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###
### Running command:
###
###   /home/biocbuild/bbs-3.14-bioc/R/bin/R CMD check --install=check:RProtoBufLib.install-out.txt --library=/home/biocbuild/bbs-3.14-bioc/R/library --no-vignettes --timings RProtoBufLib_2.6.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.14-bioc/meat/RProtoBufLib.Rcheck’
* using R version 4.1.3 (2022-03-10)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘RProtoBufLib/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘RProtoBufLib’ version ‘2.6.0’
* 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 for sufficient/correct file permissions ... OK
* checking whether package ‘RProtoBufLib’ can be installed ... OK
* checking installed package size ... NOTE
  installed size is 174.4Mb
  sub-directories of 1Mb or more:
    include    3.1Mb
    lib      171.1Mb
* 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 ... WARNING
---- unloading
Warning message:
.onUnload failed in unloadNamespace() for 'RProtoBufLib', details:
  call: dll[["path"]]
  error: subscript out of bounds 
* 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 is not available
* 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: 1 WARNING, 3 NOTEs
See
  ‘/home/biocbuild/bbs-3.14-bioc/meat/RProtoBufLib.Rcheck/00check.log’
for details.

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###
### Running command:
###
###   /home/biocbuild/bbs-3.14-bioc/R/bin/R CMD INSTALL RProtoBufLib
###
##############################################################################
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* installing to library ‘/home/biocbuild/bbs-3.14-bioc/R/library’
* installing *source* package ‘RProtoBufLib’ ...
** using staged installation
checking for gcc... gcc
checking whether the C compiler works... yes
checking for C compiler default output file name... a.out
checking for suffix of executables... 
checking whether we are cross compiling... no
checking for suffix of object files... o
checking whether we are using the GNU C compiler... yes
checking whether gcc accepts -g... yes
checking for gcc option to accept ISO C89... none needed
checking whether we are using the GNU C++ compiler... yes
checking whether g++ -std=gnu++14 accepts -g... yes
untarring protobuf ...
building protobuf...
checking whether to enable maintainer-specific portions of Makefiles... yes
checking build system type... x86_64-pc-linux-gnu
checking host system type... x86_64-pc-linux-gnu
checking target system type... x86_64-pc-linux-gnu
checking for a BSD-compatible install... /usr/bin/install -c
checking whether build environment is sane... yes
checking for a thread-safe mkdir -p... /usr/bin/mkdir -p
checking for gawk... gawk
checking whether make sets $(MAKE)... yes
checking whether make supports nested variables... yes
checking whether UID '1002' is supported by ustar format... yes
checking whether GID '1002' is supported by ustar format... yes
checking how to create a ustar tar archive... gnutar
checking whether make supports nested variables... (cached) yes
checking for gcc... gcc
checking whether the C compiler works... yes
checking for C compiler default output file name... a.out
checking for suffix of executables... 
checking whether we are cross compiling... no
checking for suffix of object files... o
checking whether we are using the GNU C compiler... yes
checking whether gcc accepts -g... yes
checking for gcc option to accept ISO C89... none needed
checking whether gcc understands -c and -o together... yes
checking whether make supports the include directive... yes (GNU style)
checking dependency style of gcc... gcc3
checking whether we are using the GNU C++ compiler... yes
checking whether g++ -std=gnu++14 accepts -g... yes
checking dependency style of g++ -std=gnu++14... gcc3
checking how to run the C preprocessor... gcc -E
checking for gcc... gcc
checking whether we are using the GNU C compiler... (cached) yes
checking whether gcc accepts -g... yes
checking for gcc option to accept ISO C89... (cached) none needed
checking whether gcc understands -c and -o together... (cached) yes
checking dependency style of gcc... (cached) gcc3
checking how to run the C preprocessor... gcc -E
checking how to run the C++ preprocessor... g++ -std=gnu++14 -E
checking for g++... g++
checking whether we are using the GNU C++ compiler... (cached) yes
checking whether g++ accepts -g... yes
checking dependency style of g++... (cached) gcc3
checking how to run the C++ preprocessor... g++ -E
checking for grep that handles long lines and -e... /usr/bin/grep
checking for egrep... /usr/bin/grep -E
checking for ANSI C header files... yes
checking for sys/types.h... yes
checking for sys/stat.h... yes
checking for stdlib.h... yes
checking for string.h... yes
checking for memory.h... yes
checking for strings.h... yes
checking for inttypes.h... yes
checking for stdint.h... yes
checking for unistd.h... yes
checking minix/config.h usability... no
checking minix/config.h presence... no
checking for minix/config.h... no
checking whether it is safe to define __EXTENSIONS__... yes
checking for ar... ar
checking the archiver (ar) interface... ar
checking for gcc... gcc
checking whether we are using the GNU Objective C compiler... yes
checking whether gcc accepts -g... yes
checking dependency style of gcc... gcc3
checking C++ compiler flags...... use user-supplied: -g -O2 -Wall
checking whether __SUNPRO_CC is declared... no
checking how to print strings... printf
checking for a sed that does not truncate output... /usr/bin/sed
checking for fgrep... /usr/bin/grep -F
checking for ld used by gcc... /usr/bin/ld
checking if the linker (/usr/bin/ld) is GNU ld... yes
checking for BSD- or MS-compatible name lister (nm)... /usr/bin/nm -B
