rglab / rprotobuflib Goto Github PK
View Code? Open in Web Editor NEWbundled Protocol buffers library as an R package
License: Other
bundled Protocol buffers library as an R package
License: Other
It is triggered by dynamic linked libprotobuf(ad22c36) and won't necessarily affect end users since multiple library(flowWorkspace)
calls won't cause the lib to be reloaded.
Loading flowWorkspace
[libprotobuf ERROR google/protobuf/descriptor_database.cc:57] File already exists in database: GatingSet.proto
[libprotobuf FATAL google/protobuf/descriptor.cc:1018] CHECK failed: generated_database_->Add(encoded_file_descriptor, size):
terminate called after throwing an instance of 'google::protobuf::FatalException'
what(): CHECK failed: generated_database_->Add(encoded_file_descriptor, size):
Aborted (core dumped)
It's been discussed here protocolbuffers/protobuf/issues/4126 and I will try to build GatingSet.pb.cc as shared lib as well to see if it will address the issue.
Should libtool
be listed in SystemRequirements
? I was having some trouble installing RProtoBufLib on my Ubuntu machine, until I examined the build reports and realized libtoolize
was not being found. Not sure that libtool
is automatically part of GNU make.
See the log here: http://paste.opensuse.org/85901062
I am trying to install RProtoBufLib on Ubuntu 16.04.
When I typed devtools::install_github("RGLab/RProtoBufLib", ref="trunk")
I got this:
config.status: error: cannot find input file: `config.h.in'
CDPATH="${ZSH_VERSION+.}:" && cd . && /bin/bash /media/malisa/SharedStorage/tmp/RtmpqD9CNM/devtools7e570bcf89f/RGLab-RProtoBufLib-5bdb09a/src/protobuf-2.6.0/missing aclocal-1.14 -I m4
/media/malisa/SharedStorage/tmp/RtmpqD9CNM/devtools7e570bcf89f/RGLab-RProtoBufLib-5bdb09a/src/protobuf-2.6.0/missing: line 81: aclocal-1.14: command not found
WARNING: 'aclocal-1.14' is missing on your system.
You should only need it if you modified 'acinclude.m4' or
'configure.ac' or m4 files included by 'configure.ac'.
The 'aclocal' program is part of the GNU Automake package:
<http://www.gnu.org/software/automake>
It also requires GNU Autoconf, GNU m4 and Perl in order to run:
<http://www.gnu.org/software/autoconf>
<http://www.gnu.org/software/m4/>
<http://www.perl.org/>
Makefile:407: recipe for target 'aclocal.m4' failed
make: *** [aclocal.m4] Error 127
configure: creating ./config.status
config.status: creating src/Makevars
** libs
mkdir -p "/home/malisa/R/x86_64-pc-linux-gnu-library/3.4/RProtoBufLib/include"
cp -r /media/malisa/SharedStorage/tmp/RtmpqD9CNM/devtools7e570bcf89f/RGLab-RProtoBufLib-5bdb09a/src/pb_build/include/google /home/malisa/R/x86_64-pc-linux-gnu-library/3.4/RProtoBufLib/include
cp: cannot stat '/media/malisa/SharedStorage/tmp/RtmpqD9CNM/devtools7e570bcf89f/RGLab-RProtoBufLib-5bdb09a/src/pb_build/include/google': No such file or directory
Makevars:9: recipe for target 'copying' failed
make: *** [copying] Error 1
ERROR: compilation failed for package ‘RProtoBufLib’
* removing ‘/home/malisa/R/x86_64-pc-linux-gnu-library/3.4/RProtoBufLib’
Installation failed: Command failed (1)
One of the warning error messages above says that it can't find aclocal-1.14
. I had aclocal (GNU automake) 1.15
installed......This warning disappeared when I followed the directions for installing aclocal-1.14 here using: https://ftp.gnu.org/gnu/automake/automake-1.14.tar.gz .
However, I'm still getting errors:
config.status: error: cannot find input file: `config.h.in'
CDPATH="${ZSH_VERSION+.}:" && cd . && /bin/bash /media/malisa/SharedStorage/tmp/RtmpFqTEer/devtools7f21280a7ad7/RGLab-RProtoBufLib-5bdb09a/src/protobuf-2.6.0/missing aclocal-1.14 -I m4
cd . && /bin/bash /media/malisa/SharedStorage/tmp/RtmpFqTEer/devtools7f21280a7ad7/RGLab-RProtoBufLib-5bdb09a/src/protobuf-2.6.0/missing automake-1.14 --foreign
Unescaped left brace in regex is deprecated, passed through in regex; marked by <-- HERE in m/\${ <-- HERE ([^ \t=:+{}]+)}/ at /usr/local/bin/automake-1.14 line 3930.
configure.ac:20: error: required file 'config.h.in' not found
Makefile:378: recipe for target 'Makefile.in' failed
make: *** [Makefile.in] Error 1
configure: creating ./config.status
config.status: creating src/Makevars
** libs
mkdir -p "/home/malisa/R/x86_64-pc-linux-gnu-library/3.4/RProtoBufLib/include"
cp -r /media/malisa/SharedStorage/tmp/RtmpFqTEer/devtools7f21280a7ad7/RGLab-RProtoBufLib-5bdb09a/src/pb_build/include/google /home/malisa/R/x86_64-pc-linux-gnu-library/3.4/RProtoBufLib/include
cp: cannot stat '/media/malisa/SharedStorage/tmp/RtmpFqTEer/devtools7f21280a7ad7/RGLab-RProtoBufLib-5bdb09a/src/pb_build/include/google': No such file or directory
Makevars:9: recipe for target 'copying' failed
make: *** [copying] Error 1
ERROR: compilation failed for package ‘RProtoBufLib’
* removing ‘/home/malisa/R/x86_64-pc-linux-gnu-library/3.4/RProtoBufLib’
Installation failed: Command failed (1)
Thanks for your help!
