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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:mzR.install-out.txt --library=F:\biocbuild\bbs-3.20-bioc\R\library --no-vignettes --timings mzR_2.39.0.tar.gz
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* using log directory 'F:/biocbuild/bbs-3.20-bioc/meat/mzR.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 'mzR/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'mzR' version '2.39.0'
* 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 ... 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 'mzR' can be installed ... WARNING
Found the following significant warnings:
  RcppPwiz.cpp:408:56: warning: format '%d' expects argument of type 'int', but argument 2 has type 'size_t' {aka 'long long unsigned int'} [-Wformat=]
  RcppPwiz.cpp:854:55: warning: format '%d' expects argument of type 'int', but argument 2 has type 'size_t' {aka 'long long unsigned int'} [-Wformat=]
  ./boost/container_hash/hash.hpp:131:33: warning: 'template<class _Arg, class _Result> struct std::unary_function' is deprecated [-Wdeprecated-declarations]
  pwiz/data/msdata/mz5/Datastructures_mz5.cpp:373:16: warning: 'char* strncpy(char*, const char*, size_t)' output may be truncated copying 255 bytes from a string of length 255 [-Wstringop-truncation]
  pwiz/data/msdata/mz5/Datastructures_mz5.cpp:377:16: warning: 'char* strncpy(char*, const char*, size_t)' output may be truncated copying 127 bytes from a string of length 127 [-Wstringop-truncation]
  pwiz/data/msdata/mz5/Datastructures_mz5.cpp:381:16: warning: 'char* strncpy(char*, const char*, size_t)' output may be truncated copying 63 bytes from a string of length 63 [-Wstringop-truncation]
  pwiz/data/msdata/MSData.cpp:1115:1: warning: control reaches end of non-void function [-Wreturn-type]
  pwiz/data/msdata/SpectrumList_mzXML.cpp:84:30: warning: catching polymorphic type 'struct pwiz::msdata::SpectrumList_mzXML::index_not_found' by value [-Wcatch-value=]
  pwiz/data/identdata/Serializer_protXML.cpp:478:10: warning: 'pwiz::identdata::{anonymous}::Handler_protXML::strict' will be initialized after [-Wreorder]
  pwiz/data/identdata/Serializer_protXML.cpp:85:9: warning:   'int pwiz::identdata::{anonymous}::Handler_protXML::nPeptides' [-Wreorder]
  pwiz/data/identdata/Serializer_protXML.cpp:91:5: warning:   when initialized here [-Wreorder]
  pwiz/data/proteome/Modification.cpp:89:5: warning: 'template<class> class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
  pwiz/utility/misc/Filesystem.cpp:156:78: warning: ISO C++ forbids converting a string constant to 'PSTR' {aka 'char*'} [-Wwrite-strings]
  pwiz/utility/misc/Filesystem.cpp:156:91: warning: ISO C++ forbids converting a string constant to 'PSTR' {aka 'char*'} [-Wwrite-strings]
  pwiz/utility/misc/Filesystem.cpp:238:34: warning: ISO C++ forbids converting a string constant to 'PSTR' {aka 'char*'} [-Wwrite-strings]
  pwiz/utility/misc/Filesystem.cpp:238:47: warning: ISO C++ forbids converting a string constant to 'PSTR' {aka 'char*'} [-Wwrite-strings]
  pwiz/utility/misc/Filesystem.cpp:251:107: warning: ISO C++ forbids converting a string constant to 'PSTR' {aka 'char*'} [-Wwrite-strings]
  pwiz/utility/misc/Filesystem.cpp:251:120: warning: ISO C++ forbids converting a string constant to 'PSTR' {aka 'char*'} [-Wwrite-strings]
  pwiz/utility/misc/Filesystem.cpp:262:77: warning: ISO C++ forbids converting a string constant to 'PSTR' {aka 'char*'} [-Wwrite-strings]
  pwiz/utility/misc/Filesystem.cpp:262:90: warning: ISO C++ forbids converting a string constant to 'PSTR' {aka 'char*'} [-Wwrite-strings]
  pwiz/utility/misc/Filesystem.cpp:269:73: warning: ISO C++ forbids converting a string constant to 'PSTR' {aka 'char*'} [-Wwrite-strings]
  pwiz/utility/misc/Filesystem.cpp:269:86: warning: ISO C++ forbids converting a string constant to 'PSTR' {aka 'char*'} [-Wwrite-strings]
See 'F:/biocbuild/bbs-3.20-bioc/meat/mzR.Rcheck/00install.out' for details.
* used C++ compiler: 'G__~1.EXE (GCC) 13.2.0'
* checking C++ specification ... NOTE
  Specified C++11: please drop specification unless essential
* checking installed package size ... NOTE
  installed size is 10.0Mb
  sub-directories of 1Mb or more:
    libs   9.4Mb
* 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 whether startup messages can be suppressed ... 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 ... WARNING
Non-portable flags in variable 'PKG_CPPFLAGS':
  -fpermissive
* 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 include directives 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/mzR/libs/x64/mzR.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 'runTests.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 WARNINGs, 5 NOTEs
See
  'F:/biocbuild/bbs-3.20-bioc/meat/mzR.Rcheck/00check.log'
for details.