NOTE checkRd: (-1) brmcoda.Rd:23: Lost braces 23 | {\code{CompILR}}{ An object of class \code{compilr} used in the \code{brm} model. } | ^ checkRd: (-1) brmcoda.Rd:24-25: Lost braces 24 | {\code{Model}}{ An object of class \code{brmsfit}, which contains the posterior draws | ^ checkRd: (-1) bsub.Rd:55: Lost braces 55 | {\code{Mean}}{ Posterior means.} | ^ checkRd: (-1) bsub.Rd:56: Lost braces 56 | {\code{CI_low} and \code{CI_high}}{ 95\% credible intervals.} | ^ checkRd: (-1) bsub.Rd:56: Lost braces 56 | {\code{CI_low} and \code{CI_high}}{ 95\% credible intervals.} | ^ checkRd: (-1) bsub.Rd:57: Lost braces 57 | {\code{Delta}}{ Amount substituted across compositional parts.} | ^ checkRd: (-1) bsub.Rd:58: Lost braces 58 | {\code{From}}{ Compositional part that is substituted from.} | ^ checkRd: (-1) bsub.Rd:59: Lost braces 59 | {\code{To}}{ Compositional parts that is substituted to.} | ^ checkRd: (-1) bsub.Rd:60: Lost braces 60 | {\code{Level}}{ Level where changes in composition takes place. Either \code{between} or \code{within}.} | ^ checkRd: (-1) bsub.Rd:61: Lost braces 61 | {\code{Reference}}{ Either \code{grandmean}, \code{clustermean}, or \code{users}.} | ^ checkRd: (-1) bsubmargins.Rd:47: Lost braces 47 | {\code{Mean}}{ Posterior means.} | ^ checkRd: (-1) bsubmargins.Rd:48: Lost braces 48 | {\code{CI_low} and \code{CI_high}}{ 95\% credible intervals.} | ^ checkRd: (-1) bsubmargins.Rd:48: Lost braces 48 | {\code{CI_low} and \code{CI_high}}{ 95\% credible intervals.} | ^ checkRd: (-1) bsubmargins.Rd:49: Lost braces 49 | {\code{Delta}}{ Amount substituted across compositional parts.} | ^ checkRd: (-1) bsubmargins.Rd:50: Lost braces 50 | {\code{From}}{ Compositional part that is substituted from.} | ^ checkRd: (-1) bsubmargins.Rd:51: Lost braces 51 | {\code{To}}{ Compositional parts that is substituted to.} | ^ checkRd: (-1) bsubmargins.Rd:52: Lost braces 52 | {\code{Level}}{ Level where changes in composition takes place. Either \code{between} or \code{within}.} | ^ checkRd: (-1) bsubmargins.Rd:53: Lost braces 53 | {\code{Reference}}{ Either \code{grandmean}, \code{clustermean}, or \code{users}.} | ^ checkRd: (-1) compilr.Rd:27-28: Lost braces 27 | {\code{BetweenComp}}{ A vector of class \code{acomp} representing one closed between-person composition | ^ checkRd: (-1) compilr.Rd:29-30: Lost braces 29 | {\code{WithinComp}}{ A vector of class \code{acomp} representing one closed within-person composition | ^ checkRd: (-1) compilr.Rd:31-32: Lost braces 31 | {\code{TotalComp}}{ A vector of class \code{acomp} representing one closed total composition | ^ checkRd: (-1) compilr.Rd:33: Lost braces 33 | {\code{BetweenILR}}{ Isometric log ratio transform of between-person composition.} | ^ checkRd: (-1) compilr.Rd:34: Lost braces 34 | {\code{WithinILR}}{ Isometric log ratio transform of within-person composition.} | ^ checkRd: (-1) compilr.Rd:35: Lost braces 35 | {\code{TotalILR}}{ Isometric log ratio transform of total composition.} | ^ checkRd: (-1) compilr.Rd:36: Lost braces 36 | {\code{data}}{ The user's dataset or imputed dataset if the input data contains zeros.} | ^ checkRd: (-1) compilr.Rd:37: Lost braces 37 | {\code{psi}}{ A ILR matrix associated with user-defined partition structure.} | ^ checkRd: (-1) compilr.Rd:38: Lost braces 38 | {\code{sbp}}{ The user-defined sequential binary partition matrix.} | ^ checkRd: (-1) compilr.Rd:39: Lost braces 39 | {\code{parts}}{ Names of compositional variables.} | ^ checkRd: (-1) compilr.Rd:40: Lost braces 40 | {\code{idvar}}{ Name of the variable containing IDs.