Trying to build it on R 4.1.2 with gcc 10.3.0 and getting the error:
CXX google/protobuf/compiler/csharp/csharp_wrapper_field.lo
CXXLD libprotoc.la
CXXLD protoc
./.libs/libprotoc.so: error: undefined reference to 'scc_info_FileDescriptorProto_google_2fprotobuf_2fdescri
ptor_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/RtmpOoKxyP/R.INSTALL2c35616a567e5/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/RtmpOoKxyP/R.INSTALL2c35616a567e5/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:17:2: error: #error This file was generated by an older version of pr
otoc which is
17 | #error This file was generated by an older version of protoc which is
| ^~~~~
../inst/include/cytolib/GatingSet.pb.h:18:2: error: #error incompatible with your Protocol Buffer headers. P
lease
18 | #error incompatible with your Protocol Buffer headers. Please
| ^~~~~
../inst/include/cytolib/GatingSet.pb.h:19:2: error: #error regenerate this file with a newer version of prot
oc.
19 | #error regenerate this file with a newer version of protoc.
| ^~~~~
In file included from GatingSet_pb_lib/GatingSet.pb.cc:4:
../inst/include/cytolib/GatingSet.pb.h:28:10: fatal error: google/protobuf/inlined_string_field.h: No such f
ile or directory
28 | #include <google/protobuf/inlined_string_field.h>
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
compilation terminated.
ERROR: compilation failed for package ‘RProtoBufLib’
* removing ‘/apps/prod/easybuild/sl7.x86_64.foss-2021a/software/BiocLibrary/3.14-foss-2021a-R-4.1.2/site-lib
rary/RProtoBufLib’
let me know what other info do you need.
See: RGLab/cytolib#37 (comment)
Another problem with the current code is that, in the case that the libGatingSet.pb library is actually missing, gsLibPath()
will return an empty string so testing with if (!file.exists(gs))
in the .onLoad()
hook is bogus. Should rather be done with something like if (gs == "")
. Or, a better solution would be to use file.path()
instead of system.file()
in the gsLibPath()
function, so the relative path to the library is always returned, even if the file doesn't exist. Then you can test with if (system.file(gs, "RProtoBufLib") == "")
in the .onLoad()
hook. Another advantage of doing this is that the warning message would actually display the path (right now it doesn't because gs
is the empty string).
The code for detecting the presence of the libprotobuf library (pbLibPath()
) has the same problems.
Hi, I successfully installed flowCore few day ago (using biocLite installation) to analyse data from flow cytometry. To visualize them I'd like to use ggcyto, however I had issues to install it. I tracked back that the basic dependency I need is RProtoBufLib (which is needed for flowWorkspace, which is the only dependency for ggcyto I don't have). I installed libhdf5-dev as I read in some previous thread it might help, it didn't in my case. Running the installation using:
> install_github("RGLab/RProtoBufLib@trunk")
gives fatal error because common.h file is not found or so...:
Downloading GitHub repo RGLab/RProtoBufLib@trunk
from URL https://api.github.com/repos/RGLab/RProtoBufLib/zipball/trunk
Installing RProtoBufLib
'/usr/local/Cellar/r/3.4.1_1/lib/R/bin/R' --no-site-file --no-environ \
--no-save --no-restore --quiet CMD INSTALL \
'/private/var/folders/k_/2qtkrd6j5y3b4l08zr0kt0r098_z_b/T/RtmpDAHsrN/devtools12e75626b308/RGLab-RProtoBufLib-6bf618b' \
--library='/usr/local/lib/R/3.4/site-library' --install-tests
* installing *source* package ‘RProtoBufLib’ ...
checking for gcc... clang
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 clang accepts -g... yes
checking for clang option to accept ISO C89... none needed
checking for g++... g++
checking whether we are using the GNU C++ compiler... yes
checking whether g++ accepts -g... yes
untarring protobuf ...
./autogen.sh: line 19: autoreconf: command not found
./configure: line 2861: automake: command not found
building protobuf...
