Package: RProtoBufLib

Version: 1.4.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:RProtoBufLib.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings RProtoBufLib_1.4.0.tar.gz

StartedAt: 2019-04-16 02:29:35 -0400 (Tue, 16 Apr 2019)

EndedAt: 2019-04-16 02:29:52 -0400 (Tue, 16 Apr 2019)

EllapsedTime: 16.7 seconds

RetCode: 0

Status:  WARNINGS

CheckDir: RProtoBufLib.Rcheck

Warnings: 1

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###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:RProtoBufLib.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings RProtoBufLib_1.4.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.8-bioc/meat/RProtoBufLib.Rcheck’
* using R version 3.5.3 (2019-03-11)
* using platform: x86_64-apple-darwin15.6.0 (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 19.4Mb
  sub-directories of 1Mb or more:
    include   1.2Mb
    lib      18.1Mb
* 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
  ‘/Users/biocbuild/bbs-3.8-bioc/meat/RProtoBufLib.Rcheck/00check.log’
for details.

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL RProtoBufLib
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* installing to library ‘/Library/Frameworks/R.framework/Versions/3.5/Resources/library’
* installing *source* package ‘RProtoBufLib’ ...
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checking whether the C compiler works... yes
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checking whether clang++ accepts -g... yes
untarring protobuf ...
building protobuf...
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checking build system type... x86_64-apple-darwin15.6.0
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configure: WARNING: Impossible to determine how to use pthreads with shared libraries and -nostdlib
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configure: creating ./config.status
config.status: creating Makefile
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Making install in .
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make[2]: Nothing to be done for `install-data-am'.
Making install in src
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google/protobuf/stubs/stringprintf.cc:164:59: warning: unused typedef 'arg_count_mismatch' [-Wunused-local-typedef]
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                                                          ^
1 warning generated.
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libtool: compile:  clang++ -DHAVE_CONFIG_H -I. -I.. -D_THREAD_SAFE -Wall -Wwrite-strings -Woverloaded-virtual -Wno-sign-compare -Wno-return-type -Wall -g -O2 -MT google/protobuf/extension_set.lo -MD -MP -MF google/protobuf/.deps/extension_set.Tpo -c google/protobuf/extension_set.cc  -fno-common -DPIC -o google/protobuf/extension_set.o
In file included from google/protobuf/extension_set.cc:43:
./google/protobuf/stubs/map_util.h:356:43: warning: unused typedef 'value_type' [-Wunused-local-typedef]
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                                          ^
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                                          ^
2 warnings generated.
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libtool: compile:  clang++ -DHAVE_CONFIG_H -I. -I.. -D_THREAD_SAFE -Wall -Wwrite-strings -Woverloaded-virtual -Wno-sign-compare -Wno-return-type -Wall -g -O2 -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  -fno-common -DPIC -o google/protobuf/io/zero_copy_stream_impl_lite.o
depbase=`echo google/protobuf/stubs/strutil.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\
	/bin/sh ../libtool  --tag=CXX   --mode=compile clang++ -DHAVE_CONFIG_H -I. -I..    -D_THREAD_SAFE  -Wall -Wwrite-strings -Woverloaded-virtual -Wno-sign-compare -Wno-return-type  -Wall -g -O2 -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 $depbase.Plo
libtool: compile:  clang++ -DHAVE_CONFIG_H -I. -I.. -D_THREAD_SAFE -Wall -Wwrite-strings -Woverloaded-virtual -Wno-sign-compare -Wno-return-type -Wall -g -O2 -MT google/protobuf/stubs/strutil.lo -MD -MP -MF google/protobuf/stubs/.deps/strutil.Tpo -c google/protobuf/stubs/strutil.cc  -fno-common -DPIC -o google/protobuf/stubs/strutil.o
google/protobuf/stubs/strutil.cc:846:21: warning: unused function 'PlaceNum' [-Wunused-function]
static inline char* PlaceNum(char* p, int num, char prev_sep) {
                    ^
In file included from google/protobuf/stubs/strutil.cc:33:
./google/protobuf/stubs/strutil.h:341:25: warning: unused typedef 'sizeof_int64_is_not_sizeof_long_long' [-Wunused-local-typedef]
                        sizeof_int64_is_not_sizeof_long_long);
                        ^
./google/protobuf/stubs/strutil.h:347:25: warning: unused typedef 'sizeof_uint64_is_not_sizeof_long_long' [-Wunused-local-typedef]
                        sizeof_uint64_is_not_sizeof_long_long);
                        ^
google/protobuf/stubs/strutil.cc:1172:39: warning: unused typedef 'DBL_DIG_is_too_big' [-Wunused-local-typedef]
  GOOGLE_COMPILE_ASSERT(DBL_DIG < 20, DBL_DIG_is_too_big);
                                      ^
google/protobuf/stubs/strutil.cc:1227:39: warning: unused typedef 'FLT_DIG_is_too_big' [-Wunused-local-typedef]
  GOOGLE_COMPILE_ASSERT(FLT_DIG < 10, FLT_DIG_is_too_big);
                                      ^
5 warnings generated.
