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Installation fails on CentOS 7.8 #16

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ivanek opened this issue Jun 7, 2021 · 3 comments
Open

Installation fails on CentOS 7.8 #16

ivanek opened this issue Jun 7, 2021 · 3 comments

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@ivanek
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ivanek commented Jun 7, 2021

Hi,

I am not able to install the recent versions of packages required for analysis of flow data (Bioc 3.13).
Namely the installation of package RProtoBufLib fails with following error:

iocManager::install("RProtoBufLib")
Bioconductor version 3.13 (BiocManager 1.30.15), R 4.1.0 (2021-05-18)
Installing package(s) 'RProtoBufLib'
trying URL 'https://bioconductor.org/packages/3.13/bioc/src/contrib/RProtoBufLib_2.4.0.tar.gz'
Content type 'application/x-gzip' length 5238829 bytes (5.0 MB)
==================================================
downloaded 5.0 MB

* installing *source* package ‘RProtoBufLib’ ...
** using staged installation
checking for gcc... gcc
checking whether the C compiler works... yes
checking for C compiler default output file name... a.out
checking for suffix of executables...
checking whether we are cross compiling... no
checking for suffix of object files... o
checking whether we are using the GNU C compiler... yes
checking whether gcc accepts -g... yes
checking for gcc option to accept ISO C89... none needed
checking whether we are using the GNU C++ compiler... yes
checking whether g++ -std=gnu++14 accepts -g... yes
untarring protobuf ...
building protobuf...
checking whether to enable maintainer-specific portions of Makefiles... yes
checking build system type... x86_64-pc-linux-gnu
checking host system type... x86_64-pc-linux-gnu
checking target system type... x86_64-pc-linux-gnu
checking for a BSD-compatible install... /usr/bin/install -c
checking whether build environment is sane... yes
checking for a thread-safe mkdir -p... /usr/bin/mkdir -p
checking for gawk... gawk
checking whether make sets $(MAKE)... yes
checking whether make supports nested variables... yes
checking whether UID '45381' is supported by ustar format... yes
checking whether GID '2919' is supported by ustar format... yes
checking how to create a ustar tar archive... gnutar
checking whether make supports nested variables... (cached) yes
checking for gcc... gcc
checking whether the C compiler works... yes
checking for C compiler default output file name... a.out
checking for suffix of executables...
checking whether we are cross compiling... no
checking for suffix of object files... o
checking whether we are using the GNU C compiler... yes
checking whether gcc accepts -g... yes
checking for gcc option to accept ISO C89... none needed
checking whether gcc understands -c and -o together... yes
checking whether make supports the include directive... yes (GNU style)
checking dependency style of gcc... gcc3
checking whether we are using the GNU C++ compiler... yes
checking whether g++ -std=gnu++14 accepts -g... yes
checking dependency style of g++ -std=gnu++14... gcc3
checking how to run the C preprocessor... gcc -E
checking for gcc... gcc
checking whether we are using the GNU C compiler... (cached) yes
checking whether gcc accepts -g... yes
checking for gcc option to accept ISO C89... (cached) none needed
checking whether gcc understands -c and -o together... (cached) yes
checking dependency style of gcc... (cached) gcc3
checking how to run the C preprocessor... gcc -E
checking how to run the C++ preprocessor... g++ -std=gnu++14 -E
checking for g++... g++
checking whether we are using the GNU C++ compiler... (cached) yes
checking whether g++ accepts -g... yes
checking dependency style of g++... (cached) gcc3
checking how to run the C++ preprocessor... g++ -E
checking for grep that handles long lines and -e... /usr/bin/grep
checking for egrep... /usr/bin/grep -E
checking for ANSI C header files... yes
checking for sys/types.h... yes
checking for sys/stat.h... yes
checking for stdlib.h... yes
checking for string.h... yes
checking for memory.h... yes
checking for strings.h... yes
checking for inttypes.h... yes
checking for stdint.h... yes
checking for unistd.h... yes
checking minix/config.h usability... no
checking minix/config.h presence... no
checking for minix/config.h... no
checking whether it is safe to define __EXTENSIONS__... yes
checking for ar... ar
checking the archiver (ar) interface... ar
checking for gcc... gcc
checking whether we are using the GNU Objective C compiler... no
checking whether gcc accepts -g... no
checking dependency style of gcc... gcc3
checking C++ compiler flags...... use user-supplied: -O2 -ftree-vectorize -march=x86-64 -mtune=generic -fno-math-errno
checking whether __SUNPRO_CC is declared... no
checking how to print strings... printf
checking for a sed that does not truncate output... /bin/sed
checking for fgrep... /usr/bin/grep -F
checking for ld used by gcc... /scicore/soft/apps/binutils/2.30-GCCcore-7.3.0/bin/ld
checking if the linker (/scicore/soft/apps/binutils/2.30-GCCcore-7.3.0/bin/ld) is GNU ld... yes
checking for BSD- or MS-compatible name lister (nm)... /scicore/soft/apps/binutils/2.30-GCCcore-7.3.0/bin/nm -B
checking the name lister (/scicore/soft/apps/binutils/2.30-GCCcore-7.3.0/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 /scicore/soft/apps/binutils/2.30-GCCcore-7.3.0/bin/ld option to reload object files... -r
checking for objdump... objdump
checking how to recognize dependent libraries... pass_all
checking for dlltool... no
checking how to associate runtime and link libraries... printf %s\n
checking for archiver @FILE support... @
checking for strip... strip
checking for ranlib... ranlib
checking command to parse /scicore/soft/apps/binutils/2.30-GCCcore-7.3.0/bin/nm -B output from gcc object... ok
checking for sysroot... no
checking for a working dd... /usr/bin/dd
checking how to truncate binary pipes... /usr/bin/dd bs=4096 count=1
checking for mt... no
checking if : is a manifest tool... no
checking for dlfcn.h... yes
checking for objdir... .libs
checking if gcc supports -fno-rtti -fno-exceptions... no
checking for gcc option to produce PIC... -fPIC -DPIC
checking if gcc PIC flag -fPIC -DPIC works... yes
checking if gcc static flag -static works... yes
checking if gcc supports -c -o file.o... yes
checking if gcc supports -c -o file.o... (cached) yes
checking whether the gcc linker (/scicore/soft/apps/binutils/2.30-GCCcore-7.3.0/bin/ld -m elf_x86_64) supports shared libraries... yes
checking whether -lc should be explicitly linked in... no
checking dynamic linker characteristics... GNU/Linux ld.so
checking how to hardcode library paths into programs... immediate
checking whether stripping libraries is possible... yes
checking if libtool supports shared libraries... yes
checking whether to build shared libraries... yes
checking whether to build static libraries... no
checking how to run the C++ preprocessor... g++ -std=gnu++14 -E
checking for ld used by g++ -std=gnu++14... /scicore/soft/apps/binutils/2.30-GCCcore-7.3.0/bin/ld -m elf_x86_64
checking if the linker (/scicore/soft/apps/binutils/2.30-GCCcore-7.3.0/bin/ld -m elf_x86_64) is GNU ld... yes
checking whether the g++ -std=gnu++14 linker (/scicore/soft/apps/binutils/2.30-GCCcore-7.3.0/bin/ld -m elf_x86_64) supports shared libraries... yes
checking for g++ -std=gnu++14 option to produce PIC... -fPIC -DPIC
checking if g++ -std=gnu++14 PIC flag -fPIC -DPIC works... yes
checking if g++ -std=gnu++14 static flag -static works... yes
checking if g++ -std=gnu++14 supports -c -o file.o... yes
checking if g++ -std=gnu++14 supports -c -o file.o... (cached) yes
checking whether the g++ -std=gnu++14 linker (/scicore/soft/apps/binutils/2.30-GCCcore-7.3.0/bin/ld -m elf_x86_64) supports shared libraries... yes
checking dynamic linker characteristics... (cached) GNU/Linux ld.so
checking how to hardcode library paths into programs... immediate
checking whether the linker supports version scripts... yes
checking for ANSI C header files... (cached) yes
checking fcntl.h usability... yes
checking fcntl.h presence... yes
checking for fcntl.h... yes
checking for inttypes.h... (cached) yes
checking limits.h usability... yes
checking limits.h presence... yes
checking for limits.h... yes
checking for stdlib.h... (cached) yes
checking for unistd.h... (cached) yes
checking for working memcmp... yes
checking for working strtod... yes
checking for ftruncate... yes
checking for memset... yes
checking for mkdir... yes
checking for strchr... yes
checking for strerror... yes
checking for strtol... yes
checking zlib version... ok (1.2.0.4 or later)
checking for library containing zlibVersion... -lz
checking whether g++ -std=gnu++14 supports C++11 features by default... yes
checking whether -latomic is needed... no
checking whether gcc is Clang... no
checking whether pthreads work with -pthread... yes
checking for joinable pthread attribute... PTHREAD_CREATE_JOINABLE
checking whether more special flags are required for pthreads... no
checking for PTHREAD_PRIO_INHERIT... yes
checking the location of hash_map... <unordered_map>
checking that generated files are newer than configure... done
configure: creating ./config.status
config.status: creating Makefile
config.status: creating src/Makefile
config.status: creating benchmarks/Makefile
config.status: creating conformance/Makefile
config.status: creating protobuf.pc
config.status: creating protobuf-lite.pc
config.status: creating config.h
config.status: executing depfiles commands
config.status: executing libtool commands
=== configuring in third_party/googletest (/scratch/RtmpLkLBfc/R.INSTALL32ad6c00103d/RProtoBufLib/src/protobuf-3.13.0/third_party/googletest)
configure: running /bin/sh ./configure --disable-option-checking '--prefix=/scratch/RtmpLkLBfc/R.INSTALL32ad6c00103d/RProtoBufLib/src/pb_build'  '--enable-static=no' '--with-pic=yes' '--enable-shared=yes' '--libdir=/scratch/RtmpLkLBfc/R.INSTALL32ad6c00103d/RProtoBufLib/src/pb_build/lib' 'CXX=g++ -std=gnu++14' 'CXXFLAGS=-O2 -ftree-vectorize -march=x86-64 -mtune=generic -fno-math-errno' 'CC=gcc' 'CFLAGS=-O2 -ftree-vectorize -march=x86-64 -mtune=generic -fno-math-errno' --cache-file=/dev/null --srcdir=.
checking for a BSD-compatible install... /usr/bin/install -c
checking whether build environment is sane... yes
checking for a thread-safe mkdir -p... /usr/bin/mkdir -p
checking for gawk... gawk
checking whether make sets $(MAKE)... yes
checking whether make supports nested variables... yes
checking that generated files are newer than configure... done
configure: creating ./config.status
config.status: creating Makefile
=== configuring in googletest (/scratch/RtmpLkLBfc/R.INSTALL32ad6c00103d/RProtoBufLib/src/protobuf-3.13.0/third_party/googletest/googletest)
configure: running /bin/sh ./configure --disable-option-checking '--prefix=/scratch/RtmpLkLBfc/R.INSTALL32ad6c00103d/RProtoBufLib/src/pb_build'  '--enable-static=no' '--with-pic=yes' '--enable-shared=yes' '--libdir=/scratch/RtmpLkLBfc/R.INSTALL32ad6c00103d/RProtoBufLib/src/pb_build/lib' 'CXX=g++ -std=gnu++14' 'CXXFLAGS=-O2 -ftree-vectorize -march=x86-64 -mtune=generic -fno-math-errno' 'CC=gcc' 'CFLAGS=-O2 -ftree-vectorize -march=x86-64 -mtune=generic -fno-math-errno' --cache-file=/dev/null --srcdir=.