checking whether to enable maintainer-specific portions of Makefiles... yes
checking build system type... x86_64-apple-darwin16.7.0
checking host system type... x86_64-apple-darwin16.7.0
checking target system type... x86_64-apple-darwin16.7.0
checking for a BSD-compatible install... /usr/bin/install -c
checking whether build environment is sane... yes
checking for a thread-safe mkdir -p... ./install-sh -c -d
checking for gawk... no
checking for mawk... no
checking for nawk... no
checking for awk... awk
checking whether make sets $(MAKE)... yes
checking whether make supports nested variables... yes
checking for gcc... clang
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 clang accepts -g... yes
checking for clang option to accept ISO C89... none needed
checking whether clang understands -c and -o together... rm: conftest.dSYM: is a directory
yes
checking for style of include used by make... GNU
checking dependency style of clang... gcc3
checking whether we are using the GNU C++ compiler... yes
checking whether g++ accepts -g... yes
checking dependency style of g++... gcc3
checking how to run the C++ preprocessor... g++ -E
checking for grep that handles long lines and -e... /usr/bin/grep
checking for egrep... /usr/bin/grep -E
checking for ANSI C header files... rm: conftest.dSYM: is a directory
rm: conftest.dSYM: is a directory
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 C++ compiler flags...... use user-supplied: -g -O2
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 clang... /Library/Developer/CommandLineTools/usr/bin/ld
checking if the linker (/Library/Developer/CommandLineTools/usr/bin/ld) is GNU ld... no
checking for BSD- or MS-compatible name lister (nm)... /usr/bin/nm -B
checking the name lister (/usr/bin/nm -B) interface... BSD nm
checking whether ln -s works... yes
checking the maximum length of command line arguments... 196608
checking whether the shell understands some XSI constructs... yes
checking whether the shell understands "+="... yes
checking how to convert x86_64-apple-darwin16.7.0 file names to x86_64-apple-darwin16.7.0 format... func_convert_file_noop
checking how to convert x86_64-apple-darwin16.7.0 file names to toolchain format... func_convert_file_noop
checking for /Library/Developer/CommandLineTools/usr/bin/ld option to reload object files... -r
checking for objdump... objdump
checking how to recognize dependent libraries... pass_all
checking for dlltool... no
checking how to associate runtime and link libraries... printf %s\n
checking for ar... ar
checking for archiver @FILE support... no
checking for strip... strip
checking for ranlib... ranlib
checking command to parse /usr/bin/nm -B output from clang object... ok
checking for sysroot... no
checking for mt... no
checking if : is a manifest tool... no
checking for dsymutil... dsymutil
checking for nmedit... nmedit
checking for lipo... lipo
checking for otool... otool
checking for otool64... no
checking for -single_module linker flag... yes
checking for -exported_symbols_list linker flag... yes
checking for -force_load linker flag... yes
checking for dlfcn.h... yes
checking for objdir... .libs
checking if clang supports -fno-rtti -fno-exceptions... yes
checking for clang option to produce PIC... -fno-common -DPIC
checking if clang PIC flag -fno-common -DPIC works... yes
checking if clang static flag -static works... no
checking if clang supports -c -o file.o... yes
checking if clang supports -c -o file.o... (cached) yes
checking whether the clang linker (/Library/Developer/CommandLineTools/usr/bin/ld) supports shared libraries... yes
checking dynamic linker characteristics... darwin16.7.0 dyld
checking how to hardcode library paths into programs... immediate
checking whether stripping libraries is possible... yes
checking if libtool supports shared libraries... yes
checking whether to build shared libraries... no
checking whether to build static libraries... yes
checking how to run the C++ preprocessor... g++ -E
checking for ld used by g++... /Library/Developer/CommandLineTools/usr/bin/ld
checking if the linker (/Library/Developer/CommandLineTools/usr/bin/ld) is GNU ld... no
checking whether the g++ linker (/Library/Developer/CommandLineTools/usr/bin/ld) supports shared libraries... yes
checking for g++ option to produce PIC... -fno-common -DPIC
checking if g++ PIC flag -fno-common -DPIC works... yes
checking if g++ static flag -static works... no
checking if g++ supports -c -o file.o... yes
checking if g++ supports -c -o file.o... (cached) yes
checking whether the g++ linker (/Library/Developer/CommandLineTools/usr/bin/ld) supports shared libraries... yes
checking dynamic linker characteristics... darwin16.7.0 dyld
checking how to hardcode library paths into programs... immediate
checking for ANSI C header files... (cached) yes
checking fcntl.h usability... yes
checking fcntl.h presence... yes
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 for the pthreads library -lpthreads... no
checking whether pthreads work without any flags... yes
checking for joinable pthread attribute... PTHREAD_CREATE_JOINABLE
checking if more special flags are required for pthreads... -D_THREAD_SAFE
checking whether to check for GCC pthread/shared inconsistencies... no
checking whether what we have so far is sufficient with -nostdlib... no
checking whether -lpthread saves the day... no
configure: WARNING: Impossible to determine how to use pthreads with shared libraries and -nostdlib
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 protobuf.pc
config.status: creating protobuf-lite.pc
config.status: error: cannot find input file: `config.h.in'
CDPATH="${ZSH_VERSION+.}:" && cd . && /bin/sh /private/var/folders/k_/2qtkrd6j5y3b4l08zr0kt0r098_z_b/T/RtmpDAHsrN/devtools12e75626b308/RGLab-RProtoBufLib-6bf618b/src/protobuf-2.6.0/missing aclocal-1.14 -I m4
/private/var/folders/k_/2qtkrd6j5y3b4l08zr0kt0r098_z_b/T/RtmpDAHsrN/devtools12e75626b308/RGLab-RProtoBufLib-6bf618b/src/protobuf-2.6.0/missing: line 81: aclocal-1.14: command not found
WARNING: 'aclocal-1.14' is missing on your system.
You should only need it if you modified 'acinclude.m4' or
'configure.ac' or m4 files included by 'configure.ac'.
The 'aclocal' program is part of the GNU Automake package:
<http://www.gnu.org/software/automake>
It also requires GNU Autoconf, GNU m4 and Perl in order to run:
<http://www.gnu.org/software/autoconf>
<http://www.gnu.org/software/m4/>
<http://www.perl.org/>
make: *** [aclocal.m4] Error 127
configure: creating ./config.status
config.status: creating src/Makevars
** libs
clang++ -I/usr/local/Cellar/r/3.4.1_1/lib/R/include -DNDEBUG -I../inst/include/ -I/private/var/folders/k_/2qtkrd6j5y3b4l08zr0kt0r098_z_b/T/RtmpDAHsrN/devtools12e75626b308/RGLab-RProtoBufLib-6bf618b/src/pb_build/include/ -I/usr/local/opt/gettext/include -I/usr/local/opt/readline/include -I/usr/local/include -fPIC -g -O2 -c GatingSet_pb_lib/GatingSet.pb.cc -o GatingSet_pb_lib/GatingSet.pb.o
In file included from GatingSet_pb_lib/GatingSet.pb.cc:5:
../inst/include/GatingSet.pb.h:9:10: fatal error:
'google/protobuf/stubs/common.h' file not found
#include <google/protobuf/stubs/common.h>
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1 error generated.
make: *** [GatingSet_pb_lib/GatingSet.pb.o] Error 1
ERROR: compilation failed for package ‘RProtoBufLib’
* removing ‘/usr/local/lib/R/3.4/site-library/RProtoBufLib’
Installation failed: Command failed (1)
using:
> biocLite("RProtoBufLib")
fails to compile RProtoBufLib package...:
BioC_mirror: https://bioconductor.org
Using Bioconductor 3.6 (BiocInstaller 1.28.0), R 3.4.1 (2017-06-30).