depbase=`echo google/protobuf/stubs/substitute.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\
	/bin/sh ../libtool  --tag=CXX   --mode=compile clang++ -DHAVE_CONFIG_H -I. -I..    -D_THREAD_SAFE  -Wall -Wwrite-strings -Woverloaded-virtual -Wno-sign-compare -Wno-return-type  -Wall -g -O2 -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 $depbase.Plo
libtool: compile:  clang++ -DHAVE_CONFIG_H -I. -I.. -D_THREAD_SAFE -Wall -Wwrite-strings -Woverloaded-virtual -Wno-sign-compare -Wno-return-type -Wall -g -O2 -MT google/protobuf/stubs/substitute.lo -MD -MP -MF google/protobuf/stubs/.deps/substitute.Tpo -c google/protobuf/stubs/substitute.cc  -fno-common -DPIC -o google/protobuf/stubs/substitute.o
In file included from google/protobuf/stubs/substitute.cc:33:
In file included from ./google/protobuf/stubs/substitute.h:36:
./google/protobuf/stubs/strutil.h:341:25: warning: unused typedef 'sizeof_int64_is_not_sizeof_long_long' [-Wunused-local-typedef]
                        sizeof_int64_is_not_sizeof_long_long);
                        ^
./google/protobuf/stubs/strutil.h:347:25: warning: unused typedef 'sizeof_uint64_is_not_sizeof_long_long' [-Wunused-local-typedef]
                        sizeof_uint64_is_not_sizeof_long_long);
                        ^
2 warnings generated.
depbase=`echo google/protobuf/stubs/structurally_valid.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\
	/bin/sh ../libtool  --tag=CXX   --mode=compile clang++ -DHAVE_CONFIG_H -I. -I..    -D_THREAD_SAFE  -Wall -Wwrite-strings -Woverloaded-virtual -Wno-sign-compare -Wno-return-type  -Wall -g -O2 -MT google/protobuf/stubs/structurally_valid.lo -MD -MP -MF $depbase.Tpo -c -o google/protobuf/stubs/structurally_valid.lo google/protobuf/stubs/structurally_valid.cc &&\
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libtool: compile:  clang++ -DHAVE_CONFIG_H -I. -I.. -D_THREAD_SAFE -Wall -Wwrite-strings -Woverloaded-virtual -Wno-sign-compare -Wno-return-type -Wall -g -O2 -MT google/protobuf/stubs/structurally_valid.lo -MD -MP -MF google/protobuf/stubs/.deps/structurally_valid.Tpo -c google/protobuf/stubs/structurally_valid.cc  -fno-common -DPIC -o google/protobuf/stubs/structurally_valid.o
depbase=`echo google/protobuf/descriptor.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\
	/bin/sh ../libtool  --tag=CXX   --mode=compile clang++ -DHAVE_CONFIG_H -I. -I..    -D_THREAD_SAFE  -Wall -Wwrite-strings -Woverloaded-virtual -Wno-sign-compare -Wno-return-type  -Wall -g -O2 -MT google/protobuf/descriptor.lo -MD -MP -MF $depbase.Tpo -c -o google/protobuf/descriptor.lo google/protobuf/descriptor.cc &&\
	mv -f $depbase.Tpo $depbase.Plo
libtool: compile:  clang++ -DHAVE_CONFIG_H -I. -I.. -D_THREAD_SAFE -Wall -Wwrite-strings -Woverloaded-virtual -Wno-sign-compare -Wno-return-type -Wall -g -O2 -MT google/protobuf/descriptor.lo -MD -MP -MF google/protobuf/.deps/descriptor.Tpo -c google/protobuf/descriptor.cc  -fno-common -DPIC -o google/protobuf/descriptor.o
In file included from google/protobuf/descriptor.cc:57:
./google/protobuf/stubs/strutil.h:341:25: warning: unused typedef 'sizeof_int64_is_not_sizeof_long_long' [-Wunused-local-typedef]
