Package: RProtoBufLib

Version: 1.4.0

Command: /home/biocbuild/bbs-3.8-bioc/R/bin/R CMD check --install=check:RProtoBufLib.install-out.txt --library=/home/biocbuild/bbs-3.8-bioc/R/library --no-vignettes --timings RProtoBufLib_1.4.0.tar.gz

StartedAt: 2019-04-16 02:44:38 -0400 (Tue, 16 Apr 2019)

EndedAt: 2019-04-16 02:44:49 -0400 (Tue, 16 Apr 2019)

EllapsedTime: 10.5 seconds

RetCode: 0

Status:  WARNINGS

CheckDir: RProtoBufLib.Rcheck

Warnings: 1

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###
### Running command:
###
###   /home/biocbuild/bbs-3.8-bioc/R/bin/R CMD check --install=check:RProtoBufLib.install-out.txt --library=/home/biocbuild/bbs-3.8-bioc/R/library --no-vignettes --timings RProtoBufLib_1.4.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.8-bioc/meat/RProtoBufLib.Rcheck’
* using R version 3.5.3 (2019-03-11)
* 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 ‘1.4.0’
* 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 24.8Mb
  sub-directories of 1Mb or more:
    include   1.3Mb
    lib      23.4Mb
* checking package 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 compiled code ... NOTE
Note: information on .o files is not available
* checking files in ‘vignettes’ ... WARNING
Files in the 'vignettes' directory but no files in 'inst/doc':
  ‘UsingRProtoBufLib.Rmd’
Package has no Sweave vignette sources and no VignetteBuilder field.
* checking examples ... OK
* checking PDF version of manual ... OK
* DONE

Status: 1 WARNING, 3 NOTEs
See
  ‘/home/biocbuild/bbs-3.8-bioc/meat/RProtoBufLib.Rcheck/00check.log’
for details.

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### Running command:
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###   /home/biocbuild/bbs-3.8-bioc/R/bin/R CMD INSTALL RProtoBufLib
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* installing to library ‘/home/biocbuild/bbs-3.8-bioc/R/library’
* installing *source* package ‘RProtoBufLib’ ...
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++ 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... /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... 
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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 for style of include used by make... GNU
checking dependency style of gcc... gcc3
checking whether we are using the GNU C++ compiler... yes
checking whether g++ accepts -g... yes
checking dependency style of g++... gcc3
checking how to run the C++ preprocessor... g++ -E
checking for grep that handles long lines and -e... /bin/grep
checking for egrep... /bin/grep -E
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checking for stdlib.h... yes
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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
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checking how to associate runtime and link libraries... printf %s\n
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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
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checking how to truncate binary pipes... /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
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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 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... no
checking whether to build static libraries... yes
checking how to run the C++ preprocessor... g++ -E
checking for ld used by g++... /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++ linker (/usr/bin/ld -m elf_x86_64) supports shared libraries... yes
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checking if g++ PIC flag -fPIC -DPIC works... yes
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checking if g++ supports -c -o file.o... yes
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checking whether the g++ 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 ANSI C header files... (cached) yes
checking fcntl.h usability... yes
checking fcntl.h presence... yes
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checking for inttypes.h... (cached) yes
checking limits.h usability... yes
checking limits.h presence... yes
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checking for stdlib.h... (cached) yes
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checking zlib version... ok (1.2.0.4 or later)
checking for library containing zlibVersion... -lz
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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 whether what we have so far is sufficient with -nostdlib... no
checking whether -lpthread saves the day... yes
checking the location of hash_map... <tr1/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 protobuf.pc
config.status: creating protobuf-lite.pc
config.status: creating config.h
config.status: executing depfiles commands
config.status: executing libtool commands
Making install in .
make[1]: Entering directory '/home/biocbuild/bbs-3.8-bioc/meat/RProtoBufLib/src/protobuf-2.6.0'
make[2]: Entering directory '/home/biocbuild/bbs-3.8-bioc/meat/RProtoBufLib/src/protobuf-2.6.0'
make[2]: Nothing to be done for 'install-exec-am'.
make[2]: Nothing to be done for 'install-data-am'.
make[2]: Leaving directory '/home/biocbuild/bbs-3.8-bioc/meat/RProtoBufLib/src/protobuf-2.6.0'
make[1]: Leaving directory '/home/biocbuild/bbs-3.8-bioc/meat/RProtoBufLib/src/protobuf-2.6.0'
Making install in src
make[1]: Entering directory '/home/biocbuild/bbs-3.8-bioc/meat/RProtoBufLib/src/protobuf-2.6.0/src'
depbase=`echo google/protobuf/stubs/atomicops_internals_x86_gcc.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\
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libtool: compile:  g++ -DHAVE_CONFIG_H -I. -I.. -pthread -Wall -Wwrite-strings -Woverloaded-virtual -Wno-sign-compare -Wno-return-type -g -O2 -Wall -MT google/protobuf/stubs/atomicops_internals_x86_gcc.lo -MD -MP -MF google/protobuf/stubs/.deps/atomicops_internals_x86_gcc.Tpo -c google/protobuf/stubs/atomicops_internals_x86_gcc.cc  -fPIC -DPIC -o google/protobuf/stubs/atomicops_internals_x86_gcc.o
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libtool: compile:  g++ -DHAVE_CONFIG_H -I. -I.. -pthread -Wall -Wwrite-strings -Woverloaded-virtual -Wno-sign-compare -Wno-return-type -g -O2 -Wall -MT google/protobuf/stubs/common.lo -MD -MP -MF google/protobuf/stubs/.deps/common.Tpo -c google/protobuf/stubs/common.cc  -fPIC -DPIC -o google/protobuf/stubs/common.o
depbase=`echo google/protobuf/stubs/once.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\
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libtool: compile:  g++ -DHAVE_CONFIG_H -I. -I.. -pthread -Wall -Wwrite-strings -Woverloaded-virtual -Wno-sign-compare -Wno-return-type -g -O2 -Wall -MT google/protobuf/stubs/once.lo -MD -MP -MF google/protobuf/stubs/.deps/once.Tpo -c google/protobuf/stubs/once.cc  -fPIC -DPIC -o google/protobuf/stubs/once.o
