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###
### Running command:
###
###   F:\biocbuild\bbs-3.17-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:alabaster.base.install-out.txt --library=F:\biocbuild\bbs-3.17-bioc\R\library --no-vignettes --timings alabaster.base_1.0.0.tar.gz
###
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* using log directory 'F:/biocbuild/bbs-3.17-bioc/meat/alabaster.base.Rcheck'
* using R version 4.3.1 (2023-06-16 ucrt)
* using platform: x86_64-w64-mingw32 (64-bit)
* R was compiled by
    gcc.exe (GCC) 12.2.0
    GNU Fortran (GCC) 12.2.0
* running under: Windows Server 2022 x64 (build 20348)
* using session charset: UTF-8
* using option '--no-vignettes'
* 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 whether package 'alabaster.base' can be installed ... OK
* used C++ compiler: 'G__~1.EXE (GCC) 12.2.0'
* checking C++ specification ... OK
  Not all R platforms support C++17
* 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 ... 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 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 ... NOTE
Note: information on .o files for x64 is not available
File 'F:/biocbuild/bbs-3.17-bioc/R/library/alabaster.base/libs/x64/alabaster.base.dll':
  Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
  Found 'exit', possibly from 'exit' (C), 'stop' (Fortran)

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 ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 2 NOTEs
See
  'F:/biocbuild/bbs-3.17-bioc/meat/alabaster.base.Rcheck/00check.log'
for details.

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###
### Running command:
###
###   F:\biocbuild\bbs-3.17-bioc\R\bin\R.exe CMD INSTALL alabaster.base
###
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* installing to library 'F:/biocbuild/bbs-3.17-bioc/R/library'
* installing *source* package 'alabaster.base' ...
** using staged installation
** libs
using C++ compiler: 'G__~1.EXE (GCC) 12.2.0'
using C++17
g++  -std=gnu++17 -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I../inst/include -I'F:/biocbuild/bbs-3.17-bioc/R/library/Rcpp/include' -I'F:/biocbuild/bbs-3.17-bioc/R/library/Rhdf5lib/include'   -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c RcppExports.cpp -o RcppExports.o
g++  -std=gnu++17 -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I../inst/include -I'F:/biocbuild/bbs-3.17-bioc/R/library/Rcpp/include' -I'F:/biocbuild/bbs-3.17-bioc/R/library/Rhdf5lib/include'   -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c check_csv.cpp -o check_csv.o
g++  -std=gnu++17 -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I../inst/include -I'F:/biocbuild/bbs-3.17-bioc/R/library/Rcpp/include' -I'F:/biocbuild/bbs-3.17-bioc/R/library/Rhdf5lib/include'   -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -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 std::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 std::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"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I../inst/include -I'F:/biocbuild/bbs-3.17-bioc/R/library/Rcpp/include' -I'F:/biocbuild/bbs-3.17-bioc/R/library/Rhdf5lib/include'   -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -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 long unsigned int'} and 'R_xlen_t' {aka 'long 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 long unsigned int'} and 'R_xlen_t' {aka 'long 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 long unsigned int'} and 'R_xlen_t' {aka 'long 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 long unsigned int'} and 'R_xlen_t' {aka 'long 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 long unsigned int'} and 'R_xlen_t' {aka 'long 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 long unsigned int'} and 'R_xlen_t' {aka 'long 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 long unsigned int'} and 'R_xlen_t' {aka 'long long int'} [-Wsign-compare]
   28 |         if (position >= store.size()) {
      |             ~~~~~~~~~^~~~~~~~~~~~~~~
g++  -std=gnu++17 -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I../inst/include -I'F:/biocbuild/bbs-3.17-bioc/R/library/Rcpp/include' -I'F:/biocbuild/bbs-3.17-bioc/R/library/Rhdf5lib/include'   -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -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 std::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 std::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 std::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 std::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 std::string&, const std::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"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I../inst/include -I'F:/biocbuild/bbs-3.17-bioc/R/library/Rcpp/include' -I'F:/biocbuild/bbs-3.17-bioc/R/library/Rhdf5lib/include'   -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c write_scalar.cpp -o write_scalar.o
g++ -shared -s -static-libgcc -o alabaster.base.dll tmp.def RcppExports.o check_csv.o check_list.o load_csv.o load_list.o write_scalar.o -LF:/biocbuild/bbs-3.17-bioc/R/library/Rhdf5lib/lib/x64-ucrt -lhdf5_cpp -lhdf5 -lcurl -lssh2 -lssl -lcrypto -lwldap32 -lws2_32 -lcrypt32 -lsz -laec -lz -lpsapi -lz -LC:/rtools43/x86_64-w64-mingw32.static.posix/lib/x64 -LC:/rtools43/x86_64-w64-mingw32.static.posix/lib -LF:/biocbuild/bbs-3.17-bioc/R/bin/x64 -lR
installing to F:/biocbuild/bbs-3.17-bioc/R/library/00LOCK-alabaster.base/00new/alabaster.base/libs/x64
** 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
** 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 ucrt) -- "Beagle Scouts"
Copyright (C) 2023 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64 (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 172 ]
> 
> proc.time()
   user  system elapsed 
  20.65    1.70   24.84