##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/R/R/bin/R CMD check --install=check:NanoMethViz.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings NanoMethViz_3.3.2.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.21-bioc/meat/NanoMethViz.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 ‘NanoMethViz/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘NanoMethViz’ version ‘3.3.2’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... INFO
Imports includes 31 non-default packages.
Importing from so many packages makes the package vulnerable to any of
them becoming unavailable.  Move as many as possible to Suggests and
use conditionally.
* 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 ‘NanoMethViz’ can be installed ... OK
* used C++ compiler: ‘aarch64-unknown-linux-gnu-g++ (GCC) 14.2.0’
* checking C++ specification ... OK
  Not all R platforms support C++20
* checking installed package size ... INFO
  installed size is 10.5Mb
  sub-directories of 1Mb or more:
    libs   3.9Mb
* 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
 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 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
reformat_modkit: no visible binding for global variable ‘ref_position’
Undefined global functions or variables:
  ref_position
* 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 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 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
get_exons              55.590  1.486  59.147
filter_methy           29.786  0.203  31.097
get_exons_mus_musculus 16.317  0.080  16.746
get_exons_homo_sapiens 15.350  0.343  15.788
plot_gene              14.687  0.846  15.567
plot_gene_heatmap      11.475  0.595  12.094
plot_grange             9.511  0.312   9.840
plot_region             9.278  0.371   9.665
plot_grange_heatmap     7.956  0.375   8.348
plot_region_heatmap     7.888  0.167   8.070
plot_agg_regions        7.338  0.408   7.763
cluster_regions         6.694  0.148   7.077
NanoMethResult-class    4.809  0.152   5.106
* 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: 3 NOTEs
See
  ‘/home/biocbuild/bbs-3.21-bioc/meat/NanoMethViz.Rcheck/00check.log’
for details.

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


* installing to library ‘/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library’
* installing *source* package ‘NanoMethViz’ ...
** using staged installation
** libs
using C++ compiler: ‘aarch64-unknown-linux-gnu-g++ (GCC) 14.2.0’
using C++20
g++ -std=gnu++20 -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 -DR_NO_REMAP -c RcppExports.cpp -o RcppExports.o
g++ -std=gnu++20 -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 -DR_NO_REMAP -c convert_methy_to_dss.cpp -o convert_methy_to_dss.o
g++ -std=gnu++20 -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 -DR_NO_REMAP -c count_cg.cpp -o count_cg.o
g++ -std=gnu++20 -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 -DR_NO_REMAP -c genome.cpp -o genome.o
g++ -std=gnu++20 -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 -DR_NO_REMAP -c modbam.cpp -o modbam.o
g++ -std=gnu++20 -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 -DR_NO_REMAP -c utils.cpp -o utils.o
g++ -std=gnu++20 -shared -L/home/biocbuild/R/R/lib -L/usr/local/lib -o NanoMethViz.so RcppExports.o convert_methy_to_dss.o count_cg.o genome.o modbam.o utils.o -lz -L/home/biocbuild/R/R/lib -lR
installing to /home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/00LOCK-NanoMethViz/00new/NanoMethViz/libs
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
*** copying figures
** 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 (NanoMethViz)

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(NanoMethViz)
Loading required package: ggplot2
> 
> test_check("NanoMethViz")
Starting 2 test processes
[ FAIL 0 | WARN 0 | SKIP 3 | PASS 457 ]

══ Skipped tests (3) ═══════════════════════════════════════════════════════════
• empty test (3): 'test-cluster_regions.R:1:1', 'test-plot_agg_regions.R:1:1',
  'test-plot_region_heatmap.R:28:1'

[ FAIL 0 | WARN 0 | SKIP 3 | PASS 457 ]
> 
> proc.time()
   user  system elapsed 
254.927   5.877 170.037