depbase=`echo google/protobuf/stubs/stringprintf.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\
/bin/bash ../libtool  --tag=CXX   --mode=compile g++ -DHAVE_CONFIG_H -I. -I..    -pthread -Wall -Wwrite-strings -Woverloaded-virtual -Wno-sign-compare -Wno-return-type  -g -O2 -Wall -MT google/protobuf/stubs/stringprintf.lo -MD -MP -MF $depbase.Tpo -c -o google/protobuf/stubs/stringprintf.lo google/protobuf/stubs/stringprintf.cc &&\
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libtool: compile:  g++ -DHAVE_CONFIG_H -I. -I.. -pthread -Wall -Wwrite-strings -Woverloaded-virtual -Wno-sign-compare -Wno-return-type -g -O2 -Wall -MT google/protobuf/stubs/stringprintf.lo -MD -MP -MF google/protobuf/stubs/.deps/stringprintf.Tpo -c google/protobuf/stubs/stringprintf.cc  -fPIC -DPIC -o google/protobuf/stubs/stringprintf.o
In file included from ./google/protobuf/stubs/stringprintf.h:47:0,
                 from google/protobuf/stubs/stringprintf.cc:33:
google/protobuf/stubs/stringprintf.cc: In function 'std::__cxx11::string google::protobuf::StringPrintfVector(const char*, const std::vector<std::__cxx11::basic_string<char> >&)':
google/protobuf/stubs/stringprintf.cc:164:59: warning: typedef 'arg_count_mismatch' locally defined but not used [-Wunused-local-typedefs]
   GOOGLE_COMPILE_ASSERT(kStringPrintfVectorMaxArgs == 32, arg_count_mismatch);
                                                           ^
./google/protobuf/stubs/common.h:382:11: note: in definition of macro 'GOOGLE_COMPILE_ASSERT'
           msg[bool(expr) ? 1 : -1]
           ^
depbase=`echo google/protobuf/extension_set.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\
/bin/bash ../libtool  --tag=CXX   --mode=compile g++ -DHAVE_CONFIG_H -I. -I..    -pthread -Wall -Wwrite-strings -Woverloaded-virtual -Wno-sign-compare -Wno-return-type  -g -O2 -Wall -MT google/protobuf/extension_set.lo -MD -MP -MF $depbase.Tpo -c -o google/protobuf/extension_set.lo google/protobuf/extension_set.cc &&\
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libtool: compile:  g++ -DHAVE_CONFIG_H -I. -I.. -pthread -Wall -Wwrite-strings -Woverloaded-virtual -Wno-sign-compare -Wno-return-type -g -O2 -Wall -MT google/protobuf/extension_set.lo -MD -MP -MF google/protobuf/.deps/extension_set.Tpo -c google/protobuf/extension_set.cc  -fPIC -DPIC -o google/protobuf/extension_set.o
In file included from google/protobuf/extension_set.cc:43:0:
./google/protobuf/stubs/map_util.h: In function 'void google::protobuf::InsertOrDie(Collection*, const typename Collection::value_type::first_type&, const typename Collection::value_type::second_type&)':
./google/protobuf/stubs/map_util.h:356:43: warning: typedef 'value_type' locally defined but not used [-Wunused-local-typedefs]
   typedef typename Collection::value_type value_type;
                                           ^
./google/protobuf/stubs/map_util.h: In function 'void google::protobuf::InsertOrDieNoPrint(Collection*, const typename Collection::value_type::first_type&, const typename Collection::value_type::second_type&)':
./google/protobuf/stubs/map_util.h:367:43: warning: typedef 'value_type' locally defined but not used [-Wunused-local-typedefs]
   typedef typename Collection::value_type value_type;
                                           ^
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/bin/bash ../libtool  --tag=CXX   --mode=compile g++ -DHAVE_CONFIG_H -I. -I..    -pthread -Wall -Wwrite-strings -Woverloaded-virtual -Wno-sign-compare -Wno-return-type  -g -O2 -Wall -MT google/protobuf/io/zero_copy_stream_impl_lite.lo -MD -MP -MF $depbase.Tpo -c -o google/protobuf/io/zero_copy_stream_impl_lite.lo google/protobuf/io/zero_copy_stream_impl_lite.cc &&\
mv -f $depbase.Tpo $depbase.Plo
libtool: compile:  g++ -DHAVE_CONFIG_H -I. -I.. -pthread -Wall -Wwrite-strings -Woverloaded-virtual -Wno-sign-compare -Wno-return-type -g -O2 -Wall -MT google/protobuf/io/zero_copy_stream_impl_lite.lo -MD -MP -MF google/protobuf/io/.deps/zero_copy_stream_impl_lite.Tpo -c google/protobuf/io/zero_copy_stream_impl_lite.cc  -fPIC -DPIC -o google/protobuf/io/zero_copy_stream_impl_lite.o
depbase=`echo google/protobuf/stubs/strutil.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\
/bin/bash ../libtool  --tag=CXX   --mode=compile g++ -DHAVE_CONFIG_H -I. -I..    -pthread -Wall -Wwrite-strings -Woverloaded-virtual -Wno-sign-compare -Wno-return-type  -g -O2 -Wall -MT google/protobuf/stubs/strutil.lo -MD -MP -MF $depbase.Tpo -c -o google/protobuf/stubs/strutil.lo google/protobuf/stubs/strutil.cc &&\
mv -f $depbase.Tpo $depbase.Plo
libtool: compile:  g++ -DHAVE_CONFIG_H -I. -I.. -pthread -Wall -Wwrite-strings -Woverloaded-virtual -Wno-sign-compare -Wno-return-type -g -O2 -Wall -MT google/protobuf/stubs/strutil.lo -MD -MP -MF google/protobuf/stubs/.deps/strutil.Tpo -c google/protobuf/stubs/strutil.cc  -fPIC -DPIC -o google/protobuf/stubs/strutil.o
In file included from ./google/protobuf/stubs/strutil.h:38:0,
                 from google/protobuf/stubs/strutil.cc:33:
./google/protobuf/stubs/strutil.h: In function 'google::protobuf::int64 google::protobuf::strto64(const char*, char**, int)':
./google/protobuf/stubs/strutil.h:341:25: warning: typedef 'sizeof_int64_is_not_sizeof_long_long' locally defined but not used [-Wunused-local-typedefs]
                         sizeof_int64_is_not_sizeof_long_long);
                         ^
./google/protobuf/stubs/common.h:382:11: note: in definition of macro 'GOOGLE_COMPILE_ASSERT'
           msg[bool(expr) ? 1 : -1]
           ^
./google/protobuf/stubs/strutil.h: In function 'google::protobuf::uint64 google::protobuf::strtou64(const char*, char**, int)':
./google/protobuf/stubs/strutil.h:347:25: warning: typedef 'sizeof_uint64_is_not_sizeof_long_long' locally defined but not used [-Wunused-local-typedefs]
                         sizeof_uint64_is_not_sizeof_long_long);
                         ^
./google/protobuf/stubs/common.h:382:11: note: in definition of macro 'GOOGLE_COMPILE_ASSERT'
           msg[bool(expr) ? 1 : -1]
           ^
google/protobuf/stubs/strutil.cc: In function 'char* google::protobuf::DoubleToBuffer(double, char*)':
google/protobuf/stubs/strutil.cc:1172:39: warning: typedef 'DBL_DIG_is_too_big' locally defined but not used [-Wunused-local-typedefs]
   GOOGLE_COMPILE_ASSERT(DBL_DIG < 20, DBL_DIG_is_too_big);
                                       ^
./google/protobuf/stubs/common.h:382:11: note: in definition of macro 'GOOGLE_COMPILE_ASSERT'
           msg[bool(expr) ? 1 : -1]
           ^