                        sizeof_int64_is_not_sizeof_long_long);
                        ^
./google/protobuf/stubs/strutil.h:347:25: warning: unused typedef 'sizeof_uint64_is_not_sizeof_long_long' [-Wunused-local-typedef]
                        sizeof_uint64_is_not_sizeof_long_long);
                        ^
In file included from google/protobuf/descriptor.cc:59:
./google/protobuf/stubs/map_util.h:356:43: warning: unused typedef 'value_type' [-Wunused-local-typedef]
  typedef typename Collection::value_type value_type;
                                          ^
./google/protobuf/stubs/map_util.h:367:43: warning: unused typedef 'value_type' [-Wunused-local-typedef]
  typedef typename Collection::value_type value_type;
                                          ^
4 warnings generated.
depbase=`echo google/protobuf/descriptor.pb.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\
	/bin/sh ../libtool  --tag=CXX   --mode=compile clang++ -DHAVE_CONFIG_H -I. -I..    -D_THREAD_SAFE  -Wall -Wwrite-strings -Woverloaded-virtual -Wno-sign-compare -Wno-return-type  -Wall -g -O2 -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 $depbase.Plo
libtool: compile:  clang++ -DHAVE_CONFIG_H -I. -I.. -D_THREAD_SAFE -Wall -Wwrite-strings -Woverloaded-virtual -Wno-sign-compare -Wno-return-type -Wall -g -O2 -MT google/protobuf/descriptor.pb.lo -MD -MP -MF google/protobuf/.deps/descriptor.pb.Tpo -c google/protobuf/descriptor.pb.cc  -fno-common -DPIC -o google/protobuf/descriptor.pb.o
depbase=`echo google/protobuf/descriptor_database.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\
	/bin/sh ../libtool  --tag=CXX   --mode=compile clang++ -DHAVE_CONFIG_H -I. -I..    -D_THREAD_SAFE  -Wall -Wwrite-strings -Woverloaded-virtual -Wno-sign-compare -Wno-return-type  -Wall -g -O2 -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 $depbase.Plo
libtool: compile:  clang++ -DHAVE_CONFIG_H -I. -I.. -D_THREAD_SAFE -Wall -Wwrite-strings -Woverloaded-virtual -Wno-sign-compare -Wno-return-type -Wall -g -O2 -MT google/protobuf/descriptor_database.lo -MD -MP -MF google/protobuf/.deps/descriptor_database.Tpo -c google/protobuf/descriptor_database.cc  -fno-common -DPIC -o google/protobuf/descriptor_database.o
In file included from google/protobuf/descriptor_database.cc:41:
./google/protobuf/stubs/strutil.h:341:25: warning: unused typedef 'sizeof_int64_is_not_sizeof_long_long' [-Wunused-local-typedef]
                        sizeof_int64_is_not_sizeof_long_long);
                        ^
./google/protobuf/stubs/strutil.h:347:25: warning: unused typedef 'sizeof_uint64_is_not_sizeof_long_long' [-Wunused-local-typedef]
                        sizeof_uint64_is_not_sizeof_long_long);
                        ^
In file included from google/protobuf/descriptor_database.cc:43:
./google/protobuf/stubs/map_util.h:356:43: warning: unused typedef 'value_type' [-Wunused-local-typedef]
  typedef typename Collection::value_type value_type;
                                          ^
./google/protobuf/stubs/map_util.h:367:43: warning: unused typedef 'value_type' [-Wunused-local-typedef]
  typedef typename Collection::value_type value_type;
                                          ^
4 warnings generated.
