Installation issue in WSL2 Ubuntu Focal

[akhst7]

Trying to install either Cran or Github versions fail with a following error output:

* installing *source* package ‘RcppParallel’ ...
** package ‘RcppParallel’ successfully unpacked and MD5 sums checked
** 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]: warning: jobserver unavailable: using -j1.  Add '+' to parent make rule.
make[1]: Entering directory '/tmp/Rtmp5qQvY4/R.INSTALL2dd142741c97/RcppParallel/src/tbb/src'
OS: linux
arch=intel64
compiler=gcc
runtime=cc9.3.0_libc2.31_kernel5.4.72
tbb_build_prefix=linux_intel64_gcc_cc9.3.0_libc2.31_kernel5.4.72
work_dir=/tmp/Rtmp5qQvY4/R.INSTALL2dd142741c97/RcppParallel/src/build/linux_intel64_gcc_cc9.3.0_libc2.31_kernel5.4.72_release
make[1]: Leaving directory '/tmp/Rtmp5qQvY4/R.INSTALL2dd142741c97/RcppParallel/src/tbb/src'
make[1]: warning: jobserver unavailable: using -j1.  Add '+' to parent make rule.
make[1]: Entering directory '/tmp/Rtmp5qQvY4/R.INSTALL2dd142741c97/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/Rtmp5qQvY4/R.INSTALL2dd142741c97/RcppParallel/src/tbb/build/lib_release'
../../build/Makefile.tbb:28: CONFIG: cfg=release arch=intel64 compiler=gcc target=linux runtime=cc9.3.0_libc2.31_kernel5.4.72
/usr/bin/clang++ -I../inst/include -I/usr/lib/llvm-13/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 -Wno-parentheses -Wno-sized-deallocation -g -O2 -fdebug-prefix-map=/build/r-base-i2PIHO/r-base-4.1.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -DTBB_NO_LEGACY=1   -I../../src -I../../src/rml/include -I../../include ../../src/tbb/concurrent_hash_map.cpp
clang: error: unknown argument: '-flifetime-dse=1'
make[2]: *** [../../build/common_rules.inc:76: concurrent_hash_map.o] Error 1
make[2]: Leaving directory '/tmp/Rtmp5qQvY4/R.INSTALL2dd142741c97/RcppParallel/src/tbb/build/lib_release'
make[1]: *** [Makefile:100: tbb_release] Error 2
make[1]: Leaving directory '/tmp/Rtmp5qQvY4/R.INSTALL2dd142741c97/RcppParallel/src/tbb/src'
/usr/bin/clang++ -I"/usr/share/R/include" -DNDEBUG -I../inst/include  -I"/usr/lib/llvm-13/include"  -std=gnu++11 -DRCPP_PARALLEL_USE_TBB=1 -DTBB_SUPPRESS_DEPRECATED_MESSAGES=1 -fpic  -g -O3 -Wall -pedantic -mtune=native -pipe -c init.cpp -o init.o
/usr/bin/clang++ -I"/usr/share/R/include" -DNDEBUG -I../inst/include  -I"/usr/lib/llvm-13/include"  -std=gnu++11 -DRCPP_PARALLEL_USE_TBB=1 -DTBB_SUPPRESS_DEPRECATED_MESSAGES=1 -fpic  -g -O3 -Wall -pedantic -mtune=native -pipe -c options.cpp -o options.o
/usr/bin/clang++ -shared -L/usr/lib/R/lib -L/usr/lib/llvm-13/lib -Wl,-rpath,/usr/lib/llvm-13/lib -o RcppParallel.so init.o options.o -L/usr/lib/R/lib -lR
installing via 'install.libs.R' to /home/rstudio/R/x86_64-pc-linux-gnu-library/4.1/00LOCK-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/rstudio/R/x86_64-pc-linux-gnu-library/4.1/00LOCK-RcppParallel/00new/RcppParallel/libs/RcppParallel.so':
  /home/rstudio/R/x86_64-pc-linux-gnu-library/4.1/00LOCK-RcppParallel/00new/RcppParallel/libs/RcppParallel.so: undefined symbol: _ZN3tbb10interface78internal15task_arena_base24internal_max_concurrencyEPKNS0_10task_arenaE
Error: loading failed
Execution halted
ERROR: loading failed
* removing ‘/home/rstudio/R/x86_64-pc-linux-gnu-library/4.1/RcppParallel’
Warning in install.packages :
  installation of package ‘RcppParallel’ had non-zero exit status

The issue probably is with clang ;

clang: error: unknown argument: '-flifetime-dse=1'

Any help will be appreciated.