google/protobuf/stubs/strutil.cc: In function 'char* google::protobuf::FloatToBuffer(float, char*)':
google/protobuf/stubs/strutil.cc:1227:39: warning: typedef 'FLT_DIG_is_too_big' locally defined but not used [-Wunused-local-typedefs]
   GOOGLE_COMPILE_ASSERT(FLT_DIG < 10, FLT_DIG_is_too_big);
                                       ^
./google/protobuf/stubs/common.h:382:11: note: in definition of macro 'GOOGLE_COMPILE_ASSERT'
           msg[bool(expr) ? 1 : -1]
           ^
depbase=`echo google/protobuf/stubs/substitute.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\
/bin/bash ../libtool  --tag=CXX   --mode=compile g++ -DHAVE_CONFIG_H -I. -I..    -pthread -Wall -Wwrite-strings -Woverloaded-virtual -Wno-sign-compare -Wno-return-type  -g -O2 -Wall -MT google/protobuf/stubs/substitute.lo -MD -MP -MF $depbase.Tpo -c -o google/protobuf/stubs/substitute.lo google/protobuf/stubs/substitute.cc &&\
mv -f $depbase.Tpo $depbase.Plo
libtool: compile:  g++ -DHAVE_CONFIG_H -I. -I.. -pthread -Wall -Wwrite-strings -Woverloaded-virtual -Wno-sign-compare -Wno-return-type -g -O2 -Wall -MT google/protobuf/stubs/substitute.lo -MD -MP -MF google/protobuf/stubs/.deps/substitute.Tpo -c google/protobuf/stubs/substitute.cc  -fPIC -DPIC -o google/protobuf/stubs/substitute.o
In file included from ./google/protobuf/stubs/substitute.h:35:0,
                 from google/protobuf/stubs/substitute.cc:33:
./google/protobuf/stubs/strutil.h: In function 'google::protobuf::int64 google::protobuf::strto64(const char*, char**, int)':
./google/protobuf/stubs/strutil.h:341:25: warning: typedef 'sizeof_int64_is_not_sizeof_long_long' locally defined but not used [-Wunused-local-typedefs]
                         sizeof_int64_is_not_sizeof_long_long);
                         ^
./google/protobuf/stubs/common.h:382:11: note: in definition of macro 'GOOGLE_COMPILE_ASSERT'
           msg[bool(expr) ? 1 : -1]
           ^
./google/protobuf/stubs/strutil.h: In function 'google::protobuf::uint64 google::protobuf::strtou64(const char*, char**, int)':
./google/protobuf/stubs/strutil.h:347:25: warning: typedef 'sizeof_uint64_is_not_sizeof_long_long' locally defined but not used [-Wunused-local-typedefs]
                         sizeof_uint64_is_not_sizeof_long_long);
                         ^
./google/protobuf/stubs/common.h:382:11: note: in definition of macro 'GOOGLE_COMPILE_ASSERT'
           msg[bool(expr) ? 1 : -1]
           ^
depbase=`echo google/protobuf/stubs/structurally_valid.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\
/bin/bash ../libtool  --tag=CXX   --mode=compile g++ -DHAVE_CONFIG_H -I. -I..    -pthread -Wall -Wwrite-strings -Woverloaded-virtual -Wno-sign-compare -Wno-return-type  -g -O2 -Wall -MT google/protobuf/stubs/structurally_valid.lo -MD -MP -MF $depbase.Tpo -c -o google/protobuf/stubs/structurally_valid.lo google/protobuf/stubs/structurally_valid.cc &&\
mv -f $depbase.Tpo $depbase.Plo
libtool: compile:  g++ -DHAVE_CONFIG_H -I. -I.. -pthread -Wall -Wwrite-strings -Woverloaded-virtual -Wno-sign-compare -Wno-return-type -g -O2 -Wall -MT google/protobuf/stubs/structurally_valid.lo -MD -MP -MF google/protobuf/stubs/.deps/structurally_valid.Tpo -c google/protobuf/stubs/structurally_valid.cc  -fPIC -DPIC -o google/protobuf/stubs/structurally_valid.o
depbase=`echo google/protobuf/descriptor.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\
/bin/bash ../libtool  --tag=CXX   --mode=compile g++ -DHAVE_CONFIG_H -I. -I..    -pthread -Wall -Wwrite-strings -Woverloaded-virtual -Wno-sign-compare -Wno-return-type  -g -O2 -Wall -MT google/protobuf/descriptor.lo -MD -MP -MF $depbase.Tpo -c -o google/protobuf/descriptor.lo google/protobuf/descriptor.cc &&\
mv -f $depbase.Tpo $depbase.Plo
libtool: compile:  g++ -DHAVE_CONFIG_H -I. -I.. -pthread -Wall -Wwrite-strings -Woverloaded-virtual -Wno-sign-compare -Wno-return-type -g -O2 -Wall -MT google/protobuf/descriptor.lo -MD -MP -MF google/protobuf/.deps/descriptor.Tpo -c google/protobuf/descriptor.cc  -fPIC -DPIC -o google/protobuf/descriptor.o
In file included from ./google/protobuf/stubs/hash.h:39:0,
                 from google/protobuf/descriptor.cc:35:
./google/protobuf/stubs/strutil.h: In function 'google::protobuf::int64 google::protobuf::strto64(const char*, char**, int)':
./google/protobuf/stubs/strutil.h:341:25: warning: typedef 'sizeof_int64_is_not_sizeof_long_long' locally defined but not used [-Wunused-local-typedefs]
                         sizeof_int64_is_not_sizeof_long_long);
                         ^
./google/protobuf/stubs/common.h:382:11: note: in definition of macro 'GOOGLE_COMPILE_ASSERT'
           msg[bool(expr) ? 1 : -1]
           ^
./google/protobuf/stubs/strutil.h: In function 'google::protobuf::uint64 google::protobuf::strtou64(const char*, char**, int)':
./google/protobuf/stubs/strutil.h:347:25: warning: typedef 'sizeof_uint64_is_not_sizeof_long_long' locally defined but not used [-Wunused-local-typedefs]
                         sizeof_uint64_is_not_sizeof_long_long);
                         ^
./google/protobuf/stubs/common.h:382:11: note: in definition of macro 'GOOGLE_COMPILE_ASSERT'
           msg[bool(expr) ? 1 : -1]
           ^
In file included from google/protobuf/descriptor.cc:59:0:
./google/protobuf/stubs/map_util.h: In function 'void google::protobuf::InsertOrDie(Collection*, const typename Collection::value_type::first_type&, const typename Collection::value_type::second_type&)':
./google/protobuf/stubs/map_util.h:356:43: warning: typedef 'value_type' locally defined but not used [-Wunused-local-typedefs]
   typedef typename Collection::value_type value_type;
                                           ^
./google/protobuf/stubs/map_util.h: In function 'void google::protobuf::InsertOrDieNoPrint(Collection*, const typename Collection::value_type::first_type&, const typename Collection::value_type::second_type&)':
./google/protobuf/stubs/map_util.h:367:43: warning: typedef 'value_type' locally defined but not used [-Wunused-local-typedefs]
   typedef typename Collection::value_type value_type;
                                           ^
depbase=`echo google/protobuf/descriptor.pb.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\
/bin/bash ../libtool  --tag=CXX   --mode=compile g++ -DHAVE_CONFIG_H -I. -I..    -pthread -Wall -Wwrite-strings -Woverloaded-virtual -Wno-sign-compare -Wno-return-type  -g -O2 -Wall -MT google/protobuf/descriptor.pb.lo -MD -MP -MF $depbase.Tpo -c -o google/protobuf/descriptor.pb.lo google/protobuf/descriptor.pb.cc &&\
mv -f $depbase.Tpo $depbase.Plo
libtool: compile:  g++ -DHAVE_CONFIG_H -I. -I.. -pthread -Wall -Wwrite-strings -Woverloaded-virtual -Wno-sign-compare -Wno-return-type -g -O2 -Wall -MT google/protobuf/descriptor.pb.lo -MD -MP -MF google/protobuf/.deps/descriptor.pb.Tpo -c google/protobuf/descriptor.pb.cc  -fPIC -DPIC -o google/protobuf/descriptor.pb.o