checking the name lister (/usr/bin/nm -B) interface... BSD nm
checking whether ln -s works... yes
checking the maximum length of command line arguments... 1572864
checking how to convert x86_64-pc-linux-gnu file names to x86_64-pc-linux-gnu format... func_convert_file_noop
checking how to convert x86_64-pc-linux-gnu file names to toolchain format... func_convert_file_noop
checking for /usr/bin/ld option to reload object files... -r
checking for objdump... objdump
checking how to recognize dependent libraries... pass_all
checking for dlltool... no
checking how to associate runtime and link libraries... printf %s\n
checking for archiver @FILE support... @
checking for strip... strip
checking for ranlib... ranlib
checking command to parse /usr/bin/nm -B output from gcc object... ok
checking for sysroot... no
checking for a working dd... /usr/bin/dd
checking how to truncate binary pipes... /usr/bin/dd bs=4096 count=1
checking for mt... mt
checking if mt is a manifest tool... no
checking for dlfcn.h... yes
checking for objdir... .libs
checking if gcc supports -fno-rtti -fno-exceptions... no
checking for gcc option to produce PIC... -fPIC -DPIC
checking if gcc PIC flag -fPIC -DPIC works... yes
checking if gcc static flag -static works... yes
checking if gcc supports -c -o file.o... yes
checking if gcc supports -c -o file.o... (cached) yes
checking whether the gcc linker (/usr/bin/ld -m elf_x86_64) supports shared libraries... yes
checking whether -lc should be explicitly linked in... no
checking dynamic linker characteristics... GNU/Linux ld.so
checking how to hardcode library paths into programs... immediate
checking whether stripping libraries is possible... yes
checking if libtool supports shared libraries... yes
checking whether to build shared libraries... yes
checking whether to build static libraries... no
checking how to run the C++ preprocessor... g++ -std=gnu++14 -E
checking for ld used by g++ -std=gnu++14... /usr/bin/ld -m elf_x86_64
checking if the linker (/usr/bin/ld -m elf_x86_64) is GNU ld... yes
checking whether the g++ -std=gnu++14 linker (/usr/bin/ld -m elf_x86_64) supports shared libraries... yes
checking for g++ -std=gnu++14 option to produce PIC... -fPIC -DPIC
checking if g++ -std=gnu++14 PIC flag -fPIC -DPIC works... yes
checking if g++ -std=gnu++14 static flag -static works... yes
checking if g++ -std=gnu++14 supports -c -o file.o... yes
checking if g++ -std=gnu++14 supports -c -o file.o... (cached) yes
checking whether the g++ -std=gnu++14 linker (/usr/bin/ld -m elf_x86_64) supports shared libraries... yes
checking dynamic linker characteristics... (cached) GNU/Linux ld.so
checking how to hardcode library paths into programs... immediate
checking whether the linker supports version scripts... yes
checking for ANSI C header files... (cached) yes
checking fcntl.h usability... yes
checking fcntl.h presence... yes
checking for fcntl.h... yes
checking for inttypes.h... (cached) yes
checking limits.h usability... yes
checking limits.h presence... yes
checking for limits.h... yes
checking for stdlib.h... (cached) yes
checking for unistd.h... (cached) yes
checking for working memcmp... yes
checking for working strtod... yes
checking for ftruncate... yes
checking for memset... yes
checking for mkdir... yes
checking for strchr... yes
checking for strerror... yes
checking for strtol... yes
checking zlib version... ok (1.2.0.4 or later)
checking for library containing zlibVersion... -lz
checking whether g++ -std=gnu++14 supports C++11 features by default... yes
checking whether -latomic is needed... no
checking whether gcc is Clang... no
checking whether pthreads work with -pthread... yes
checking for joinable pthread attribute... PTHREAD_CREATE_JOINABLE
checking whether more special flags are required for pthreads... no
checking for PTHREAD_PRIO_INHERIT... yes
checking the location of hash_map... <unordered_map>
checking that generated files are newer than configure... done
configure: creating ./config.status
config.status: creating Makefile
config.status: creating src/Makefile
config.status: creating benchmarks/Makefile
config.status: creating conformance/Makefile
config.status: creating protobuf.pc
config.status: creating protobuf-lite.pc
config.status: creating config.h
config.status: executing depfiles commands
config.status: executing libtool commands
=== configuring in third_party/googletest (/home/biocbuild/bbs-3.14-bioc/meat/RProtoBufLib/src/protobuf-3.13.0/third_party/googletest)
configure: running /bin/bash ./configure --disable-option-checking '--prefix=/home/biocbuild/bbs-3.14-bioc/meat/RProtoBufLib/src/pb_build'  '--enable-static=no' '--with-pic=yes' '--enable-shared=yes' '--libdir=/home/biocbuild/bbs-3.14-bioc/meat/RProtoBufLib/src/pb_build/lib' 'CXX=g++ -std=gnu++14' 'CXXFLAGS=-g -O2 -Wall' 'CC=gcc' 'CFLAGS=-g -O2 -Wall' --cache-file=/dev/null --srcdir=.
checking for a BSD-compatible install... /usr/bin/install -c
checking whether build environment is sane... yes
checking for a thread-safe mkdir -p... /usr/bin/mkdir -p
checking for gawk... gawk
checking whether make sets $(MAKE)... yes
checking whether make supports nested variables... yes
checking that generated files are newer than configure... done
configure: creating ./config.status
config.status: creating Makefile
=== configuring in googletest (/home/biocbuild/bbs-3.14-bioc/meat/RProtoBufLib/src/protobuf-3.13.0/third_party/googletest/googletest)
configure: running /bin/bash ./configure --disable-option-checking '--prefix=/home/biocbuild/bbs-3.14-bioc/meat/RProtoBufLib/src/pb_build'  '--enable-static=no' '--with-pic=yes' '--enable-shared=yes' '--libdir=/home/biocbuild/bbs-3.14-bioc/meat/RProtoBufLib/src/pb_build/lib' 'CXX=g++ -std=gnu++14' 'CXXFLAGS=-g -O2 -Wall' 'CC=gcc' 'CFLAGS=-g -O2 -Wall' --cache-file=/dev/null --srcdir=.