depbase=`echo google/protobuf/dynamic_message.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\
	/bin/sh ../libtool  --tag=CXX   --mode=compile clang++ -DHAVE_CONFIG_H -I. -I..    -D_THREAD_SAFE  -Wall -Wwrite-strings -Woverloaded-virtual -Wno-sign-compare -Wno-return-type  -Wall -g -O2 -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 $depbase.Plo
libtool: compile:  clang++ -DHAVE_CONFIG_H -I. -I.. -D_THREAD_SAFE -Wall -Wwrite-strings -Woverloaded-virtual -Wno-sign-compare -Wno-return-type -Wall -g -O2 -MT google/protobuf/dynamic_message.lo -MD -MP -MF google/protobuf/.deps/dynamic_message.Tpo -c google/protobuf/dynamic_message.cc  -fno-common -DPIC -o google/protobuf/dynamic_message.o
depbase=`echo google/protobuf/extension_set_heavy.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\
	/bin/sh ../libtool  --tag=CXX   --mode=compile clang++ -DHAVE_CONFIG_H -I. -I..    -D_THREAD_SAFE  -Wall -Wwrite-strings -Woverloaded-virtual -Wno-sign-compare -Wno-return-type  -Wall -g -O2 -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 $depbase.Plo
libtool: compile:  clang++ -DHAVE_CONFIG_H -I. -I.. -D_THREAD_SAFE -Wall -Wwrite-strings -Woverloaded-virtual -Wno-sign-compare -Wno-return-type -Wall -g -O2 -MT google/protobuf/extension_set_heavy.lo -MD -MP -MF google/protobuf/.deps/extension_set_heavy.Tpo -c google/protobuf/extension_set_heavy.cc  -fno-common -DPIC -o google/protobuf/extension_set_heavy.o
depbase=`echo google/protobuf/generated_message_reflection.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\
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	mv -f $depbase.Tpo $depbase.Plo
libtool: compile:  clang++ -DHAVE_CONFIG_H -I. -I.. -D_THREAD_SAFE -Wall -Wwrite-strings -Woverloaded-virtual -Wno-sign-compare -Wno-return-type -Wall -g -O2 -MT google/protobuf/generated_message_reflection.lo -MD -MP -MF google/protobuf/.deps/generated_message_reflection.Tpo -c google/protobuf/generated_message_reflection.cc  -fno-common -DPIC -o google/protobuf/generated_message_reflection.o
depbase=`echo google/protobuf/message.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\
	/bin/sh ../libtool  --tag=CXX   --mode=compile clang++ -DHAVE_CONFIG_H -I. -I..    -D_THREAD_SAFE  -Wall -Wwrite-strings -Woverloaded-virtual -Wno-sign-compare -Wno-return-type  -Wall -g -O2 -MT google/protobuf/message.lo -MD -MP -MF $depbase.Tpo -c -o google/protobuf/message.lo google/protobuf/message.cc &&\
	mv -f $depbase.Tpo $depbase.Plo
libtool: compile:  clang++ -DHAVE_CONFIG_H -I. -I.. -D_THREAD_SAFE -Wall -Wwrite-strings -Woverloaded-virtual -Wno-sign-compare -Wno-return-type -Wall -g -O2 -MT google/protobuf/message.lo -MD -MP -MF google/protobuf/.deps/message.Tpo -c google/protobuf/message.cc  -fno-common -DPIC -o google/protobuf/message.o
In file included from google/protobuf/message.cc:50:
./google/protobuf/stubs/strutil.h:341:25: warning: unused typedef 'sizeof_int64_is_not_sizeof_long_long' [-Wunused-local-typedef]
                        sizeof_int64_is_not_sizeof_long_long);
                        ^
./google/protobuf/stubs/strutil.h:347:25: warning: unused typedef 'sizeof_uint64_is_not_sizeof_long_long' [-Wunused-local-typedef]
                        sizeof_uint64_is_not_sizeof_long_long);
                        ^
In file included from google/protobuf/message.cc:51:
./google/protobuf/stubs/map_util.h:356:43: warning: unused typedef 'value_type' [-Wunused-local-typedef]
  typedef typename Collection::value_type value_type;
                                          ^
./google/protobuf/stubs/map_util.h:367:43: warning: unused typedef 'value_type' [-Wunused-local-typedef]
  typedef typename Collection::value_type value_type;
                                          ^
4 warnings generated.