depbase=`echo google/protobuf/descriptor_database.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\
/bin/bash ../libtool  --tag=CXX   --mode=compile g++ -DHAVE_CONFIG_H -I. -I..    -pthread -Wall -Wwrite-strings -Woverloaded-virtual -Wno-sign-compare -Wno-return-type  -g -O2 -Wall -MT google/protobuf/descriptor_database.lo -MD -MP -MF $depbase.Tpo -c -o google/protobuf/descriptor_database.lo google/protobuf/descriptor_database.cc &&\
mv -f $depbase.Tpo $depbase.Plo
libtool: compile:  g++ -DHAVE_CONFIG_H -I. -I.. -pthread -Wall -Wwrite-strings -Woverloaded-virtual -Wno-sign-compare -Wno-return-type -g -O2 -Wall -MT google/protobuf/descriptor_database.lo -MD -MP -MF google/protobuf/.deps/descriptor_database.Tpo -c google/protobuf/descriptor_database.cc  -fPIC -DPIC -o google/protobuf/descriptor_database.o
In file included from ./google/protobuf/descriptor_database.h:44:0,
                 from google/protobuf/descriptor_database.cc:35:
./google/protobuf/stubs/strutil.h: In function 'google::protobuf::int64 google::protobuf::strto64(const char*, char**, int)':
./google/protobuf/stubs/strutil.h:341:25: warning: typedef 'sizeof_int64_is_not_sizeof_long_long' locally defined but not used [-Wunused-local-typedefs]
                         sizeof_int64_is_not_sizeof_long_long);
                         ^
./google/protobuf/stubs/common.h:382:11: note: in definition of macro 'GOOGLE_COMPILE_ASSERT'
           msg[bool(expr) ? 1 : -1]
           ^
./google/protobuf/stubs/strutil.h: In function 'google::protobuf::uint64 google::protobuf::strtou64(const char*, char**, int)':
./google/protobuf/stubs/strutil.h:347:25: warning: typedef 'sizeof_uint64_is_not_sizeof_long_long' locally defined but not used [-Wunused-local-typedefs]
                         sizeof_uint64_is_not_sizeof_long_long);
                         ^
./google/protobuf/stubs/common.h:382:11: note: in definition of macro 'GOOGLE_COMPILE_ASSERT'
           msg[bool(expr) ? 1 : -1]
           ^
In file included from google/protobuf/descriptor_database.cc:43:0:
./google/protobuf/stubs/map_util.h: In function 'void google::protobuf::InsertOrDie(Collection*, const typename Collection::value_type::first_type&, const typename Collection::value_type::second_type&)':
./google/protobuf/stubs/map_util.h:356:43: warning: typedef 'value_type' locally defined but not used [-Wunused-local-typedefs]
   typedef typename Collection::value_type value_type;
                                           ^
./google/protobuf/stubs/map_util.h: In function 'void google::protobuf::InsertOrDieNoPrint(Collection*, const typename Collection::value_type::first_type&, const typename Collection::value_type::second_type&)':
./google/protobuf/stubs/map_util.h:367:43: warning: typedef 'value_type' locally defined but not used [-Wunused-local-typedefs]
   typedef typename Collection::value_type value_type;
                                           ^
depbase=`echo google/protobuf/dynamic_message.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\
/bin/bash ../libtool  --tag=CXX   --mode=compile g++ -DHAVE_CONFIG_H -I. -I..    -pthread -Wall -Wwrite-strings -Woverloaded-virtual -Wno-sign-compare -Wno-return-type  -g -O2 -Wall -MT google/protobuf/dynamic_message.lo -MD -MP -MF $depbase.Tpo -c -o google/protobuf/dynamic_message.lo google/protobuf/dynamic_message.cc &&\
mv -f $depbase.Tpo $depbase.Plo
libtool: compile:  g++ -DHAVE_CONFIG_H -I. -I.. -pthread -Wall -Wwrite-strings -Woverloaded-virtual -Wno-sign-compare -Wno-return-type -g -O2 -Wall -MT google/protobuf/dynamic_message.lo -MD -MP -MF google/protobuf/.deps/dynamic_message.Tpo -c google/protobuf/dynamic_message.cc  -fPIC -DPIC -o google/protobuf/dynamic_message.o
depbase=`echo google/protobuf/extension_set_heavy.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\
/bin/bash ../libtool  --tag=CXX   --mode=compile g++ -DHAVE_CONFIG_H -I. -I..    -pthread -Wall -Wwrite-strings -Woverloaded-virtual -Wno-sign-compare -Wno-return-type  -g -O2 -Wall -MT google/protobuf/extension_set_heavy.lo -MD -MP -MF $depbase.Tpo -c -o google/protobuf/extension_set_heavy.lo google/protobuf/extension_set_heavy.cc &&\
mv -f $depbase.Tpo $depbase.Plo
libtool: compile:  g++ -DHAVE_CONFIG_H -I. -I.. -pthread -Wall -Wwrite-strings -Woverloaded-virtual -Wno-sign-compare -Wno-return-type -g -O2 -Wall -MT google/protobuf/extension_set_heavy.lo -MD -MP -MF google/protobuf/.deps/extension_set_heavy.Tpo -c google/protobuf/extension_set_heavy.cc  -fPIC -DPIC -o google/protobuf/extension_set_heavy.o
depbase=`echo google/protobuf/generated_message_reflection.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\
/bin/bash ../libtool  --tag=CXX   --mode=compile g++ -DHAVE_CONFIG_H -I. -I..    -pthread -Wall -Wwrite-strings -Woverloaded-virtual -Wno-sign-compare -Wno-return-type  -g -O2 -Wall -MT google/protobuf/generated_message_reflection.lo -MD -MP -MF $depbase.Tpo -c -o google/protobuf/generated_message_reflection.lo google/protobuf/generated_message_reflection.cc &&\
mv -f $depbase.Tpo $depbase.Plo
libtool: compile:  g++ -DHAVE_CONFIG_H -I. -I.. -pthread -Wall -Wwrite-strings -Woverloaded-virtual -Wno-sign-compare -Wno-return-type -g -O2 -Wall -MT google/protobuf/generated_message_reflection.lo -MD -MP -MF google/protobuf/.deps/generated_message_reflection.Tpo -c google/protobuf/generated_message_reflection.cc  -fPIC -DPIC -o google/protobuf/generated_message_reflection.o
google/protobuf/generated_message_reflection.cc: In member function 'void google::protobuf::internal::GeneratedMessageReflection::SwapOneofField(google::protobuf::Message*, google::protobuf::Message*, const google::protobuf::OneofDescriptor*) const':
google/protobuf/generated_message_reflection.cc:503:54: warning: 'field1' may be used uninitialized in this function [-Wmaybe-uninitialized]
         SetField<TYPE>(message2, field1, temp_##TYPE);                  \
                                                      ^
google/protobuf/generated_message_reflection.cc:516:60: warning: 'temp_message' may be used uninitialized in this function [-Wmaybe-uninitialized]
         SetAllocatedMessage(message2, temp_message, field1);
                                                            ^
depbase=`echo google/protobuf/message.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\
/bin/bash ../libtool  --tag=CXX   --mode=compile g++ -DHAVE_CONFIG_H -I. -I..    -pthread -Wall -Wwrite-strings -Woverloaded-virtual -Wno-sign-compare -Wno-return-type  -g -O2 -Wall -MT google/protobuf/message.lo -MD -MP -MF $depbase.Tpo -c -o google/protobuf/message.lo google/protobuf/message.cc &&\
mv -f $depbase.Tpo $depbase.Plo