checking for a BSD-compatible install... /usr/bin/install -c
checking whether build environment is sane... yes
checking for a thread-safe mkdir -p... /usr/bin/mkdir -p
checking for gawk... gawk
checking whether make sets $(MAKE)... yes
checking whether make supports nested variables... yes
checking for gcc... gcc
checking whether the C compiler works... yes
checking for C compiler default output file name... a.out
checking for suffix of executables...
checking whether we are cross compiling... no
checking for suffix of object files... o
checking whether we are using the GNU C compiler... yes
checking whether gcc accepts -g... yes
checking for gcc option to accept ISO C89... none needed
checking whether gcc understands -c and -o together... yes
checking whether make supports the include directive... yes (GNU style)
checking dependency style of gcc... gcc3
checking whether we are using the GNU C++ compiler... yes
checking whether g++ -std=gnu++14 accepts -g... yes
checking dependency style of g++ -std=gnu++14... gcc3
checking build system type... x86_64-pc-linux-gnu
checking host system type... x86_64-pc-linux-gnu
checking how to print strings... printf
checking for a sed that does not truncate output... /bin/sed
checking for grep that handles long lines and -e... /usr/bin/grep
checking for egrep... /usr/bin/grep -E
checking for fgrep... /usr/bin/grep -F
checking for ld used by gcc... /scicore/soft/apps/binutils/2.30-GCCcore-7.3.0/bin/ld
checking if the linker (/scicore/soft/apps/binutils/2.30-GCCcore-7.3.0/bin/ld) is GNU ld... yes
checking for BSD- or MS-compatible name lister (nm)... /scicore/soft/apps/binutils/2.30-GCCcore-7.3.0/bin/nm -B
checking the name lister (/scicore/soft/apps/binutils/2.30-GCCcore-7.3.0/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 /scicore/soft/apps/binutils/2.30-GCCcore-7.3.0/bin/ld option to reload object files... -r
checking for objdump... objdump
checking how to recognize dependent libraries... pass_all
checking for dlltool... no
checking how to associate runtime and link libraries... printf %s\n
checking for ar... ar
checking for archiver @FILE support... @
checking for strip... strip
checking for ranlib... ranlib
checking command to parse /scicore/soft/apps/binutils/2.30-GCCcore-7.3.0/bin/nm -B output from gcc object... ok
checking for sysroot... no
checking for a working dd... /usr/bin/dd
checking how to truncate binary pipes... /usr/bin/dd bs=4096 count=1
checking for mt... no
checking if : is a manifest tool... no
checking how to run the C preprocessor... gcc -E
checking for ANSI C header files... yes
checking for sys/types.h... yes
checking for sys/stat.h... yes
checking for stdlib.h... yes
checking for string.h... yes
checking for memory.h... yes
checking for strings.h... yes
checking for inttypes.h... yes
checking for stdint.h... yes
checking for unistd.h... yes
checking for dlfcn.h... yes
checking for objdir... .libs
checking if gcc supports -fno-rtti -fno-exceptions... no
checking for gcc option to produce PIC... -fPIC -DPIC
checking if gcc PIC flag -fPIC -DPIC works... yes
checking if gcc static flag -static works... yes
checking if gcc supports -c -o file.o... yes
checking if gcc supports -c -o file.o... (cached) yes
checking whether the gcc linker (/scicore/soft/apps/binutils/2.30-GCCcore-7.3.0/bin/ld -m elf_x86_64) supports shared libraries... yes
checking whether -lc should be explicitly linked in... no
checking dynamic linker characteristics... GNU/Linux ld.so
checking how to hardcode library paths into programs... immediate
checking whether stripping libraries is possible... yes
checking if libtool supports shared libraries... yes
checking whether to build shared libraries... yes
checking whether to build static libraries... no
checking how to run the C++ preprocessor... g++ -std=gnu++14 -E
checking for ld used by g++ -std=gnu++14... /scicore/soft/apps/binutils/2.30-GCCcore-7.3.0/bin/ld -m elf_x86_64
checking if the linker (/scicore/soft/apps/binutils/2.30-GCCcore-7.3.0/bin/ld -m elf_x86_64) is GNU ld... yes
checking whether the g++ -std=gnu++14 linker (/scicore/soft/apps/binutils/2.30-GCCcore-7.3.0/bin/ld -m elf_x86_64) supports shared libraries... yes
checking for g++ -std=gnu++14 option to produce PIC... -fPIC -DPIC
checking if g++ -std=gnu++14 PIC flag -fPIC -DPIC works... yes
checking if g++ -std=gnu++14 static flag -static works... yes
checking if g++ -std=gnu++14 supports -c -o file.o... yes
checking if g++ -std=gnu++14 supports -c -o file.o... (cached) yes
checking whether the g++ -std=gnu++14 linker (/scicore/soft/apps/binutils/2.30-GCCcore-7.3.0/bin/ld -m elf_x86_64) supports shared libraries... yes
checking dynamic linker characteristics... (cached) GNU/Linux ld.so
checking how to hardcode library paths into programs... immediate
checking for python... /scicore/home/ivanek/ivanek/miniconda3/bin/python
checking for the pthreads library -lpthreads... no
checking whether pthreads work without any flags... no
checking whether pthreads work with -Kthread... no
checking whether pthreads work with -kthread... no
checking for the pthreads library -llthread... no
checking whether pthreads work with -pthread... yes
checking for joinable pthread attribute... PTHREAD_CREATE_JOINABLE
checking if more special flags are required for pthreads... no
checking whether to check for GCC pthread/shared inconsistencies... yes
checking whether -pthread is sufficient with -shared... yes
checking that generated files are newer than configure... done
configure: creating ./config.status
config.status: creating Makefile
config.status: creating scripts/gtest-config
config.status: creating build-aux/config.h
config.status: executing depfiles commands
config.status: executing libtool commands
=== configuring in googlemock (/scratch/RtmpLkLBfc/R.INSTALL32ad6c00103d/RProtoBufLib/src/protobuf-3.13.0/third_party/googletest/googlemock)
configure: running /bin/sh ./configure --disable-option-checking '--prefix=/scratch/RtmpLkLBfc/R.INSTALL32ad6c00103d/RProtoBufLib/src/pb_build'  '--enable-static=no' '--with-pic=yes' '--enable-shared=yes' '--libdir=/scratch/RtmpLkLBfc/R.INSTALL32ad6c00103d/RProtoBufLib/src/pb_build/lib' 'CXX=g++ -std=gnu++14' 'CXXFLAGS=-O2 -ftree-vectorize -march=x86-64 -mtune=generic -fno-math-errno' 'CC=gcc' 'CFLAGS=-O2 -ftree-vectorize -march=x86-64 -mtune=generic -fno-math-errno' --cache-file=/dev/null --srcdir=.
checking for a BSD-compatible install... /usr/bin/install -c
checking whether build environment is sane... yes
checking for a thread-safe mkdir -p... /usr/bin/mkdir -p
checking for gawk... gawk
checking whether make sets $(MAKE)... yes
checking whether make supports nested variables... yes
checking for gcc... gcc
checking whether the C compiler works... yes
checking for C compiler default output file name... a.out
checking for suffix of executables...
checking whether we are cross compiling... no
checking for suffix of object files... o
checking whether we are using the GNU C compiler... yes
checking whether gcc accepts -g... yes
checking for gcc option to accept ISO C89... none needed
checking whether gcc understands -c and -o together... yes
checking whether make supports the include directive... yes (GNU style)
checking dependency style of gcc... gcc3
checking whether we are using the GNU C++ compiler... yes
checking whether g++ -std=gnu++14 accepts -g... yes
checking dependency style of g++ -std=gnu++14... gcc3
checking build system type... x86_64-pc-linux-gnu
checking host system type... x86_64-pc-linux-gnu
checking how to print strings... printf
checking for a sed that does not truncate output... /bin/sed
checking for grep that handles long lines and -e... /usr/bin/grep
checking for egrep... /usr/bin/grep -E
checking for fgrep... /usr/bin/grep -F
checking for ld used by gcc... /scicore/soft/apps/binutils/2.30-GCCcore-7.3.0/bin/ld
checking if the linker (/scicore/soft/apps/binutils/2.30-GCCcore-7.3.0/bin/ld) is GNU ld... yes
checking for BSD- or MS-compatible name lister (nm)... /scicore/soft/apps/binutils/2.30-GCCcore-7.3.0/bin/nm -B
checking the name lister (/scicore/soft/apps/binutils/2.30-GCCcore-7.3.0/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 /scicore/soft/apps/binutils/2.30-GCCcore-7.3.0/bin/ld option to reload object files... -r
checking for objdump... objdump
checking how to recognize dependent libraries... pass_all
checking for dlltool... no
checking how to associate runtime and link libraries... printf %s\n
checking for ar... ar
checking for archiver @FILE support... @
checking for strip... strip
checking for ranlib... ranlib
checking command to parse /scicore/soft/apps/binutils/2.30-GCCcore-7.3.0/bin/nm -B output from gcc object... ok
checking for sysroot... no
checking for a working dd... /usr/bin/dd
checking how to truncate binary pipes... /usr/bin/dd bs=4096 count=1
checking for mt... no
checking if : is a manifest tool... no
checking how to run the C preprocessor... gcc -E
checking for ANSI C header files... yes
checking for sys/types.h... yes
checking for sys/stat.h... yes
checking for stdlib.h... yes
checking for string.h... yes
checking for memory.h... yes
checking for strings.h... yes
checking for inttypes.h... yes
checking for stdint.h... yes
checking for unistd.h... yes
checking for dlfcn.h... yes
checking for objdir... .libs
checking if gcc supports -fno-rtti -fno-exceptions... no
checking for gcc option to produce PIC... -fPIC -DPIC
checking if gcc PIC flag -fPIC -DPIC works... yes
checking if gcc static flag -static works... yes
checking if gcc supports -c -o file.o... yes
checking if gcc supports -c -o file.o... (cached) yes
checking whether the gcc linker (/scicore/soft/apps/binutils/2.30-GCCcore-7.3.0/bin/ld -m elf_x86_64) supports shared libraries... yes
checking whether -lc should be explicitly linked in... no
checking dynamic linker characteristics... GNU/Linux ld.so
checking how to hardcode library paths into programs... immediate
checking whether stripping libraries is possible... yes
checking if libtool supports shared libraries... yes
checking whether to build shared libraries... yes
checking whether to build static libraries... no
checking how to run the C++ preprocessor... g++ -std=gnu++14 -E
checking for ld used by g++ -std=gnu++14... /scicore/soft/apps/binutils/2.30-GCCcore-7.3.0/bin/ld -m elf_x86_64
checking if the linker (/scicore/soft/apps/binutils/2.30-GCCcore-7.3.0/bin/ld -m elf_x86_64) is GNU ld... yes
checking whether the g++ -std=gnu++14 linker (/scicore/soft/apps/binutils/2.30-GCCcore-7.3.0/bin/ld -m elf_x86_64) supports shared libraries... yes
checking for g++ -std=gnu++14 option to produce PIC... -fPIC -DPIC
checking if g++ -std=gnu++14 PIC flag -fPIC -DPIC works... yes
checking if g++ -std=gnu++14 static flag -static works... yes
checking if g++ -std=gnu++14 supports -c -o file.o... yes
checking if g++ -std=gnu++14 supports -c -o file.o... (cached) yes
checking whether the g++ -std=gnu++14 linker (/scicore/soft/apps/binutils/2.30-GCCcore-7.3.0/bin/ld -m elf_x86_64) supports shared libraries... yes
checking dynamic linker characteristics... (cached) GNU/Linux ld.so
checking how to hardcode library paths into programs... immediate
checking for python... /scicore/home/ivanek/ivanek/miniconda3/bin/python
checking for the pthreads library -lpthreads... no
checking whether pthreads work without any flags... no
