Cannot install RccpParallel

[ytakemon]

Hello,

I've tried to install your package from github using devtools::install_github("RcppCore/RcppParallel") and from CRAN, but neither method has worked for me. Do you have any suggestions for how I could troubleshoot this?
I've listed my R version and machine used as well as the error message below.

Thank you in advance!
Yuka

R version/ Machine used:
R version 4.0.2 (2020-06-22)
Platform: x86_64-centos7-linux-gnu (64-bit)
Running under: CentOS Linux 7 (Core)

Error message:

> devtools::install_github("RcppCore/RcppParallel")
Using github PAT from envvar GITHUB_PAT
Downloading GitHub repo RcppCore/RcppParallel@HEAD
✔  checking for file ‘/tmp/RtmpkUICWI/remotes24eff3242c46e/RcppCore-RcppParallel-878b6e7/DESCRIPTION’ (508ms)
─  preparing ‘RcppParallel’:
✔  checking DESCRIPTION meta-information ...
─  cleaning src
─  running ‘cleanup’
─  checking for LF line-endings in source and make files and shell scripts (549ms)
─  checking for empty or unneeded directories
─  building ‘RcppParallel_5.1.5.tar.gz’

Installing package into ‘/home/ytakemon/R/x86_64-centos7-linux-gnu-library/4.0’
(as ‘lib’ is unspecified)
* installing *source* package ‘RcppParallel’ ...
** using staged installation
** preparing to configure package 'RcppParallel' ...
*** configured file: 'src/Makevars.in' => 'src/Makevars'
** finished configure for package 'RcppParallel'
** libs
(tbb) Building TBB using bundled sources ...
make[1]: Entering directory `/tmp/RtmpN2WSXT/R.INSTALL250a73a2216f7/RcppParallel/src/tbb/src'
OS: linux
arch=intel64
compiler=gcc
runtime=cc4.8.5_libc2.17_kernel3.10.0
tbb_build_prefix=linux_intel64_gcc_cc4.8.5_libc2.17_kernel3.10.0
work_dir=/tmp/RtmpN2WSXT/R.INSTALL250a73a2216f7/RcppParallel/src/build/linux_intel64_gcc_cc4.8.5_libc2.17_kernel3.10.0_release
make[1]: Leaving directory `/tmp/RtmpN2WSXT/R.INSTALL250a73a2216f7/RcppParallel/src/tbb/src'
make[1]: Entering directory `/tmp/RtmpN2WSXT/R.INSTALL250a73a2216f7/RcppParallel/src/tbb/src'
Created ../build/lib_release directory
make -C "../build/lib_release"  -r -f ../../build/Makefile.tbb cfg=release
make[2]: Entering directory `/tmp/RtmpN2WSXT/R.INSTALL250a73a2216f7/RcppParallel/src/tbb/build/lib_release'
../../build/Makefile.tbb:28: CONFIG: cfg=release arch=intel64 compiler=gcc target=linux runtime=cc4.8.5_libc2.17_kernel3.10.0
/usr/bin/g++ -I../inst/include  -o concurrent_hash_map.o -c -MMD -DDO_ITT_NOTIFY -O2 -DUSE_PTHREAD -m64 -mrtm  -fpic -flifetime-dse=1 -D__TBB_BUILD=1 -Wall -Wextra  -L/gsc/software/linux-x86_64-centos7/gcc-7.2.0/lib64 -DTBB_NO_LEGACY=1   -I../../src -I../../src/rml/include -I../../include ../../src/tbb/concurrent_hash_map.cpp
g++: error: unrecognized command line option ‘-flifetime-dse=1’
make[2]: *** [concurrent_hash_map.o] Error 1