libtool: compile:  g++ -DHAVE_CONFIG_H -I. -I.. -pthread -Wall -Wwrite-strings -Woverloaded-virtual -Wno-sign-compare -Wno-return-type -g -O2 -Wall -MT google/protobuf/message.lo -MD -MP -MF google/protobuf/.deps/message.Tpo -c google/protobuf/message.cc  -fPIC -DPIC -o google/protobuf/message.o
In file included from ./google/protobuf/stubs/hash.h:39:0,
                 from google/protobuf/message.cc:37:
./google/protobuf/stubs/strutil.h: In function 'google::protobuf::int64 google::protobuf::strto64(const char*, char**, int)':
./google/protobuf/stubs/strutil.h:341:25: warning: typedef 'sizeof_int64_is_not_sizeof_long_long' locally defined but not used [-Wunused-local-typedefs]
                         sizeof_int64_is_not_sizeof_long_long);
                         ^
./google/protobuf/stubs/common.h:382:11: note: in definition of macro 'GOOGLE_COMPILE_ASSERT'
           msg[bool(expr) ? 1 : -1]
           ^
./google/protobuf/stubs/strutil.h: In function 'google::protobuf::uint64 google::protobuf::strtou64(const char*, char**, int)':
./google/protobuf/stubs/strutil.h:347:25: warning: typedef 'sizeof_uint64_is_not_sizeof_long_long' locally defined but not used [-Wunused-local-typedefs]
                         sizeof_uint64_is_not_sizeof_long_long);
                         ^
./google/protobuf/stubs/common.h:382:11: note: in definition of macro 'GOOGLE_COMPILE_ASSERT'
           msg[bool(expr) ? 1 : -1]
           ^
In file included from google/protobuf/message.cc:51:0:
./google/protobuf/stubs/map_util.h: In function 'void google::protobuf::InsertOrDie(Collection*, const typename Collection::value_type::first_type&, const typename Collection::value_type::second_type&)':
./google/protobuf/stubs/map_util.h:356:43: warning: typedef 'value_type' locally defined but not used [-Wunused-local-typedefs]
   typedef typename Collection::value_type value_type;
                                           ^
./google/protobuf/stubs/map_util.h: In function 'void google::protobuf::InsertOrDieNoPrint(Collection*, const typename Collection::value_type::first_type&, const typename Collection::value_type::second_type&)':
./google/protobuf/stubs/map_util.h:367:43: warning: typedef 'value_type' locally defined but not used [-Wunused-local-typedefs]
   typedef typename Collection::value_type value_type;
                                           ^
depbase=`echo google/protobuf/reflection_ops.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\
/bin/bash ../libtool  --tag=CXX   --mode=compile g++ -DHAVE_CONFIG_H -I. -I..    -pthread -Wall -Wwrite-strings -Woverloaded-virtual -Wno-sign-compare -Wno-return-type  -g -O2 -Wall -MT google/protobuf/reflection_ops.lo -MD -MP -MF $depbase.Tpo -c -o google/protobuf/reflection_ops.lo google/protobuf/reflection_ops.cc &&\
mv -f $depbase.Tpo $depbase.Plo
libtool: compile:  g++ -DHAVE_CONFIG_H -I. -I.. -pthread -Wall -Wwrite-strings -Woverloaded-virtual -Wno-sign-compare -Wno-return-type -g -O2 -Wall -MT google/protobuf/reflection_ops.lo -MD -MP -MF google/protobuf/.deps/reflection_ops.Tpo -c google/protobuf/reflection_ops.cc  -fPIC -DPIC -o google/protobuf/reflection_ops.o
In file included from ./google/protobuf/reflection_ops.h:41:0,
                 from google/protobuf/reflection_ops.cc:38:
./google/protobuf/stubs/strutil.h: In function 'google::protobuf::int64 google::protobuf::strto64(const char*, char**, int)':
./google/protobuf/stubs/strutil.h:341:25: warning: typedef 'sizeof_int64_is_not_sizeof_long_long' locally defined but not used [-Wunused-local-typedefs]
                         sizeof_int64_is_not_sizeof_long_long);
                         ^
./google/protobuf/stubs/common.h:382:11: note: in definition of macro 'GOOGLE_COMPILE_ASSERT'
           msg[bool(expr) ? 1 : -1]
           ^
./google/protobuf/stubs/strutil.h: In function 'google::protobuf::uint64 google::protobuf::strtou64(const char*, char**, int)':
./google/protobuf/stubs/strutil.h:347:25: warning: typedef 'sizeof_uint64_is_not_sizeof_long_long' locally defined but not used [-Wunused-local-typedefs]
                         sizeof_uint64_is_not_sizeof_long_long);
                         ^
./google/protobuf/stubs/common.h:382:11: note: in definition of macro 'GOOGLE_COMPILE_ASSERT'
           msg[bool(expr) ? 1 : -1]
           ^
depbase=`echo google/protobuf/service.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\
/bin/bash ../libtool  --tag=CXX   --mode=compile g++ -DHAVE_CONFIG_H -I. -I..    -pthread -Wall -Wwrite-strings -Woverloaded-virtual -Wno-sign-compare -Wno-return-type  -g -O2 -Wall -MT google/protobuf/service.lo -MD -MP -MF $depbase.Tpo -c -o google/protobuf/service.lo google/protobuf/service.cc &&\
mv -f $depbase.Tpo $depbase.Plo
libtool: compile:  g++ -DHAVE_CONFIG_H -I. -I.. -pthread -Wall -Wwrite-strings -Woverloaded-virtual -Wno-sign-compare -Wno-return-type -g -O2 -Wall -MT google/protobuf/service.lo -MD -MP -MF google/protobuf/.deps/service.Tpo -c google/protobuf/service.cc  -fPIC -DPIC -o google/protobuf/service.o
depbase=`echo google/protobuf/text_format.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\
/bin/bash ../libtool  --tag=CXX   --mode=compile g++ -DHAVE_CONFIG_H -I. -I..    -pthread -Wall -Wwrite-strings -Woverloaded-virtual -Wno-sign-compare -Wno-return-type  -g -O2 -Wall -MT google/protobuf/text_format.lo -MD -MP -MF $depbase.Tpo -c -o google/protobuf/text_format.lo google/protobuf/text_format.cc &&\
mv -f $depbase.Tpo $depbase.Plo
libtool: compile:  g++ -DHAVE_CONFIG_H -I. -I.. -pthread -Wall -Wwrite-strings -Woverloaded-virtual -Wno-sign-compare -Wno-return-type -g -O2 -Wall -MT google/protobuf/text_format.lo -MD -MP -MF google/protobuf/.deps/text_format.Tpo -c google/protobuf/text_format.cc  -fPIC -DPIC -o google/protobuf/text_format.o
In file included from ./google/protobuf/text_format.h:46:0,
                 from google/protobuf/text_format.cc:43:
./google/protobuf/stubs/strutil.h: In function 'google::protobuf::int64 google::protobuf::strto64(const char*, char**, int)':
./google/protobuf/stubs/strutil.h:341:25: warning: typedef 'sizeof_int64_is_not_sizeof_long_long' locally defined but not used [-Wunused-local-typedefs]
                         sizeof_int64_is_not_sizeof_long_long);
                         ^
./google/protobuf/stubs/common.h:382:11: note: in definition of macro 'GOOGLE_COMPILE_ASSERT'
           msg[bool(expr) ? 1 : -1]
           ^
./google/protobuf/stubs/strutil.h: In function 'google::protobuf::uint64 google::protobuf::strtou64(const char*, char**, int)':
./google/protobuf/stubs/strutil.h:347:25: warning: typedef 'sizeof_uint64_is_not_sizeof_long_long' locally defined but not used [-Wunused-local-typedefs]
                         sizeof_uint64_is_not_sizeof_long_long);
                         ^