checking whether pthreads work with -Kthread... no
checking whether pthreads work with -kthread... no
checking for the pthreads library -llthread... no
checking whether pthreads work with -pthread... yes
checking for joinable pthread attribute... PTHREAD_CREATE_JOINABLE
checking if more special flags are required for pthreads... no
checking whether to check for GCC pthread/shared inconsistencies... yes
checking whether -pthread is sufficient with -shared... yes
checking for gtest-config... no
checking that generated files are newer than configure... done
configure: creating ./config.status
config.status: creating Makefile
config.status: creating scripts/gmock-config
config.status: creating build-aux/config.h
config.status: executing depfiles commands
config.status: executing libtool commands
Making install in .
make[1]: Entering directory `/scratch/RtmpLkLBfc/R.INSTALL32ad6c00103d/RProtoBufLib/src/protobuf-3.13.0'
make[2]: Entering directory `/scratch/RtmpLkLBfc/R.INSTALL32ad6c00103d/RProtoBufLib/src/protobuf-3.13.0'
make[2]: Nothing to be done for `install-exec-am'.
 /usr/bin/mkdir -p '/scratch/RtmpLkLBfc/R.INSTALL32ad6c00103d/RProtoBufLib/src/pb_build/lib/pkgconfig'
 /usr/bin/install -c -m 644 protobuf.pc protobuf-lite.pc '/scratch/RtmpLkLBfc/R.INSTALL32ad6c00103d/RProtoBufLib/src/pb_build/lib/pkgconfig'
make[2]: Leaving directory `/scratch/RtmpLkLBfc/R.INSTALL32ad6c00103d/RProtoBufLib/src/protobuf-3.13.0'
make[1]: Leaving directory `/scratch/RtmpLkLBfc/R.INSTALL32ad6c00103d/RProtoBufLib/src/protobuf-3.13.0'
Making install in src
make[1]: Entering directory `/scratch/RtmpLkLBfc/R.INSTALL32ad6c00103d/RProtoBufLib/src/protobuf-3.13.0/src'
  CXX      google/protobuf/compiler/main.o
  CXX      google/protobuf/stubs/bytestream.lo
  CXX      google/protobuf/stubs/common.lo
  CXX      google/protobuf/stubs/int128.lo
  CXX      google/protobuf/io/io_win32.lo
  CXX      google/protobuf/stubs/status.lo
  CXX      google/protobuf/stubs/statusor.lo
  CXX      google/protobuf/stubs/stringpiece.lo
  CXX      google/protobuf/stubs/stringprintf.lo
  CXX      google/protobuf/stubs/structurally_valid.lo
  CXX      google/protobuf/stubs/strutil.lo
  CXX      google/protobuf/stubs/time.lo
  CXX      google/protobuf/any_lite.lo
  CXX      google/protobuf/arena.lo
  CXX      google/protobuf/extension_set.lo
  CXX      google/protobuf/generated_enum_util.lo
  CXX      google/protobuf/generated_message_util.lo
  CXX      google/protobuf/generated_message_table_driven_lite.lo
  CXX      google/protobuf/implicit_weak_message.lo
  CXX      google/protobuf/message_lite.lo
In file included from ./google/protobuf/message_lite.h:47:0,
                 from google/protobuf/message_lite.cc:36:
In member function 'google::protobuf::uint8* google::protobuf::io::EpsCopyOutputStream::WriteRaw(const void*, int, google::protobuf::uint8*)',
    inlined from 'bool google::protobuf::MessageLite::SerializePartialToZeroCopyStream(google::protobuf::io::ZeroCopyOutputStream*) const' at ./google/protobuf/implicit_weak_message.h:86:35:
./google/protobuf/io/coded_stream.h:699:16: warning: 'void* memcpy(void*, const void*, size_t)': specified size between 18446744071562067968 and 18446744073709551615 exceeds maximum object size 9223372036854775807 [-Wstringop-overflow=]
     std::memcpy(ptr, data, size);
     ~~~~~~~~~~~^~~~~~~~~~~~~~~~~
  CXX      google/protobuf/parse_context.lo
  CXX      google/protobuf/repeated_field.lo
  CXX      google/protobuf/wire_format_lite.lo
  CXX      google/protobuf/io/coded_stream.lo
  CXX      google/protobuf/io/strtod.lo
  CXX      google/protobuf/io/zero_copy_stream.lo
  CXX      google/protobuf/io/zero_copy_stream_impl.lo
  CXX      google/protobuf/io/zero_copy_stream_impl_lite.lo
  CXX      google/protobuf/any.pb.lo
  CXX      google/protobuf/api.pb.lo
  CXX      google/protobuf/any.lo
  CXX      google/protobuf/descriptor.lo
  CXX      google/protobuf/descriptor_database.lo
  CXX      google/protobuf/descriptor.pb.lo
  CXX      google/protobuf/duration.pb.lo
  CXX      google/protobuf/dynamic_message.lo
  CXX      google/protobuf/empty.pb.lo
  CXX      google/protobuf/extension_set_heavy.lo
  CXX      google/protobuf/field_mask.pb.lo
  CXX      google/protobuf/generated_message_reflection.lo
  CXX      google/protobuf/generated_message_table_driven.lo
  CXX      google/protobuf/map_field.lo
  CXX      google/protobuf/message.lo
  CXX      google/protobuf/reflection_ops.lo
  CXX      google/protobuf/service.lo
  CXX      google/protobuf/source_context.pb.lo
  CXX      google/protobuf/struct.pb.lo
  CXX      google/protobuf/stubs/substitute.lo
  CXX      google/protobuf/text_format.lo
  CXX      google/protobuf/timestamp.pb.lo
  CXX      google/protobuf/type.pb.lo
  CXX      google/protobuf/unknown_field_set.lo
  CXX      google/protobuf/wire_format.lo
  CXX      google/protobuf/wrappers.pb.lo
  CXX      google/protobuf/io/gzip_stream.lo
  CXX      google/protobuf/io/printer.lo
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  CXX      google/protobuf/compiler/importer.lo
  CXX      google/protobuf/compiler/parser.lo
  CXX      google/protobuf/util/delimited_message_util.lo
  CXX      google/protobuf/util/field_comparator.lo
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  CXX      google/protobuf/util/internal/default_value_objectwriter.lo
  CXX      google/protobuf/util/internal/error_listener.lo
  CXX      google/protobuf/util/internal/field_mask_utility.lo
  CXX      google/protobuf/util/internal/json_escaping.lo
  CXX      google/protobuf/util/internal/json_objectwriter.lo
  CXX      google/protobuf/util/internal/json_stream_parser.lo
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  CXXLD    libprotobuf.la
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  CXX      google/protobuf/compiler/cpp/cpp_helpers.lo
google/protobuf/compiler/cpp/cpp_helpers.cc:171:6: warning: 'char google::protobuf::compiler::cpp::{anonymous}::Base63Char(int)' defined but not used [-Wunused-function]
 char Base63Char(int value) {
      ^~~~~~~~~~
  CXX      google/protobuf/compiler/cpp/cpp_map_field.lo
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  CXXLD    libprotoc.la
  CXXLD    protoc
./.libs/libprotoc.so: error: undefined reference to 'scc_info_FileDescriptorProto_google_2fprotobuf_2fdescriptor_2eproto'
./.libs/libprotoc.so: error: undefined reference to 'descriptor_table_google_2fprotobuf_2fdescriptor_2eproto'
collect2: error: ld returned 1 exit status
make[1]: *** [protoc] Error 1
make[1]: Leaving directory `/scratch/RtmpLkLBfc/R.INSTALL32ad6c00103d/RProtoBufLib/src/protobuf-3.13.0/src'
make: *** [install-recursive] Error 1
configure: creating ./config.status
config.status: creating src/Makevars
** libs
g++ -std=gnu++11 -shared -fpic -I../inst/include/ -I/scratch/RtmpLkLBfc/R.INSTALL32ad6c00103d/RProtoBufLib/src/pb_build/include/ -o GatingSet_pb_lib/libGatingSet.pb.so GatingSet_pb_lib/GatingSet.pb.cc
In file included from GatingSet_pb_lib/GatingSet.pb.cc:4:0:
../inst/include/cytolib/GatingSet.pb.h:12:2: error: #error This file was generated by a newer version of protoc which is
 #error This file was generated by a newer version of protoc which is
  ^~~~~
../inst/include/cytolib/GatingSet.pb.h:13:2: error: #error incompatible with your Protocol Buffer headers. Please update
 #error incompatible with your Protocol Buffer headers. Please update
  ^~~~~
../inst/include/cytolib/GatingSet.pb.h:14:2: error: #error your headers.
 #error your headers.
  ^~~~~
In file included from GatingSet_pb_lib/GatingSet.pb.cc:4:0:
../inst/include/cytolib/GatingSet.pb.h:39:1: error: ‘PROTOBUF_NAMESPACE_OPEN’ does not name a type; did you mean ‘PROTOBUF_USE_EXCEPTIONS’?
 PROTOBUF_NAMESPACE_OPEN
 ^~~~~~~~~~~~~~~~~~~~~~~
 PROTOBUF_USE_EXCEPTIONS
../inst/include/cytolib/GatingSet.pb.h:43:1: error: ‘PROTOBUF_NAMESPACE_CLOSE’ does not name a type; did you mean ‘PROTOBUF_USE_EXCEPTIONS’?
 PROTOBUF_NAMESPACE_CLOSE
 ^~~~~~~~~~~~~~~~~~~~~~~~
 PROTOBUF_USE_EXCEPTIONS
../inst/include/cytolib/GatingSet.pb.h:159:1: error: ‘PROTOBUF_NAMESPACE_OPEN’ does not name a type; did you mean ‘PROTOBUF_USE_EXCEPTIONS’?
 PROTOBUF_NAMESPACE_OPEN
 ^~~~~~~~~~~~~~~~~~~~~~~
 PROTOBUF_USE_EXCEPTIONS
../inst/include/cytolib/GatingSet.pb.h:161:24: error: ‘Arena’ has not been declared
 template<> ::pb::COMP* Arena::CreateMaybeMessage<::pb::COMP>(Arena*);
                        ^~~~~
../inst/include/cytolib/GatingSet.pb.h:161:49: error: expected initializer before ‘<’ token
 template<> ::pb::COMP* Arena::CreateMaybeMessage<::pb::COMP>(Arena*);
                                                 ^
../inst/include/cytolib/GatingSet.pb.h:162:29: error: ‘Arena’ has not been declared
 template<> ::pb::CytoFrame* Arena::CreateMaybeMessage<::pb::CytoFrame>(Arena*);
                             ^~~~~
../inst/include/cytolib/GatingSet.pb.h:162:54: error: expected initializer before ‘<’ token
 template<> ::pb::CytoFrame* Arena::CreateMaybeMessage<::pb::CytoFrame>(Arena*);
                                                      ^
../inst/include/cytolib/GatingSet.pb.h:163:35: error: ‘Arena’ has not been declared
 template<> ::pb::GatingHierarchy* Arena::CreateMaybeMessage<::pb::GatingHierarchy>(Arena*);
                                   ^~~~~
../inst/include/cytolib/GatingSet.pb.h:163:60: error: expected initializer before ‘<’ token
 template<> ::pb::GatingHierarchy* Arena::CreateMaybeMessage<::pb::GatingHierarchy>(Arena*);
                                                            ^
../inst/include/cytolib/GatingSet.pb.h:164:29: error: ‘Arena’ has not been declared
 template<> ::pb::GatingSet* Arena::CreateMaybeMessage<::pb::GatingSet>(Arena*);
                             ^~~~~
../inst/include/cytolib/GatingSet.pb.h:164:54: error: expected initializer before ‘<’ token
 template<> ::pb::GatingSet* Arena::CreateMaybeMessage<::pb::GatingSet>(Arena*);
                                                      ^
../inst/include/cytolib/GatingSet.pb.h:165:25: error: ‘Arena’ has not been declared
 template<> ::pb::PARAM* Arena::CreateMaybeMessage<::pb::PARAM>(Arena*);
                         ^~~~~
../inst/include/cytolib/GatingSet.pb.h:165:50: error: expected initializer before ‘<’ token
 template<> ::pb::PARAM* Arena::CreateMaybeMessage<::pb::PARAM>(Arena*);
                                                  ^
../inst/include/cytolib/GatingSet.pb.h:166:30: error: ‘Arena’ has not been declared
 template<> ::pb::POPINDICES* Arena::CreateMaybeMessage<::pb::POPINDICES>(Arena*);
                              ^~~~~
../inst/include/cytolib/GatingSet.pb.h:166:55: error: expected initializer before ‘<’ token
 template<> ::pb::POPINDICES* Arena::CreateMaybeMessage<::pb::POPINDICES>(Arena*);
                                                       ^
../inst/include/cytolib/GatingSet.pb.h:167:28: error: ‘Arena’ has not been declared
 template<> ::pb::POPSTATS* Arena::CreateMaybeMessage<::pb::POPSTATS>(Arena*);
                            ^~~~~
../inst/include/cytolib/GatingSet.pb.h:167:53: error: expected initializer before ‘<’ token
 template<> ::pb::POPSTATS* Arena::CreateMaybeMessage<::pb::POPSTATS>(Arena*);
                                                     ^
../inst/include/cytolib/GatingSet.pb.h:168:29: error: ‘Arena’ has not been declared
 template<> ::pb::TRANS_TBL* Arena::CreateMaybeMessage<::pb::TRANS_TBL>(Arena*);
