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###
### Running command:
###
###   E:\biocbuild\bbs-3.19-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:Rhdf5lib.install-out.txt --library=E:\biocbuild\bbs-3.19-bioc\R\library --no-vignettes --timings Rhdf5lib_1.26.0.tar.gz
###
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* using log directory 'E:/biocbuild/bbs-3.19-bioc/meat/Rhdf5lib.Rcheck'
* using R version 4.4.1 (2024-06-14 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 'Rhdf5lib/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'Rhdf5lib' version '1.26.0'
* 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 whether package 'Rhdf5lib' can be installed ... OK
* used C compiler: 'gcc.exe (GCC) 13.2.0'
* checking installed package size ... NOTE
  installed size is 18.9Mb
  sub-directories of 1Mb or more:
    include   2.5Mb
    lib      13.4Mb
    libs      2.8Mb
* 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 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 shell scripts ... 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 for x64 is not available
File 'E:/biocbuild/bbs-3.19-bioc/R/library/Rhdf5lib/libs/x64/Rhdf5lib.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 'tinytest.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
  'E:/biocbuild/bbs-3.19-bioc/meat/Rhdf5lib.Rcheck/00check.log'
for details.

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###
### Running command:
###
###   E:\biocbuild\bbs-3.19-bioc\R\bin\R.exe CMD INSTALL Rhdf5lib
###
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* installing to library 'E:/biocbuild/bbs-3.19-bioc/R/library'
* installing *source* package 'Rhdf5lib' ...
** using staged installation
untarring hdf5_headers_1.10.7.tar.gz ...
** libs
using C compiler: 'gcc.exe (GCC) 13.2.0'
mkdir -p "E:/biocbuild/bbs-3.19-bioc/R/library/00LOCK-Rhdf5lib/00new/Rhdf5lib/lib/x64-ucrt" "E:/biocbuild/bbs-3.19-bioc/R/library/00LOCK-Rhdf5lib/00new/Rhdf5lib/include"
"E:/biocbuild/bbs-3.19-bioc/R/bin/x64/Rscript.exe" "../tools/copy_hdf5_files.R" "E:/biocbuild/bbs-3.19-bioc/R/library/00LOCK-Rhdf5lib/00new/Rhdf5lib/lib/x64-ucrt" "E:/biocbuild/bbs-3.19-bioc/R/library/00LOCK-Rhdf5lib/00new/Rhdf5lib/include"
Copying libraries
Copying headers
Done
"E:/biocbuild/bbs-3.19-bioc/R/bin/x64/Rscript.exe" "../tools/winlibs.R" "E:/biocbuild/bbs-3.19-bioc/R/library/00LOCK-Rhdf5lib/00new/Rhdf5lib/lib/x64-ucrt"
Copying libcurl etc
gcc  -I"E:/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG     -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"  -I"E:/biocbuild/bbs-3.19-bioc/R/library/00LOCK-Rhdf5lib/00new/Rhdf5lib/include"   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c Rhdf5lib.c -o Rhdf5lib.o
gcc -shared -s -static-libgcc -o Rhdf5lib.dll tmp.def Rhdf5lib.o E:/biocbuild/bbs-3.19-bioc/R/library/00LOCK-Rhdf5lib/00new/Rhdf5lib/lib/x64-ucrt/libhdf5.a E:/biocbuild/bbs-3.19-bioc/R/library/00LOCK-Rhdf5lib/00new/Rhdf5lib/lib/x64-ucrt/libsz.a E:/biocbuild/bbs-3.19-bioc/R/library/00LOCK-Rhdf5lib/00new/Rhdf5lib/lib/x64-ucrt/libaec.a -lpsapi -lz -LC:/rtools44/x86_64-w64-mingw32.static.posix/lib/x64 -LC:/rtools44/x86_64-w64-mingw32.static.posix/lib -LE:/biocbuild/bbs-3.19-bioc/R/bin/x64 -lR
installing to E:/biocbuild/bbs-3.19-bioc/R/library/00LOCK-Rhdf5lib/00new/Rhdf5lib/libs/x64
** 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
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (Rhdf5lib)

R version 4.4.1 (2024-06-14 ucrt) -- "Race for Your Life"
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.

> if ( requireNamespace("tinytest", quietly=TRUE) ) {
+   tinytest::test_package("Rhdf5lib")
+ }

test_library_version.R........    1 tests OK 
test_library_version.R........    2 tests OK 75ms

test_link_flags.R.............    0 tests    
test_link_flags.R.............    0 tests    
test_link_flags.R.............    0 tests    
test_link_flags.R.............    0 tests    
test_link_flags.R.............    0 tests    
test_link_flags.R.............    1 tests OK 
test_link_flags.R.............    2 tests OK 
test_link_flags.R.............    3 tests OK 
test_link_flags.R.............    4 tests OK 
test_link_flags.R.............    5 tests OK 
test_link_flags.R.............    6 tests OK 
test_link_flags.R.............    7 tests OK 
test_link_flags.R.............    8 tests OK 0.7s
All ok, 10 results (0.8s)
> 
> proc.time()
   user  system elapsed 
   0.51    0.17    1.14