./google/protobuf/stubs/common.h:382:11: note: in definition of macro 'GOOGLE_COMPILE_ASSERT'
           msg[bool(expr) ? 1 : -1]
           ^
In file included from google/protobuf/text_format.cc:54:0:
./google/protobuf/stubs/map_util.h: In function 'void google::protobuf::InsertOrDie(Collection*, const typename Collection::value_type::first_type&, const typename Collection::value_type::second_type&)':
./google/protobuf/stubs/map_util.h:356:43: warning: typedef 'value_type' locally defined but not used [-Wunused-local-typedefs]
   typedef typename Collection::value_type value_type;
                                           ^
./google/protobuf/stubs/map_util.h: In function 'void google::protobuf::InsertOrDieNoPrint(Collection*, const typename Collection::value_type::first_type&, const typename Collection::value_type::second_type&)':
./google/protobuf/stubs/map_util.h:367:43: warning: typedef 'value_type' locally defined but not used [-Wunused-local-typedefs]
   typedef typename Collection::value_type value_type;
                                           ^
depbase=`echo google/protobuf/unknown_field_set.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\
/bin/bash ../libtool  --tag=CXX   --mode=compile g++ -DHAVE_CONFIG_H -I. -I..    -pthread -Wall -Wwrite-strings -Woverloaded-virtual -Wno-sign-compare -Wno-return-type  -g -O2 -Wall -MT google/protobuf/unknown_field_set.lo -MD -MP -MF $depbase.Tpo -c -o google/protobuf/unknown_field_set.lo google/protobuf/unknown_field_set.cc &&\
mv -f $depbase.Tpo $depbase.Plo
libtool: compile:  g++ -DHAVE_CONFIG_H -I. -I.. -pthread -Wall -Wwrite-strings -Woverloaded-virtual -Wno-sign-compare -Wno-return-type -g -O2 -Wall -MT google/protobuf/unknown_field_set.lo -MD -MP -MF google/protobuf/.deps/unknown_field_set.Tpo -c google/protobuf/unknown_field_set.cc  -fPIC -DPIC -o google/protobuf/unknown_field_set.o
depbase=`echo google/protobuf/wire_format.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\
/bin/bash ../libtool  --tag=CXX   --mode=compile g++ -DHAVE_CONFIG_H -I. -I..    -pthread -Wall -Wwrite-strings -Woverloaded-virtual -Wno-sign-compare -Wno-return-type  -g -O2 -Wall -MT google/protobuf/wire_format.lo -MD -MP -MF $depbase.Tpo -c -o google/protobuf/wire_format.lo google/protobuf/wire_format.cc &&\
mv -f $depbase.Tpo $depbase.Plo
libtool: compile:  g++ -DHAVE_CONFIG_H -I. -I.. -pthread -Wall -Wwrite-strings -Woverloaded-virtual -Wno-sign-compare -Wno-return-type -g -O2 -Wall -MT google/protobuf/wire_format.lo -MD -MP -MF google/protobuf/.deps/wire_format.Tpo -c google/protobuf/wire_format.cc  -fPIC -DPIC -o google/protobuf/wire_format.o
depbase=`echo google/protobuf/io/gzip_stream.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\
/bin/bash ../libtool  --tag=CXX   --mode=compile g++ -DHAVE_CONFIG_H -I. -I..    -pthread -Wall -Wwrite-strings -Woverloaded-virtual -Wno-sign-compare -Wno-return-type  -g -O2 -Wall -MT google/protobuf/io/gzip_stream.lo -MD -MP -MF $depbase.Tpo -c -o google/protobuf/io/gzip_stream.lo google/protobuf/io/gzip_stream.cc &&\
mv -f $depbase.Tpo $depbase.Plo
libtool: compile:  g++ -DHAVE_CONFIG_H -I. -I.. -pthread -Wall -Wwrite-strings -Woverloaded-virtual -Wno-sign-compare -Wno-return-type -g -O2 -Wall -MT google/protobuf/io/gzip_stream.lo -MD -MP -MF google/protobuf/io/.deps/gzip_stream.Tpo -c google/protobuf/io/gzip_stream.cc  -fPIC -DPIC -o google/protobuf/io/gzip_stream.o
depbase=`echo google/protobuf/io/printer.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\
/bin/bash ../libtool  --tag=CXX   --mode=compile g++ -DHAVE_CONFIG_H -I. -I..    -pthread -Wall -Wwrite-strings -Woverloaded-virtual -Wno-sign-compare -Wno-return-type  -g -O2 -Wall -MT google/protobuf/io/printer.lo -MD -MP -MF $depbase.Tpo -c -o google/protobuf/io/printer.lo google/protobuf/io/printer.cc &&\
mv -f $depbase.Tpo $depbase.Plo
libtool: compile:  g++ -DHAVE_CONFIG_H -I. -I.. -pthread -Wall -Wwrite-strings -Woverloaded-virtual -Wno-sign-compare -Wno-return-type -g -O2 -Wall -MT google/protobuf/io/printer.lo -MD -MP -MF google/protobuf/io/.deps/printer.Tpo -c google/protobuf/io/printer.cc  -fPIC -DPIC -o google/protobuf/io/printer.o
depbase=`echo google/protobuf/io/strtod.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\
/bin/bash ../libtool  --tag=CXX   --mode=compile g++ -DHAVE_CONFIG_H -I. -I..    -pthread -Wall -Wwrite-strings -Woverloaded-virtual -Wno-sign-compare -Wno-return-type  -g -O2 -Wall -MT google/protobuf/io/strtod.lo -MD -MP -MF $depbase.Tpo -c -o google/protobuf/io/strtod.lo google/protobuf/io/strtod.cc &&\
mv -f $depbase.Tpo $depbase.Plo
libtool: compile:  g++ -DHAVE_CONFIG_H -I. -I.. -pthread -Wall -Wwrite-strings -Woverloaded-virtual -Wno-sign-compare -Wno-return-type -g -O2 -Wall -MT google/protobuf/io/strtod.lo -MD -MP -MF google/protobuf/io/.deps/strtod.Tpo -c google/protobuf/io/strtod.cc  -fPIC -DPIC -o google/protobuf/io/strtod.o
depbase=`echo google/protobuf/io/tokenizer.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\
/bin/bash ../libtool  --tag=CXX   --mode=compile g++ -DHAVE_CONFIG_H -I. -I..    -pthread -Wall -Wwrite-strings -Woverloaded-virtual -Wno-sign-compare -Wno-return-type  -g -O2 -Wall -MT google/protobuf/io/tokenizer.lo -MD -MP -MF $depbase.Tpo -c -o google/protobuf/io/tokenizer.lo google/protobuf/io/tokenizer.cc &&\
mv -f $depbase.Tpo $depbase.Plo
libtool: compile:  g++ -DHAVE_CONFIG_H -I. -I.. -pthread -Wall -Wwrite-strings -Woverloaded-virtual -Wno-sign-compare -Wno-return-type -g -O2 -Wall -MT google/protobuf/io/tokenizer.lo -MD -MP -MF google/protobuf/io/.deps/tokenizer.Tpo -c google/protobuf/io/tokenizer.cc  -fPIC -DPIC -o google/protobuf/io/tokenizer.o
In file included from ./google/protobuf/io/tokenizer.h:42:0,
                 from google/protobuf/io/tokenizer.cc:91:
./google/protobuf/stubs/strutil.h: In function 'google::protobuf::int64 google::protobuf::strto64(const char*, char**, int)':
./google/protobuf/stubs/strutil.h:341:25: warning: typedef 'sizeof_int64_is_not_sizeof_long_long' locally defined but not used [-Wunused-local-typedefs]
                         sizeof_int64_is_not_sizeof_long_long);
                         ^
./google/protobuf/stubs/common.h:382:11: note: in definition of macro 'GOOGLE_COMPILE_ASSERT'
           msg[bool(expr) ? 1 : -1]
           ^
./google/protobuf/stubs/strutil.h: In function 'google::protobuf::uint64 google::protobuf::strtou64(const char*, char**, int)':
./google/protobuf/stubs/strutil.h:347:25: warning: typedef 'sizeof_uint64_is_not_sizeof_long_long' locally defined but not used [-Wunused-local-typedefs]
                         sizeof_uint64_is_not_sizeof_long_long);
                         ^
./google/protobuf/stubs/common.h:382:11: note: in definition of macro 'GOOGLE_COMPILE_ASSERT'