depbase=`echo google/protobuf/reflection_ops.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\
	/bin/sh ../libtool  --tag=CXX   --mode=compile clang++ -DHAVE_CONFIG_H -I. -I..    -D_THREAD_SAFE  -Wall -Wwrite-strings -Woverloaded-virtual -Wno-sign-compare -Wno-return-type  -Wall -g -O2 -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 $depbase.Plo
libtool: compile:  clang++ -DHAVE_CONFIG_H -I. -I.. -D_THREAD_SAFE -Wall -Wwrite-strings -Woverloaded-virtual -Wno-sign-compare -Wno-return-type -Wall -g -O2 -MT google/protobuf/reflection_ops.lo -MD -MP -MF google/protobuf/.deps/reflection_ops.Tpo -c google/protobuf/reflection_ops.cc  -fno-common -DPIC -o google/protobuf/reflection_ops.o
In file included from google/protobuf/reflection_ops.cc:42:
./google/protobuf/stubs/strutil.h:341:25: warning: unused typedef 'sizeof_int64_is_not_sizeof_long_long' [-Wunused-local-typedef]
                        sizeof_int64_is_not_sizeof_long_long);
                        ^
./google/protobuf/stubs/strutil.h:347:25: warning: unused typedef 'sizeof_uint64_is_not_sizeof_long_long' [-Wunused-local-typedef]
                        sizeof_uint64_is_not_sizeof_long_long);
                        ^
2 warnings generated.
depbase=`echo google/protobuf/service.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\
	/bin/sh ../libtool  --tag=CXX   --mode=compile clang++ -DHAVE_CONFIG_H -I. -I..    -D_THREAD_SAFE  -Wall -Wwrite-strings -Woverloaded-virtual -Wno-sign-compare -Wno-return-type  -Wall -g -O2 -MT google/protobuf/service.lo -MD -MP -MF $depbase.Tpo -c -o google/protobuf/service.lo google/protobuf/service.cc &&\
	mv -f $depbase.Tpo $depbase.Plo
libtool: compile:  clang++ -DHAVE_CONFIG_H -I. -I.. -D_THREAD_SAFE -Wall -Wwrite-strings -Woverloaded-virtual -Wno-sign-compare -Wno-return-type -Wall -g -O2 -MT google/protobuf/service.lo -MD -MP -MF google/protobuf/.deps/service.Tpo -c google/protobuf/service.cc  -fno-common -DPIC -o google/protobuf/service.o
depbase=`echo google/protobuf/text_format.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\
	/bin/sh ../libtool  --tag=CXX   --mode=compile clang++ -DHAVE_CONFIG_H -I. -I..    -D_THREAD_SAFE  -Wall -Wwrite-strings -Woverloaded-virtual -Wno-sign-compare -Wno-return-type  -Wall -g -O2 -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 $depbase.Plo
libtool: compile:  clang++ -DHAVE_CONFIG_H -I. -I.. -D_THREAD_SAFE -Wall -Wwrite-strings -Woverloaded-virtual -Wno-sign-compare -Wno-return-type -Wall -g -O2 -MT google/protobuf/text_format.lo -MD -MP -MF google/protobuf/.deps/text_format.Tpo -c google/protobuf/text_format.cc  -fno-common -DPIC -o google/protobuf/text_format.o
In file included from google/protobuf/text_format.cc:53:
./google/protobuf/stubs/strutil.h:341:25: warning: unused typedef 'sizeof_int64_is_not_sizeof_long_long' [-Wunused-local-typedef]
                        sizeof_int64_is_not_sizeof_long_long);
                        ^
./google/protobuf/stubs/strutil.h:347:25: warning: unused typedef 'sizeof_uint64_is_not_sizeof_long_long' [-Wunused-local-typedef]
                        sizeof_uint64_is_not_sizeof_long_long);
                        ^
In file included from google/protobuf/text_format.cc:54:
./google/protobuf/stubs/map_util.h:356:43: warning: unused typedef 'value_type' [-Wunused-local-typedef]
  typedef typename Collection::value_type value_type;
                                          ^
./google/protobuf/stubs/map_util.h:367:43: warning: unused typedef 'value_type' [-Wunused-local-typedef]
  typedef typename Collection::value_type value_type;
                                          ^
4 warnings generated.