Installing package(s) ‘RProtoBufLib’
trying URL 'https://bioconductor.org/packages/3.6/bioc/src/contrib/RProtoBufLib_1.0.1.tar.gz'
Content type 'application/x-gzip' length 1930285 bytes (1.8 MB)
==================================================
downloaded 1.8 MB
* installing *source* package ‘RProtoBufLib’ ...
checking for gcc... clang
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 clang accepts -g... yes
checking for clang option to accept ISO C89... none needed
checking for g++... g++
checking whether we are using the GNU C++ compiler... yes
checking whether g++ accepts -g... yes
untarring protobuf ...
./autogen.sh: line 19: autoreconf: command not found
./configure: line 2861: automake: command not found
building protobuf...
checking whether to enable maintainer-specific portions of Makefiles... yes
checking build system type... x86_64-apple-darwin16.7.0
checking host system type... x86_64-apple-darwin16.7.0
checking target system type... x86_64-apple-darwin16.7.0
checking for a BSD-compatible install... /usr/bin/install -c
checking whether build environment is sane... yes
checking for a thread-safe mkdir -p... ./install-sh -c -d
checking for gawk... no
checking for mawk... no
checking for nawk... no
checking for awk... awk
checking whether make sets $(MAKE)... yes
checking whether make supports nested variables... yes
checking for gcc... clang
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 clang accepts -g... yes
checking for clang option to accept ISO C89... none needed
checking whether clang understands -c and -o together... rm: conftest.dSYM: is a directory
yes
checking for style of include used by make... GNU
checking dependency style of clang... gcc3
checking whether we are using the GNU C++ compiler... yes
checking whether g++ accepts -g... yes
checking dependency style of g++... gcc3
checking how to run the C++ preprocessor... g++ -E
checking for grep that handles long lines and -e... /usr/bin/grep
checking for egrep... /usr/bin/grep -E
checking for ANSI C header files... rm: conftest.dSYM: is a directory
rm: conftest.dSYM: is a directory
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 C++ compiler flags...... use user-supplied: -g -O2
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 clang... /Library/Developer/CommandLineTools/usr/bin/ld
checking if the linker (/Library/Developer/CommandLineTools/usr/bin/ld) is GNU ld... no
checking for BSD- or MS-compatible name lister (nm)... /usr/bin/nm -B
checking the name lister (/usr/bin/nm -B) interface... BSD nm
checking whether ln -s works... yes
checking the maximum length of command line arguments... 196608
checking whether the shell understands some XSI constructs... yes
checking whether the shell understands "+="... yes
checking how to convert x86_64-apple-darwin16.7.0 file names to x86_64-apple-darwin16.7.0 format... func_convert_file_noop
checking how to convert x86_64-apple-darwin16.7.0 file names to toolchain format... func_convert_file_noop
checking for /Library/Developer/CommandLineTools/usr/bin/ld option to reload object files... -r
checking for objdump... objdump
checking how to recognize dependent libraries... pass_all
checking for dlltool... no
checking how to associate runtime and link libraries... printf %s\n
checking for ar... ar
checking for archiver @FILE support... no
checking for strip... strip
checking for ranlib... ranlib
checking command to parse /usr/bin/nm -B output from clang object... ok
checking for sysroot... no
checking for mt... no
checking if : is a manifest tool... no
checking for dsymutil... dsymutil
checking for nmedit... nmedit
checking for lipo... lipo
checking for otool... otool
checking for otool64... no
checking for -single_module linker flag... yes
checking for -exported_symbols_list linker flag... yes
checking for -force_load linker flag... yes
checking for dlfcn.h... yes
checking for objdir... .libs
checking if clang supports -fno-rtti -fno-exceptions... yes
checking for clang option to produce PIC... -fno-common -DPIC
checking if clang PIC flag -fno-common -DPIC works... yes
checking if clang static flag -static works... no
checking if clang supports -c -o file.o... yes
checking if clang supports -c -o file.o... (cached) yes
checking whether the clang linker (/Library/Developer/CommandLineTools/usr/bin/ld) supports shared libraries... yes
checking dynamic linker characteristics... darwin16.7.0 dyld
checking how to hardcode library paths into programs... immediate
checking whether stripping libraries is possible... yes
checking if libtool supports shared libraries... yes
checking whether to build shared libraries... no
checking whether to build static libraries... yes
checking how to run the C++ preprocessor... g++ -E
checking for ld used by g++... /Library/Developer/CommandLineTools/usr/bin/ld
checking if the linker (/Library/Developer/CommandLineTools/usr/bin/ld) is GNU ld... no
checking whether the g++ linker (/Library/Developer/CommandLineTools/usr/bin/ld) supports shared libraries... yes
checking for g++ option to produce PIC... -fno-common -DPIC
checking if g++ PIC flag -fno-common -DPIC works... yes
checking if g++ static flag -static works... no
checking if g++ supports -c -o file.o... yes
checking if g++ supports -c -o file.o... (cached) yes
checking whether the g++ linker (/Library/Developer/CommandLineTools/usr/bin/ld) supports shared libraries... yes
checking dynamic linker characteristics... darwin16.7.0 dyld
checking how to hardcode library paths into programs... immediate
checking for ANSI C header files... (cached) yes
checking fcntl.h usability... yes
checking fcntl.h presence... yes
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 for the pthreads library -lpthreads... no
checking whether pthreads work without any flags... yes
checking for joinable pthread attribute... PTHREAD_CREATE_JOINABLE
checking if more special flags are required for pthreads... -D_THREAD_SAFE
checking whether to check for GCC pthread/shared inconsistencies... no
checking whether what we have so far is sufficient with -nostdlib... no
checking whether -lpthread saves the day... no
configure: WARNING: Impossible to determine how to use pthreads with shared libraries and -nostdlib
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 protobuf.pc
config.status: creating protobuf-lite.pc
config.status: error: cannot find input file: `config.h.in'
CDPATH="${ZSH_VERSION+.}:" && cd . && /bin/sh /private/var/folders/k_/2qtkrd6j5y3b4l08zr0kt0r098_z_b/T/Rtmpcz8XrI/R.INSTALLa979535b1f24/RProtoBufLib/src/protobuf-2.6.0/missing aclocal-1.14 -I m4
/private/var/folders/k_/2qtkrd6j5y3b4l08zr0kt0r098_z_b/T/Rtmpcz8XrI/R.INSTALLa979535b1f24/RProtoBufLib/src/protobuf-2.6.0/missing: line 81: aclocal-1.14: command not found
WARNING: 'aclocal-1.14' is missing on your system.