           msg[bool(expr) ? 1 : -1]
           ^
depbase=`echo google/protobuf/io/zero_copy_stream_impl.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\
/bin/bash ../libtool  --tag=CXX   --mode=compile g++ -DHAVE_CONFIG_H -I. -I..    -pthread -Wall -Wwrite-strings -Woverloaded-virtual -Wno-sign-compare -Wno-return-type  -g -O2 -Wall -MT google/protobuf/io/zero_copy_stream_impl.lo -MD -MP -MF $depbase.Tpo -c -o google/protobuf/io/zero_copy_stream_impl.lo google/protobuf/io/zero_copy_stream_impl.cc &&\
mv -f $depbase.Tpo $depbase.Plo
libtool: compile:  g++ -DHAVE_CONFIG_H -I. -I.. -pthread -Wall -Wwrite-strings -Woverloaded-virtual -Wno-sign-compare -Wno-return-type -g -O2 -Wall -MT google/protobuf/io/zero_copy_stream_impl.lo -MD -MP -MF google/protobuf/io/.deps/zero_copy_stream_impl.Tpo -c google/protobuf/io/zero_copy_stream_impl.cc  -fPIC -DPIC -o google/protobuf/io/zero_copy_stream_impl.o
/bin/bash ../libtool  --tag=CXX   --mode=link g++ -pthread -Wall -Wwrite-strings -Woverloaded-virtual -Wno-sign-compare -Wno-return-type  -g -O2 -Wall -version-info 9:0:0 -export-dynamic -no-undefined  -o libprotobuf.la -rpath /home/biocbuild/bbs-3.8-bioc/meat/RProtoBufLib/src/pb_build/lib google/protobuf/stubs/atomicops_internals_x86_gcc.lo google/protobuf/stubs/atomicops_internals_x86_msvc.lo google/protobuf/stubs/common.lo google/protobuf/stubs/once.lo google/protobuf/stubs/stringprintf.lo google/protobuf/extension_set.lo google/protobuf/generated_message_util.lo google/protobuf/message_lite.lo google/protobuf/repeated_field.lo google/protobuf/wire_format_lite.lo google/protobuf/io/coded_stream.lo google/protobuf/io/zero_copy_stream.lo google/protobuf/io/zero_copy_stream_impl_lite.lo google/protobuf/stubs/strutil.lo google/protobuf/stubs/substitute.lo google/protobuf/stubs/structurally_valid.lo google/protobuf/descriptor.lo google/protobuf/descriptor.pb.lo google/protobuf/descriptor_database.lo google/protobuf/dynamic_message.lo google/protobuf/extension_set_heavy.lo google/protobuf/generated_message_reflection.lo google/protobuf/message.lo google/protobuf/reflection_ops.lo google/protobuf/service.lo google/protobuf/text_format.lo google/protobuf/unknown_field_set.lo google/protobuf/wire_format.lo google/protobuf/io/gzip_stream.lo google/protobuf/io/printer.lo google/protobuf/io/strtod.lo google/protobuf/io/tokenizer.lo google/protobuf/io/zero_copy_stream_impl.lo -lpthread -lz 
libtool: link: ar cru .libs/libprotobuf.a  google/protobuf/stubs/atomicops_internals_x86_gcc.o google/protobuf/stubs/atomicops_internals_x86_msvc.o google/protobuf/stubs/common.o google/protobuf/stubs/once.o google/protobuf/stubs/stringprintf.o google/protobuf/extension_set.o google/protobuf/generated_message_util.o google/protobuf/message_lite.o google/protobuf/repeated_field.o google/protobuf/wire_format_lite.o google/protobuf/io/coded_stream.o google/protobuf/io/zero_copy_stream.o google/protobuf/io/zero_copy_stream_impl_lite.o google/protobuf/stubs/strutil.o google/protobuf/stubs/substitute.o google/protobuf/stubs/structurally_valid.o google/protobuf/descriptor.o google/protobuf/descriptor.pb.o google/protobuf/descriptor_database.o google/protobuf/dynamic_message.o google/protobuf/extension_set_heavy.o google/protobuf/generated_message_reflection.o google/protobuf/message.o google/protobuf/reflection_ops.o google/protobuf/service.o google/protobuf/text_format.o google/protobuf/unknown_field_set.o google/protobuf/wire_format.o google/protobuf/io/gzip_stream.o google/protobuf/io/printer.o google/protobuf/io/strtod.o google/protobuf/io/tokenizer.o google/protobuf/io/zero_copy_stream_impl.o
ar: `u' modifier ignored since `D' is the default (see `U')
libtool: link: ranlib .libs/libprotobuf.a
libtool: link: ( cd ".libs" && rm -f "libprotobuf.la" && ln -s "../libprotobuf.la" "libprotobuf.la" )
make[2]: Entering directory '/home/biocbuild/bbs-3.8-bioc/meat/RProtoBufLib/src/protobuf-2.6.0/src'
 /bin/mkdir -p '/home/biocbuild/bbs-3.8-bioc/meat/RProtoBufLib/src/pb_build/lib'
 /bin/bash ../libtool   --mode=install /usr/bin/install -c   libprotobuf.la '/home/biocbuild/bbs-3.8-bioc/meat/RProtoBufLib/src/pb_build/lib'
libtool: install: /usr/bin/install -c .libs/libprotobuf.lai /home/biocbuild/bbs-3.8-bioc/meat/RProtoBufLib/src/pb_build/lib/libprotobuf.la
libtool: install: /usr/bin/install -c .libs/libprotobuf.a /home/biocbuild/bbs-3.8-bioc/meat/RProtoBufLib/src/pb_build/lib/libprotobuf.a
libtool: install: chmod 644 /home/biocbuild/bbs-3.8-bioc/meat/RProtoBufLib/src/pb_build/lib/libprotobuf.a
libtool: install: ranlib /home/biocbuild/bbs-3.8-bioc/meat/RProtoBufLib/src/pb_build/lib/libprotobuf.a
libtool: finish: PATH="/usr/bin:/bin:/usr/local/bin:/snap/bin:/usr/local/root/bin:/usr/local/ensembl-vep:/sbin" ldconfig -n /home/biocbuild/bbs-3.8-bioc/meat/RProtoBufLib/src/pb_build/lib
----------------------------------------------------------------------
Libraries have been installed in:
   /home/biocbuild/bbs-3.8-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.
----------------------------------------------------------------------
 /bin/mkdir -p '/home/biocbuild/bbs-3.8-bioc/meat/RProtoBufLib/src/pb_build/include'
 /bin/mkdir -p '/home/biocbuild/bbs-3.8-bioc/meat/RProtoBufLib/src/pb_build/include/google/protobuf'
 /usr/bin/install -c -m 644  google/protobuf/descriptor.h google/protobuf/descriptor.pb.h google/protobuf/descriptor_database.h google/protobuf/dynamic_message.h google/protobuf/extension_set.h google/protobuf/generated_enum_reflection.h google/protobuf/generated_message_util.h google/protobuf/generated_message_reflection.h google/protobuf/message.h google/protobuf/message_lite.h google/protobuf/reflection_ops.h google/protobuf/repeated_field.h google/protobuf/service.h google/protobuf/text_format.h google/protobuf/unknown_field_set.h google/protobuf/wire_format.h google/protobuf/wire_format_lite.h google/protobuf/wire_format_lite_inl.h '/home/biocbuild/bbs-3.8-bioc/meat/RProtoBufLib/src/pb_build/include/google/protobuf'
 /bin/mkdir -p '/home/biocbuild/bbs-3.8-bioc/meat/RProtoBufLib/src/pb_build/include/google/protobuf/stubs'
 /usr/bin/install -c -m 644  google/protobuf/stubs/atomicops.h google/protobuf/stubs/atomicops_internals_arm_gcc.h google/protobuf/stubs/atomicops_internals_arm64_gcc.h google/protobuf/stubs/atomicops_internals_arm_qnx.h google/protobuf/stubs/atomicops_internals_atomicword_compat.h google/protobuf/stubs/atomicops_internals_generic_gcc.h google/protobuf/stubs/atomicops_internals_macosx.h google/protobuf/stubs/atomicops_internals_mips_gcc.h google/protobuf/stubs/atomicops_internals_pnacl.h google/protobuf/stubs/atomicops_internals_tsan.h google/protobuf/stubs/atomicops_internals_x86_gcc.h google/protobuf/stubs/atomicops_internals_x86_msvc.h google/protobuf/stubs/common.h google/protobuf/stubs/platform_macros.h google/protobuf/stubs/once.h google/protobuf/stubs/stl_util.h google/protobuf/stubs/template_util.h google/protobuf/stubs/type_traits.h '/home/biocbuild/bbs-3.8-bioc/meat/RProtoBufLib/src/pb_build/include/google/protobuf/stubs'
