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###
### Running command:
###
###   F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:CardinalIO.install-out.txt --library=F:\biocbuild\bbs-3.20-bioc\R\library --no-vignettes --timings CardinalIO_1.3.0.tar.gz
###
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* using log directory 'F:/biocbuild/bbs-3.20-bioc/meat/CardinalIO.Rcheck'
* using R version 4.4.0 RC (2024-04-16 r86468 ucrt)
* using platform: x86_64-w64-mingw32
* R was compiled by
    gcc.exe (GCC) 13.2.0
    GNU Fortran (GCC) 13.2.0
* running under: Windows Server 2022 x64 (build 20348)
* using session charset: UTF-8
* using option '--no-vignettes'
* checking for file 'CardinalIO/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'CardinalIO' version '1.3.0'
* 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 'CardinalIO' can be installed ... OK
* used C++ compiler: 'G__~1.EXE (GCC) 13.2.0'
* 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 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 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 compiled code ... NOTE
Note: information on .o files for x64 is not available
File 'F:/biocbuild/bbs-3.20-bioc/R/library/CardinalIO/libs/x64/CardinalIO.dll':
  Found '_exit', possibly from '_exit' (C)
  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'
 ERROR
Running the tests in 'tests/testthat.R' failed.
Last 13 lines of output:
  Loading required package: BiocParallel
  Loading required package: Matrix
  Loading required package: ontologyIndex
  > 
  > test_check("CardinalIO")
  [ FAIL 1 | WARN 0 | SKIP 0 | PASS 140 ]
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Failure ('test-Analyze75.R:28:2'): Analyze 7.5 - write/parse ────────────────
  `intensity` not equal to `intensity2`.
  Attributes: < Component "dim": Numeric: lengths (3, 4) differ >
  
  [ FAIL 1 | WARN 0 | SKIP 0 | PASS 140 ]
  Error: Test failures
  Execution halted
* 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: 1 ERROR, 1 NOTE
See
  'F:/biocbuild/bbs-3.20-bioc/meat/CardinalIO.Rcheck/00check.log'
for details.

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###
### Running command:
###
###   F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD INSTALL CardinalIO
###
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* installing to library 'F:/biocbuild/bbs-3.20-bioc/R/library'
* installing *source* package 'CardinalIO' ...
** using staged installation
** libs
using C++ compiler: 'G__~1.EXE (GCC) 13.2.0'
g++ -std=gnu++17  -I"F:/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG     -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c CardinalIO.cpp -o CardinalIO.o
In file included from CardinalIO.h:5,
                 from CardinalIO.cpp:2:
imzML.h: In member function 'int imzML::get_params(pugi::xml_node, int, SEXP, SEXP)':
imzML.h:346:43: warning: comparison of integer expressions of different signedness: 'size_t' {aka 'long long unsigned int'} and 'int' [-Wsign-compare]
  346 |                         while ( node && i < count ) {
      |                                         ~~^~~~~~~
imzML.h:367:32: warning: comparison of integer expressions of different signedness: 'size_t' {aka 'long long unsigned int'} and 'int' [-Wsign-compare]
  367 |                         if ( i != count )
      |                              ~~^~~~~~~~
g++ -std=gnu++17  -I"F:/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG     -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c init.cpp -o init.o
In file included from CardinalIO.h:5,
                 from init.cpp:3:
imzML.h: In member function 'int imzML::get_params(pugi::xml_node, int, SEXP, SEXP)':
imzML.h:346:43: warning: comparison of integer expressions of different signedness: 'size_t' {aka 'long long unsigned int'} and 'int' [-Wsign-compare]
  346 |                         while ( node && i < count ) {
      |                                         ~~^~~~~~~
imzML.h:367:32: warning: comparison of integer expressions of different signedness: 'size_t' {aka 'long long unsigned int'} and 'int' [-Wsign-compare]
  367 |                         if ( i != count )
      |                              ~~^~~~~~~~
g++ -std=gnu++17  -I"F:/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG     -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c pugixml.cpp -o pugixml.o
pugixml.cpp:2303:23: warning: 'void pugi::impl::{anonymous}::as_utf8_end(char*, size_t, const wchar_t*, size_t)' defined but not used [-Wunused-function]
 2303 |         PUGI__FN void as_utf8_end(char* buffer, size_t size, const wchar_t* str, size_t length)
      |                       ^~~~~~~~~~~
pugixml.cpp:2297:25: warning: 'size_t pugi::impl::{anonymous}::as_utf8_begin(const wchar_t*, size_t)' defined but not used [-Wunused-function]
 2297 |         PUGI__FN size_t as_utf8_begin(const wchar_t* str, size_t length)
      |                         ^~~~~~~~~~~~~
pugixml.cpp:248:25: warning: 'size_t pugi::impl::{anonymous}::strlength_wide(const wchar_t*)' defined but not used [-Wunused-function]
  248 |         PUGI__FN size_t strlength_wide(const wchar_t* s)
      |                         ^~~~~~~~~~~~~~
g++ -std=gnu++17 -shared -s -static-libgcc -o CardinalIO.dll tmp.def CardinalIO.o init.o pugixml.o -LC:/rtools44/x86_64-w64-mingw32.static.posix/lib/x64 -LC:/rtools44/x86_64-w64-mingw32.static.posix/lib -LF:/biocbuild/bbs-3.20-bioc/R/bin/x64 -lR
installing to F:/biocbuild/bbs-3.20-bioc/R/library/00LOCK-CardinalIO/00new/CardinalIO/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 (CardinalIO)

R version 4.4.0 RC (2024-04-16 r86468 ucrt) -- "Puppy Cup"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64

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(CardinalIO)
Loading required package: matter
Loading required package: BiocParallel
Loading required package: Matrix
Loading required package: ontologyIndex
> 
> test_check("CardinalIO")
[ FAIL 1 | WARN 0 | SKIP 0 | PASS 140 ]

══ Failed tests ════════════════════════════════════════════════════════════════
── Failure ('test-Analyze75.R:28:2'): Analyze 7.5 - write/parse ────────────────
`intensity` not equal to `intensity2`.
Attributes: < Component "dim": Numeric: lengths (3, 4) differ >

[ FAIL 1 | WARN 0 | SKIP 0 | PASS 140 ]
Error: Test failures
Execution halted