                             ^~~~~
../inst/include/cytolib/GatingSet.pb.h:168:54: error: expected initializer before ‘<’ token
 template<> ::pb::TRANS_TBL* Arena::CreateMaybeMessage<::pb::TRANS_TBL>(Arena*);
                                                      ^
../inst/include/cytolib/GatingSet.pb.h:169:30: error: ‘Arena’ has not been declared
 template<> ::pb::biexpTrans* Arena::CreateMaybeMessage<::pb::biexpTrans>(Arena*);
                              ^~~~~
../inst/include/cytolib/GatingSet.pb.h:169:55: error: expected initializer before ‘<’ token
 template<> ::pb::biexpTrans* Arena::CreateMaybeMessage<::pb::biexpTrans>(Arena*);
                                                       ^
../inst/include/cytolib/GatingSet.pb.h:170:28: error: ‘Arena’ has not been declared
 template<> ::pb::boolGate* Arena::CreateMaybeMessage<::pb::boolGate>(Arena*);
                            ^~~~~
../inst/include/cytolib/GatingSet.pb.h:170:53: error: expected initializer before ‘<’ token
 template<> ::pb::boolGate* Arena::CreateMaybeMessage<::pb::boolGate>(Arena*);
                                                     ^
../inst/include/cytolib/GatingSet.pb.h:171:36: error: ‘Arena’ has not been declared
 template<> ::pb::calibrationTable* Arena::CreateMaybeMessage<::pb::calibrationTable>(Arena*);
                                    ^~~~~
../inst/include/cytolib/GatingSet.pb.h:171:61: error: expected initializer before ‘<’ token
 template<> ::pb::calibrationTable* Arena::CreateMaybeMessage<::pb::calibrationTable>(Arena*);
                                                             ^
../inst/include/cytolib/GatingSet.pb.h:172:31: error: ‘Arena’ has not been declared
 template<> ::pb::clusterGate* Arena::CreateMaybeMessage<::pb::clusterGate>(Arena*);
                               ^~~~~
../inst/include/cytolib/GatingSet.pb.h:172:56: error: expected initializer before ‘<’ token
 template<> ::pb::clusterGate* Arena::CreateMaybeMessage<::pb::clusterGate>(Arena*);
                                                        ^
../inst/include/cytolib/GatingSet.pb.h:173:30: error: ‘Arena’ has not been declared
 template<> ::pb::coordinate* Arena::CreateMaybeMessage<::pb::coordinate>(Arena*);
                              ^~~~~
../inst/include/cytolib/GatingSet.pb.h:173:55: error: expected initializer before ‘<’ token
 template<> ::pb::coordinate* Arena::CreateMaybeMessage<::pb::coordinate>(Arena*);
                                                       ^
../inst/include/cytolib/GatingSet.pb.h:174:31: error: ‘Arena’ has not been declared
 template<> ::pb::ellipseGate* Arena::CreateMaybeMessage<::pb::ellipseGate>(Arena*);
                               ^~~~~
../inst/include/cytolib/GatingSet.pb.h:174:56: error: expected initializer before ‘<’ token
 template<> ::pb::ellipseGate* Arena::CreateMaybeMessage<::pb::ellipseGate>(Arena*);
                                                        ^
../inst/include/cytolib/GatingSet.pb.h:175:31: error: ‘Arena’ has not been declared
 template<> ::pb::fasinhTrans* Arena::CreateMaybeMessage<::pb::fasinhTrans>(Arena*);
                               ^~~~~
../inst/include/cytolib/GatingSet.pb.h:175:56: error: expected initializer before ‘<’ token
 template<> ::pb::fasinhTrans* Arena::CreateMaybeMessage<::pb::fasinhTrans>(Arena*);
                                                        ^
../inst/include/cytolib/GatingSet.pb.h:176:29: error: ‘Arena’ has not been declared
 template<> ::pb::flinTrans* Arena::CreateMaybeMessage<::pb::flinTrans>(Arena*);
                             ^~~~~
../inst/include/cytolib/GatingSet.pb.h:176:54: error: expected initializer before ‘<’ token
 template<> ::pb::flinTrans* Arena::CreateMaybeMessage<::pb::flinTrans>(Arena*);
                                                      ^
../inst/include/cytolib/GatingSet.pb.h:177:24: error: ‘Arena’ has not been declared
 template<> ::pb::gate* Arena::CreateMaybeMessage<::pb::gate>(Arena*);
                        ^~~~~
../inst/include/cytolib/GatingSet.pb.h:177:49: error: expected initializer before ‘<’ token
 template<> ::pb::gate* Arena::CreateMaybeMessage<::pb::gate>(Arena*);
                                                 ^
../inst/include/cytolib/GatingSet.pb.h:178:32: error: ‘Arena’ has not been declared
 template<> ::pb::logGML2Trans* Arena::CreateMaybeMessage<::pb::logGML2Trans>(Arena*);
                                ^~~~~
../inst/include/cytolib/GatingSet.pb.h:178:57: error: expected initializer before ‘<’ token
 template<> ::pb::logGML2Trans* Arena::CreateMaybeMessage<::pb::logGML2Trans>(Arena*);
                                                         ^
../inst/include/cytolib/GatingSet.pb.h:179:28: error: ‘Arena’ has not been declared
 template<> ::pb::logTrans* Arena::CreateMaybeMessage<::pb::logTrans>(Arena*);
                            ^~~~~
../inst/include/cytolib/GatingSet.pb.h:179:53: error: expected initializer before ‘<’ token
 template<> ::pb::logTrans* Arena::CreateMaybeMessage<::pb::logTrans>(Arena*);
                                                     ^
../inst/include/cytolib/GatingSet.pb.h:180:32: error: ‘Arena’ has not been declared
 template<> ::pb::logicleTrans* Arena::CreateMaybeMessage<::pb::logicleTrans>(Arena*);
                                ^~~~~
../inst/include/cytolib/GatingSet.pb.h:180:57: error: expected initializer before ‘<’ token
 template<> ::pb::logicleTrans* Arena::CreateMaybeMessage<::pb::logicleTrans>(Arena*);
                                                         ^
../inst/include/cytolib/GatingSet.pb.h:181:34: error: ‘Arena’ has not been declared
 template<> ::pb::nodeProperties* Arena::CreateMaybeMessage<::pb::nodeProperties>(Arena*);
                                  ^~~~~
../inst/include/cytolib/GatingSet.pb.h:181:59: error: expected initializer before ‘<’ token
 template<> ::pb::nodeProperties* Arena::CreateMaybeMessage<::pb::nodeProperties>(Arena*);
                                                           ^
../inst/include/cytolib/GatingSet.pb.h:182:29: error: ‘Arena’ has not been declared
 template<> ::pb::paramPoly* Arena::CreateMaybeMessage<::pb::paramPoly>(Arena*);
                             ^~~~~
../inst/include/cytolib/GatingSet.pb.h:182:54: error: expected initializer before ‘<’ token
 template<> ::pb::paramPoly* Arena::CreateMaybeMessage<::pb::paramPoly>(Arena*);
                                                      ^
../inst/include/cytolib/GatingSet.pb.h:183:30: error: ‘Arena’ has not been declared
 template<> ::pb::paramRange* Arena::CreateMaybeMessage<::pb::paramRange>(Arena*);
                              ^~~~~
../inst/include/cytolib/GatingSet.pb.h:183:55: error: expected initializer before ‘<’ token
 template<> ::pb::paramRange* Arena::CreateMaybeMessage<::pb::paramRange>(Arena*);
                                                       ^
../inst/include/cytolib/GatingSet.pb.h:184:31: error: ‘Arena’ has not been declared
 template<> ::pb::polygonGate* Arena::CreateMaybeMessage<::pb::polygonGate>(Arena*);
                               ^~~~~
../inst/include/cytolib/GatingSet.pb.h:184:56: error: expected initializer before ‘<’ token
 template<> ::pb::polygonGate* Arena::CreateMaybeMessage<::pb::polygonGate>(Arena*);
                                                        ^
../inst/include/cytolib/GatingSet.pb.h:185:34: error: ‘Arena’ has not been declared
 template<> ::pb::populationTree* Arena::CreateMaybeMessage<::pb::populationTree>(Arena*);
                                  ^~~~~
../inst/include/cytolib/GatingSet.pb.h:185:59: error: expected initializer before ‘<’ token
 template<> ::pb::populationTree* Arena::CreateMaybeMessage<::pb::populationTree>(Arena*);
                                                           ^
../inst/include/cytolib/GatingSet.pb.h:186:28: error: ‘Arena’ has not been declared
 template<> ::pb::quadGate* Arena::CreateMaybeMessage<::pb::quadGate>(Arena*);
                            ^~~~~
../inst/include/cytolib/GatingSet.pb.h:186:53: error: expected initializer before ‘<’ token
 template<> ::pb::quadGate* Arena::CreateMaybeMessage<::pb::quadGate>(Arena*);
                                                     ^
../inst/include/cytolib/GatingSet.pb.h:187:29: error: ‘Arena’ has not been declared
 template<> ::pb::rangeGate* Arena::CreateMaybeMessage<::pb::rangeGate>(Arena*);
                             ^~~~~
../inst/include/cytolib/GatingSet.pb.h:187:54: error: expected initializer before ‘<’ token
 template<> ::pb::rangeGate* Arena::CreateMaybeMessage<::pb::rangeGate>(Arena*);
                                                      ^
../inst/include/cytolib/GatingSet.pb.h:188:30: error: ‘Arena’ has not been declared
 template<> ::pb::scaleTrans* Arena::CreateMaybeMessage<::pb::scaleTrans>(Arena*);
                              ^~~~~
../inst/include/cytolib/GatingSet.pb.h:188:55: error: expected initializer before ‘<’ token
 template<> ::pb::scaleTrans* Arena::CreateMaybeMessage<::pb::scaleTrans>(Arena*);
                                                       ^
../inst/include/cytolib/GatingSet.pb.h:189:31: error: ‘Arena’ has not been declared
 template<> ::pb::trans_local* Arena::CreateMaybeMessage<::pb::trans_local>(Arena*);
                               ^~~~~
../inst/include/cytolib/GatingSet.pb.h:189:56: error: expected initializer before ‘<’ token
 template<> ::pb::trans_local* Arena::CreateMaybeMessage<::pb::trans_local>(Arena*);
                                                        ^
../inst/include/cytolib/GatingSet.pb.h:190:30: error: ‘Arena’ has not been declared
 template<> ::pb::trans_pair* Arena::CreateMaybeMessage<::pb::trans_pair>(Arena*);
                              ^~~~~
../inst/include/cytolib/GatingSet.pb.h:190:55: error: expected initializer before ‘<’ token
 template<> ::pb::trans_pair* Arena::CreateMaybeMessage<::pb::trans_pair>(Arena*);
                                                       ^
../inst/include/cytolib/GatingSet.pb.h:191:34: error: ‘Arena’ has not been declared
 template<> ::pb::transformation* Arena::CreateMaybeMessage<::pb::transformation>(Arena*);
                                  ^~~~~
../inst/include/cytolib/GatingSet.pb.h:191:59: error: expected initializer before ‘<’ token
 template<> ::pb::transformation* Arena::CreateMaybeMessage<::pb::transformation>(Arena*);
                                                           ^
../inst/include/cytolib/GatingSet.pb.h:192:29: error: ‘Arena’ has not been declared
 template<> ::pb::treeNodes* Arena::CreateMaybeMessage<::pb::treeNodes>(Arena*);
                             ^~~~~
../inst/include/cytolib/GatingSet.pb.h:192:54: error: expected initializer before ‘<’ token
 template<> ::pb::treeNodes* Arena::CreateMaybeMessage<::pb::treeNodes>(Arena*);
                                                      ^
../inst/include/cytolib/GatingSet.pb.h:193:1: error: ‘PROTOBUF_NAMESPACE_CLOSE’ does not name a type; did you mean ‘PROTOBUF_USE_EXCEPTIONS’?
 PROTOBUF_NAMESPACE_CLOSE
 ^~~~~~~~~~~~~~~~~~~~~~~~
 PROTOBUF_USE_EXCEPTIONS
../inst/include/cytolib/GatingSet.pb.h:6598:30: error: expected declaration before end of line
   #pragma GCC diagnostic push
                              ^
make: *** [libGatingSet.pb] Error 1
ERROR: compilation failed for package ‘RProtoBufLib’
* removing ‘/scicore/home/ivanek/GROUP/R-libraries/4.1.0-foss-2018b-bare-bioc-3.13/RProtoBufLib’

