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###
### Running command:
###
###   /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:alabaster.base.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/site-library --timings alabaster.base_1.0.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.17-bioc/meat/alabaster.base.Rcheck’
* using R version 4.3.1 (2023-06-16)
* using platform: x86_64-pc-linux-gnu (64-bit)
* R was compiled by
    gcc (Ubuntu 11.3.0-1ubuntu1~22.04.1) 11.3.0
    GNU Fortran (Ubuntu 11.3.0-1ubuntu1~22.04.1) 11.3.0
* running under: Ubuntu 22.04.3 LTS
* using session charset: UTF-8
* checking for file ‘alabaster.base/DESCRIPTION’ ... OK
* this is package ‘alabaster.base’ version ‘1.0.0’
* 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 ‘alabaster.base’ 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++17
* checking installed package size ... NOTE
  installed size is 13.4Mb
  sub-directories of 1Mb or more:
    libs  13.0Mb
* 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 line endings in Makefiles ... OK
* checking compilation flags in Makevars ... OK
* checking for GNU extensions in Makefiles ... NOTE
GNU make is a SystemRequirements.
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking use of PKG_*FLAGS in Makefiles ... OK
* checking compiled code ... WARNING
Note: information on .o files is not available
File ‘/home/biocbuild/bbs-3.17-bioc/R/site-library/alabaster.base/libs/alabaster.base.so’:
  Found ‘_ZSt4cerr’, possibly from ‘std::cerr’ (C++)
  Found ‘__sprintf_chk’, possibly from ‘sprintf’ (C)
  Found ‘abort’, possibly from ‘abort’ (C)
  Found ‘exit’, possibly from ‘exit’ (C)
  Found ‘rand_r’, possibly from ‘rand_r’ (C)
  Found ‘stderr’, possibly from ‘stderr’ (C)
  Found ‘stdout’, possibly from ‘stdout’ (C)

Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console, nor use Fortran I/O
nor system RNGs nor [v]sprintf. The detected symbols are linked into
the code but might come from libraries and not actually be called.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
* 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 ...
  ‘applications.Rmd’ using ‘UTF-8’... OK
  ‘extensions.Rmd’ using ‘UTF-8’... OK
  ‘userguide.Rmd’ using ‘UTF-8’... OK
 NONE
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: 1 WARNING, 2 NOTEs
See
  ‘/home/biocbuild/bbs-3.17-bioc/meat/alabaster.base.Rcheck/00check.log’
for details.

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### Running command:
###
###   /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD INSTALL alabaster.base
###
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* installing to library ‘/home/biocbuild/bbs-3.17-bioc/R/site-library’
* installing *source* package ‘alabaster.base’ ...
** using staged installation
** libs
using C++ compiler: ‘g++ (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’
using C++17
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I../inst/include -I'/home/biocbuild/bbs-3.17-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.17-bioc/R/site-library/Rhdf5lib/include' -I/usr/local/include    -fpic  -g -O2  -Wall -c RcppExports.cpp -o RcppExports.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I../inst/include -I'/home/biocbuild/bbs-3.17-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.17-bioc/R/site-library/Rhdf5lib/include' -I/usr/local/include    -fpic  -g -O2  -Wall -c check_csv.cpp -o check_csv.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I../inst/include -I'/home/biocbuild/bbs-3.17-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.17-bioc/R/site-library/Rhdf5lib/include' -I/usr/local/include    -fpic  -g -O2  -Wall -c check_list.cpp -o check_list.o
In file included from ../inst/include/uzuki2/uzuki2.hpp:14,
                 from check_list.cpp:3:
../inst/include/uzuki2/parse_hdf5.hpp: In instantiation of ‘std::shared_ptr<uzuki2::Base> uzuki2::hdf5::parse_inner(const H5::Group&, Externals&, const string&) [with Provisioner = uzuki2::DummyProvisioner; Externals = uzuki2::ExternalTracker<uzuki2::DummyExternals>; std::string = std::__cxx11::basic_string<char>]’:
../inst/include/uzuki2/parse_hdf5.hpp:442:50:   required from ‘std::shared_ptr<uzuki2::Base> uzuki2::Hdf5Parser::parse(const H5::Group&, const string&, Externals) [with Provisioner = uzuki2::DummyProvisioner; Externals = uzuki2::DummyExternals; std::string = std::__cxx11::basic_string<char>]’
../inst/include/uzuki2/parse_hdf5.hpp:521:32:   required from here
../inst/include/uzuki2/parse_hdf5.hpp:227:27: warning: comparison of integer expressions of different signedness: ‘int’ and ‘long long unsigned int’ [-Wsign-compare]
  227 |         for (int i = 0; i < len; ++i) {
      |                         ~~^~~~~
../inst/include/uzuki2/parse_hdf5.hpp:295:32: warning: comparison of integer expressions of different signedness: ‘int32_t’ {aka ‘int’} and ‘long long unsigned int’ [-Wsign-compare]
  295 |                 if (x < 0 || x >= levlen) {
      |                              ~~^~~~~~~~~
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I../inst/include -I'/home/biocbuild/bbs-3.17-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.17-bioc/R/site-library/Rhdf5lib/include' -I/usr/local/include    -fpic  -g -O2  -Wall -c load_csv.cpp -o load_csv.o
load_csv.cpp: In instantiation of ‘void RFilledField<T, tt, RVector>::add_missing() [with T = std::complex<double>; comservatory::Type tt = comservatory::COMPLEX; RVector = Rcpp::Vector<15>]’:
load_csv.cpp:36:10:   required from here
load_csv.cpp:37:22: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘R_xlen_t’ {aka ‘long int’} [-Wsign-compare]
   37 |         if (position >= store.size()) {
      |             ~~~~~~~~~^~~~~~~~~~~~~~~
load_csv.cpp: In instantiation of ‘void RFilledField<T, tt, RVector>::add_missing() [with T = bool; comservatory::Type tt = comservatory::BOOLEAN; RVector = Rcpp::Vector<10, Rcpp::PreserveStorage>]’:
load_csv.cpp:36:10:   required from here
load_csv.cpp:37:22: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘R_xlen_t’ {aka ‘long int’} [-Wsign-compare]
load_csv.cpp: In instantiation of ‘void RFilledField<T, tt, RVector>::push_back(T) [with T = bool; comservatory::Type tt = comservatory::BOOLEAN; RVector = Rcpp::Vector<10, Rcpp::PreserveStorage>]’:
load_csv.cpp:27:10:   required from here
load_csv.cpp:28:22: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘R_xlen_t’ {aka ‘long int’} [-Wsign-compare]
   28 |         if (position >= store.size()) {
      |             ~~~~~~~~~^~~~~~~~~~~~~~~
load_csv.cpp: In instantiation of ‘void RFilledField<T, tt, RVector>::add_missing() [with T = double; comservatory::Type tt = comservatory::NUMBER; RVector = Rcpp::Vector<14, Rcpp::PreserveStorage>]’:
load_csv.cpp:36:10:   required from here
load_csv.cpp:37:22: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘R_xlen_t’ {aka ‘long int’} [-Wsign-compare]
   37 |         if (position >= store.size()) {
      |             ~~~~~~~~~^~~~~~~~~~~~~~~
load_csv.cpp: In instantiation of ‘void RFilledField<T, tt, RVector>::push_back(T) [with T = double; comservatory::Type tt = comservatory::NUMBER; RVector = Rcpp::Vector<14, Rcpp::PreserveStorage>]’:
load_csv.cpp:27:10:   required from here
load_csv.cpp:28:22: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘R_xlen_t’ {aka ‘long int’} [-Wsign-compare]
   28 |         if (position >= store.size()) {
      |             ~~~~~~~~~^~~~~~~~~~~~~~~
load_csv.cpp: In instantiation of ‘void RFilledField<T, tt, RVector>::add_missing() [with T = std::__cxx11::basic_string<char>; comservatory::Type tt = comservatory::STRING; RVector = Rcpp::Vector<16>]’:
load_csv.cpp:36:10:   required from here
load_csv.cpp:37:22: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘R_xlen_t’ {aka ‘long int’} [-Wsign-compare]
   37 |         if (position >= store.size()) {
      |             ~~~~~~~~~^~~~~~~~~~~~~~~
load_csv.cpp: In instantiation of ‘void RFilledField<T, tt, RVector>::push_back(T) [with T = std::__cxx11::basic_string<char>; comservatory::Type tt = comservatory::STRING; RVector = Rcpp::Vector<16>]’:
load_csv.cpp:27:10:   required from here
load_csv.cpp:28:22: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘R_xlen_t’ {aka ‘long int’} [-Wsign-compare]
   28 |         if (position >= store.size()) {
      |             ~~~~~~~~~^~~~~~~~~~~~~~~