> sessionInfo()
R version 4.1.2 (2021-11-01)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 20.04.3 LTS

Matrix products: default
BLAS:   /usr/lib/x86_64-linux-gnu/blas/libblas.so.3.9.0
LAPACK: /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.9.0

locale:
 [1] LC_CTYPE=C.UTF-8       LC_NUMERIC=C           LC_TIME=C.UTF-8        LC_COLLATE=C.UTF-8     LC_MONETARY=C.UTF-8   
 [6] LC_MESSAGES=C.UTF-8    LC_PAPER=C.UTF-8       LC_NAME=C              LC_ADDRESS=C           LC_TELEPHONE=C        
[11] LC_MEASUREMENT=C.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_4.1.2 tools_4.1.2    curl_4.3.2     remotes_2.4.2 

~ neofetch
            .-/+oossssoo+/-.               root@204152
        `:+ssssssssssssssssss+:`           ------------------
      -+ssssssssssssssssssyyssss+-         OS: Ubuntu 20.04.3 LTS on Windows 10 x86_64
    .ossssssssssssssssssdMMMNysssso.       Kernel: 5.4.72-microsoft-standard-WSL2
   /ssssssssssshdmmNNmmyNMMMMhssssss/      Uptime: 6 days, 1 hour, 47 mins
  +ssssssssshmydMMMMMMMNddddyssssssss+     Packages: 1325 (dpkg)
 /sssssssshNMMMyhhyyyyhmNMMMNhssssssss/    Shell: zsh 5.8
.ssssssssdMMMNhsssssssssshNMMMdssssssss.   Terminal: /dev/pts/0
+sssshhhyNMMNyssssssssssssyNMMMysssssss+   CPU: Intel Xeon Gold 6230 (40) @ 2.094GHz
ossyNMMMNyMMhsssssssssssssshmmmhssssssso   Memory: 619MiB / 102724MiB
ossyNMMMNyMMhsssssssssssssshmmmhssssssso
+sssshhhyNMMNyssssssssssssyNMMMysssssss+
.ssssssssdMMMNhsssssssssshNMMMdssssssss.
 /sssssssshNMMMyhhyyyyhdNMMMNhssssssss/
  +sssssssssdmydMMMMMMMMddddyssssssss+
   /ssssssssssshdmNNNNmyNMMMMhssssss/
    .ossssssssssssssssssdMMMNysssso.
      -+sssssssssssssssssyyyssss+-
        `:+ssssssssssssssssss+:`
            .-/+oossssoo+/-.

[kevinushey]

clang: error: unknown argument: '-flifetime-dse=1'

Probably happening because you're building with clang instead of gcc, or something similar like that. Patches would be welcomed.

[akhst7]

@kevinushey

Initially, I thought so too but RcppParallel does get installed in my Mac, fully running clang. I have to dig a bit more but this could be specific to the WSL2 Ubuntu.

[kevinushey]

Note also that TBB seems to think you're using a gcc compiler:

arch=intel64
compiler=gcc
runtime=cc9.3.0_libc2.31_kernel5.4.72
tbb_build_prefix=linux_intel64_gcc_cc9.3.0_libc2.31_kernel5.4.72

Have you changed your compiler settings for R in any other way? Why is clang being used rather than gcc?

[akhst7]

@kevinushey,

My Markevars has a compiler switch from gcc to clang, and by disabling it, gcc kicked in and I was able to compile RcppParallel. I have not figured out why clang works just fine in my Mac though.

[eddelbuettel]

RcppParallel is a somewhat more complex package with sub-Makefiles and whatnot and may have a subtle preference for gcc. You can probably switch back to clang in your Makevars if you prefer that -- mixing and matching is generally fine -- if you just keep it in mind for 'odd' breakage. (I have used a ccache prefix for a decade or longer and every few hundred packages something stumbles so ....).