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cannot install RProtoBufLib as dependency for ggcyto and flowWorkspace #4

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marketavlkova opened this issue Feb 25, 2018 · 8 comments
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cannot install RProtoBufLib as dependency for ggcyto and flowWorkspace #4

marketavlkova opened this issue Feb 25, 2018 · 8 comments

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@marketavlkova
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marketavlkova commented Feb 25, 2018 •
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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
@marketavlkova marketavlkova changed the title cannot install as RProtoBufLib dependency for ggcyto and flowWorkspace cannot install RProtoBufLib as dependency for ggcyto and flowWorkspace Feb 25, 2018
@mikejiang
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You need libtool see https://github.com/RGLab/RProtoBufLib/blob/trunk/DESCRIPTION#L12
and #2

@marketavlkova
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marketavlkova commented Feb 26, 2018 •
edited
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libtool installed, but installation through both biocLite("RProtoBufLib") and install_github("RGLab/RProtoBufLib@trunk") still has the same errors

@mikejiang
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Since you are mac, you can manually download/install the prebuilt binary from the latest bioconductor release http://bioconductor.org/packages/3.6/bioc/html/RProtoBufLib.html. Or if you upgrade your R to 3.4.3, then biocLite should automatically pull the binary for you.

@marketavlkova
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Upgraded to R 3.4.3 and still have the same errors using biocLite. I don't know how to install it manually using the prebuilt binary.

@mikejiang
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You need to make sure to use the latest version of Bioconductor 3.6 by biocLite("BiocUpgrade")
see details https://www.bioconductor.org/install/

@marketavlkova
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I already have Bioconductor 3.6

> biocLite("BiocUpgrade")
Error: Bioconductor version 3.6 cannot be upgraded with R version 3.4.3

@RGLab RGLab deleted a comment from marketavlkova Feb 27, 2018
@mikejiang
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Ok. I don't know what was the reason for you Mac OSX not being able to pull the binary version. To do it manually, just download the package from http://bioconductor.org/packages/3.6/bioc/bin/macosx/el-capitan/contrib/3.4/RProtoBufLib_1.0.1.tgz

and run R CMD INSTALL RProtoBufLib_1.0.1.tgz

@marketavlkova
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good, this worked. Thanks.

@mikejiang mikejiang mentioned this issue Apr 17, 2018
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@mikejiang @marketavlkova