checking for a BSD-compatible install... /usr/bin/install -c
checking whether build environment is sane... yes
checking for a thread-safe mkdir -p... /usr/bin/mkdir -p
checking for gawk... gawk
checking whether make sets $(MAKE)... yes
checking whether make supports nested variables... yes
checking for gcc... gcc
checking whether the C compiler works... yes
checking for C compiler default output file name... a.out
checking for suffix of executables... 
checking whether we are cross compiling... no
checking for suffix of object files... o
checking whether we are using the GNU C compiler... yes
checking whether gcc accepts -g... yes
checking for gcc option to accept ISO C89... none needed
checking whether gcc understands -c and -o together... yes
checking whether make supports the include directive... yes (GNU style)
checking dependency style of gcc... gcc3
checking whether we are using the GNU C++ compiler... yes
checking whether g++ -std=gnu++14 accepts -g... yes
checking dependency style of g++ -std=gnu++14... gcc3
checking build system type... x86_64-pc-linux-gnu
checking host system type... x86_64-pc-linux-gnu
checking how to print strings... printf
checking for a sed that does not truncate output... /usr/bin/sed
checking for grep that handles long lines and -e... /usr/bin/grep
checking for egrep... /usr/bin/grep -E
checking for fgrep... /usr/bin/grep -F
checking for ld used by gcc... /usr/bin/ld
checking if the linker (/usr/bin/ld) is GNU ld... yes
checking for BSD- or MS-compatible name lister (nm)... /usr/bin/nm -B
checking the name lister (/usr/bin/nm -B) interface... BSD nm
checking whether ln -s works... yes
checking the maximum length of command line arguments... 1572864
checking how to convert x86_64-pc-linux-gnu file names to x86_64-pc-linux-gnu format... func_convert_file_noop
checking how to convert x86_64-pc-linux-gnu file names to toolchain format... func_convert_file_noop
checking for /usr/bin/ld option to reload object files... -r
checking for objdump... objdump
checking how to recognize dependent libraries... pass_all
checking for dlltool... no
checking how to associate runtime and link libraries... printf %s\n
checking for ar... ar
checking for archiver @FILE support... @
checking for strip... strip
checking for ranlib... ranlib
checking command to parse /usr/bin/nm -B output from gcc object... ok
checking for sysroot... no
checking for a working dd... /usr/bin/dd
checking how to truncate binary pipes... /usr/bin/dd bs=4096 count=1
checking for mt... mt
checking if mt is a manifest tool... no
checking how to run the C preprocessor... gcc -E
checking for ANSI C header files... yes
checking for sys/types.h... yes
checking for sys/stat.h... yes
checking for stdlib.h... yes
checking for string.h... yes
checking for memory.h... yes
checking for strings.h... yes
checking for inttypes.h... yes
checking for stdint.h... yes
checking for unistd.h... yes
checking for dlfcn.h... yes
checking for objdir... .libs
checking if gcc supports -fno-rtti -fno-exceptions... no
checking for gcc option to produce PIC... -fPIC -DPIC
checking if gcc PIC flag -fPIC -DPIC works... yes
checking if gcc static flag -static works... yes
checking if gcc supports -c -o file.o... yes
checking if gcc supports -c -o file.o... (cached) yes
checking whether the gcc linker (/usr/bin/ld -m elf_x86_64) supports shared libraries... yes
checking whether -lc should be explicitly linked in... no
checking dynamic linker characteristics... GNU/Linux ld.so
checking how to hardcode library paths into programs... immediate
checking whether stripping libraries is possible... yes
checking if libtool supports shared libraries... yes
checking whether to build shared libraries... yes
checking whether to build static libraries... no
checking how to run the C++ preprocessor... g++ -std=gnu++14 -E
checking for ld used by g++ -std=gnu++14... /usr/bin/ld -m elf_x86_64
checking if the linker (/usr/bin/ld -m elf_x86_64) is GNU ld... yes
checking whether the g++ -std=gnu++14 linker (/usr/bin/ld -m elf_x86_64) supports shared libraries... yes
checking for g++ -std=gnu++14 option to produce PIC... -fPIC -DPIC
checking if g++ -std=gnu++14 PIC flag -fPIC -DPIC works... yes
checking if g++ -std=gnu++14 static flag -static works... yes
checking if g++ -std=gnu++14 supports -c -o file.o... yes
checking if g++ -std=gnu++14 supports -c -o file.o... (cached) yes
checking whether the g++ -std=gnu++14 linker (/usr/bin/ld -m elf_x86_64) supports shared libraries... yes
checking dynamic linker characteristics... (cached) GNU/Linux ld.so
checking how to hardcode library paths into programs... immediate
checking for python... :
checking for the pthreads library -lpthreads... no
checking whether pthreads work without any flags... no
checking whether pthreads work with -Kthread... no
checking whether pthreads work with -kthread... no
checking for the pthreads library -llthread... no
checking whether pthreads work with -pthread... yes
checking for joinable pthread attribute... PTHREAD_CREATE_JOINABLE
checking if more special flags are required for pthreads... no
checking whether to check for GCC pthread/shared inconsistencies... yes
checking whether -pthread is sufficient with -shared... yes
checking that generated files are newer than configure... done
configure: creating ./config.status
config.status: creating Makefile
config.status: creating scripts/gtest-config
config.status: creating build-aux/config.h
config.status: executing depfiles commands
config.status: executing libtool commands
=== configuring in googlemock (/home/biocbuild/bbs-3.14-bioc/meat/RProtoBufLib/src/protobuf-3.13.0/third_party/googletest/googlemock)
configure: running /bin/bash ./configure --disable-option-checking '--prefix=/home/biocbuild/bbs-3.14-bioc/meat/RProtoBufLib/src/pb_build'  '--enable-static=no' '--with-pic=yes' '--enable-shared=yes' '--libdir=/home/biocbuild/bbs-3.14-bioc/meat/RProtoBufLib/src/pb_build/lib' 'CXX=g++ -std=gnu++14' 'CXXFLAGS=-g -O2 -Wall' 'CC=gcc' 'CFLAGS=-g -O2 -Wall' --cache-file=/dev/null --srcdir=.