You should only need it if you modified 'acinclude.m4' or
'configure.ac' or m4 files included by 'configure.ac'.
The 'aclocal' program is part of the GNU Automake package:
<http://www.gnu.org/software/automake>
It also requires GNU Autoconf, GNU m4 and Perl in order to run:
<http://www.gnu.org/software/autoconf>
<http://www.gnu.org/software/m4/>
<http://www.perl.org/>
make: *** [aclocal.m4] Error 127
configure: creating ./config.status
config.status: creating src/Makevars
** libs
mkdir -p "/usr/local/lib/R/3.4/site-library/RProtoBufLib/include"
cp -r /private/var/folders/k_/2qtkrd6j5y3b4l08zr0kt0r098_z_b/T/Rtmpcz8XrI/R.INSTALLa979535b1f24/RProtoBufLib/src/pb_build/include/google /usr/local/lib/R/3.4/site-library/RProtoBufLib/include
cp: /private/var/folders/k_/2qtkrd6j5y3b4l08zr0kt0r098_z_b/T/Rtmpcz8XrI/R.INSTALLa979535b1f24/RProtoBufLib/src/pb_build/include/google: No such file or directory
make: *** [copying] Error 1
ERROR: compilation failed for package ‘RProtoBufLib’
* removing ‘/usr/local/lib/R/3.4/site-library/RProtoBufLib’
The downloaded source packages are in
‘/private/var/folders/k_/2qtkrd6j5y3b4l08zr0kt0r098_z_b/T/RtmpDAHsrN/downloaded_packages’
Warning message:
In install.packages(pkgs = doing, lib = lib, ...) :
installation of package ‘RProtoBufLib’ had non-zero exit status
Could you help me to solve this, please?
PS: I'm using mac and R version 3.4.1
It's been the most frequent complain regarding to this system library dependencies (#1 #2 #4 and from Prof Brian Ripley).
It is currently required by protobuf c++ library https://github.com/google/protobuf/blob/master/src/README.md
I can try to dig into build script and makefiles to see if these dependencies can be dropped.
The existing binaries are still 2.6.
And the previous cross-compiling process on linux no longer works for 3.7 due to the error
$ protobuf-3.7.0/configure --host=x86_64-w64-mingw32 --enable-shared=yes --enable-static=no
$ make
../../../protobuf-3.7.0/src/google/protobuf/stubs/common.cc:48:2: error: #error "No suitable threading library available."
Trying to build it from windows through MinGW
, and the compiling seems to be ok but freezes at linking stage for libprotobuf-lite.la
vcpkg
only has 3.10 available which won't be compatible with 3.7
So I will try to build it with vs from scratch...
Hi,
I am having problems installing on both Windows and Mac using the:
devtools::install_github("RGLab/RProtoBufLib")
and
devtools::install_github("RGLab/RProtoBufLib", ref = "trunk")
devtools::install_github("RGLab/RProtoBufLib") does not work at all with the following error in windows:
Error: Failed to install 'unknown package' from GitHub:
HTTP error 404.
No commit found for the ref master
Did you spell the repo owner (`RGLab`) and repo name (`RProtoBufLib`) correctly?
- If spelling is correct, check that you have the required permissions to access the repo.
I get a similar error on Mac saying there is no master tarball.
