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### Running command:
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###   F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:HDF5Array.install-out.txt --library=F:\biocbuild\bbs-3.20-bioc\R\library --no-vignettes --timings HDF5Array_1.34.0.tar.gz
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* using log directory 'F:/biocbuild/bbs-3.20-bioc/meat/HDF5Array.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 'HDF5Array/DESCRIPTION' ... OK
* this is package 'HDF5Array' version '1.34.0'
* 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 ... NOTE
Found the following hidden files and directories:
  .BBSoptions
These were most likely included in error. See section 'Package
structure' in the 'Writing R Extensions' manual.
* checking for portable file names ... OK
* checking whether package 'HDF5Array' can be installed ... WARNING
Found the following significant warnings:
  H5DSetDescriptor.c:698:38: warning: format '%ld' expects argument of type 'long int', but argument 3 has type 'hid_t' {aka 'long long int'} [-Wformat=]
  H5DSetDescriptor.c:700:40: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'size_t' {aka 'long long unsigned int'} [-Wformat=]
  H5DSetDescriptor.c:740:47: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'size_t' {aka 'long long unsigned int'} [-Wformat=]
  H5DSetDescriptor.c:755:45: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'size_t' {aka 'long long unsigned int'} [-Wformat=]
  H5DSetDescriptor.c:1166:32: warning: format '%ld' expects argument of type 'long int', but argument 2 has type 'hid_t' {aka 'long long int'} [-Wformat=]
  H5DSetDescriptor.c:1184:35: warning: format '%ld' expects argument of type 'long int', but argument 2 has type 'hid_t' {aka 'long long int'} [-Wformat=]
  H5DSetDescriptor.c:1188:35: warning: format '%ld' expects argument of type 'long int', but argument 2 has type 'hid_t' {aka 'long long int'} [-Wformat=]
  H5DSetDescriptor.c:1210:37: warning: format '%lu' expects argument of type 'long unsigned int', but argument 2 has type 'size_t' {aka 'long long unsigned int'} [-Wformat=]
  uaselection.c:53:45: warning: format '%ld' expects argument of type 'long int', but argument 5 has type 'R_xlen_t' {aka 'long long int'} [-Wformat=]
  uaselection.c:55:45: warning: format '%ld' expects argument of type 'long int', but argument 6 has type 'R_xlen_t' {aka 'long long int'} [-Wformat=]
  uaselection.c:64:45: warning: format '%ld' expects argument of type 'long int', but argument 5 has type 'R_xlen_t' {aka 'long long int'} [-Wformat=]
  uaselection.c:68:45: warning: format '%ld' expects argument of type 'long int', but argument 6 has type 'R_xlen_t' {aka 'long long int'} [-Wformat=]
  uaselection.c:75:45: warning: format '%ld' expects argument of type 'long int', but argument 5 has type 'R_xlen_t' {aka 'long long int'} [-Wformat=]
  uaselection.c:78:45: warning: format '%ld' expects argument of type 'long int', but argument 6 has type 'R_xlen_t' {aka 'long long int'} [-Wformat=]
  uaselection.c:199:25: warning: format '%ld' expects argument of type 'long int', but argument 6 has type 'R_xlen_t' {aka 'long long int'} [-Wformat=]
  uaselection.c:204:25: warning: format '%ld' expects argument of type 'long int', but argument 6 has type 'R_xlen_t' {aka 'long long int'} [-Wformat=]
  uaselection.c:204:25: warning: format '%ld' expects argument of type 'long int', but argument 8 has type 'R_xlen_t' {aka 'long long int'} [-Wformat=]
  uaselection.c:217:37: warning: format '%ld' expects argument of type 'long int', but argument 6 has type 'R_xlen_t' {aka 'long long int'} [-Wformat=]
  uaselection.c:217:37: warning: format '%ld' expects argument of type 'long int', but argument 8 has type 'R_xlen_t' {aka 'long long int'} [-Wformat=]
  uaselection.c:220:37: warning: format '%ld' expects argument of type 'long int', but argument 6 has type 'R_xlen_t' {aka 'long long int'} [-Wformat=]
  uaselection.c:220:37: warning: format '%ld' expects argument of type 'long int', but argument 8 has type 'R_xlen_t' {aka 'long long int'} [-Wformat=]
  uaselection.c:220:37: warning: format '%ld' expects argument of type 'long int', but argument 10 has type 'R_xlen_t' {aka 'long long int'} [-Wformat=]
  uaselection.c:233:37: warning: format '%ld' expects argument of type 'long int', but argument 5 has type 'R_xlen_t' {aka 'long long int'} [-Wformat=]
  uaselection.c:288:45: warning: format '%ld' expects argument of type 'long int', but argument 5 has type 'R_xlen_t' {aka 'long long int'} [-Wformat=]
  uaselection.c:428:53: warning: format '%ld' expects argument of type 'long int', but argument 5 has type 'R_xlen_t' {aka 'long long int'} [-Wformat=]
  ChunkIterator.c:457:28: warning: format '%lu' expects argument of type 'long unsigned int', but argument 2 has type 'size_t' {aka 'long long unsigned int'} [-Wformat=]
  ChunkIterator.c:457:32: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'size_t' {aka 'long long unsigned int'} [-Wformat=]
See 'F:/biocbuild/bbs-3.20-bioc/meat/HDF5Array.Rcheck/00install.out' for details.
* used C compiler: 'gcc.exe (GCC) 13.2.0'
* checking installed package size ... NOTE
  installed size is 15.3Mb
  sub-directories of 1Mb or more:
    extdata   7.7Mb
    libs      6.6Mb
* checking package 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 whether startup messages can be suppressed ... OK
* checking dependencies in R code ... NOTE
Unexported object imported by a ':::' call: 'rhdf5:::h5checktypeOrOpenLocS3'
  See the note in ?`:::` about the use of this operator.
* 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-3.20-bioc/R/library/HDF5Array/libs/x64/HDF5Array.dll':
  Found '_assert', possibly from 'assert' (C)
  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 examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                  user system elapsed
h5mread          53.86   5.21   80.18
TENxMatrix-class 36.23   7.77  182.90
writeTENxMatrix  21.92   1.25   24.64
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
  Running 'run_unitTests.R'
 OK
* checking PDF version of manual ... OK
* DONE

Status: 1 WARNING, 5 NOTEs
See
  'F:/biocbuild/bbs-3.20-bioc/meat/HDF5Array.Rcheck/00check.log'
for details.