In .inet_warning(msg) :
  installation of package ‘RProtoBufLib’ had non-zero exit status

My session info is:

R version 4.1.0 (2021-05-18)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: CentOS Linux 7 (Core)

Matrix products: default
BLAS/LAPACK: /scicore/soft/apps/OpenBLAS/0.3.1-GCC-7.3.0-2.30/lib/libopenblas_sandybridgep-r0.3.1.so

locale:
 [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C               LC_TIME=en_US.UTF-8
 [4] LC_COLLATE=en_US.UTF-8     LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8
 [7] LC_PAPER=en_US.UTF-8       LC_NAME=C                  LC_ADDRESS=C
[10] LC_TELEPHONE=C             LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base

loaded via a namespace (and not attached):
[1] compiler_4.1.0

And the Bioc Installation seems to be valid otherwise. Thanks for your help.

Best, Robert
@pineappleburger
Copy link

I seem to have the same problem after updating to R 4.1 under CentOS 7:

> devtools::install_github("RGLab/RProtoBufLib")
Downloading GitHub repo RGLab/RProtoBufLib@HEAD
✓  checking for file ‘/tmp/RtmpvdUXKp/remotes4f144d148678/RGLab-RProtoBufLib-30a9fbd/DESCRIPTION’ (529ms)
─  preparing ‘RProtoBufLib’:
✓  checking DESCRIPTION meta-information
─  cleaning src
─  running ‘cleanup’
─  checking for LF line-endings in source and make files and shell scripts
─  checking for empty or unneeded directories
─  building ‘RProtoBufLib_2.5.1.tar.gz’
   