depbase=`echo google/protobuf/unknown_field_set.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\
	/bin/sh ../libtool  --tag=CXX   --mode=compile clang++ -DHAVE_CONFIG_H -I. -I..    -D_THREAD_SAFE  -Wall -Wwrite-strings -Woverloaded-virtual -Wno-sign-compare -Wno-return-type  -Wall -g -O2 -MT google/protobuf/unknown_field_set.lo -MD -MP -MF $depbase.Tpo -c -o google/protobuf/unknown_field_set.lo google/protobuf/unknown_field_set.cc &&\
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libtool: compile:  clang++ -DHAVE_CONFIG_H -I. -I.. -D_THREAD_SAFE -Wall -Wwrite-strings -Woverloaded-virtual -Wno-sign-compare -Wno-return-type -Wall -g -O2 -MT google/protobuf/unknown_field_set.lo -MD -MP -MF google/protobuf/.deps/unknown_field_set.Tpo -c google/protobuf/unknown_field_set.cc  -fno-common -DPIC -o google/protobuf/unknown_field_set.o
depbase=`echo google/protobuf/wire_format.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\
	/bin/sh ../libtool  --tag=CXX   --mode=compile clang++ -DHAVE_CONFIG_H -I. -I..    -D_THREAD_SAFE  -Wall -Wwrite-strings -Woverloaded-virtual -Wno-sign-compare -Wno-return-type  -Wall -g -O2 -MT google/protobuf/wire_format.lo -MD -MP -MF $depbase.Tpo -c -o google/protobuf/wire_format.lo google/protobuf/wire_format.cc &&\
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libtool: compile:  clang++ -DHAVE_CONFIG_H -I. -I.. -D_THREAD_SAFE -Wall -Wwrite-strings -Woverloaded-virtual -Wno-sign-compare -Wno-return-type -Wall -g -O2 -MT google/protobuf/wire_format.lo -MD -MP -MF google/protobuf/.deps/wire_format.Tpo -c google/protobuf/wire_format.cc  -fno-common -DPIC -o google/protobuf/wire_format.o
google/protobuf/wire_format.cc:60:12: warning: unused function 'GetEnumNumber' [-Wunused-function]
inline int GetEnumNumber(const EnumValueDescriptor* descriptor) {
           ^
1 warning generated.
depbase=`echo google/protobuf/io/gzip_stream.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\
	/bin/sh ../libtool  --tag=CXX   --mode=compile clang++ -DHAVE_CONFIG_H -I. -I..    -D_THREAD_SAFE  -Wall -Wwrite-strings -Woverloaded-virtual -Wno-sign-compare -Wno-return-type  -Wall -g -O2 -MT google/protobuf/io/gzip_stream.lo -MD -MP -MF $depbase.Tpo -c -o google/protobuf/io/gzip_stream.lo google/protobuf/io/gzip_stream.cc &&\
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libtool: compile:  clang++ -DHAVE_CONFIG_H -I. -I.. -D_THREAD_SAFE -Wall -Wwrite-strings -Woverloaded-virtual -Wno-sign-compare -Wno-return-type -Wall -g -O2 -MT google/protobuf/io/gzip_stream.lo -MD -MP -MF google/protobuf/io/.deps/gzip_stream.Tpo -c google/protobuf/io/gzip_stream.cc  -fno-common -DPIC -o google/protobuf/io/gzip_stream.o
depbase=`echo google/protobuf/io/printer.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\
	/bin/sh ../libtool  --tag=CXX   --mode=compile clang++ -DHAVE_CONFIG_H -I. -I..    -D_THREAD_SAFE  -Wall -Wwrite-strings -Woverloaded-virtual -Wno-sign-compare -Wno-return-type  -Wall -g -O2 -MT google/protobuf/io/printer.lo -MD -MP -MF $depbase.Tpo -c -o google/protobuf/io/printer.lo google/protobuf/io/printer.cc &&\
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libtool: compile:  clang++ -DHAVE_CONFIG_H -I. -I.. -D_THREAD_SAFE -Wall -Wwrite-strings -Woverloaded-virtual -Wno-sign-compare -Wno-return-type -Wall -g -O2 -MT google/protobuf/io/printer.lo -MD -MP -MF google/protobuf/io/.deps/printer.Tpo -c google/protobuf/io/printer.cc  -fno-common -DPIC -o google/protobuf/io/printer.o