make[2]: Leaving directory `/tmp/RtmpN2WSXT/R.INSTALL250a73a2216f7/RcppParallel/src/tbb/build/lib_release'
make[1]: *** [tbb_release] Error 2
make[1]: Leaving directory `/tmp/RtmpN2WSXT/R.INSTALL250a73a2216f7/RcppParallel/src/tbb/src'
/gsc/software/linux-x86_64-centos7/gcc-7.2.0/bin/g++ -std=gnu++11 -I"/gsc/software/linux-x86_64-centos7/R-4.0.2/lib64/R/include" -DNDEBUG -I../inst/include  -I/usr/local/include  -std=gnu++11 -DRCPP_PARALLEL_USE_TBB=1 -DTBB_SUPPRESS_DEPRECATED_MESSAGES=1 -fpic  -L/gsc/software/linux-x86_64-centos7/gcc-7.2.0/lib64  -c init.cpp -o init.o
/gsc/software/linux-x86_64-centos7/gcc-7.2.0/bin/g++ -std=gnu++11 -I"/gsc/software/linux-x86_64-centos7/R-4.0.2/lib64/R/include" -DNDEBUG -I../inst/include  -I/usr/local/include  -std=gnu++11 -DRCPP_PARALLEL_USE_TBB=1 -DTBB_SUPPRESS_DEPRECATED_MESSAGES=1 -fpic  -L/gsc/software/linux-x86_64-centos7/gcc-7.2.0/lib64  -c options.cpp -o options.o
/gsc/software/linux-x86_64-centos7/gcc-7.2.0/bin/g++ -std=gnu++11 -shared -L/gsc/software/linux-x86_64-centos7/R-4.0.2/lib64/R/lib -L/gsc/software/linux-x86_64-centos7/gcc-7.2.0/lib64 -o RcppParallel.so init.o options.o -L/gsc/software/linux-x86_64-centos7/R-4.0.2/lib64/R/lib -lR
installing via 'install.libs.R' to /home/ytakemon/R/x86_64-centos7-linux-gnu-library/4.0/00LOCK-RcppParallel/00new/RcppParallel
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** testing if installed package can be loaded from temporary location
Error: package or namespace load failed for ‘RcppParallel’:
 .onLoad failed in loadNamespace() for 'RcppParallel', details:
  call: dyn.load(file, DLLpath = DLLpath, ...)
  error: unable to load shared object '/home/ytakemon/R/x86_64-centos7-linux-gnu-library/4.0/00LOCK-RcppParallel/00new/RcppParallel/libs/RcppParallel.so':
  /home/ytakemon/R/x86_64-centos7-linux-gnu-library/4.0/00LOCK-RcppParallel/00new/RcppParallel/libs/RcppParallel.so: undefined symbol: _ZN3tbb4task13note_affinityEt
Error: loading failed
Execution halted
ERROR: loading failed
* removing ‘/home/ytakemon/R/x86_64-centos7-linux-gnu-library/4.0/RcppParallel’
Warning message:
In i.p(...) :
  installation of package ‘/tmp/RtmpkUICWI/file24eff72505ea4/RcppParallel_5.1.5.tar.gz’ had non-zero exit status

[eddelbuettel]

You need to use a less old operating system, or at least provide it with more recent compilers -- which you can do via something called devtoolset.

[ytakemon]

Thanks for your response. Could you share what the minimum version requirements are for OS and compilers? This will help me communicate with the IT department which has sudo privileges.

[eddelbuettel]

I think the devtoolsset for CentOS 7 gets you gcc/g++ 8.* which should be good enough. CRAN uses newer versions (10 and later). Also note that your R version is also two years behind so you may get other trouble from other packages.