Installing package into ‘/g/huber/users/mammen/proj/diagnFACS/renv/library/R-4.1/x86_64-pc-linux-gnu’
(as ‘lib’ is unspecified)
* installing *source* package ‘RProtoBufLib’ ...
** using staged installation
checking for gcc... gcc
checking whether the C compiler works... yes
checking for C compiler default output file name... a.out
checking for suffix of executables... 
checking whether we are cross compiling... no
checking for suffix of object files... o
checking whether we are using the GNU C compiler... yes
checking whether gcc accepts -g... yes
checking for gcc option to accept ISO C89... none needed
checking whether we are using the GNU C++ compiler... yes
checking whether g++ -std=gnu++14 accepts -g... yes
untarring protobuf ...
building protobuf...
checking whether to enable maintainer-specific portions of Makefiles... yes
checking build system type... x86_64-pc-linux-gnu
checking host system type... x86_64-pc-linux-gnu
checking target system type... x86_64-pc-linux-gnu
checking for a BSD-compatible install... /usr/bin/install -c
checking whether build environment is sane... yes
checking for a thread-safe mkdir -p... /usr/bin/mkdir -p
checking for gawk... gawk
checking whether make sets $(MAKE)... yes
checking whether make supports nested variables... yes
checking whether UID '24602' is supported by ustar format... yes
checking whether GID '987' is supported by ustar format... yes
checking how to create a ustar tar archive... gnutar
checking whether make supports nested variables... (cached) yes
checking for gcc... gcc
checking whether the C compiler works... yes
checking for C compiler default output file name... a.out
checking for suffix of executables... 
checking whether we are cross compiling... no
checking for suffix of object files... o
checking whether we are using the GNU C compiler... yes
checking whether gcc accepts -g... yes
checking for gcc option to accept ISO C89... none needed
checking whether gcc understands -c and -o together... yes
checking whether make supports the include directive... yes (GNU style)
checking dependency style of gcc... gcc3
checking whether we are using the GNU C++ compiler... yes
checking whether g++ -std=gnu++14 accepts -g... yes
checking dependency style of g++ -std=gnu++14... gcc3
checking how to run the C preprocessor... gcc -E
checking for gcc... gcc
checking whether we are using the GNU C compiler... (cached) yes
checking whether gcc accepts -g... yes
checking for gcc option to accept ISO C89... (cached) none needed
checking whether gcc understands -c and -o together... (cached) yes
checking dependency style of gcc... (cached) gcc3
checking how to run the C preprocessor... gcc -E
checking how to run the C++ preprocessor... g++ -std=gnu++14 -E
checking for g++... g++
checking whether we are using the GNU C++ compiler... (cached) yes
checking whether g++ accepts -g... yes
checking dependency style of g++... (cached) gcc3
checking how to run the C++ preprocessor... g++ -E
checking for grep that handles long lines and -e... /usr/bin/grep
checking for egrep... /usr/bin/grep -E
checking for ANSI C header files... yes
checking for sys/types.h... yes
checking for sys/stat.h... yes
checking for stdlib.h... yes
checking for string.h... yes
checking for memory.h... yes
checking for strings.h... yes
checking for inttypes.h... yes
checking for stdint.h... yes
checking for unistd.h... yes
checking minix/config.h usability... no
checking minix/config.h presence... no
checking for minix/config.h... no
checking whether it is safe to define __EXTENSIONS__... yes
checking for ar... ar
checking the archiver (ar) interface... ar
checking for gcc... gcc
checking whether we are using the GNU Objective C compiler... no
checking whether gcc accepts -g... no
checking dependency style of gcc... gcc3
checking C++ compiler flags...... use user-supplied: -O2 -ftree-vectorize -march=native -fno-math-errno
checking whether __SUNPRO_CC is declared... no
checking how to print strings... printf
checking for a sed that does not truncate output... /usr/bin/sed
checking for fgrep... /usr/bin/grep -F
checking for ld used by gcc... /g/easybuild/x86_64/CentOS/7/haswell/software/binutils/2.36.1-GCCcore-10.3.0/bin/ld
checking if the linker (/g/easybuild/x86_64/CentOS/7/haswell/software/binutils/2.36.1-GCCcore-10.3.0/bin/ld) is GNU ld... yes
checking for BSD- or MS-compatible name lister (nm)... /g/easybuild/x86_64/CentOS/7/haswell/software/binutils/2.36.1-GCCcore-10.3.0/bin/nm -B
checking the name lister (/g/easybuild/x86_64/CentOS/7/haswell/software/binutils/2.36.1-GCCcore-10.3.0/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 /g/easybuild/x86_64/CentOS/7/haswell/software/binutils/2.36.1-GCCcore-10.3.0/bin/ld option to reload object files... -r
checking for objdump... objdump
checking how to recognize dependent libraries... pass_all
checking for dlltool... no
checking how to associate runtime and link libraries... printf %s\n
checking for archiver @FILE support... @
checking for strip... strip
checking for ranlib... ranlib
checking command to parse /g/easybuild/x86_64/CentOS/7/haswell/software/binutils/2.36.1-GCCcore-10.3.0/bin/nm -B output from gcc object... ok
checking for sysroot... no
checking for a working dd... /usr/bin/dd
checking how to truncate binary pipes... /usr/bin/dd bs=4096 count=1
checking for mt... no
checking if : is a manifest tool... no
checking for dlfcn.h... yes
checking for objdir... .libs
checking if gcc supports -fno-rtti -fno-exceptions... no
checking for gcc option to produce PIC... -fPIC -DPIC
checking if gcc PIC flag -fPIC -DPIC works... yes
checking if gcc static flag -static works... no
checking if gcc supports -c -o file.o... yes
checking if gcc supports -c -o file.o... (cached) yes
checking whether the gcc linker (/g/easybuild/x86_64/CentOS/7/haswell/software/binutils/2.36.1-GCCcore-10.3.0/bin/ld -m elf_x86_64) supports shared libraries... yes
checking whether -lc should be explicitly linked in... no
checking dynamic linker characteristics... GNU/Linux ld.so
checking how to hardcode library paths into programs... immediate
checking whether stripping libraries is possible... yes
checking if libtool supports shared libraries... yes
checking whether to build shared libraries... yes
checking whether to build static libraries... no
checking how to run the C++ preprocessor... g++ -std=gnu++14 -E
checking for ld used by g++ -std=gnu++14... /g/easybuild/x86_64/CentOS/7/haswell/software/binutils/2.36.1-GCCcore-10.3.0/bin/ld -m elf_x86_64
checking if the linker (/g/easybuild/x86_64/CentOS/7/haswell/software/binutils/2.36.1-GCCcore-10.3.0/bin/ld -m elf_x86_64) is GNU ld... yes
checking whether the g++ -std=gnu++14 linker (/g/easybuild/x86_64/CentOS/7/haswell/software/binutils/2.36.1-GCCcore-10.3.0/bin/ld -m elf_x86_64) supports shared libraries... yes
checking for g++ -std=gnu++14 option to produce PIC... -fPIC -DPIC
checking if g++ -std=gnu++14 PIC flag -fPIC -DPIC works... yes
checking if g++ -std=gnu++14 static flag -static works... no
checking if g++ -std=gnu++14 supports -c -o file.o... yes
checking if g++ -std=gnu++14 supports -c -o file.o... (cached) yes
checking whether the g++ -std=gnu++14 linker (/g/easybuild/x86_64/CentOS/7/haswell/software/binutils/2.36.1-GCCcore-10.3.0/bin/ld -m elf_x86_64) supports shared libraries... yes
checking dynamic linker characteristics... (cached) GNU/Linux ld.so
checking how to hardcode library paths into programs... immediate
checking whether the linker supports version scripts... yes
checking for ANSI C header files... (cached) yes
checking fcntl.h usability... yes
checking fcntl.h presence... yes
checking for fcntl.h... yes
checking for inttypes.h... (cached) yes
checking limits.h usability... yes
checking limits.h presence... yes
checking for limits.h... yes
checking for stdlib.h... (cached) yes
checking for unistd.h... (cached) yes
checking for working memcmp... yes
checking for working strtod... yes
checking for ftruncate... yes
checking for memset... yes
checking for mkdir... yes
checking for strchr... yes
checking for strerror... yes
checking for strtol... yes
checking zlib version... ok (1.2.0.4 or later)
checking for library containing zlibVersion... -lz
checking whether g++ -std=gnu++14 supports C++11 features by default... yes
checking whether -latomic is needed... no
checking whether gcc is Clang... no
checking whether pthreads work with -pthread... yes
checking for joinable pthread attribute... PTHREAD_CREATE_JOINABLE
checking whether more special flags are required for pthreads... no
checking for PTHREAD_PRIO_INHERIT... yes
checking the location of hash_map... <unordered_map>
checking that generated files are newer than configure... done
configure: creating ./config.status
config.status: creating Makefile
config.status: creating src/Makefile
config.status: creating benchmarks/Makefile
config.status: creating conformance/Makefile
config.status: creating protobuf.pc
config.status: creating protobuf-lite.pc
config.status: creating config.h
config.status: executing depfiles commands
config.status: executing libtool commands
=== configuring in third_party/googletest (/tmp/Rtmps1sO12/R.INSTALLe84f62e0d5bd/RProtoBufLib/src/protobuf-3.13.0/third_party/googletest)
configure: running /bin/sh ./configure --disable-option-checking '--prefix=/tmp/Rtmps1sO12/R.INSTALLe84f62e0d5bd/RProtoBufLib/src/pb_build'  '--enable-static=no' '--with-pic=yes' '--enable-shared=yes' '--libdir=/tmp/Rtmps1sO12/R.INSTALLe84f62e0d5bd/RProtoBufLib/src/pb_build/lib' 'CXX=g++ -std=gnu++14' 'CXXFLAGS=-O2 -ftree-vectorize -march=native -fno-math-errno' 'CC=gcc' 'CFLAGS=-O2 -ftree-vectorize -march=native -fno-math-errno' --cache-file=/dev/null --srcdir=.
checking for a BSD-compatible install... /usr/bin/install -c
checking whether build environment is sane... yes
checking for a thread-safe mkdir -p... /usr/bin/mkdir -p
checking for gawk... gawk
checking whether make sets $(MAKE)... yes
checking whether make supports nested variables... yes
checking that generated files are newer than configure... done
configure: creating ./config.status
config.status: creating Makefile
=== configuring in googletest (/tmp/Rtmps1sO12/R.INSTALLe84f62e0d5bd/RProtoBufLib/src/protobuf-3.13.0/third_party/googletest/googletest)
configure: running /bin/sh ./configure --disable-option-checking '--prefix=/tmp/Rtmps1sO12/R.INSTALLe84f62e0d5bd/RProtoBufLib/src/pb_build'  '--enable-static=no' '--with-pic=yes' '--enable-shared=yes' '--libdir=/tmp/Rtmps1sO12/R.INSTALLe84f62e0d5bd/RProtoBufLib/src/pb_build/lib' 'CXX=g++ -std=gnu++14' 'CXXFLAGS=-O2 -ftree-vectorize -march=native -fno-math-errno' 'CC=gcc' 'CFLAGS=-O2 -ftree-vectorize -march=native -fno-math-errno' --cache-file=/dev/null --srcdir=.
checking for a BSD-compatible install... /usr/bin/install -c
checking whether build environment is sane... yes
checking for a thread-safe mkdir -p... /usr/bin/mkdir -p
checking for gawk... gawk
checking whether make sets $(MAKE)... yes
checking whether make supports nested variables... yes
checking for gcc... gcc
checking whether the C compiler works... yes
checking for C compiler default output file name... a.out
checking for suffix of executables... 
checking whether we are cross compiling... no
checking for suffix of object files... o
checking whether we are using the GNU C compiler... yes
checking whether gcc accepts -g... yes
checking for gcc option to accept ISO C89... none needed
checking whether gcc understands -c and -o together... yes
checking whether make supports the include directive... yes (GNU style)
checking dependency style of gcc... gcc3
checking whether we are using the GNU C++ compiler... yes
checking whether g++ -std=gnu++14 accepts -g... yes
checking dependency style of g++ -std=gnu++14... gcc3
checking build system type... x86_64-pc-linux-gnu
checking host system type... x86_64-pc-linux-gnu
checking how to print strings... printf
checking for a sed that does not truncate output... /usr/bin/sed
checking for grep that handles long lines and -e... /usr/bin/grep
checking for egrep... /usr/bin/grep -E
checking for fgrep... /usr/bin/grep -F
checking for ld used by gcc... /g/easybuild/x86_64/CentOS/7/haswell/software/binutils/2.36.1-GCCcore-10.3.0/bin/ld
checking if the linker (/g/easybuild/x86_64/CentOS/7/haswell/software/binutils/2.36.1-GCCcore-10.3.0/bin/ld) is GNU ld... yes
checking for BSD- or MS-compatible name lister (nm)... /g/easybuild/x86_64/CentOS/7/haswell/software/binutils/2.36.1-GCCcore-10.3.0/bin/nm -B
checking the name lister (/g/easybuild/x86_64/CentOS/7/haswell/software/binutils/2.36.1-GCCcore-10.3.0/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 /g/easybuild/x86_64/CentOS/7/haswell/software/binutils/2.36.1-GCCcore-10.3.0/bin/ld option to reload object files... -r
checking for objdump... objdump
checking how to recognize dependent libraries... pass_all
checking for dlltool... no
checking how to associate runtime and link libraries... printf %s\n
checking for ar... ar