checking for a BSD-compatible install... /usr/bin/install -c
checking whether build environment is sane... yes
checking for a thread-safe mkdir -p... /usr/bin/mkdir -p
checking for gawk... gawk
checking whether make sets $(MAKE)... yes
checking whether make supports nested variables... yes
checking for gcc... gcc
checking whether the C compiler works... yes
checking for C compiler default output file name... a.out
checking for suffix of executables... 
checking whether we are cross compiling... no
checking for suffix of object files... o
checking whether we are using the GNU C compiler... yes
checking whether gcc accepts -g... yes
checking for gcc option to accept ISO C89... none needed
checking whether gcc understands -c and -o together... yes
checking whether make supports the include directive... yes (GNU style)
checking dependency style of gcc... gcc3
checking whether we are using the GNU C++ compiler... yes
checking whether g++ -std=gnu++14 accepts -g... yes
checking dependency style of g++ -std=gnu++14... gcc3
checking build system type... x86_64-pc-linux-gnu
checking host system type... x86_64-pc-linux-gnu
checking how to print strings... printf
checking for a sed that does not truncate output... /usr/bin/sed
checking for grep that handles long lines and -e... /usr/bin/grep
checking for egrep... /usr/bin/grep -E
checking for fgrep... /usr/bin/grep -F
checking for ld used by gcc... /usr/bin/ld
checking if the linker (/usr/bin/ld) is GNU ld... yes
checking for BSD- or MS-compatible name lister (nm)... /usr/bin/nm -B
checking the name lister (/usr/bin/nm -B) interface... BSD nm
checking whether ln -s works... yes
checking the maximum length of command line arguments... 1572864
checking how to convert x86_64-pc-linux-gnu file names to x86_64-pc-linux-gnu format... func_convert_file_noop
checking how to convert x86_64-pc-linux-gnu file names to toolchain format... func_convert_file_noop
checking for /usr/bin/ld option to reload object files... -r
checking for objdump... objdump
checking how to recognize dependent libraries... pass_all
checking for dlltool... no
checking how to associate runtime and link libraries... printf %s\n
checking for ar... ar
checking for archiver @FILE support... @
checking for strip... strip
checking for ranlib... ranlib
checking command to parse /usr/bin/nm -B output from gcc object... ok
checking for sysroot... no
checking for a working dd... /usr/bin/dd
checking how to truncate binary pipes... /usr/bin/dd bs=4096 count=1
checking for mt... mt
checking if mt is a manifest tool... no
checking how to run the C preprocessor... gcc -E
checking for ANSI C header files... yes
checking for sys/types.h... yes
checking for sys/stat.h... yes
checking for stdlib.h... yes
checking for string.h... yes
checking for memory.h... yes
checking for strings.h... yes
checking for inttypes.h... yes
checking for stdint.h... yes
checking for unistd.h... yes
checking for dlfcn.h... yes
checking for objdir... .libs
checking if gcc supports -fno-rtti -fno-exceptions... no
checking for gcc option to produce PIC... -fPIC -DPIC
checking if gcc PIC flag -fPIC -DPIC works... yes
checking if gcc static flag -static works... yes
checking if gcc supports -c -o file.o... yes
checking if gcc supports -c -o file.o... (cached) yes
checking whether the gcc linker (/usr/bin/ld -m elf_x86_64) supports shared libraries... yes
checking whether -lc should be explicitly linked in... no
checking dynamic linker characteristics... GNU/Linux ld.so
checking how to hardcode library paths into programs... immediate
checking whether stripping libraries is possible... yes
checking if libtool supports shared libraries... yes
checking whether to build shared libraries... yes
checking whether to build static libraries... no
checking how to run the C++ preprocessor... g++ -std=gnu++14 -E
checking for ld used by g++ -std=gnu++14... /usr/bin/ld -m elf_x86_64
checking if the linker (/usr/bin/ld -m elf_x86_64) is GNU ld... yes
checking whether the g++ -std=gnu++14 linker (/usr/bin/ld -m elf_x86_64) supports shared libraries... yes
checking for g++ -std=gnu++14 option to produce PIC... -fPIC -DPIC
checking if g++ -std=gnu++14 PIC flag -fPIC -DPIC works... yes
checking if g++ -std=gnu++14 static flag -static works... yes
checking if g++ -std=gnu++14 supports -c -o file.o... yes
checking if g++ -std=gnu++14 supports -c -o file.o... (cached) yes
checking whether the g++ -std=gnu++14 linker (/usr/bin/ld -m elf_x86_64) supports shared libraries... yes
checking dynamic linker characteristics... (cached) GNU/Linux ld.so
checking how to hardcode library paths into programs... immediate
checking for python... :
checking for the pthreads library -lpthreads... no
checking whether pthreads work without any flags... no
checking whether pthreads work with -Kthread... no
checking whether pthreads work with -kthread... no
checking for the pthreads library -llthread... no
checking whether pthreads work with -pthread... yes
checking for joinable pthread attribute... PTHREAD_CREATE_JOINABLE
checking if more special flags are required for pthreads... no
checking whether to check for GCC pthread/shared inconsistencies... yes
checking whether -pthread is sufficient with -shared... yes
checking for gtest-config... no
checking that generated files are newer than configure... done
configure: creating ./config.status
config.status: creating Makefile
config.status: creating scripts/gmock-config
config.status: creating build-aux/config.h
config.status: executing depfiles commands
config.status: executing libtool commands
Making install in .
make[1]: Entering directory '/home/biocbuild/bbs-3.14-bioc/meat/RProtoBufLib/src/protobuf-3.13.0'
make[2]: Entering directory '/home/biocbuild/bbs-3.14-bioc/meat/RProtoBufLib/src/protobuf-3.13.0'
make[2]: Nothing to be done for 'install-exec-am'.