Using devtools::install_github("RGLab/RProtoBufLib", ref = "trunk") on windows gives the following error:
*** arch - i386
mkdir -p "C:/R363/Packages/00LOCK-RProtoBufLib/00new/RProtoBufLib/include"
cp -r /include/google "C:/R363/Packages/00LOCK-RProtoBufLib/00new/RProtoBufLib/include"
cp: cannot stat '/include/google': No such file or directory
make: *** [Makevars.win:12: copying] Error 1
ERROR: compilation failed for package 'RProtoBufLib'
* removing 'C:/R363/Packages/RProtoBufLib'
Error: Failed to install 'RProtoBufLib' from GitHub:
(converted from warning) installation of package ‘C:/Users/chall/AppData/Local/Temp/RtmpOm1N4t/file164c60802664/RProtoBufLib_1.9.7.tar.gz’ had non-zero exit status
and on mac
mkdir -p "/Library/Frameworks/R.framework/Versions/3.6/Resources/library/00LOCK-RProtoBufLib/00new/RProtoBufLib/include"
cp -r /private/var/folders/38/ctpzr4rx38j0cgzcj5rnl0vr0000gq/T/RtmpwG2Ktw/R.INSTALL350660ea4ca5/RProtoBufLib/src/pb_build/include/google /Library/Frameworks/R.framework/Versions/3.6/Resources/library/00LOCK-RProtoBufLib/00new/RProtoBufLib/include
cp: /private/var/folders/38/ctpzr4rx38j0cgzcj5rnl0vr0000gq/T/RtmpwG2Ktw/R.INSTALL350660ea4ca5/RProtoBufLib/src/pb_build/include/google: No such file or directory
make: *** [copying] Error 1
ERROR: compilation failed for package ‘RProtoBufLib’
* removing ‘/Library/Frameworks/R.framework/Versions/3.6/Resources/library/RProtoBufLib’
* restoring previous ‘/Library/Frameworks/R.framework/Versions/3.6/Resources/library/RProtoBufLib’
Error: Failed to install 'RProtoBufLib' from GitHub:
(converted from warning) installation of package ‘/var/folders/38/ctpzr4rx38j0cgzcj5rnl0vr0000gq/T//Rtmpue3j42/file5a22f12ae42/RProtoBufLib_1.9.7.tar.gz’ had non-zero exit status
I am using R 3.6.3 on Windows and 3.6.1 on Mac.
This seems to be the same(ish) issue as "Windows Installation Problems #9", except I can't get it working on Mac either. Not at all coincidentally I am trying to install CytoRSuite(2).
Kind regards
Chris
p.s. As soon as I submitted it I spotted the odd looking space in the second line of the Mac error, after the '/google '. I wonder if that is the issue (bearing in mind I know very little about how Mac file structure works). Ignore this comment.
make[1]: Entering directory '/tmp/Rtmp3C2eJD/R.INSTALL1d778a7bed94/RProtoBufLib/src/protobuf-3.10.0/src'
CXX google/protobuf/stubs/bytestream.lo
CXX google/protobuf/stubs/common.lo
google/protobuf/stubs/common.cc: In function 'void google::protobuf::internal::OnShutdown(void ()())':
google/protobuf/stubs/common.cc:345:3: error: 'OnShutdownRun' was not declared in this scope
OnShutdownRun(RunZeroArgFunc, reinterpret_cast<void>(func));
^~~~~~~~~~~~~
google/protobuf/stubs/common.cc:345:3: note: suggested alternative: 'OnShutdown'
OnShutdownRun(RunZeroArgFunc, reinterpret_cast<void*>(func));
^~~~~~~~~~~~~
OnShutdown
make[1]: *** [Makefile:915: google/protobuf/stubs/common.lo] Error 1
make[1]: Leaving directory '/tmp/Rtmp3C2eJD/R.INSTALL1d778a7bed94/RProtoBufLib/src/protobuf-3.10.0/src'
make: *** [Makefile:1714: install-recursive] Error 1
configure: creating ./config.status
config.status: creating src/Makevars
** libs
mkdir -p "/public/packages/R-4.0.3/lib/00LOCK-RProtoBufLib/00new/RProtoBufLib/include"
cp -r /tmp/Rtmp3C2eJD/R.INSTALL1d778a7bed94/RProtoBufLib/src/pb_build/include/google /public/packages/R-4.0.3/lib/00LOCK-RProtoBufLib/00new/RProtoBufLib/include
cp: cannot stat ‘/tmp/Rtmp3C2eJD/R.INSTALL1d778a7bed94/RProtoBufLib/src/pb_build/include/google’: No such file or directory
make: *** [Makevars:12: copying] Error 1
ERROR: compilation failed for package ‘RProtoBufLib’
Hi @mikejiang & @jacobpwagner,
I pulled down the latest protobuf
binaries, extracted to C:/ and set environment variable as always. When I try to install RProtoBufLib
I get compilation errors:
> devtools::install_github("RGLab/RProtoBufLib")
Downloading GitHub repo RGLab/RProtoBufLib@master
√ checking for file 'C:\Users\localuseradmin.JCSMR-028197PL\AppData\Local\Temp\Rtmpg5uvjO\remotes3d4c572542b\RGLab-RProtoBufLib-d7d10f8/DESCRIPTION' (683ms)
- preparing 'RProtoBufLib':
√ checking DESCRIPTION meta-information ...
- cleaning src
- running 'cleanup.win'
- checking for LF line-endings in source and make files and shell scripts
- checking for empty or unneeded directories
- building 'RProtoBufLib_2.1.0.tar.gz'
Warning: file 'RProtoBufLib/cleanup' did not have execute permissions: corrected
Warning: file 'RProtoBufLib/configure' did not have execute permissions: corrected
* installing *source* package 'RProtoBufLib' ...
