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### Running command:
###
###   /home/biocbuild/bbs-3.18-bioc/R/bin/R CMD check --install=check:HiLDA.install-out.txt --library=/home/biocbuild/bbs-3.18-bioc/R/site-library --timings HiLDA_1.16.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.18-bioc/meat/HiLDA.Rcheck’
* using R version 4.3.3 (2024-02-29)
* using platform: x86_64-pc-linux-gnu (64-bit)
* R was compiled by
    gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
    GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
* running under: Ubuntu 22.04.4 LTS
* using session charset: UTF-8
* checking for file ‘HiLDA/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘HiLDA’ version ‘1.16.0’
* package encoding: UTF-8
* 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 for sufficient/correct file permissions ... OK
* checking whether package ‘HiLDA’ can be installed ... OK
* used C++ compiler: ‘g++ (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’
* checking installed package size ... OK
* checking package directory ... 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 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 ... OK
* checking Rd files ... OK
* checking Rd metadata ... 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 line endings in C/C++/Fortran sources/headers ... OK
* checking compiled code ... NOTE
Note: information on .o files is not available
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                    user system elapsed
hildaTest         75.611  0.120  75.732
hildaGlobalResult 38.310  0.108  38.758
hildaReadMPFile   14.867  0.544  15.428
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’
 OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ...
  ‘HiLDA.Rmd’ using ‘UTF-8’... OK
 OK
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: 1 NOTE
See
  ‘/home/biocbuild/bbs-3.18-bioc/meat/HiLDA.Rcheck/00check.log’
for details.

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### Running command:
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###   /home/biocbuild/bbs-3.18-bioc/R/bin/R CMD INSTALL HiLDA
###
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* installing to library ‘/home/biocbuild/bbs-3.18-bioc/R/site-library’
* installing *source* package ‘HiLDA’ ...
** using staged installation
** libs
using C++ compiler: ‘g++ (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.18-bioc/R/site-library/Rcpp/include' -I/usr/local/include    -fpic  -g -O2  -Wall -c EMalgorithm.cpp -o EMalgorithm.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.18-bioc/R/site-library/Rcpp/include' -I/usr/local/include    -fpic  -g -O2  -Wall -c RcppExports.cpp -o RcppExports.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.18-bioc/R/site-library/Rcpp/include' -I/usr/local/include    -fpic  -g -O2  -Wall -c checkBoundary.cpp -o checkBoundary.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.18-bioc/R/site-library/Rcpp/include' -I/usr/local/include    -fpic  -g -O2  -Wall -c convertFromToVector.cpp -o convertFromToVector.o
g++ -std=gnu++17 -shared -L/home/biocbuild/bbs-3.18-bioc/R/lib -L/usr/local/lib -o HiLDA.so EMalgorithm.o RcppExports.o checkBoundary.o convertFromToVector.o -L/home/biocbuild/bbs-3.18-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.18-bioc/R/site-library/00LOCK-HiLDA/00new/HiLDA/libs
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (HiLDA)

R version 4.3.3 (2024-02-29) -- "Angel Food Cake"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> library(testthat)
> library(HiLDA)
Loading required package: ggplot2
> 
> test_check("HiLDA")
#trial:  1; #iteration:   16; time(s): 0.03; convergence: TRUE; loglikelihood: -8202.3313
#trial:  2; #iteration:   13; time(s): 0.02; convergence: TRUE; loglikelihood: -8202.3334
#trial:  3; #iteration:   39; time(s): 0.07; convergence: TRUE; loglikelihood: -8202.3184
#trial:  4; #iteration:   22; time(s): 0.03; convergence: TRUE; loglikelihood: -8202.3185
#trial:  5; #iteration:   15; time(s): 0.02; convergence: TRUE; loglikelihood: -8202.3184
#trial:  6; #iteration:   16; time(s): 0.02; convergence: TRUE; loglikelihood: -8202.5202
#trial:  7; #iteration:   22; time(s): 0.04; convergence: TRUE; loglikelihood: -8202.3185
#trial:  8; #iteration:   12; time(s): 0.02; convergence: TRUE; loglikelihood: -8202.3184
#trial:  9; #iteration:   11; time(s): 0.02; convergence: TRUE; loglikelihood: -8202.3184
#trial: 10; #iteration:   13; time(s): 0.02; convergence: TRUE; loglikelihood: -8202.3330
[ FAIL 0 | WARN 2 | SKIP 0 | PASS 4 ]

[ FAIL 0 | WARN 2 | SKIP 0 | PASS 4 ]
> 
> proc.time()
   user  system elapsed 
  3.093   0.121   3.205