 /usr/bin/mkdir -p '/home/biocbuild/bbs-3.14-bioc/meat/RProtoBufLib/src/pb_build/lib/pkgconfig'
 /usr/bin/install -c -m 644 protobuf.pc protobuf-lite.pc '/home/biocbuild/bbs-3.14-bioc/meat/RProtoBufLib/src/pb_build/lib/pkgconfig'
make[2]: Leaving directory '/home/biocbuild/bbs-3.14-bioc/meat/RProtoBufLib/src/protobuf-3.13.0'
make[1]: Leaving directory '/home/biocbuild/bbs-3.14-bioc/meat/RProtoBufLib/src/protobuf-3.13.0'
Making install in src
make[1]: Entering directory '/home/biocbuild/bbs-3.14-bioc/meat/RProtoBufLib/src/protobuf-3.13.0/src'
  CXX      google/protobuf/compiler/main.o
  CXX      google/protobuf/stubs/bytestream.lo
  CXX      google/protobuf/stubs/common.lo
  CXX      google/protobuf/stubs/int128.lo
  CXX      google/protobuf/io/io_win32.lo
  CXX      google/protobuf/stubs/status.lo
  CXX      google/protobuf/stubs/statusor.lo
  CXX      google/protobuf/stubs/stringpiece.lo
  CXX      google/protobuf/stubs/stringprintf.lo
  CXX      google/protobuf/stubs/structurally_valid.lo
  CXX      google/protobuf/stubs/strutil.lo
  CXX      google/protobuf/stubs/time.lo
  CXX      google/protobuf/any_lite.lo
  CXX      google/protobuf/arena.lo
  CXX      google/protobuf/extension_set.lo
  CXX      google/protobuf/generated_enum_util.lo
  CXX      google/protobuf/generated_message_util.lo
  CXX      google/protobuf/generated_message_table_driven_lite.lo
  CXX      google/protobuf/implicit_weak_message.lo
  CXX      google/protobuf/message_lite.lo
In file included from /usr/include/string.h:495,
                 from ./google/protobuf/stubs/port.h:39,
                 from ./google/protobuf/stubs/macros.h:34,
                 from ./google/protobuf/stubs/common.h:46,
                 from ./google/protobuf/message_lite.h:45,
                 from google/protobuf/message_lite.cc:36:
In function 'void* memcpy(void*, const void*, size_t)',
    inlined from 'google::protobuf::uint8* google::protobuf::io::EpsCopyOutputStream::WriteRaw(const void*, int, google::protobuf::uint8*)' at ./google/protobuf/io/coded_stream.h:699:16,
    inlined from 'virtual google::protobuf::uint8* google::protobuf::internal::ImplicitWeakMessage::_InternalSerialize(google::protobuf::uint8*, google::protobuf::io::EpsCopyOutputStream*) const' at ./google/protobuf/implicit_weak_message.h:85:28,
    inlined from 'bool google::protobuf::MessageLite::SerializePartialToZeroCopyStream(google::protobuf::io::ZeroCopyOutputStream*) const' at google/protobuf/message_lite.cc:419:30:
/usr/include/x86_64-linux-gnu/bits/string_fortified.h:34:33: warning: 'void* __builtin___memcpy_chk(void*, const void*, long unsigned int, long unsigned int)' specified size between 18446744071562067968 and 18446744073709551615 exceeds maximum object size 9223372036854775807 [-Wstringop-overflow=]
   34 |   return __builtin___memcpy_chk (__dest, __src, __len, __bos0 (__dest));
      |          ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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make[2]: Entering directory '/home/biocbuild/bbs-3.14-bioc/meat/RProtoBufLib/src/protobuf-3.13.0/src'
 /usr/bin/mkdir -p '/home/biocbuild/bbs-3.14-bioc/meat/RProtoBufLib/src/pb_build/lib'
 /bin/bash ../libtool   --mode=install /usr/bin/install -c   libprotobuf-lite.la libprotobuf.la libprotoc.la '/home/biocbuild/bbs-3.14-bioc/meat/RProtoBufLib/src/pb_build/lib'
libtool: install: /usr/bin/install -c .libs/libprotobuf-lite.so.24.0.0 /home/biocbuild/bbs-3.14-bioc/meat/RProtoBufLib/src/pb_build/lib/libprotobuf-lite.so.24.0.0
libtool: install: (cd /home/biocbuild/bbs-3.14-bioc/meat/RProtoBufLib/src/pb_build/lib && { ln -s -f libprotobuf-lite.so.24.0.0 libprotobuf-lite.so.24 || { rm -f libprotobuf-lite.so.24 && ln -s libprotobuf-lite.so.24.0.0 libprotobuf-lite.so.24; }; })
libtool: install: (cd /home/biocbuild/bbs-3.14-bioc/meat/RProtoBufLib/src/pb_build/lib && { ln -s -f libprotobuf-lite.so.24.0.0 libprotobuf-lite.so || { rm -f libprotobuf-lite.so && ln -s libprotobuf-lite.so.24.0.0 libprotobuf-lite.so; }; })
libtool: install: /usr/bin/install -c .libs/libprotobuf-lite.lai /home/biocbuild/bbs-3.14-bioc/meat/RProtoBufLib/src/pb_build/lib/libprotobuf-lite.la
libtool: install: /usr/bin/install -c .libs/libprotobuf.so.24.0.0 /home/biocbuild/bbs-3.14-bioc/meat/RProtoBufLib/src/pb_build/lib/libprotobuf.so.24.0.0
libtool: install: (cd /home/biocbuild/bbs-3.14-bioc/meat/RProtoBufLib/src/pb_build/lib && { ln -s -f libprotobuf.so.24.0.0 libprotobuf.so.24 || { rm -f libprotobuf.so.24 && ln -s libprotobuf.so.24.0.0 libprotobuf.so.24; }; })