** using staged installation
**********************************************
WARNING: this package has a configure script
It probably needs manual configuration
**********************************************
** libs
*** arch - i386
mkdir -p "C:/Program Files/R/R-4.0.0/library/00LOCK-RProtoBufLib/00new/RProtoBufLib/include"
cp -r C:/protobuf/include/google "C:/Program Files/R/R-4.0.0/library/00LOCK-RProtoBufLib/00new/RProtoBufLib/include"
mkdir -p "C:/Program Files/R/R-4.0.0/library/00LOCK-RProtoBufLib/00new/RProtoBufLib/lib/i386"
cp C:/protobuf/lib/i386/libprotobuf-lite.a "C:/Program Files/R/R-4.0.0/library/00LOCK-RProtoBufLib/00new/RProtoBufLib/lib/i386/libprotobuf-lite.a"
"C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/PROGRA~1/R/R-40~1.0/include" -DNDEBUG -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c dummy.cpp -o dummy.o
C:/rtools40/mingw32/bin/g++ -std=gnu++11 -shared -s -static-libgcc -o RProtoBufLib.dll tmp.def dummy.o -LC:/PROGRA~1/R/R-40~1.0/bin/i386 -lR
: symbol not definedbin/../lib/gcc/i686-w64-mingw32/8.3.0/../../../../i686-w64-mingw32/bin/ld.exe: cannot export _Z19dummy_RProtobuf_funv
collect2.exe: error: ld returned 1 exit status
no DLL was created
ERROR: compilation failed for package 'RProtoBufLib'
* removing 'C:/Program Files/R/R-4.0.0/library/RProtoBufLib'
* restoring previous 'C:/Program Files/R/R-4.0.0/library/RProtoBufLib'
Error: Failed to install 'RProtoBufLib' from GitHub:
(converted from warning) installation of package ‘C:/Users/LOCALU~1.JCS/AppData/Local/Temp/Rtmpg5uvjO/file3d4c4195424d/RProtoBufLib_2.1.0.tar.gz’ had non-zero exit status
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
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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
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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
CXX google/protobuf/io/tokenizer.lo
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
CXX google/protobuf/util/field_mask_util.lo
CXX google/protobuf/util/internal/datapiece.lo
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
CXX google/protobuf/util/internal/object_writer.lo
CXX google/protobuf/util/internal/protostream_objectsource.lo
CXX google/protobuf/util/internal/protostream_objectwriter.lo
CXX google/protobuf/util/internal/proto_writer.lo
CXX google/protobuf/util/internal/type_info.lo
CXX google/protobuf/util/internal/type_info_test_helper.lo
CXX google/protobuf/util/internal/utility.lo
CXX google/protobuf/util/json_util.lo
CXX google/protobuf/util/message_differencer.lo
CXX google/protobuf/util/time_util.lo
CXX google/protobuf/util/type_resolver_util.lo
CXXLD libprotobuf.la
CXX google/protobuf/compiler/code_generator.lo
CXX google/protobuf/compiler/command_line_interface.lo
CXX google/protobuf/compiler/plugin.lo
CXX google/protobuf/compiler/plugin.pb.lo
CXX google/protobuf/compiler/subprocess.lo
CXX google/protobuf/compiler/zip_writer.lo
CXX google/protobuf/compiler/cpp/cpp_enum.lo
CXX google/protobuf/compiler/cpp/cpp_enum_field.lo
CXX google/protobuf/compiler/cpp/cpp_extension.lo
CXX google/protobuf/compiler/cpp/cpp_field.lo
CXX google/protobuf/compiler/cpp/cpp_file.lo
CXX google/protobuf/compiler/cpp/cpp_generator.lo
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
CXX google/protobuf/compiler/cpp/cpp_message.lo
CXX google/protobuf/compiler/cpp/cpp_message_field.lo
CXX google/protobuf/compiler/cpp/cpp_padding_optimizer.lo
CXX google/protobuf/compiler/cpp/cpp_primitive_field.lo
CXX google/protobuf/compiler/cpp/cpp_service.lo
CXX google/protobuf/compiler/cpp/cpp_string_field.lo
CXX google/protobuf/compiler/java/java_context.lo
CXX google/protobuf/compiler/java/java_enum.lo
CXX google/protobuf/compiler/java/java_enum_lite.lo
CXX google/protobuf/compiler/java/java_enum_field.lo
CXX google/protobuf/compiler/java/java_enum_field_lite.lo
CXX google/protobuf/compiler/java/java_extension.lo
CXX google/protobuf/compiler/java/java_extension_lite.lo
CXX google/protobuf/compiler/java/java_field.lo
CXX google/protobuf/compiler/java/java_file.lo
CXX google/protobuf/compiler/java/java_generator.lo
CXX google/protobuf/compiler/java/java_generator_factory.lo
CXX google/protobuf/compiler/java/java_helpers.lo
CXX google/protobuf/compiler/java/java_map_field.lo
CXX google/protobuf/compiler/java/java_map_field_lite.lo
CXX google/protobuf/compiler/java/java_message.lo
CXX google/protobuf/compiler/java/java_message_lite.lo
CXX google/protobuf/compiler/java/java_message_builder.lo
CXX google/protobuf/compiler/java/java_message_builder_lite.lo
CXX google/protobuf/compiler/java/java_message_field.lo
CXX google/protobuf/compiler/java/java_message_field_lite.lo
CXX google/protobuf/compiler/java/java_name_resolver.lo
CXX google/protobuf/compiler/java/java_primitive_field.lo
CXX google/protobuf/compiler/java/java_primitive_field_lite.lo
CXX google/protobuf/compiler/java/java_shared_code_generator.lo
CXX google/protobuf/compiler/java/java_service.lo
CXX google/protobuf/compiler/java/java_string_field.lo
CXX google/protobuf/compiler/java/java_string_field_lite.lo
CXX google/protobuf/compiler/java/java_doc_comment.lo
CXX google/protobuf/compiler/js/js_generator.lo
