* using log directory 'd:/RCompile/CRANincoming/R-devel/iClusterVB.Rcheck' * using R Under development (unstable) (2024-07-20 r86909 ucrt) * using platform: x86_64-w64-mingw32 * R was compiled by gcc.exe (GCC) 13.2.0 GNU Fortran (GCC) 13.2.0 * running under: Windows Server 2022 x64 (build 20348) * using session charset: UTF-8 * checking for file 'iClusterVB/DESCRIPTION' ... OK * checking extension type ... Package * this is package 'iClusterVB' version '0.1.0' * package encoding: UTF-8 * checking CRAN incoming feasibility ... NOTE Maintainer: 'Abdalkarim Alnajjar ' New submission Possibly misspelled words in DESCRIPTION: iClusterVB (14:18) variational (14:53) Size of tarball: 16741579 bytes * 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 hidden files and directories ... OK * checking for portable file names ... OK * checking serialization versions ... OK * checking whether package 'iClusterVB' can be installed ... OK * used C++ compiler: 'g++.exe (GCC) 13.2.0' * checking installed package size ... OK * checking package directory ... OK * checking for future file timestamps ... OK * checking DESCRIPTION meta-information ... NOTE License components which are templates and need '+ file LICENSE': MIT * checking top-level files ... NOTE File LICENSE is not mentioned in the DESCRIPTION file. Non-standard files/directories found at top level: 'README.Rmd' 'README_files' 'sim_data.rda' * 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 ... 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 ... OK * checking S3 generic/method consistency ... WARNING plot: function(x, ...) plot.iClusterVB: function(fit) See section 'Generic functions and methods' in the 'Writing R Extensions' manual. * checking replacement functions ... OK * checking foreign function calls ... OK * checking R code for possible problems ... [11s] NOTE iClusterVB: no visible global function definition for 'kproto_gower' piplot: no visible binding for global variable 'varid' piplot: no visible binding for global variable 'rho' Undefined global functions or variables: kproto_gower rho varid * checking Rd files ... NOTE checkRd: (-1) iClusterVB.Rd:62: Lost braces; missing escapes or markup? 62 | {dim=c(N, p[[r]])}. Here, N is the sample size and p[[r]] is the number of | ^ checkRd: (-1) iClusterVB.Rd:88: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) iClusterVB.Rd:89: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) iClusterVB.Rd:90: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) iClusterVB.Rd:91: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) iClusterVB.Rd:92-97: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) laml.Rd:11-12: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) laml.Rd:13-14: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) laml.Rd:15-18: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) laml.Rd:19-23: Lost braces in \itemize; \value handles \item{}{} directly * checking Rd metadata ... OK * checking Rd line widths ... OK * checking Rd cross-references ... OK * checking for missing documentation entries ... WARNING Undocumented code objects: 'gene_symbols_500' 'laml.cli' 'laml.exp' 'laml.mut' Undocumented data sets: 'gene_symbols_500' 'laml.cli' 'laml.exp' 'laml.mut' All user-level objects in a package should have documentation entries. See chapter 'Writing R documentation files' in the 'Writing R Extensions' manual. * 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 ... OK * checking LazyData ... WARNING LazyData DB of 15.8 MB without LazyDataCompression set See ยง1.1.6 of 'Writing R Extensions' * checking data for ASCII and uncompressed saves ... WARNING Note: significantly better compression could be obtained by using R CMD build --resave-data old_size new_size compress laml.rda 12.0Mb 7.3Mb xz sim_data.rda 3.7Mb 1.8Mb xz * checking line endings in C/C++/Fortran sources/headers ... OK * checking line endings in Makefiles ... OK * checking compilation flags in Makevars ... OK * checking for GNU extensions in Makefiles ... OK * checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK * checking use of PKG_*FLAGS in Makefiles ... OK * checking use of SHLIB_OPENMP_*FLAGS in Makefiles ... OK * checking pragmas in C/C++ headers and code ... OK * checking compilation flags used ... OK * checking compiled code ... OK * checking examples ... OK * checking PDF version of manual ... [14s] OK * checking HTML version of manual ... OK * DONE Status: 4 WARNINGs, 5 NOTEs