libtool: install: (cd /home/biocbuild/bbs-3.14-bioc/meat/RProtoBufLib/src/pb_build/lib && { ln -s -f libprotobuf.so.24.0.0 libprotobuf.so || { rm -f libprotobuf.so && ln -s libprotobuf.so.24.0.0 libprotobuf.so; }; })
libtool: install: /usr/bin/install -c .libs/libprotobuf.lai /home/biocbuild/bbs-3.14-bioc/meat/RProtoBufLib/src/pb_build/lib/libprotobuf.la
libtool: warning: relinking 'libprotoc.la'
libtool: install: (cd /home/biocbuild/bbs-3.14-bioc/meat/RProtoBufLib/src/protobuf-3.13.0/src; /bin/bash "/home/biocbuild/bbs-3.14-bioc/meat/RProtoBufLib/src/protobuf-3.13.0/libtool"  --silent --tag CXX --mode=relink g++ -std=gnu++14 -pthread -DHAVE_PTHREAD=1 -DHAVE_ZLIB=1 -Wall -Wno-sign-compare -g -O2 -Wall -version-info 24:0:0 -export-dynamic -no-undefined -Wl,--version-script=./libprotoc.map -o libprotoc.la -rpath /home/biocbuild/bbs-3.14-bioc/meat/RProtoBufLib/src/pb_build/lib google/protobuf/compiler/code_generator.lo google/protobuf/compiler/command_line_interface.lo google/protobuf/compiler/plugin.lo google/protobuf/compiler/plugin.pb.lo google/protobuf/compiler/subprocess.lo google/protobuf/compiler/zip_writer.lo google/protobuf/compiler/cpp/cpp_enum.lo google/protobuf/compiler/cpp/cpp_enum_field.lo google/protobuf/compiler/cpp/cpp_extension.lo google/protobuf/compiler/cpp/cpp_field.lo google/protobuf/compiler/cpp/cpp_file.lo google/protobuf/compiler/cpp/cpp_generator.lo google/protobuf/compiler/cpp/cpp_helpers.lo google/protobuf/compiler/cpp/cpp_map_field.lo google/protobuf/compiler/cpp/cpp_message.lo google/protobuf/compiler/cpp/cpp_message_field.lo google/protobuf/compiler/cpp/cpp_padding_optimizer.lo google/protobuf/compiler/cpp/cpp_primitive_field.lo google/protobuf/compiler/cpp/cpp_service.lo google/protobuf/compiler/cpp/cpp_string_field.lo google/protobuf/compiler/java/java_context.lo google/protobuf/compiler/java/java_enum.lo google/protobuf/compiler/java/java_enum_lite.lo google/protobuf/compiler/java/java_enum_field.lo google/protobuf/compiler/java/java_enum_field_lite.lo google/protobuf/compiler/java/java_extension.lo google/protobuf/compiler/java/java_extension_lite.lo google/protobuf/compiler/java/java_field.lo google/protobuf/compiler/java/java_file.lo google/protobuf/compiler/java/java_generator.lo google/protobuf/compiler/java/java_generator_factory.lo google/protobuf/compiler/java/java_helpers.lo google/protobuf/compiler/java/java_map_field.lo google/protobuf/compiler/java/java_map_field_lite.lo google/protobuf/compiler/java/java_message.lo google/protobuf/compiler/java/java_message_lite.lo google/protobuf/compiler/java/java_message_builder.lo google/protobuf/compiler/java/java_message_builder_lite.lo google/protobuf/compiler/java/java_message_field.lo google/protobuf/compiler/java/java_message_field_lite.lo google/protobuf/compiler/java/java_name_resolver.lo google/protobuf/compiler/java/java_primitive_field.lo google/protobuf/compiler/java/java_primitive_field_lite.lo google/protobuf/compiler/java/java_shared_code_generator.lo google/protobuf/compiler/java/java_service.lo google/protobuf/compiler/java/java_string_field.lo google/protobuf/compiler/java/java_string_field_lite.lo google/protobuf/compiler/java/java_doc_comment.lo google/protobuf/compiler/js/js_generator.lo google/protobuf/compiler/js/well_known_types_embed.lo google/protobuf/compiler/objectivec/objectivec_enum.lo google/protobuf/compiler/objectivec/objectivec_enum_field.lo google/protobuf/compiler/objectivec/objectivec_extension.lo google/protobuf/compiler/objectivec/objectivec_field.lo google/protobuf/compiler/objectivec/objectivec_file.lo google/protobuf/compiler/objectivec/objectivec_generator.lo google/protobuf/compiler/objectivec/objectivec_helpers.lo google/protobuf/compiler/objectivec/objectivec_map_field.lo google/protobuf/compiler/objectivec/objectivec_message.lo google/protobuf/compiler/objectivec/objectivec_message_field.lo google/protobuf/compiler/objectivec/objectivec_oneof.lo google/protobuf/compiler/objectivec/objectivec_primitive_field.lo google/protobuf/compiler/php/php_generator.lo google/protobuf/compiler/python/python_generator.lo google/protobuf/compiler/ruby/ruby_generator.lo google/protobuf/compiler/csharp/csharp_doc_comment.lo google/protobuf/compiler/csharp/csharp_enum.lo google/protobuf/compiler/csharp/csharp_enum_field.lo google/protobuf/compiler/csharp/csharp_field_base.lo google/protobuf/compiler/csharp/csharp_generator.lo google/protobuf/compiler/csharp/csharp_helpers.lo google/protobuf/compiler/csharp/csharp_map_field.lo google/protobuf/compiler/csharp/csharp_message.lo google/protobuf/compiler/csharp/csharp_message_field.lo google/protobuf/compiler/csharp/csharp_primitive_field.lo google/protobuf/compiler/csharp/csharp_reflection_class.lo google/protobuf/compiler/csharp/csharp_repeated_enum_field.lo google/protobuf/compiler/csharp/csharp_repeated_message_field.lo google/protobuf/compiler/csharp/csharp_repeated_primitive_field.lo google/protobuf/compiler/csharp/csharp_source_generator_base.lo google/protobuf/compiler/csharp/csharp_wrapper_field.lo libprotobuf.la -lz )
