##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/R/R/bin/R CMD check --install=check:TEKRABber.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings TEKRABber_1.11.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.21-bioc/meat/TEKRABber.Rcheck’
* using R Under development (unstable) (2024-11-24 r87369)
* using platform: aarch64-unknown-linux-gnu
* R was compiled by
    aarch64-unknown-linux-gnu-gcc (GCC) 14.2.0
    GNU Fortran (GCC) 14.2.0
* running under: openEuler 24.03 (LTS)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘TEKRABber/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘TEKRABber’ version ‘1.11.0’
* 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 ‘TEKRABber’ can be installed ... OK
* used C++ compiler: ‘aarch64-unknown-linux-gnu-g++ (GCC) 14.2.0’
* 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 ...Warning: program compiled against libxml 212 using older 211
 NOTE
Problems with news in ‘NEWS.md’:
No news entries found.
* 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 whether startup messages can be suppressed ... OK
* checking dependencies in R code ... NOTE
Warning: program compiled against libxml 212 using older 211
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
File ‘TEKRABber/R/zzz.R’:
  .onLoad calls:
    packageStartupMessage(paste(messages, collapse = "\n"))

See section ‘Good practice’ in '?.onAttach'.

appTEKRABber: no visible global function definition for ‘grid_page’
appTEKRABber: no visible global function definition for
  ‘grid_card_text’
appTEKRABber: no visible global function definition for ‘grid_card’
appTEKRABber: no visible global function definition for ‘card_header’
appTEKRABber: no visible global function definition for ‘card_body’
appTEKRABber: no visible global function definition for
  ‘selectizeInput’
appTEKRABber: no visible global function definition for ‘actionButton’
appTEKRABber: no visible global function definition for ‘plotlyOutput’
appTEKRABber: no visible global function definition for ‘plotOutput’
appTEKRABber : server: no visible global function definition for
  ‘renderPlotly’
appTEKRABber : server: no visible global function definition for
  ‘plot_ly’
appTEKRABber : server: no visible global function definition for
  ‘observeEvent’
appTEKRABber : server: no visible global function definition for
  ‘renderPlot’
appTEKRABber : server: no visible global function definition for
  ‘ggplot’
appTEKRABber : server: no visible global function definition for ‘aes’
appTEKRABber : server: no visible binding for global variable ‘gene’
appTEKRABber : server: no visible binding for global variable ‘TE’
appTEKRABber : server: no visible global function definition for
  ‘geom_point’
appTEKRABber : server: no visible global function definition for ‘labs’
appTEKRABber : server: no visible global function definition for
  ‘geom_smooth’
appTEKRABber : server: no visible global function definition for
  ‘theme_bw’
appTEKRABber : server: no visible global function definition for
  ‘ggtitle’
appTEKRABber : server: no visible global function definition for
  ‘ggviolin’
appTEKRABber : server: no visible global function definition for ‘ylab’
appTEKRABber : server: no visible global function definition for ‘xlab’
appTEKRABber : server: no visible global function definition for
  ‘theme’
appTEKRABber: no visible global function definition for ‘shinyApp’
corrOrthologTE: no visible binding for global variable ‘i’
corrOrthologTE: no visible binding for global variable ‘j’
corrOrthologTE: no visible global function definition for ‘cor.test’
orthologScale: no visible global function definition for ‘desc’
orthologScale: no visible binding for global variable
  ‘orthologyConfidence’
orthologScale: no visible binding for global variable ‘refLength’
orthologScale: no visible binding for global variable ‘compareLength’
orthologScale: no visible global function definition for ‘across’
orthologScale: no visible binding for global variable ‘refLen’
orthologScale: no visible binding for global variable ‘compareLen’
prepareRMSK: no visible binding for global variable ‘repEnd’
prepareRMSK: no visible binding for global variable ‘repStart’
prepareRMSK: no visible binding for global variable ‘repName’
prepareRMSK: no visible binding for global variable ‘repClass’
prepareRMSK: no visible binding for global variable ‘rLen’
prepareRMSK: no visible binding for global variable ‘cLen’
Undefined global functions or variables:
  TE across actionButton aes cLen card_body card_header compareLen
  compareLength cor.test desc gene geom_point geom_smooth ggplot
  ggtitle ggviolin grid_card grid_card_text grid_page i j labs
  observeEvent orthologyConfidence plotOutput plot_ly plotlyOutput rLen
  refLen refLength renderPlot renderPlotly repClass repEnd repName
  repStart selectizeInput shinyApp theme theme_bw xlab ylab
Consider adding
  importFrom("stats", "cor.test")
to your NAMESPACE file.
* 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 contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... 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
prepareRMSK    530.031 14.571 909.117
DECorrInputs    61.721  1.602  77.606
orthologScale   56.949  1.576  76.629
corrOrthologTE  55.833  0.335  56.293
DEgeneTE        35.425  0.471  35.977
appTEKRABber    34.747  0.267  35.085
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’
 OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 4 NOTEs
See
  ‘/home/biocbuild/bbs-3.21-bioc/meat/TEKRABber.Rcheck/00check.log’
for details.

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/R/R/bin/R CMD INSTALL TEKRABber
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library’
* installing *source* package ‘TEKRABber’ ...
** using staged installation
** libs
using C++ compiler: ‘aarch64-unknown-linux-gnu-g++ (GCC) 14.2.0’
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-g++ -std=gnu++17 -I"/home/biocbuild/R/R/include" -DNDEBUG  -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/Rcpp/include' -I/usr/local/include    -fPIC  -g -O2  -Wall -Werror=format-security -DR_NO_REMAP -c RcppExports.cpp -o RcppExports.o
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-g++ -std=gnu++17 -I"/home/biocbuild/R/R/include" -DNDEBUG  -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/Rcpp/include' -I/usr/local/include    -fPIC  -g -O2  -Wall -Werror=format-security -DR_NO_REMAP -c rcpp_corr.cpp -o rcpp_corr.o
rcpp_corr.cpp:23: warning: ignoring ‘#pragma omp parallel’ [-Wunknown-pragmas]
   23 |     #pragma omp parallel for
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-g++ -std=gnu++17 -shared -L/home/biocbuild/R/R/lib -L/usr/local/lib -o TEKRABber.so RcppExports.o rcpp_corr.o -L/home/biocbuild/R/R/lib -lR
installing to /home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/00LOCK-TEKRABber/00new/TEKRABber/libs
** R
** data
** 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 (TEKRABber)

R Under development (unstable) (2024-11-24 r87369) -- "Unsuffered Consequences"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: aarch64-unknown-linux-gnu

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("TEKRABber")
Welcome to TEKRABber version 1.8.0
+ New function: prepareRMSK() for getting repeatmasker
+ New parameter: `numCore` in corrOrthologTE() for parallel computing
> test_check("TEKRABber")
Warning: program compiled against libxml 212 using older 211
[ FAIL 0 | WARN 0 | SKIP 1 | PASS 10 ]

══ Skipped tests (1) ═══════════════════════════════════════════════════════════
• On CRAN (1): 'test-corrOrthologTE.R:31:5'

[ FAIL 0 | WARN 0 | SKIP 1 | PASS 10 ]
> 
> proc.time()
   user  system elapsed 
188.938   1.984 212.866