##############################################################################
##############################################################################
###
### 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_3.3.4.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.21-bioc/meat/NanoMethViz.Rcheck’
* using R Under development (unstable) (2025-02-19 r87757)
* 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-SP1)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘NanoMethViz/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘NanoMethViz’ version ‘3.3.4’
* 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 ... 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 ... OK
* 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              63.139  1.628  89.936
filter_methy           30.169  0.222  39.198
get_exons_mus_musculus 16.764  0.242  21.873
get_exons_homo_sapiens 16.423  0.067  21.007
plot_gene              14.476  0.678  17.543
plot_gene_heatmap      12.512  0.327  14.700
plot_grange            10.609  0.127  12.834
plot_region            10.170  0.143  12.425
plot_region_heatmap    10.015  0.281  12.596
plot_grange_heatmap     8.595  0.155  10.628
plot_agg_regions        7.526  0.451  10.269
cluster_regions         5.670  0.036   7.042
NanoMethResult-class    4.885  0.188   6.318
* 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: 2 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-devel_2025-02-19/site-library’
* installing *source* package ‘NanoMethViz’ ...
** this is package ‘NanoMethViz’ version ‘3.3.4’
** using staged installation
** libs
using C++ compiler: ‘aarch64-unknown-linux-gnu-g++ (GCC) 14.2.0’
using C++20
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-g++ -std=gnu++20 -I"/home/biocbuild/R/R/include" -DNDEBUG  -I'/home/biocbuild/R/R-devel_2025-02-19/site-library/Rcpp/include' -I/usr/local/include    -fPIC  -g -O2  -Wall -Werror=format-security  -c RcppExports.cpp -o RcppExports.o
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-g++ -std=gnu++20 -I"/home/biocbuild/R/R/include" -DNDEBUG  -I'/home/biocbuild/R/R-devel_2025-02-19/site-library/Rcpp/include' -I/usr/local/include    -fPIC  -g -O2  -Wall -Werror=format-security  -c convert_methy_to_dss.cpp -o convert_methy_to_dss.o
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-g++ -std=gnu++20 -I"/home/biocbuild/R/R/include" -DNDEBUG  -I'/home/biocbuild/R/R-devel_2025-02-19/site-library/Rcpp/include' -I/usr/local/include    -fPIC  -g -O2  -Wall -Werror=format-security  -c count_cg.cpp -o count_cg.o
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-g++ -std=gnu++20 -I"/home/biocbuild/R/R/include" -DNDEBUG  -I'/home/biocbuild/R/R-devel_2025-02-19/site-library/Rcpp/include' -I/usr/local/include    -fPIC  -g -O2  -Wall -Werror=format-security  -c genome.cpp -o genome.o
genome.cpp: In member function ‘bool Genome::check_if_motif(const std::string&, int, const std::string&, int)’:
genome.cpp:43:21: warning: variable ‘chrom_view’ set but not used [-Wunused-but-set-variable]
   43 |         string_view chrom_view = this->bases_at(chrom, motif_start, motif_end);
      |                     ^~~~~~~~~~
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-g++ -std=gnu++20 -I"/home/biocbuild/R/R/include" -DNDEBUG  -I'/home/biocbuild/R/R-devel_2025-02-19/site-library/Rcpp/include' -I/usr/local/include    -fPIC  -g -O2  -Wall -Werror=format-security  -c modbam.cpp -o modbam.o
modbam.cpp: In function ‘GenomicModPos parse_bam(const std::string&, const std::string&, const std::string&, const std::string&, const std::string&, int)’:
modbam.cpp:331:44: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::basic_string_view<char>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  331 |                     while ( mod_string_end < mm_tok.size() && std::isalnum(mm_tok[mod_string_end]) ) {
      |                             ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~
modbam.cpp:339:40: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::basic_string_view<char>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  339 |                     if (mod_string_end == mm_tok.size() || mm_tok[mod_string_end] == '?') {
      |                         ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~
modbam.cpp:363:17: warning: ‘target_base’ may be used uninitialized [-Wmaybe-uninitialized]
  363 |                 if (seq.at(seq_ind) == target_base) {
      |                 ^~
modbam.cpp:305:14: note: ‘target_base’ was declared here
  305 |         char target_base;
      |              ^~~~~~~~~~~
modbam.cpp:364:21: warning: ‘parse_mode’ may be used uninitialized [-Wmaybe-uninitialized]
  364 |                     switch (parse_mode) {
      |                     ^~~~~~
modbam.cpp:308:19: note: ‘parse_mode’ was declared here
  308 |         ParseMode parse_mode;
      |                   ^~~~~~~~~~
In file included from /opt/ohpc/pub/compiler/gcc/14.2.0/include/c++/14.2.0/bits/stl_iterator.h:78,
                 from /opt/ohpc/pub/compiler/gcc/14.2.0/include/c++/14.2.0/bits/stl_algobase.h:67,
                 from /opt/ohpc/pub/compiler/gcc/14.2.0/include/c++/14.2.0/algorithm:60,
                 from modbam.cpp:1:
In function ‘constexpr decltype (::new(void*(0)) _Tp) std::construct_at(_Tp*, _Args&& ...) [with _Tp = char; _Args = {const char&}]’,
    inlined from ‘static constexpr void std::allocator_traits<std::allocator<_CharT> >::construct(allocator_type&, _Up*, _Args&& ...) [with _Up = char; _Args = {const char&}; _Tp = char]’ at /opt/ohpc/pub/compiler/gcc/14.2.0/include/c++/14.2.0/bits/alloc_traits.h:536:21,
    inlined from ‘constexpr void std::vector<_Tp, _Alloc>::_M_realloc_append(_Args&& ...) [with _Args = {const char&}; _Tp = char; _Alloc = std::allocator<char>]’ at /opt/ohpc/pub/compiler/gcc/14.2.0/include/c++/14.2.0/bits/vector.tcc:634:26,
    inlined from ‘constexpr void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = char; _Alloc = std::allocator<char>]’ at /opt/ohpc/pub/compiler/gcc/14.2.0/include/c++/14.2.0/bits/stl_vector.h:1294:21,
    inlined from ‘GenomicModPos parse_bam(const std::string&, const std::string&, const std::string&, const std::string&, const std::string&, int)’ at modbam.cpp:368:50:
/opt/ohpc/pub/compiler/gcc/14.2.0/include/c++/14.2.0/bits/stl_construct.h:97:14: warning: ‘current_base’ may be used uninitialized [-Wmaybe-uninitialized]
   97 |     { return ::new((void*)__location) _Tp(std::forward<_Args>(__args)...); }
      |              ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
modbam.cpp: In function ‘GenomicModPos parse_bam(const std::string&, const std::string&, const std::string&, const std::string&, const std::string&, int)’:
modbam.cpp:304:14: note: ‘current_base’ was declared here
  304 |         char current_base;
      |              ^~~~~~~~~~~~
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-g++ -std=gnu++20 -I"/home/biocbuild/R/R/include" -DNDEBUG  -I'/home/biocbuild/R/R-devel_2025-02-19/site-library/Rcpp/include' -I/usr/local/include    -fPIC  -g -O2  -Wall -Werror=format-security  -c utils.cpp -o utils.o
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-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-devel_2025-02-19/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) (2025-02-19 r87757) -- "Unsuffered Consequences"
Copyright (C) 2025 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 0 | PASS 631 ]
> 
> proc.time()
   user  system elapsed 
269.128   7.033 217.030