libtool: install: /usr/bin/install -c .libs/libprotoc.so.24.0.0T /home/biocbuild/bbs-3.14-bioc/meat/RProtoBufLib/src/pb_build/lib/libprotoc.so.24.0.0
libtool: install: (cd /home/biocbuild/bbs-3.14-bioc/meat/RProtoBufLib/src/pb_build/lib && { ln -s -f libprotoc.so.24.0.0 libprotoc.so.24 || { rm -f libprotoc.so.24 && ln -s libprotoc.so.24.0.0 libprotoc.so.24; }; })
libtool: install: (cd /home/biocbuild/bbs-3.14-bioc/meat/RProtoBufLib/src/pb_build/lib && { ln -s -f libprotoc.so.24.0.0 libprotoc.so || { rm -f libprotoc.so && ln -s libprotoc.so.24.0.0 libprotoc.so; }; })
libtool: install: /usr/bin/install -c .libs/libprotoc.lai /home/biocbuild/bbs-3.14-bioc/meat/RProtoBufLib/src/pb_build/lib/libprotoc.la
libtool: finish: PATH="/home/biocbuild/bin:/usr/local/bin:/usr/bin:/bin:/snap/bin:/usr/local/ensembl-vep:/sbin" ldconfig -n /home/biocbuild/bbs-3.14-bioc/meat/RProtoBufLib/src/pb_build/lib
----------------------------------------------------------------------
Libraries have been installed in:
   /home/biocbuild/bbs-3.14-bioc/meat/RProtoBufLib/src/pb_build/lib

If you ever happen to want to link against installed libraries
in a given directory, LIBDIR, you must either use libtool, and
specify the full pathname of the library, or use the '-LLIBDIR'
flag during linking and do at least one of the following:
   - add LIBDIR to the 'LD_LIBRARY_PATH' environment variable
     during execution
   - add LIBDIR to the 'LD_RUN_PATH' environment variable
     during linking
   - use the '-Wl,-rpath -Wl,LIBDIR' linker flag
   - have your system administrator add LIBDIR to '/etc/ld.so.conf'

See any operating system documentation about shared libraries for
more information, such as the ld(1) and ld.so(8) manual pages.
----------------------------------------------------------------------
 /usr/bin/mkdir -p '/home/biocbuild/bbs-3.14-bioc/meat/RProtoBufLib/src/pb_build/bin'
  /bin/bash ../libtool   --mode=install /usr/bin/install -c protoc '/home/biocbuild/bbs-3.14-bioc/meat/RProtoBufLib/src/pb_build/bin'
libtool: install: /usr/bin/install -c .libs/protoc /home/biocbuild/bbs-3.14-bioc/meat/RProtoBufLib/src/pb_build/bin/protoc
 /usr/bin/mkdir -p '/home/biocbuild/bbs-3.14-bioc/meat/RProtoBufLib/src/pb_build/include'
 /usr/bin/mkdir -p '/home/biocbuild/bbs-3.14-bioc/meat/RProtoBufLib/src/pb_build/include/google/protobuf'
 /usr/bin/install -c -m 644  google/protobuf/descriptor.proto google/protobuf/any.proto google/protobuf/api.proto google/protobuf/duration.proto google/protobuf/empty.proto google/protobuf/field_mask.proto google/protobuf/source_context.proto google/protobuf/struct.proto google/protobuf/timestamp.proto google/protobuf/type.proto google/protobuf/wrappers.proto '/home/biocbuild/bbs-3.14-bioc/meat/RProtoBufLib/src/pb_build/include/google/protobuf'
 /usr/bin/mkdir -p '/home/biocbuild/bbs-3.14-bioc/meat/RProtoBufLib/src/pb_build/include/google/protobuf/compiler'
 /usr/bin/install -c -m 644  google/protobuf/compiler/plugin.proto '/home/biocbuild/bbs-3.14-bioc/meat/RProtoBufLib/src/pb_build/include/google/protobuf/compiler'
 /usr/bin/mkdir -p '/home/biocbuild/bbs-3.14-bioc/meat/RProtoBufLib/src/pb_build/include'
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 /usr/bin/mkdir -p '/home/biocbuild/bbs-3.14-bioc/meat/RProtoBufLib/src/pb_build/include/google/protobuf/stubs'
 /usr/bin/install -c -m 644  google/protobuf/stubs/callback.h google/protobuf/stubs/bytestream.h google/protobuf/stubs/casts.h google/protobuf/stubs/common.h google/protobuf/stubs/fastmem.h google/protobuf/stubs/hash.h google/protobuf/stubs/logging.h google/protobuf/stubs/macros.h google/protobuf/stubs/map_util.h google/protobuf/stubs/mutex.h google/protobuf/stubs/once.h google/protobuf/stubs/platform_macros.h google/protobuf/stubs/port.h google/protobuf/stubs/status.h google/protobuf/stubs/stl_util.h google/protobuf/stubs/stringpiece.h google/protobuf/stubs/strutil.h google/protobuf/stubs/template_util.h '/home/biocbuild/bbs-3.14-bioc/meat/RProtoBufLib/src/pb_build/include/google/protobuf/stubs'