[kevinushey]

For reference, the relevant error:

g++: error: unrecognized command line option ‘-flifetime-dse=1’

But that flag should only be turned on if using gcc 6 or newer:

RcppParallel/src/tbb/build/linux.gcc.inc

Lines 60 to 65 in c5d3b57

	# gcc 6.0 and later have -flifetime-dse option that controls
	# elimination of stores done outside the object lifetime
	ifneq (,$(shell $(CONLY) -dumpfullversion -dumpversion | egrep "^([6-9])"))
	# keep pre-contruction stores for zero initialization
	DSE_KEY = -flifetime-dse=1
	endif

It looks like the R-related files are being compiled using gcc 7:

/gsc/software/linux-x86_64-centos7/gcc-7.2.0/bin/g++ -std=gnu++11 -I"/gsc/software/linux-x86_64-centos7/R-4.0.2/lib64/R/include" -DNDEBUG -I../inst/include -I/usr/local/include -std=gnu++11 -DRCPP_PARALLEL_USE_TBB=1 -DTBB_SUPPRESS_DEPRECATED_MESSAGES=1 -fpic -L/gsc/software/linux-x86_64-centos7/gcc-7.2.0/lib64 -c init.cpp -o init.o

But, for whatever reason, TBB itself is seeing (and using) the "system" gcc installation:

/usr/bin/g++ -I../inst/include -o concurrent_hash_map.o -c -MMD -DDO_ITT_NOTIFY -O2 -DUSE_PTHREAD -m64 -mrtm -fpic -flifetime-dse=1 -D__TBB_BUILD=1 -Wall -Wextra -L/gsc/software/linux-x86_64-centos7/gcc-7.2.0/lib64 -DTBB_NO_LEGACY=1 -I../../src -I../../src/rml/include -I../../include ../../src/tbb/concurrent_hash_map.cpp

Can you share the output of:

R CMD config --all

I wonder if we're somehow failing to pass along the right path to the C++ compiler to TBB here.

[eddelbuettel]

I wonder if we're somehow failing to pass along the right path to the C++ compiler to TBB here.

That's a very good observation. It's been a few years since I saw a devtoolset-enhance CentOS but I also recall that a) these are installed off the path and b) require sourcing a shell script to 'activate' and so c) may not be found in R's own compile time config as R may not have been recompiled.

[ytakemon]

Can you share the output of:
R CMD config --all

Below are the outputs:

CC = /gsc/software/linux-x86_64-centos7/gcc-7.2.0/bin/gcc
CFLAGS = -g -O2
CPICFLAGS = -fpic
CPPFLAGS = -I/usr/local/include
CXX = /gsc/software/linux-x86_64-centos7/gcc-7.2.0/bin/g++ -std=gnu++11
CXXFLAGS = -L/gsc/software/linux-x86_64-centos7/gcc-7.2.0/lib64
CXXPICFLAGS = -fpic
CXX11 = /usr/bin/g++
CXX11STD = -std=gnu++11
CXX11FLAGS = -L/gsc/software/linux-x86_64-centos7/gcc-7.2.0/lib64
CXX11PICFLAGS = -fpic
CXX14 = /gsc/software/linux-x86_64-centos7/gcc-7.2.0/bin/g++
CXX14STD = -std=gnu++14
CXX14FLAGS = -L/gsc/software/linux-x86_64-centos7/gcc-7.2.0/lib64
CXX14PICFLAGS = -fpic
CXX17 = /gsc/software/linux-x86_64-centos7/gcc-7.2.0/bin/g++
CXX17STD = -std=gnu++17
CXX17FLAGS = -L/gsc/software/linux-x86_64-centos7/gcc-7.2.0/lib64
CXX17PICFLAGS = -fpic
CXX20 =
CXX20STD =
CXX20FLAGS =
CXX20PICFLAGS =
DYLIB_EXT = .so
DYLIB_LD = /gsc/software/linux-x86_64-centos7/gcc-7.2.0/bin/gcc
DYLIB_LDFLAGS = -shared -fopenmp
FC = /gsc/software/linux-x86_64-centos7/gcc-7.2.0/bin/gfortran
FFLAGS = -g -O2
FPICFLAGS = -fpic
FLIBS = -lgfortran -lm -lquadmath
FCFLAGS = -g -O2
SAFE_FFLAGS = -g -O2 -msse2 -mfpmath=sse
OBJC =
OBJCFLAGS =
JAVA = /gsc/software/linux-x86_64-centos7/jdk1.8.0_172/jre/bin/java
JAVAC = /gsc/software/linux-x86_64-centos7/jdk1.8.0_172/jre/../bin/javac
JAVAH = /gsc/software/linux-x86_64-centos7/jdk1.8.0_172/jre/../bin/javah
JAR = /gsc/software/linux-x86_64-centos7/jdk1.8.0_172/jre/../bin/jar
JAVA_HOME = /gsc/software/linux-x86_64-centos7/jdk1.8.0_172/jre
JAVA_LIBS = -L/gsc/software/linux-x86_64-centos7/jdk1.8.0_172/jre/lib/amd64/server -ljvm
JAVA_CPPFLAGS = -I/gsc/software/linux-x86_64-centos7/jdk1.8.0_172/jre/../include -I/gsc/software/linux-x86_64-centos7/jdk1.8.0_172/jre/../include/linux
LDFLAGS = -L/gsc/software/linux-x86_64-centos7/gcc-7.2.0/lib64
SHLIB_CFLAGS =
SHLIB_CXXFLAGS =
SHLIB_CXXLD = /gsc/software/linux-x86_64-centos7/gcc-7.2.0/bin/g++ -std=gnu++11
SHLIB_CXXLDFLAGS = -shared
SHLIB_CXX11LD = /usr/bin/g++ -std=gnu++11
SHLIB_CXX11LDFLAGS = -shared
SHLIB_CXX14LD = /gsc/software/linux-x86_64-centos7/gcc-7.2.0/bin/g++ -std=gnu++14
SHLIB_CXX14LDFLAGS = -shared
SHLIB_CXX17LD = /gsc/software/linux-x86_64-centos7/gcc-7.2.0/bin/g++ -std=gnu++17
SHLIB_CXX17LDFLAGS = -shared
SHLIB_CXX20LD =
SHLIB_CXX20LDFLAGS = -shared
SHLIB_EXT = .so
SHLIB_FFLAGS =
SHLIB_LD = /gsc/software/linux-x86_64-centos7/gcc-7.2.0/bin/gcc
SHLIB_LDFLAGS = -shared
TCLTK_CPPFLAGS =
TCLTK_LIBS =
BLAS_LIBS = -L/gsc/software/linux-x86_64-centos7/R-4.0.2/lib64/R/lib -lRblas
LAPACK_LIBS = -L/gsc/software/linux-x86_64-centos7/R-4.0.2/lib64/R/lib -lRlapack
MAKE = make
LIBnn = lib64
AR = ar
RANLIB = ranlib
## The following variables are deprecated
CPP = /gsc/software/linux-x86_64-centos7/gcc-7.2.0/bin/gcc -E
CXXCPP = /gsc/software/linux-x86_64-centos7/gcc-7.2.0/bin/g++ -std=gnu++11 -E

I also tried installing RccpParallel using the most recent R installation we have on our system, which is R-4.1.0, and I am seeing the same errors there as well.

[kevinushey]

I think this explains it:

CXX11 = /usr/bin/g++

CXX11 wasn't updated to use the new compiler. You can try overriding this in e.g. your ~/.R/Makevars file, to point at the compiler you want to use.

[ytakemon]

I've now installed your tool successfully! I did exactly what you suggested and changed the path on ~/.R/Makevars to :

CXX11 = /gsc/software/linux-x86_64-centos7/gcc-7.2.0/bin/g++ 

Thank you both for taking the time to help me solve the problem!

[eddelbuettel]

Thanks to you for persevering! Turns out your IT folks did try to help and had a newer compiler, but one went astray.

One thing I find helps is to not just 'fail' at the top-level (in your case via remotes) but to try to run install.packages() directly, or, better still, unpack the source tar.gz and run R CMD INSTALL . and/or ./configure -- all in order to get closer to the actual error messages to have a better handle on what may have caused it.