depbase=`echo google/protobuf/io/strtod.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\
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libtool: compile:  clang++ -DHAVE_CONFIG_H -I. -I.. -D_THREAD_SAFE -Wall -Wwrite-strings -Woverloaded-virtual -Wno-sign-compare -Wno-return-type -Wall -g -O2 -MT google/protobuf/io/strtod.lo -MD -MP -MF google/protobuf/io/.deps/strtod.Tpo -c google/protobuf/io/strtod.cc  -fno-common -DPIC -o google/protobuf/io/strtod.o
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	/bin/sh ../libtool  --tag=CXX   --mode=compile clang++ -DHAVE_CONFIG_H -I. -I..    -D_THREAD_SAFE  -Wall -Wwrite-strings -Woverloaded-virtual -Wno-sign-compare -Wno-return-type  -Wall -g -O2 -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 $depbase.Plo
libtool: compile:  clang++ -DHAVE_CONFIG_H -I. -I.. -D_THREAD_SAFE -Wall -Wwrite-strings -Woverloaded-virtual -Wno-sign-compare -Wno-return-type -Wall -g -O2 -MT google/protobuf/io/tokenizer.lo -MD -MP -MF google/protobuf/io/.deps/tokenizer.Tpo -c google/protobuf/io/tokenizer.cc  -fno-common -DPIC -o google/protobuf/io/tokenizer.o
In file included from google/protobuf/io/tokenizer.cc:96:
./google/protobuf/stubs/strutil.h:341:25: warning: unused typedef 'sizeof_int64_is_not_sizeof_long_long' [-Wunused-local-typedef]
                        sizeof_int64_is_not_sizeof_long_long);
                        ^
./google/protobuf/stubs/strutil.h:347:25: warning: unused typedef 'sizeof_uint64_is_not_sizeof_long_long' [-Wunused-local-typedef]
                        sizeof_uint64_is_not_sizeof_long_long);
                        ^
2 warnings generated.
depbase=`echo google/protobuf/io/zero_copy_stream_impl.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\
	/bin/sh ../libtool  --tag=CXX   --mode=compile clang++ -DHAVE_CONFIG_H -I. -I..    -D_THREAD_SAFE  -Wall -Wwrite-strings -Woverloaded-virtual -Wno-sign-compare -Wno-return-type  -Wall -g -O2 -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:  clang++ -DHAVE_CONFIG_H -I. -I.. -D_THREAD_SAFE -Wall -Wwrite-strings -Woverloaded-virtual -Wno-sign-compare -Wno-return-type -Wall -g -O2 -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  -fno-common -DPIC -o google/protobuf/io/zero_copy_stream_impl.o
/bin/sh ../libtool  --tag=CXX   --mode=link clang++ -D_THREAD_SAFE  -Wall -Wwrite-strings -Woverloaded-virtual -Wno-sign-compare -Wno-return-type  -Wall -g -O2 -version-info 9:0:0 -export-dynamic -no-undefined  -o libprotobuf.la -rpath /Users/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  -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
/Library/Developer/CommandLineTools/usr/bin/ranlib: file: .libs/libprotobuf.a(atomicops_internals_x86_gcc.o) has no symbols
/Library/Developer/CommandLineTools/usr/bin/ranlib: file: .libs/libprotobuf.a(atomicops_internals_x86_msvc.o) has no symbols
libtool: link: ranlib .libs/libprotobuf.a
/Library/Developer/CommandLineTools/usr/bin/ranlib: file: .libs/libprotobuf.a(atomicops_internals_x86_gcc.o) has no symbols
/Library/Developer/CommandLineTools/usr/bin/ranlib: file: .libs/libprotobuf.a(atomicops_internals_x86_msvc.o) has no symbols