 /bin/mkdir -p '/home/biocbuild/bbs-3.8-bioc/meat/RProtoBufLib/src/pb_build/include/google/protobuf/io'
 /usr/bin/install -c -m 644  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-3.8-bioc/meat/RProtoBufLib/src/pb_build/include/google/protobuf/io'
make[2]: Leaving directory '/home/biocbuild/bbs-3.8-bioc/meat/RProtoBufLib/src/protobuf-2.6.0/src'
make[1]: Leaving directory '/home/biocbuild/bbs-3.8-bioc/meat/RProtoBufLib/src/protobuf-2.6.0/src'
configure: creating ./config.status
config.status: creating src/Makevars
** libs
g++  -I"/home/biocbuild/bbs-3.8-bioc/R/include" -DNDEBUG -I../inst/include/ -I/home/biocbuild/bbs-3.8-bioc/meat/RProtoBufLib/src/pb_build/include/  -I/usr/local/include   -fpic  -g -O2  -Wall -c GatingSet_pb_lib/GatingSet.pb.cc -o GatingSet_pb_lib/GatingSet.pb.o
In file included from GatingSet_pb_lib/GatingSet.pb.cc:12:0:
/home/biocbuild/bbs-3.8-bioc/meat/RProtoBufLib/src/pb_build/include/google/protobuf/wire_format_lite_inl.h: In instantiation of ‘static bool google::protobuf::internal::WireFormatLite::ReadPackedFixedSizePrimitive(google::protobuf::io::CodedInputStream*, google::protobuf::RepeatedField<T>*) [with CType = unsigned int; google::protobuf::internal::WireFormatLite::FieldType DeclaredType = (google::protobuf::internal::WireFormatLite::FieldType)7u]’:
/home/biocbuild/bbs-3.8-bioc/meat/RProtoBufLib/src/pb_build/include/google/protobuf/wire_format_lite_inl.h:413:1:   required from here
/home/biocbuild/bbs-3.8-bioc/meat/RProtoBufLib/src/pb_build/include/google/protobuf/wire_format_lite_inl.h:393:23: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     for (int i = 0; i < new_entries; ++i) {
                       ^
/home/biocbuild/bbs-3.8-bioc/meat/RProtoBufLib/src/pb_build/include/google/protobuf/wire_format_lite_inl.h: In instantiation of ‘static bool google::protobuf::internal::WireFormatLite::ReadPackedFixedSizePrimitive(google::protobuf::io::CodedInputStream*, google::protobuf::RepeatedField<T>*) [with CType = long unsigned int; google::protobuf::internal::WireFormatLite::FieldType DeclaredType = (google::protobuf::internal::WireFormatLite::FieldType)6u]’:
/home/biocbuild/bbs-3.8-bioc/meat/RProtoBufLib/src/pb_build/include/google/protobuf/wire_format_lite_inl.h:414:1:   required from here
/home/biocbuild/bbs-3.8-bioc/meat/RProtoBufLib/src/pb_build/include/google/protobuf/wire_format_lite_inl.h:393:23: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
/home/biocbuild/bbs-3.8-bioc/meat/RProtoBufLib/src/pb_build/include/google/protobuf/wire_format_lite_inl.h: In instantiation of ‘static bool google::protobuf::internal::WireFormatLite::ReadPackedFixedSizePrimitive(google::protobuf::io::CodedInputStream*, google::protobuf::RepeatedField<T>*) [with CType = int; google::protobuf::internal::WireFormatLite::FieldType DeclaredType = (google::protobuf::internal::WireFormatLite::FieldType)15u]’:
/home/biocbuild/bbs-3.8-bioc/meat/RProtoBufLib/src/pb_build/include/google/protobuf/wire_format_lite_inl.h:415:1:   required from here
/home/biocbuild/bbs-3.8-bioc/meat/RProtoBufLib/src/pb_build/include/google/protobuf/wire_format_lite_inl.h:393:23: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
/home/biocbuild/bbs-3.8-bioc/meat/RProtoBufLib/src/pb_build/include/google/protobuf/wire_format_lite_inl.h: In instantiation of ‘static bool google::protobuf::internal::WireFormatLite::ReadPackedFixedSizePrimitive(google::protobuf::io::CodedInputStream*, google::protobuf::RepeatedField<T>*) [with CType = long int; google::protobuf::internal::WireFormatLite::FieldType DeclaredType = (google::protobuf::internal::WireFormatLite::FieldType)16u]’:
/home/biocbuild/bbs-3.8-bioc/meat/RProtoBufLib/src/pb_build/include/google/protobuf/wire_format_lite_inl.h:416:1:   required from here
/home/biocbuild/bbs-3.8-bioc/meat/RProtoBufLib/src/pb_build/include/google/protobuf/wire_format_lite_inl.h:393:23: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
/home/biocbuild/bbs-3.8-bioc/meat/RProtoBufLib/src/pb_build/include/google/protobuf/wire_format_lite_inl.h: In instantiation of ‘static bool google::protobuf::internal::WireFormatLite::ReadPackedFixedSizePrimitive(google::protobuf::io::CodedInputStream*, google::protobuf::RepeatedField<T>*) [with CType = float; google::protobuf::internal::WireFormatLite::FieldType DeclaredType = (google::protobuf::internal::WireFormatLite::FieldType)2u]’:
/home/biocbuild/bbs-3.8-bioc/meat/RProtoBufLib/src/pb_build/include/google/protobuf/wire_format_lite_inl.h:417:1:   required from here
/home/biocbuild/bbs-3.8-bioc/meat/RProtoBufLib/src/pb_build/include/google/protobuf/wire_format_lite_inl.h:393:23: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
/home/biocbuild/bbs-3.8-bioc/meat/RProtoBufLib/src/pb_build/include/google/protobuf/wire_format_lite_inl.h: In instantiation of ‘static bool google::protobuf::internal::WireFormatLite::ReadPackedFixedSizePrimitive(google::protobuf::io::CodedInputStream*, google::protobuf::RepeatedField<T>*) [with CType = double; google::protobuf::internal::WireFormatLite::FieldType DeclaredType = (google::protobuf::internal::WireFormatLite::FieldType)1u]’:
/home/biocbuild/bbs-3.8-bioc/meat/RProtoBufLib/src/pb_build/include/google/protobuf/wire_format_lite_inl.h:418:1:   required from here
/home/biocbuild/bbs-3.8-bioc/meat/RProtoBufLib/src/pb_build/include/google/protobuf/wire_format_lite_inl.h:393:23: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
mkdir -p "/home/biocbuild/bbs-3.8-bioc/R/library/RProtoBufLib/include"
cp -r /home/biocbuild/bbs-3.8-bioc/meat/RProtoBufLib/src/pb_build/include/google /home/biocbuild/bbs-3.8-bioc/R/library/RProtoBufLib/include
mkdir -p "/home/biocbuild/bbs-3.8-bioc/R/library/RProtoBufLib/lib/"
cp /home/biocbuild/bbs-3.8-bioc/meat/RProtoBufLib/src/pb_build/lib/* /home/biocbuild/bbs-3.8-bioc/R/library/RProtoBufLib/lib/
cp GatingSet_pb_lib/GatingSet.pb.o /home/biocbuild/bbs-3.8-bioc/R/library/RProtoBufLib/lib//GatingSet.pb.o
g++  -I"/home/biocbuild/bbs-3.8-bioc/R/include" -DNDEBUG -I../inst/include/ -I/home/biocbuild/bbs-3.8-bioc/meat/RProtoBufLib/src/pb_build/include/  -I/usr/local/include   -fpic  -g -O2  -Wall -c dummy.cpp -o dummy.o
g++ -shared -L/home/biocbuild/bbs-3.8-bioc/R/lib -L/usr/local/lib -o RProtoBufLib.so dummy.o -L/home/biocbuild/bbs-3.8-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.8-bioc/R/library/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
* DONE (RProtoBufLib)

name	user	system	elapsed
LdFlags	0.016	0.004	0.017