} | ^ checkRd: (-1) compilr.Rd:41: Lost braces 41 | {\code{total}}{ Total amount to which the compositions is closed.} | ^ checkRd: (-1) submargins.Rd:47: Lost braces 47 | {\code{Mean}}{ Posterior means.} | ^ checkRd: (-1) submargins.Rd:48: Lost braces 48 | {\code{CI_low} and \code{CI_high}}{ 95\% credible intervals.} | ^ checkRd: (-1) submargins.Rd:48: Lost braces 48 | {\code{CI_low} and \code{CI_high}}{ 95\% credible intervals.} | ^ checkRd: (-1) submargins.Rd:49: Lost braces 49 | {\code{Delta}}{ Amount substituted across compositional parts.} | ^ checkRd: (-1) submargins.Rd:50: Lost braces 50 | {\code{From}}{ Compositional part that is substituted from.} | ^ checkRd: (-1) submargins.Rd:51: Lost braces 51 | {\code{To}}{ Compositional parts that is substituted to.} | ^ checkRd: (-1) submargins.Rd:52: Lost braces 52 | {\code{Level}}{ Level where changes in composition takes place. Either \code{between} or \code{within}.} | ^ checkRd: (-1) submargins.Rd:53: Lost braces 53 | {\code{Reference}}{ Either \code{grandmean}, \code{clustermean}, or \code{users}.} | ^ checkRd: (-1) substitution.Rd:55: Lost braces 55 | {\code{Mean}}{ Posterior means.} | ^ checkRd: (-1) substitution.Rd:56: Lost braces 56 | {\code{CI_low} and \code{CI_high}}{ 95\% credible intervals.} | ^ checkRd: (-1) substitution.Rd:56: Lost braces 56 | {\code{CI_low} and \code{CI_high}}{ 95\% credible intervals.} | ^ checkRd: (-1) substitution.Rd:57: Lost braces 57 | {\code{Delta}}{ Amount substituted across compositional parts.} | ^ checkRd: (-1) substitution.Rd:58: Lost braces 58 | {\code{From}}{ Compositional part that is substituted from.} | ^ checkRd: (-1) substitution.Rd:59: Lost braces 59 | {\code{To}}{ Compositional parts that is substituted to.} | ^ checkRd: (-1) substitution.Rd:60: Lost braces 60 | {\code{Level}}{ Level where changes in composition takes place. Either \code{between} or \code{within}.} | ^ checkRd: (-1) substitution.Rd:61: Lost braces 61 | {\code{Reference}}{ Either \code{grandmean}, \code{clustermean}, or \code{users}.} | ^ checkRd: (-1) summary.substitution.Rd:35: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) summary.substitution.Rd:36: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) summary.substitution.Rd:37: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) summary.substitution.Rd:38: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) summary.substitution.Rd:39: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) summary.substitution.Rd:40: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) summary.substitution.Rd:41: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) update.brmcoda.Rd:26: Lost braces 26 | {\code{CompILR}}{ An object of class \code{compilr} used in the \code{brm} model. } | ^ checkRd: (-1) update.brmcoda.Rd:27-28: Lost braces 27 | {\code{Model}}{ An object of class \code{brmsfit}, which contains the posterior draws | ^ checkRd: (-1) update.compilr.Rd:21-22: Lost braces 21 | {\code{BetweenComp}}{ A vector of class \code{acomp} representing one closed between-person composition | ^ checkRd: (-1) update.compilr.Rd:23-24: Lost braces 23 | {\code{WithinComp}}{ A vector of class \code{acomp} representing one closed within-person composition | ^ checkRd: (-1) update.compilr.Rd:25-26: Lost braces 25 | {\code{TotalComp}}{ A vector of class \code{acomp} representing one closed total composition | ^ checkRd: (-1) update.compilr.Rd:27: Lost braces 27 | {\code{BetweenILR}}{ Isometric log ratio transform of between-person composition.