libtool: link: ( cd ".libs" && rm -f "libprotobuf.la" && ln -s "../libprotobuf.la" "libprotobuf.la" )
 .././install-sh -c -d '/Users/biocbuild/bbs-3.8-bioc/meat/RProtoBufLib/src/pb_build/lib'
 /bin/sh ../libtool   --mode=install /usr/bin/install -c   libprotobuf.la '/Users/biocbuild/bbs-3.8-bioc/meat/RProtoBufLib/src/pb_build/lib'
libtool: install: /usr/bin/install -c .libs/libprotobuf.lai /Users/biocbuild/bbs-3.8-bioc/meat/RProtoBufLib/src/pb_build/lib/libprotobuf.la
libtool: install: /usr/bin/install -c .libs/libprotobuf.a /Users/biocbuild/bbs-3.8-bioc/meat/RProtoBufLib/src/pb_build/lib/libprotobuf.a
libtool: install: chmod 644 /Users/biocbuild/bbs-3.8-bioc/meat/RProtoBufLib/src/pb_build/lib/libprotobuf.a
libtool: install: ranlib /Users/biocbuild/bbs-3.8-bioc/meat/RProtoBufLib/src/pb_build/lib/libprotobuf.a
/Library/Developer/CommandLineTools/usr/bin/ranlib: file: /Users/biocbuild/bbs-3.8-bioc/meat/RProtoBufLib/src/pb_build/lib/libprotobuf.a(atomicops_internals_x86_gcc.o) has no symbols
/Library/Developer/CommandLineTools/usr/bin/ranlib: file: /Users/biocbuild/bbs-3.8-bioc/meat/RProtoBufLib/src/pb_build/lib/libprotobuf.a(atomicops_internals_x86_msvc.o) has no symbols
 .././install-sh -c -d '/Users/biocbuild/bbs-3.8-bioc/meat/RProtoBufLib/src/pb_build/include'
 .././install-sh -c -d '/Users/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 '/Users/biocbuild/bbs-3.8-bioc/meat/RProtoBufLib/src/pb_build/include/google/protobuf/stubs'
 .././install-sh -c -d '/Users/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 '/Users/biocbuild/bbs-3.8-bioc/meat/RProtoBufLib/src/pb_build/include/google/protobuf/io'
 .././install-sh -c -d '/Users/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 '/Users/biocbuild/bbs-3.8-bioc/meat/RProtoBufLib/src/pb_build/include/google/protobuf'
configure: creating ./config.status
config.status: creating src/Makevars
** libs
clang++  -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I../inst/include/ -I/Users/biocbuild/bbs-3.8-bioc/meat/RProtoBufLib/src/pb_build/include/  -I/usr/local/include   -fPIC  -Wall -g -O2  -c GatingSet_pb_lib/GatingSet.pb.cc -o GatingSet_pb_lib/GatingSet.pb.o
mkdir -p "/Library/Frameworks/R.framework/Versions/3.5/Resources/library/RProtoBufLib/include"
cp -r /Users/biocbuild/bbs-3.8-bioc/meat/RProtoBufLib/src/pb_build/include/google /Library/Frameworks/R.framework/Versions/3.5/Resources/library/RProtoBufLib/include
mkdir -p "/Library/Frameworks/R.framework/Versions/3.5/Resources/library/RProtoBufLib/lib/"
cp /Users/biocbuild/bbs-3.8-bioc/meat/RProtoBufLib/src/pb_build/lib/* /Library/Frameworks/R.framework/Versions/3.5/Resources/library/RProtoBufLib/lib/
cp GatingSet_pb_lib/GatingSet.pb.o /Library/Frameworks/R.framework/Versions/3.5/Resources/library/RProtoBufLib/lib//GatingSet.pb.o
clang++  -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I../inst/include/ -I/Users/biocbuild/bbs-3.8-bioc/meat/RProtoBufLib/src/pb_build/include/  -I/usr/local/include   -fPIC  -Wall -g -O2  -c dummy.cpp -o dummy.o
clang++ -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/Library/Frameworks/R.framework/Resources/lib -L/usr/local/lib -o RProtoBufLib.so dummy.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Library/Frameworks/R.framework/Versions/3.5/Resources/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	0.018	0.002	0.020