CXX google/protobuf/compiler/js/well_known_types_embed.lo
CXX google/protobuf/compiler/objectivec/objectivec_enum.lo
CXX google/protobuf/compiler/objectivec/objectivec_enum_field.lo
CXX google/protobuf/compiler/objectivec/objectivec_extension.lo
CXX google/protobuf/compiler/objectivec/objectivec_field.lo
CXX google/protobuf/compiler/objectivec/objectivec_file.lo
CXX google/protobuf/compiler/objectivec/objectivec_generator.lo
CXX google/protobuf/compiler/objectivec/objectivec_helpers.lo
CXX google/protobuf/compiler/objectivec/objectivec_map_field.lo
CXX google/protobuf/compiler/objectivec/objectivec_message.lo
CXX google/protobuf/compiler/objectivec/objectivec_message_field.lo
CXX google/protobuf/compiler/objectivec/objectivec_oneof.lo
CXX google/protobuf/compiler/objectivec/objectivec_primitive_field.lo
CXX google/protobuf/compiler/php/php_generator.lo
CXX google/protobuf/compiler/python/python_generator.lo
CXX google/protobuf/compiler/ruby/ruby_generator.lo
CXX google/protobuf/compiler/csharp/csharp_doc_comment.lo
CXX google/protobuf/compiler/csharp/csharp_enum.lo
CXX google/protobuf/compiler/csharp/csharp_enum_field.lo
CXX google/protobuf/compiler/csharp/csharp_field_base.lo
CXX google/protobuf/compiler/csharp/csharp_generator.lo
CXX google/protobuf/compiler/csharp/csharp_helpers.lo
CXX google/protobuf/compiler/csharp/csharp_map_field.lo
CXX google/protobuf/compiler/csharp/csharp_message.lo
CXX google/protobuf/compiler/csharp/csharp_message_field.lo
CXX google/protobuf/compiler/csharp/csharp_primitive_field.lo
CXX google/protobuf/compiler/csharp/csharp_reflection_class.lo
CXX google/protobuf/compiler/csharp/csharp_repeated_enum_field.lo
CXX google/protobuf/compiler/csharp/csharp_repeated_message_field.lo
CXX google/protobuf/compiler/csharp/csharp_repeated_primitive_field.lo
CXX google/protobuf/compiler/csharp/csharp_source_generator_base.lo
CXX google/protobuf/compiler/csharp/csharp_wrapper_field.lo
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
The current bundled pb is 2.6, which is 4 year old. We will have to test the backward compatibility (for both code and data archive) before making such upgrade.
From: Prof Brian Ripley [email protected]
Subject: BioC package RProtoBufLib 1.9.6You have in configure.ac (in BioC 3.11 versions only)
configure.ac: echo "untarring protobuf ...";
configure.ac: tar xf ${PBTGZNAME}'tar' is not required to handle .tar.gz files, and does not on Solaris.
You need to do this the old way, e.g.gzip -dc ${PBTGZNAME} | tar -xf -
or use R to do this. Otherwise the script retries until it used up the
process table .... After that, protobuf's configure is not using
CXXFLAGS correctly, as its Makefile containsCFLAGS = -O2 -m64
CXXFLAGS = -O2 -m64This is far too much work for 3 CRAN packages
Hey @mikejiang and @gfinak, just a heads up that I ran in to some simple compilation errors on macOS Big Sur with the most recent master
branch. Fortunately the errors were really informative and the gist was:
Protobuf requires at least c++11
I think it's just that clang wasn't supporting C++11 features by default. Anyway, adding CXX_STD = CXX11
to Makevars.in
fixed it right up. Just a heads up in case you start getting Mac build failures.
Hi @mikejiang,
I am struggling to install RProtoBufLib since the changes 15 days ago and I was hoping that you may be able to help. I have no issues installing the package on a mac. This is what I get when I try to install the package on windows:
> devtools::install_github("RGLab/RProtoBufLib", ref = "trunk")
Downloading GitHub repo RGLab/RProtoBufLib@trunk
√ checking for file 'C:\Users\localuseradmin.JCSMR-028197PL\AppData\Local\Temp\RtmpAp36Zy\remotes4d383c6bb33\RGLab-RProtoBufLib-0001c9f/DESCRIPTION' (518ms)
- preparing 'RProtoBufLib':
√ checking DESCRIPTION meta-information ...
- cleaning src
- running 'cleanup.win'
- checking for LF line-endings in source and make files and shell scripts
- checking for empty or unneeded directories
- building 'RProtoBufLib_1.9.6.tar.gz'
Warning: file 'RProtoBufLib/cleanup' did not have execute permissions: corrected
Warning: file 'RProtoBufLib/configure' did not have execute permissions: corrected
* installing *source* package 'RProtoBufLib' ...
** using staged installation
**********************************************
WARNING: this package has a configure script
It probably needs manual configuration
**********************************************
** libs
*** arch - i386
mkdir -p ""C:/Program Files/R/R-3.6.1/library/00LOCK-RProtoBufLib/00new/RProtoBufLib/include""
cp -r /include/google "C:/Program Files/R/R-3.6.1/library/00LOCK-RProtoBufLib/00new/RProtoBufLib/include"
cp: cannot stat '/include/google': No such file or directory
make: *** [Makevars.win:12: copying] Error 1
ERROR: compilation failed for package 'RProtoBufLib'
* removing 'C:/Program Files/R/R-3.6.1/library/RProtoBufLib'
* restoring previous 'C:/Program Files/R/R-3.6.1/library/RProtoBufLib'
Error: Failed to install 'RProtoBufLib' from GitHub:
(converted from warning) installation of package ‘C:/Users/LOCALU~1.JCS/AppData/Local/Temp/RtmpAp36Zy/file4d381ebb7636/RProtoBufLib_1.9.6.tar.gz’ had non-zero exit status
Thanks for your help.
Dillon
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