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### Running command:
###
###   /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD check --install=check:NanoMethViz.install-out.txt --library=/home/biocbuild/bbs-3.19-bioc/R/site-library --timings NanoMethViz_3.0.2.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.19-bioc/meat/NanoMethViz.Rcheck’
* using R version 4.4.1 (2024-06-14)
* using platform: x86_64-pc-linux-gnu
* 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 ‘NanoMethViz/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘NanoMethViz’ version ‘3.0.2’
* 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 ‘NanoMethViz’ can be installed ... OK
* used C++ compiler: ‘g++ (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’
* checking C++ specification ... OK
  Not all R platforms support C++20
* checking installed package size ... NOTE
  installed size is  6.9Mb
  sub-directories of 1Mb or more:
    libs   1.8Mb
* 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
read_methy_lines: no visible global function definition for
  ‘read.delim’
Undefined global functions or variables:
  read.delim
Consider adding
  importFrom("utils", "read.delim")
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 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              38.551  2.012  40.633
get_exons_homo_sapiens 11.366  0.592  11.959
get_exons_mus_musculus 11.741  0.160  11.900
plot_gene               7.596  0.084   7.680
plot_gene_heatmap       6.455  0.116   6.571
plot_grange             5.754  0.068   5.822
plot_region             5.547  0.028   5.575
* 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 re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: 3 NOTEs
See
  ‘/home/biocbuild/bbs-3.19-bioc/meat/NanoMethViz.Rcheck/00check.log’
for details.

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###
### Running command:
###
###   /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD INSTALL NanoMethViz
###
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* installing to library ‘/home/biocbuild/bbs-3.19-bioc/R/site-library’
* installing *source* package ‘NanoMethViz’ ...
** using staged installation
** libs
using C++ compiler: ‘g++ (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’
using C++20
g++ -std=gnu++20 -I"/home/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/Rcpp/include' -I/usr/local/include    -fpic  -g -O2  -Wall  -c RcppExports.cpp -o RcppExports.o
g++ -std=gnu++20 -I"/home/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/Rcpp/include' -I/usr/local/include    -fpic  -g -O2  -Wall  -c convert_methy_to_dss.cpp -o convert_methy_to_dss.o
g++ -std=gnu++20 -I"/home/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/Rcpp/include' -I/usr/local/include    -fpic  -g -O2  -Wall  -c count_cg.cpp -o count_cg.o
g++ -std=gnu++20 -I"/home/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/Rcpp/include' -I/usr/local/include    -fpic  -g -O2  -Wall  -c modbam.cpp -o modbam.o
modbam.cpp: In function ‘GenomicModPos parse_bam(const string&, const string&, const string&, const string&, const string&, int)’:
modbam.cpp:394:44: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::basic_string_view<char>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  394 |                     while ( mod_string_end < mm_tok.size() && std::isalnum(mm_tok[mod_string_end]) ) {
      |                             ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~
modbam.cpp:400:40: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::basic_string_view<char>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  400 |                     if (mod_string_end == mm_tok.size() || mm_tok[mod_string_end] == '.') {
      |                         ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~
modbam.cpp:425:17: warning: ‘parse_mode’ may be used uninitialized in this function [-Wmaybe-uninitialized]
  425 |                 if (parse_mode == ParseMode::skip_low_prob) {
      |                 ^~
modbam.cpp:426:21: warning: ‘target_base’ may be used uninitialized in this function [-Wmaybe-uninitialized]
  426 |                     if (seq.at(seq_ind) == target_base) {
      |                     ^~
g++ -std=gnu++20 -I"/home/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/Rcpp/include' -I/usr/local/include    -fpic  -g -O2  -Wall  -c utils.cpp -o utils.o
g++ -std=gnu++20 -shared -L/home/biocbuild/bbs-3.19-bioc/R/lib -L/usr/local/lib -o NanoMethViz.so RcppExports.o convert_methy_to_dss.o count_cg.o modbam.o utils.o -lz -L/home/biocbuild/bbs-3.19-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.19-bioc/R/site-library/00LOCK-NanoMethViz/00new/NanoMethViz/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 (NanoMethViz)

R version 4.4.1 (2024-06-14) -- "Race for Your Life"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-pc-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 580 ]
> 
> proc.time()
   user  system elapsed 
155.076  13.119 116.038