* using log directory ‘/srv/hornik/tmp/CRAN/iClusterVB.Rcheck’
* using R Under development (unstable) (2024-07-20 r86909)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    Debian clang version 18.1.8 (1+b1)
    Debian flang-new version 18.1.8 (1+b1)
* running under: Debian GNU/Linux trixie/sid
* 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 ... [3s/5s] NOTE
Maintainer: ‘Abdalkarim Alnajjar <abdalkarim.alnajjar@queensu.ca>’

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 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 ‘iClusterVB’ can be installed ... [41s/41s] WARNING
Found the following significant warnings:
  CAVI_algorithm_global_version.cpp:585:11: warning: using integer absolute value function 'abs' when argument is of floating point type [-Wabsolute-value]
  CAVI_algorithm_standard_version.cpp:472:11: warning: using integer absolute value function 'abs' when argument is of floating point type [-Wabsolute-value]
See ‘/srv/hornik/tmp/CRAN/iClusterVB.Rcheck/00install.out’ for details.
* used C++ compiler: ‘Debian clang version 18.1.8 (3)’
* 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 ... [2s/2s] OK
* checking whether the package can be loaded with stated dependencies ... [1s/1s] OK
* checking whether the package can be unloaded cleanly ... [1s/1s] OK
* checking whether the namespace can be loaded with stated dependencies ... [1s/1s] 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 ... 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 ... [8s/8s] 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 ... [0s/0s] 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 ... [0s/0s] OK
* checking LazyData ... WARNING
  LazyData DB of 15.8 MB without LazyDataCompression set
  See §1.1.6 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 ... [3s/3s] OK
* checking PDF version of manual ... [3s/3s] OK
* checking HTML version of manual ... [0s/0s] OK
* checking for non-standard things in the check directory ... OK
* checking for detritus in the temp directory ... OK
* DONE
Status: 5 WARNINGs, 5 NOTEs