checking for archiver @FILE support... @
checking for strip... strip
checking for ranlib... ranlib
checking command to parse /g/easybuild/x86_64/CentOS/7/haswell/software/binutils/2.36.1-GCCcore-10.3.0/bin/nm -B output from gcc object... ok
checking for sysroot... no
checking for a working dd... /usr/bin/dd
checking how to truncate binary pipes... /usr/bin/dd bs=4096 count=1
checking for mt... no
checking if : is a manifest tool... no
checking how to run the C preprocessor... gcc -E
checking for ANSI C header files... yes
checking for sys/types.h... yes
checking for sys/stat.h... yes
checking for stdlib.h... yes
checking for string.h... yes
checking for memory.h... yes
checking for strings.h... yes
checking for inttypes.h... yes
checking for stdint.h... yes
checking for unistd.h... yes
checking for dlfcn.h... yes
checking for objdir... .libs
checking if gcc supports -fno-rtti -fno-exceptions... no
checking for gcc option to produce PIC... -fPIC -DPIC
checking if gcc PIC flag -fPIC -DPIC works... yes
checking if gcc static flag -static works... no
checking if gcc supports -c -o file.o... yes
checking if gcc supports -c -o file.o... (cached) yes
checking whether the gcc linker (/g/easybuild/x86_64/CentOS/7/haswell/software/binutils/2.36.1-GCCcore-10.3.0/bin/ld -m elf_x86_64) supports shared libraries... yes
checking whether -lc should be explicitly linked in... no
checking dynamic linker characteristics... GNU/Linux ld.so
checking how to hardcode library paths into programs... immediate
checking whether stripping libraries is possible... yes
checking if libtool supports shared libraries... yes
checking whether to build shared libraries... yes
checking whether to build static libraries... no
checking how to run the C++ preprocessor... g++ -std=gnu++14 -E
checking for ld used by g++ -std=gnu++14... /g/easybuild/x86_64/CentOS/7/haswell/software/binutils/2.36.1-GCCcore-10.3.0/bin/ld -m elf_x86_64
checking if the linker (/g/easybuild/x86_64/CentOS/7/haswell/software/binutils/2.36.1-GCCcore-10.3.0/bin/ld -m elf_x86_64) is GNU ld... yes
checking whether the g++ -std=gnu++14 linker (/g/easybuild/x86_64/CentOS/7/haswell/software/binutils/2.36.1-GCCcore-10.3.0/bin/ld -m elf_x86_64) supports shared libraries... yes
checking for g++ -std=gnu++14 option to produce PIC... -fPIC -DPIC
checking if g++ -std=gnu++14 PIC flag -fPIC -DPIC works... yes
checking if g++ -std=gnu++14 static flag -static works... no
checking if g++ -std=gnu++14 supports -c -o file.o... yes
checking if g++ -std=gnu++14 supports -c -o file.o... (cached) yes
checking whether the g++ -std=gnu++14 linker (/g/easybuild/x86_64/CentOS/7/haswell/software/binutils/2.36.1-GCCcore-10.3.0/bin/ld -m elf_x86_64) supports shared libraries... yes
checking dynamic linker characteristics... (cached) GNU/Linux ld.so
checking how to hardcode library paths into programs... immediate
checking for python... /g/easybuild/x86_64/CentOS/7/haswell/software/Python/3.9.5-GCCcore-10.3.0/bin/python
checking for the pthreads library -lpthreads... no
checking whether pthreads work without any flags... no
checking whether pthreads work with -Kthread... no
checking whether pthreads work with -kthread... no
checking for the pthreads library -llthread... no
checking whether pthreads work with -pthread... yes
checking for joinable pthread attribute... PTHREAD_CREATE_JOINABLE
checking if more special flags are required for pthreads... no
checking whether to check for GCC pthread/shared inconsistencies... yes
checking whether -pthread is sufficient with -shared... yes
checking that generated files are newer than configure... done
configure: creating ./config.status
config.status: creating Makefile
config.status: creating scripts/gtest-config
config.status: creating build-aux/config.h
config.status: executing depfiles commands
config.status: executing libtool commands
=== configuring in googlemock (/tmp/Rtmps1sO12/R.INSTALLe84f62e0d5bd/RProtoBufLib/src/protobuf-3.13.0/third_party/googletest/googlemock)
configure: running /bin/sh ./configure --disable-option-checking '--prefix=/tmp/Rtmps1sO12/R.INSTALLe84f62e0d5bd/RProtoBufLib/src/pb_build'  '--enable-static=no' '--with-pic=yes' '--enable-shared=yes' '--libdir=/tmp/Rtmps1sO12/R.INSTALLe84f62e0d5bd/RProtoBufLib/src/pb_build/lib' 'CXX=g++ -std=gnu++14' 'CXXFLAGS=-O2 -ftree-vectorize -march=native -fno-math-errno' 'CC=gcc' 'CFLAGS=-O2 -ftree-vectorize -march=native -fno-math-errno' --cache-file=/dev/null --srcdir=.
checking for a BSD-compatible install... /usr/bin/install -c
checking whether build environment is sane... yes
checking for a thread-safe mkdir -p... /usr/bin/mkdir -p
checking for gawk... gawk
checking whether make sets $(MAKE)... yes
checking whether make supports nested variables... yes
checking for gcc... gcc
checking whether the C compiler works... yes
checking for C compiler default output file name... a.out
checking for suffix of executables... 
checking whether we are cross compiling... no
checking for suffix of object files... o
checking whether we are using the GNU C compiler... yes
checking whether gcc accepts -g... yes
checking for gcc option to accept ISO C89... none needed
checking whether gcc understands -c and -o together... yes
checking whether make supports the include directive... yes (GNU style)
checking dependency style of gcc... gcc3
checking whether we are using the GNU C++ compiler... yes
checking whether g++ -std=gnu++14 accepts -g... yes
checking dependency style of g++ -std=gnu++14... gcc3
checking build system type... x86_64-pc-linux-gnu
checking host system type... x86_64-pc-linux-gnu
checking how to print strings... printf
checking for a sed that does not truncate output... /usr/bin/sed
checking for grep that handles long lines and -e... /usr/bin/grep
checking for egrep... /usr/bin/grep -E
checking for fgrep... /usr/bin/grep -F
checking for ld used by gcc... /g/easybuild/x86_64/CentOS/7/haswell/software/binutils/2.36.1-GCCcore-10.3.0/bin/ld
checking if the linker (/g/easybuild/x86_64/CentOS/7/haswell/software/binutils/2.36.1-GCCcore-10.3.0/bin/ld) is GNU ld... yes
checking for BSD- or MS-compatible name lister (nm)... /g/easybuild/x86_64/CentOS/7/haswell/software/binutils/2.36.1-GCCcore-10.3.0/bin/nm -B
checking the name lister (/g/easybuild/x86_64/CentOS/7/haswell/software/binutils/2.36.1-GCCcore-10.3.0/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 /g/easybuild/x86_64/CentOS/7/haswell/software/binutils/2.36.1-GCCcore-10.3.0/bin/ld option to reload object files... -r
checking for objdump... objdump
checking how to recognize dependent libraries... pass_all
checking for dlltool... no
checking how to associate runtime and link libraries... printf %s\n
checking for ar... ar
checking for archiver @FILE support... @
checking for strip... strip
checking for ranlib... ranlib
checking command to parse /g/easybuild/x86_64/CentOS/7/haswell/software/binutils/2.36.1-GCCcore-10.3.0/bin/nm -B output from gcc object... ok
checking for sysroot... no
checking for a working dd... /usr/bin/dd
checking how to truncate binary pipes... /usr/bin/dd bs=4096 count=1
checking for mt... no
checking if : is a manifest tool... no
checking how to run the C preprocessor... gcc -E
checking for ANSI C header files... yes
checking for sys/types.h... yes
checking for sys/stat.h... yes
checking for stdlib.h... yes
checking for string.h... yes
checking for memory.h... yes
checking for strings.h... yes
checking for inttypes.h... yes
checking for stdint.h... yes
checking for unistd.h... yes
checking for dlfcn.h... yes
checking for objdir... .libs
checking if gcc supports -fno-rtti -fno-exceptions... no
checking for gcc option to produce PIC... -fPIC -DPIC
checking if gcc PIC flag -fPIC -DPIC works... yes
checking if gcc static flag -static works... no
checking if gcc supports -c -o file.o... yes
checking if gcc supports -c -o file.o... (cached) yes
checking whether the gcc linker (/g/easybuild/x86_64/CentOS/7/haswell/software/binutils/2.36.1-GCCcore-10.3.0/bin/ld -m elf_x86_64) supports shared libraries... yes
checking whether -lc should be explicitly linked in... no
checking dynamic linker characteristics... GNU/Linux ld.so
checking how to hardcode library paths into programs... immediate
checking whether stripping libraries is possible... yes
checking if libtool supports shared libraries... yes
checking whether to build shared libraries... yes
checking whether to build static libraries... no
checking how to run the C++ preprocessor... g++ -std=gnu++14 -E
checking for ld used by g++ -std=gnu++14... /g/easybuild/x86_64/CentOS/7/haswell/software/binutils/2.36.1-GCCcore-10.3.0/bin/ld -m elf_x86_64
checking if the linker (/g/easybuild/x86_64/CentOS/7/haswell/software/binutils/2.36.1-GCCcore-10.3.0/bin/ld -m elf_x86_64) is GNU ld... yes
checking whether the g++ -std=gnu++14 linker (/g/easybuild/x86_64/CentOS/7/haswell/software/binutils/2.36.1-GCCcore-10.3.0/bin/ld -m elf_x86_64) supports shared libraries... yes
checking for g++ -std=gnu++14 option to produce PIC... -fPIC -DPIC
checking if g++ -std=gnu++14 PIC flag -fPIC -DPIC works... yes
checking if g++ -std=gnu++14 static flag -static works... no
checking if g++ -std=gnu++14 supports -c -o file.o... yes
checking if g++ -std=gnu++14 supports -c -o file.o... (cached) yes
checking whether the g++ -std=gnu++14 linker (/g/easybuild/x86_64/CentOS/7/haswell/software/binutils/2.36.1-GCCcore-10.3.0/bin/ld -m elf_x86_64) supports shared libraries... yes
checking dynamic linker characteristics... (cached) GNU/Linux ld.so
checking how to hardcode library paths into programs... immediate
checking for python... /g/easybuild/x86_64/CentOS/7/haswell/software/Python/3.9.5-GCCcore-10.3.0/bin/python
checking for the pthreads library -lpthreads... no
checking whether pthreads work without any flags... no
checking whether pthreads work with -Kthread... no
checking whether pthreads work with -kthread... no
checking for the pthreads library -llthread... no
checking whether pthreads work with -pthread... yes
checking for joinable pthread attribute... PTHREAD_CREATE_JOINABLE
checking if more special flags are required for pthreads... no
checking whether to check for GCC pthread/shared inconsistencies... yes
checking whether -pthread is sufficient with -shared... yes
checking for gtest-config... no
checking that generated files are newer than configure... done
configure: creating ./config.status
config.status: creating Makefile
config.status: creating scripts/gmock-config
config.status: creating build-aux/config.h
config.status: executing depfiles commands
config.status: executing libtool commands
Making install in .
make[1]: Entering directory `/tmp/Rtmps1sO12/R.INSTALLe84f62e0d5bd/RProtoBufLib/src/protobuf-3.13.0'
make[2]: Entering directory `/tmp/Rtmps1sO12/R.INSTALLe84f62e0d5bd/RProtoBufLib/src/protobuf-3.13.0'
make[2]: Nothing to be done for `install-exec-am'.
 /usr/bin/mkdir -p '/tmp/Rtmps1sO12/R.INSTALLe84f62e0d5bd/RProtoBufLib/src/pb_build/lib/pkgconfig'
 /usr/bin/install -c -m 644 protobuf.pc protobuf-lite.pc '/tmp/Rtmps1sO12/R.INSTALLe84f62e0d5bd/RProtoBufLib/src/pb_build/lib/pkgconfig'
make[2]: Leaving directory `/tmp/Rtmps1sO12/R.INSTALLe84f62e0d5bd/RProtoBufLib/src/protobuf-3.13.0'
make[1]: Leaving directory `/tmp/Rtmps1sO12/R.INSTALLe84f62e0d5bd/RProtoBufLib/src/protobuf-3.13.0'
Making install in src
make[1]: Entering directory `/tmp/Rtmps1sO12/R.INSTALLe84f62e0d5bd/RProtoBufLib/src/protobuf-3.13.0/src'
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  CXXLD    libprotobuf.la
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  CXXLD    libprotoc.la
  CXXLD    protoc
./.libs/libprotoc.so: error: undefined reference to 'scc_info_FileDescriptorProto_google_2fprotobuf_2fdescriptor_2eproto'
./.libs/libprotoc.so: error: undefined reference to 'descriptor_table_google_2fprotobuf_2fdescriptor_2eproto'
collect2: error: ld returned 1 exit status
make[1]: *** [protoc] Error 1
make[1]: Leaving directory `/tmp/Rtmps1sO12/R.INSTALLe84f62e0d5bd/RProtoBufLib/src/protobuf-3.13.0/src'
make: *** [install-recursive] Error 1
configure: creating ./config.status
config.status: creating src/Makevars
** libs
g++ -std=gnu++11 -shared -fpic -I../inst/include/ -I/tmp/Rtmps1sO12/R.INSTALLe84f62e0d5bd/RProtoBufLib/src/pb_build/include/ -o GatingSet_pb_lib/libGatingSet.pb.so GatingSet_pb_lib/GatingSet.pb.cc
In file included from GatingSet_pb_lib/GatingSet.pb.cc:4:
../inst/include/cytolib/GatingSet.pb.h:10:10: fatal error: google/protobuf/port_def.inc: No such file or directory
   10 | #include <google/protobuf/port_def.inc>
      |          ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
compilation terminated.
make: *** [libGatingSet.pb] Error 1
ERROR: compilation failed for package ‘RProtoBufLib’
* removing ‘/g/huber/users/mammen/proj/diagnFACS/renv/library/R-4.1/x86_64-pc-linux-gnu/RProtoBufLib’
Warning message:
In i.p(...) :
  installation of package ‘/tmp/RtmpvdUXKp/file4f144c0124e7/RProtoBufLib_2.5.1.tar.gz’ had non-zero exit status

