* using log directory 'd:/RCompile/CRANincoming/R-devel/PCGII.Rcheck' * using R Under development (unstable) (2024-01-25 r85826 ucrt) * using platform: x86_64-w64-mingw32 * R was compiled by gcc.exe (GCC) 12.3.0 GNU Fortran (GCC) 12.3.0 * running under: Windows Server 2022 x64 (build 20348) * using session charset: UTF-8 * checking for file 'PCGII/DESCRIPTION' ... OK * checking extension type ... Package * this is package 'PCGII' version '1.1.2' * package encoding: UTF-8 * checking CRAN incoming feasibility ... NOTE Maintainer: 'Hao Wang ' New submission The Description field should not start with the package name, 'This package' or similar. * checking package namespace information ... OK * checking package dependencies ... NOTE Depends: includes the non-default packages: 'corpcor', 'igraph', 'tidyverse', 'Matrix', 'mvtnorm', 'glmnet' Adding so many packages to the search path is excessive and importing selectively is preferable. * checking if this is a source package ... OK * checking if there is a namespace ... OK * checking for hidden files and directories ... OK * checking for portable file names ... OK * checking serialization versions ... OK * checking whether package 'PCGII' can be installed ... OK * checking installed package size ... 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 ... OK * checking whether the package can be loaded with stated dependencies ... OK * checking whether the package can be unloaded cleanly ... OK * checking whether the namespace can be loaded with stated dependencies ... OK * checking whether the namespace can be unloaded cleanly ... OK * checking loading without being on the library search path ... OK * checking use of S3 registration ... OK * checking dependencies in R code ... NOTE 'library' or 'require' calls to packages already attached by Depends: 'Matrix' 'corpcor' 'glmnet' 'igraph' 'tidyverse' Please remove these calls from your code. Packages in Depends field not imported from: 'Matrix' 'corpcor' 'glmnet' 'igraph' 'mvtnorm' 'tidyverse' These packages need to be imported from (in the NAMESPACE file) for when this namespace is loaded but not attached. * checking S3 generic/method consistency ... OK * checking replacement functions ... OK * checking foreign function calls ... OK * checking R code for possible problems ... NOTE PCGII: no visible global function definition for 'sd' PCGII: no visible global function definition for 'glmnet' PCGII: no visible binding for global variable 'sd' PCGII: no visible global function definition for 'predict' clevel: no visible global function definition for 'sd' clevel: no visible global function definition for 'glmnet' clevel: no visible global function definition for 'predict' clevel: no visible binding for global variable 'sd' inference: no visible global function definition for 'pnorm' makeBlockDiag: no visible global function definition for 'runif' makeBlockDiag: no visible global function definition for 'is.positive.definite' make_random_precision_mat: no visible global function definition for 'sample_gnp' make_random_precision_mat: no visible global function definition for 'as_adjacency_matrix' make_random_precision_mat: no visible global function definition for 'runif' make_sf_precision_mat: no visible global function definition for 'sample_pa' make_sf_precision_mat: no visible global function definition for 'as_adjacency_matrix' make_sf_precision_mat: no visible global function definition for 'runif' undirected_prior: no visible global function definition for '%>%' undirected_prior: no visible global function definition for 'arrange' Undefined global functions or variables: %>% arrange as_adjacency_matrix glmnet is.positive.definite pnorm predict runif sample_gnp sample_pa sd Consider adding importFrom("stats", "pnorm", "predict", "runif", "sd") to your NAMESPACE file. * checking Rd files ... NOTE checkRd: (-1) make_sf_precision_mat.Rd:17: Lost braces; missing escapes or markup? 17 | \item{e}{Numeric constant, the number of edges to add in each time step, see sample_pa {igraph}.} | ^ checkRd: (-1) make_sf_precision_mat.Rd:19: Lost braces; missing escapes or markup? 19 | \item{power}{Numeric constant, the power of the preferential attachment for scale-free network, the default is 1, , see sample_pa {igraph}.} | ^ * checking Rd metadata ... OK * checking Rd line widths ... NOTE Rd file 'PCGII.Rd': \examples lines wider than 100 characters: net %>% plot(vertex.size=4, vertex.label.dist=0.5, vertex.color="red", edge.arrow.size=0.5, layout=layout_in_circle(net)) Rd file 'clevel.Rd': \examples lines wider than 100 characters: net %>% plot(vertex.size=4, vertex.label.dist=0.5, vertex.color="red", edge.arrow.size=0.5, layout=layout_in_circle(net)) Rd file 'inference.Rd': \examples lines wider than 100 characters: net %>% plot(vertex.size=4, vertex.label.dist=0.5, vertex.color="red", edge.arrow.size=0.5, layout=layout_in_circle(net)) Rd file 'undirected_prior.Rd': \examples lines wider than 100 characters: prior=as.data.frame(matrix(c(1,2,1,5,1,10), ncol=2, byrow=TRUE)) ## a prior set of 3 connections (1-2, 1-3, 1-10) ## Remark: this function is not necessary. Prior set should be considered carefully before running the network analysis. If the prior n ... [TRUNCATED] 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 installed files from 'inst/doc' ... OK * checking files in 'vignettes' ... OK * checking examples ... OK * checking for unstated dependencies in 'tests' ... OK * checking tests ... OK Running 'testthat.R' * checking for unstated dependencies in vignettes ... OK * checking package vignettes ... OK * checking re-building of vignette outputs ... OK * checking PDF version of manual ... [11s] WARNING LaTeX errors when creating PDF version. This typically indicates Rd problems. LaTeX errors found: ! LaTeX Error: Unicode character − (U+2212) not set up for use with LaTeX. See the LaTeX manual or LaTeX Companion for explanation. Type H for immediate help. ! LaTeX Error: Unicode character − (U+2212) not set up for use with LaTeX. See the LaTeX manual or LaTeX Companion for explanation. Type H for immediate help. ! LaTeX Error: Unicode character ∪ (U+222A) not set up for use with LaTeX. See the LaTeX manual or LaTeX Companion for explanation. Type H for immediate help. ! LaTeX Error: Unicode character − (U+2212) not set up for use with LaTeX. See the LaTeX manual or LaTeX Companion for explanation. Type H for immediate help. ! LaTeX Error: Unicode character − (U+2212) not set up for use with LaTeX. See the LaTeX manual or LaTeX Companion for explanation. Type H for immediate help. ! LaTeX Error: Unicode character ∪ (U+222A) not set up for use with LaTeX. See the LaTeX manual or LaTeX Companion for explanation. Type H for immediate help. * checking PDF version of manual without index ... ERROR * checking HTML version of manual ... OK * DONE Status: 1 ERROR, 1 WARNING, 6 NOTEs