} | ^ checkRd: (-1) update.compilr.Rd:28: Lost braces 28 | {\code{WithinILR}}{ Isometric log ratio transform of within-person composition.} | ^ checkRd: (-1) update.compilr.Rd:29: Lost braces 29 | {\code{TotalILR}}{ Isometric log ratio transform of total composition.} | ^ checkRd: (-1) update.compilr.Rd:30: Lost braces 30 | {\code{data}}{ The user's dataset or imputed dataset if the input data contains zeros.} | ^ checkRd: (-1) update.compilr.Rd:31: Lost braces 31 | {\code{psi}}{ A ILR matrix associated with user-defined partition structure.} | ^ checkRd: (-1) update.compilr.Rd:32: Lost braces 32 | {\code{sbp}}{ The user-defined sequential binary partition matrix.} | ^ checkRd: (-1) update.compilr.Rd:33: Lost braces 33 | {\code{parts}}{ Names of compositional variables.} | ^ checkRd: (-1) update.compilr.Rd:34: Lost braces 34 | {\code{idvar}}{ Name of the variable containing IDs.} | ^ checkRd: (-1) update.compilr.Rd:35: Lost braces 35 | {\code{total}}{ Total amount to which the compositions is closed.} | ^ checkRd: (-1) wsub.Rd:55: Lost braces 55 | {\code{Mean}}{ Posterior means.} | ^ checkRd: (-1) wsub.Rd:56: Lost braces 56 | {\code{CI_low} and \code{CI_high}}{ 95\% credible intervals.} | ^ checkRd: (-1) wsub.Rd:56: Lost braces 56 | {\code{CI_low} and \code{CI_high}}{ 95\% credible intervals.} | ^ checkRd: (-1) wsub.Rd:57: Lost braces 57 | {\code{Delta}}{ Amount substituted across compositional parts.} | ^ checkRd: (-1) wsub.Rd:58: Lost braces 58 | {\code{From}}{ Compositional part that is substituted from.} | ^ checkRd: (-1) wsub.Rd:59: Lost braces 59 | {\code{To}}{ Compositional parts that is substituted to.} | ^ checkRd: (-1) wsub.Rd:60: Lost braces 60 | {\code{Level}}{ Level where changes in composition takes place. Either \code{between} or \code{within}.} | ^ checkRd: (-1) wsub.Rd:61: Lost braces 61 | {\code{Reference}}{ Either \code{grandmean}, \code{clustermean}, or \code{users}.} | ^ checkRd: (-1) wsubmargins.Rd:47: Lost braces 47 | {\code{Mean}}{ Posterior means.} | ^ checkRd: (-1) wsubmargins.Rd:48: Lost braces 48 | {\code{CI_low} and \code{CI_high}}{ 95\% credible intervals.} | ^ checkRd: (-1) wsubmargins.Rd:48: Lost braces 48 | {\code{CI_low} and \code{CI_high}}{ 95\% credible intervals.} | ^ checkRd: (-1) wsubmargins.Rd:49: Lost braces 49 | {\code{Delta}}{ Amount substituted across compositional parts.} | ^ checkRd: (-1) wsubmargins.Rd:50: Lost braces 50 | {\code{From}}{ Compositional part that is substituted from.} | ^ checkRd: (-1) wsubmargins.Rd:51: Lost braces 51 | {\code{To}}{ Compositional parts that is substituted to.} | ^ checkRd: (-1) wsubmargins.Rd:52: Lost braces 52 | {\code{Level}}{ Level where changes in composition takes place. Either \code{between} or \code{within}.} | ^ checkRd: (-1) wsubmargins.Rd:53: Lost braces 53 | {\code{Reference}}{ Either \code{grandmean}, \code{clustermean}, or \code{users}.} | ^ * 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 contents of ‘data’ directory ... OK * checking data for non-ASCII characters ... [0s/0s] 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 ... [11s/11s] OK * checking for unstated dependencies in ‘tests’ ... OK * checking tests ... [16s/11s] OK Running ‘testthat.R’ [16s/11s] * checking for unstated dependencies in vignettes ... OK * checking package vignettes ... OK * checking re-building of vignette outputs ... [4s/4s] OK * checking PDF version of manual ... [4s/4s] 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: 3 NOTEs