Session Info:

> sessionInfo()
R version 4.1.0 (2021-05-18)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: CentOS Linux 7 (Core)

Matrix products: default
BLAS/LAPACK: /g/easybuild/x86_64/CentOS/7/haswell/software/FlexiBLAS/3.0.4-GCC-10.3.0/lib64/libflexiblas.so.3.0

locale:
 [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C               LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8     LC_MONETARY=en_US.UTF-8   
 [6] LC_MESSAGES=en_US.UTF-8    LC_PAPER=en_US.UTF-8       LC_NAME=C                  LC_ADDRESS=C               LC_TELEPHONE=C            
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C       

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base     

loaded via a namespace (and not attached):
 [1] rstudioapi_0.13     magrittr_2.0.1      usethis_2.0.1       devtools_2.4.2      pkgload_1.2.1       R6_2.5.0            rlang_0.4.11       
 [8] fastmap_1.1.0       tools_4.1.0         pkgbuild_1.2.0      sessioninfo_1.1.1   cli_3.0.1           withr_2.4.2         ellipsis_0.3.2     
[15] remotes_2.4.0       rprojroot_2.0.2     lifecycle_1.0.0     crayon_1.4.1        processx_3.5.2      purrr_0.3.4         BiocManager_1.30.16
[22] callr_3.7.0         fs_1.5.0            ps_1.6.0            curl_4.3.2          testthat_3.0.4      memoise_2.0.0       glue_1.4.2         
[29] cachem_1.0.5        compiler_4.1.0      desc_1.3.0          prettyunits_1.1.1   renv_0.14.0

@urielrosen
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Hi,

I am having the same issue. Does anyone know about a workaround for this ?

@jennib3
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jennib3 commented Feb 17, 2022

If anyone else sees this issue, I fixed this by make clean and then rebuilding, seemingly the file had gotten corrupted.

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@ivanek @jennib3 @pineappleburger @urielrosen