 /usr/bin/mkdir -p '/home/biocbuild/bbs-3.14-bioc/meat/RProtoBufLib/src/pb_build/include/google/protobuf/util'
 /usr/bin/install -c -m 644  google/protobuf/util/type_resolver.h google/protobuf/util/delimited_message_util.h google/protobuf/util/field_comparator.h google/protobuf/util/field_mask_util.h google/protobuf/util/json_util.h google/protobuf/util/time_util.h google/protobuf/util/type_resolver_util.h google/protobuf/util/message_differencer.h '/home/biocbuild/bbs-3.14-bioc/meat/RProtoBufLib/src/pb_build/include/google/protobuf/util'
 /usr/bin/mkdir -p '/home/biocbuild/bbs-3.14-bioc/meat/RProtoBufLib/src/pb_build/include/google/protobuf/compiler/php'
 /usr/bin/install -c -m 644  google/protobuf/compiler/php/php_generator.h '/home/biocbuild/bbs-3.14-bioc/meat/RProtoBufLib/src/pb_build/include/google/protobuf/compiler/php'
 /usr/bin/mkdir -p '/home/biocbuild/bbs-3.14-bioc/meat/RProtoBufLib/src/pb_build/include/google/protobuf/compiler'
 /usr/bin/install -c -m 644  google/protobuf/compiler/code_generator.h google/protobuf/compiler/command_line_interface.h google/protobuf/compiler/importer.h google/protobuf/compiler/parser.h google/protobuf/compiler/plugin.h google/protobuf/compiler/plugin.pb.h '/home/biocbuild/bbs-3.14-bioc/meat/RProtoBufLib/src/pb_build/include/google/protobuf/compiler'
 /usr/bin/mkdir -p '/home/biocbuild/bbs-3.14-bioc/meat/RProtoBufLib/src/pb_build/include/google/protobuf/compiler/ruby'
 /usr/bin/install -c -m 644  google/protobuf/compiler/ruby/ruby_generator.h '/home/biocbuild/bbs-3.14-bioc/meat/RProtoBufLib/src/pb_build/include/google/protobuf/compiler/ruby'
 /usr/bin/mkdir -p '/home/biocbuild/bbs-3.14-bioc/meat/RProtoBufLib/src/pb_build/include/google/protobuf/io'
 /usr/bin/install -c -m 644  google/protobuf/io/io_win32.h google/protobuf/io/coded_stream.h google/protobuf/io/gzip_stream.h google/protobuf/io/printer.h google/protobuf/io/strtod.h google/protobuf/io/tokenizer.h google/protobuf/io/zero_copy_stream.h google/protobuf/io/zero_copy_stream_impl.h google/protobuf/io/zero_copy_stream_impl_lite.h '/home/biocbuild/bbs-3.14-bioc/meat/RProtoBufLib/src/pb_build/include/google/protobuf/io'
 /usr/bin/mkdir -p '/home/biocbuild/bbs-3.14-bioc/meat/RProtoBufLib/src/pb_build/include/google/protobuf/compiler/csharp'
 /usr/bin/install -c -m 644  google/protobuf/compiler/csharp/csharp_generator.h google/protobuf/compiler/csharp/csharp_names.h '/home/biocbuild/bbs-3.14-bioc/meat/RProtoBufLib/src/pb_build/include/google/protobuf/compiler/csharp'
 /usr/bin/mkdir -p '/home/biocbuild/bbs-3.14-bioc/meat/RProtoBufLib/src/pb_build/include/google/protobuf/compiler/objectivec'
 /usr/bin/install -c -m 644  google/protobuf/compiler/objectivec/objectivec_generator.h google/protobuf/compiler/objectivec/objectivec_helpers.h '/home/biocbuild/bbs-3.14-bioc/meat/RProtoBufLib/src/pb_build/include/google/protobuf/compiler/objectivec'
make[2]: Leaving directory '/home/biocbuild/bbs-3.14-bioc/meat/RProtoBufLib/src/protobuf-3.13.0/src'
make[1]: Leaving directory '/home/biocbuild/bbs-3.14-bioc/meat/RProtoBufLib/src/protobuf-3.13.0/src'
configure: creating ./config.status
config.status: creating src/Makevars
** libs
g++ -std=gnu++11 -shared -fpic -I../inst/include/ -I/home/biocbuild/bbs-3.14-bioc/meat/RProtoBufLib/src/pb_build/include/ -o GatingSet_pb_lib/libGatingSet.pb.so GatingSet_pb_lib/GatingSet.pb.cc
mkdir -p "/home/biocbuild/bbs-3.14-bioc/R/library/00LOCK-RProtoBufLib/00new/RProtoBufLib/include"
cp -r /home/biocbuild/bbs-3.14-bioc/meat/RProtoBufLib/src/pb_build/include/google /home/biocbuild/bbs-3.14-bioc/R/library/00LOCK-RProtoBufLib/00new/RProtoBufLib/include
mkdir -p "/home/biocbuild/bbs-3.14-bioc/R/library/00LOCK-RProtoBufLib/00new/RProtoBufLib/lib/"
cp /home/biocbuild/bbs-3.14-bioc/meat/RProtoBufLib/src/pb_build/lib/libprotobuf* /home/biocbuild/bbs-3.14-bioc/R/library/00LOCK-RProtoBufLib/00new/RProtoBufLib/lib/
cp GatingSet_pb_lib/libGatingSet.pb.so /home/biocbuild/bbs-3.14-bioc/R/library/00LOCK-RProtoBufLib/00new/RProtoBufLib/lib//libGatingSet.pb.so
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG -I../inst/include/ -I/home/biocbuild/bbs-3.14-bioc/meat/RProtoBufLib/src/pb_build/include/  -I/usr/local/include   -fpic  -g -O2  -Wall -c dummy.cpp -o dummy.o
g++ -std=gnu++11 -shared -L/home/biocbuild/bbs-3.14-bioc/R/lib -L/usr/local/lib -o RProtoBufLib.so dummy.o -L/home/biocbuild/bbs-3.14-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.14-bioc/R/library/00LOCK-RProtoBufLib/00new/RProtoBufLib/libs
** 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
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (RProtoBufLib)