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###
### Running command:
###
###   D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:RProtoBufLib.install-out.txt --library=D:\biocbuild\bbs-3.15-bioc\R\library --no-vignettes --timings RProtoBufLib_2.7.1.tar.gz
###
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* using log directory 'D:/biocbuild/bbs-3.15-bioc/meat/RProtoBufLib.Rcheck'
* using R Under development (unstable) (2021-11-21 r81221)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'RProtoBufLib/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'RProtoBufLib' version '2.7.1'
* 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 ... NOTE
Found the following non-portable file paths:
  RProtoBufLib/windows/protobuf-3.13.0/include/google/protobuf/compiler/objectivec/objectivec_generator.h
  RProtoBufLib/windows/protobuf-3.13.0/include/google/protobuf/compiler/objectivec/objectivec_helpers.h

Tarballs are only required to store paths of up to 100 bytes and cannot
store those of more than 256 bytes, with restrictions including to 100
bytes for the final component.
See section 'Package structure' in the 'Writing R Extensions' manual.
* checking whether package 'RProtoBufLib' can be installed ... OK
* checking installed package size ... NOTE
  installed size is 90.0Mb
  sub-directories of 1Mb or more:
    include   3.1Mb
    lib      86.9Mb
* checking package directory ... OK
* checking 'build' directory ... OK
* checking DESCRIPTION meta-information ... NOTE
License components which are templates and need '+ file LICENSE':
  BSD_3_clause
* 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 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 'D:/biocbuild/bbs-3.15-bioc/R/library/RProtoBufLib/libs/x64/RProtoBufLib.dll':
  Found 'abort', possibly from 'abort' (C), 'runtime' (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. 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 ... NONE
* 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: 4 NOTEs
See
  'D:/biocbuild/bbs-3.15-bioc/meat/RProtoBufLib.Rcheck/00check.log'
for details.

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###
### Running command:
###
###   D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD INSTALL RProtoBufLib
###
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* installing to library 'D:/biocbuild/bbs-3.15-bioc/R/library'
* installing *source* package 'RProtoBufLib' ...
** using staged installation

   **********************************************
   WARNING: this package has a configure script
         It probably needs manual configuration
   **********************************************


** libs
"D:/biocbuild/bbs-3.15-bioc/R/bin/x64/Rscript.exe" "../tools/downloadlibs.R" 3.13.0
"C:/rtools40/mingw64/bin/"g++  -std=gnu++11 -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I../inst/include/ -I../windows/protobuf-3.13.0/include    -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition  -c GatingSet_pb_lib/GatingSet.pb.cc -o GatingSet_pb_lib/GatingSet.pb.o
mkdir -p "D:/biocbuild/bbs-3.15-bioc/R/library/00LOCK-RProtoBufLib/00new/RProtoBufLib/include"
cp -r ../windows/protobuf-3.13.0/include/google "D:/biocbuild/bbs-3.15-bioc/R/library/00LOCK-RProtoBufLib/00new/RProtoBufLib/include"
mkdir -p "D:/biocbuild/bbs-3.15-bioc/R/library/00LOCK-RProtoBufLib/00new/RProtoBufLib/lib/x64"
cp  ../windows/protobuf-3.13.0/lib/x64/libprotobuf.a "D:/biocbuild/bbs-3.15-bioc/R/library/00LOCK-RProtoBufLib/00new/RProtoBufLib/lib/x64/libprotobuf.a"
cp GatingSet_pb_lib/GatingSet.pb.o "D:/biocbuild/bbs-3.15-bioc/R/library/00LOCK-RProtoBufLib/00new/RProtoBufLib/lib/x64/GatingSet.pb.o"
"C:/rtools40/mingw64/bin/"g++  -std=gnu++11 -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I../inst/include/ -I../windows/protobuf-3.13.0/include    -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition  -c dummy.cpp -o dummy.o
C:/rtools40/mingw64/bin/g++ -shared -s -static-libgcc -o RProtoBufLib.dll tmp.def dummy.o -LC:/extsoft/lib/x64 -LC:/extsoft/lib -LD:/biocbuild/bbs-3.15-bioc/R/bin/x64 -lR
installing to D:/biocbuild/bbs-3.15-bioc/R/library/00LOCK-RProtoBufLib/00new/RProtoBufLib/libs/x64
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'RProtoBufLib'
    finding HTML links ... done
    LdFlags                                 html  
** 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 (RProtoBufLib)
Making 'packages.html' ... done