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I../inst/include -I'/home/biocbuild/bbs-3.17-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.17-bioc/R/site-library/Rhdf5lib/include' -I/usr/local/include    -fpic  -g -O2  -Wall -c load_list.cpp -o load_list.o
In file included from ../inst/include/uzuki2/uzuki2.hpp:14,
                 from load_list.cpp:3:
../inst/include/uzuki2/parse_hdf5.hpp: In instantiation of ‘std::shared_ptr<uzuki2::Base> uzuki2::hdf5::parse_inner(const H5::Group&, Externals&, const string&) [with Provisioner = uzuki2::DummyProvisioner; Externals = uzuki2::ExternalTracker<uzuki2::DummyExternals>; std::string = std::__cxx11::basic_string<char>]’:
../inst/include/uzuki2/parse_hdf5.hpp:442:50:   required from ‘std::shared_ptr<uzuki2::Base> uzuki2::Hdf5Parser::parse(const H5::Group&, const string&, Externals) [with Provisioner = uzuki2::DummyProvisioner; Externals = uzuki2::DummyExternals; std::string = std::__cxx11::basic_string<char>]’
../inst/include/uzuki2/parse_hdf5.hpp:521:32:   required from here
../inst/include/uzuki2/parse_hdf5.hpp:227:27: warning: comparison of integer expressions of different signedness: ‘int’ and ‘long long unsigned int’ [-Wsign-compare]
  227 |         for (int i = 0; i < len; ++i) {
      |                         ~~^~~~~
../inst/include/uzuki2/parse_hdf5.hpp:295:32: warning: comparison of integer expressions of different signedness: ‘int32_t’ {aka ‘int’} and ‘long long unsigned int’ [-Wsign-compare]
  295 |                 if (x < 0 || x >= levlen) {
      |                              ~~^~~~~~~~~
../inst/include/uzuki2/parse_hdf5.hpp: In instantiation of ‘std::shared_ptr<uzuki2::Base> uzuki2::hdf5::parse_inner(const H5::Group&, Externals&, const string&) [with Provisioner = RProvisioner; Externals = uzuki2::ExternalTracker<RExternals>; std::string = std::__cxx11::basic_string<char>]’:
../inst/include/uzuki2/parse_hdf5.hpp:442:50:   required from ‘std::shared_ptr<uzuki2::Base> uzuki2::Hdf5Parser::parse(const H5::Group&, const string&, Externals) [with Provisioner = RProvisioner; Externals = RExternals; std::string = std::__cxx11::basic_string<char>]’
../inst/include/uzuki2/parse_hdf5.hpp:486:34:   required from ‘std::shared_ptr<uzuki2::Base> uzuki2::Hdf5Parser::parse(const string&, const string&, Externals) [with Provisioner = RProvisioner; Externals = RExternals; std::string = std::__cxx11::basic_string<char>]’
load_list.cpp:288:56:   required from here
../inst/include/uzuki2/parse_hdf5.hpp:227:27: warning: comparison of integer expressions of different signedness: ‘int’ and ‘long long unsigned int’ [-Wsign-compare]
  227 |         for (int i = 0; i < len; ++i) {
      |                         ~~^~~~~
../inst/include/uzuki2/parse_hdf5.hpp:295:32: warning: comparison of integer expressions of different signedness: ‘int32_t’ {aka ‘int’} and ‘long long unsigned int’ [-Wsign-compare]
  295 |                 if (x < 0 || x >= levlen) {
      |                              ~~^~~~~~~~~
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I../inst/include -I'/home/biocbuild/bbs-3.17-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.17-bioc/R/site-library/Rhdf5lib/include' -I/usr/local/include    -fpic  -g -O2  -Wall -c write_scalar.cpp -o write_scalar.o
g++ -std=gnu++17 -shared -L/home/biocbuild/bbs-3.17-bioc/R/lib -L/usr/local/lib -o alabaster.base.so RcppExports.o check_csv.o check_list.o load_csv.o load_list.o write_scalar.o /home/biocbuild/bbs-3.17-bioc/R/site-library/Rhdf5lib/lib/libhdf5_cpp.a /home/biocbuild/bbs-3.17-bioc/R/site-library/Rhdf5lib/lib/libhdf5.a -lcrypto -lcurl -lsz -laec -lz -ldl -lm -lz -L/home/biocbuild/bbs-3.17-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.17-bioc/R/site-library/00LOCK-alabaster.base/00new/alabaster.base/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 (alabaster.base)

R version 4.3.1 (2023-06-16) -- "Beagle Scouts"
Copyright (C) 2023 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(alabaster.base)
> test_check("alabaster.base")
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 170 ]
> 
> proc.time()
   user  system elapsed 
 26.279   0.731  23.125