Error building `Rcall`: R cannot be found

[chriselrod]

julia> ENV["R_HOME"]
"/usr/lib64/R"

julia> run(`Rscript -e "R.home()"`)
[1] "/usr/lib64/R"
Process(`Rscript -e 'R.home()'`, ProcessExited(0))

(v1.3) pkg> build RCall
  Building Conda → `~/.julia/packages/Conda/kLXeC/deps/build.log`
  Building RCall → `~/.julia/packages/RCall/iojZI/deps/build.log`
┌ Error: Error building `RCall`: 
│ ERROR: LoadError: R cannot be found. Set the "R_HOME" environment variable to re-run Pkg.build("RCall").
│ Stacktrace:
│  [1] error(::String) at ./error.jl:33
│  [2] top-level scope at /home/chriselrod/.julia/packages/RCall/iojZI/deps/build.jl:49
│  [3] include at ./boot.jl:328 [inlined]
│  [4] include_relative(::Module, ::String) at ./loading.jl:1094
│  [5] include(::Module, ::String) at ./Base.jl:31
│  [6] include(::String) at ./client.jl:432
│  [7] top-level scope at none:5
│ in expression starting at /home/chriselrod/.julia/packages/RCall/iojZI/deps/build.jl:10
└ @ Pkg.Operations ~/Documents/languages/julia/usr/share/julia/stdlib/v1.3/Pkg/src/backwards_compatible_isolation.jl:647

julia> versioninfo()
Julia Version 1.3.0-alpha.63
Commit 7f2922eb09* (2019-08-06 03:27 UTC)
Platform Info:
  OS: Linux (x86_64-generic-linux)
  CPU: Intel(R) Core(TM) i9-7900X CPU @ 3.30GHz
  WORD_SIZE: 64
  LIBM: libopenlibm
  LLVM: libLLVM-8.0.0 (ORCJIT, skylake)

I've tried a lot of different values for "R_HOME", and have always seen the same error.

[Non-Contradiction]

Does libR.so exist somewhere in the folder? libR is needed by RCall and RCall will report the "R cannot be found" error if RCall cannot find the libR.

[chriselrod]

libR is in /usr/lib64/R/lib:

julia> ENV["R_HOME"] = "/usr/lib64/R/lib"
"/usr/lib64/R/lib"

(v1.3) pkg> build RCall
  Building Conda → `~/.julia/packages/Conda/kLXeC/deps/build.log`
  Building RCall → `~/.julia/packages/RCall/iojZI/deps/build.log`
┌ Error: Error building `RCall`: 
│ ERROR: LoadError: R cannot be found. Set the "R_HOME" environment variable to re-run Pkg.build("RCall").
│ Stacktrace:
│  [1] error(::String) at ./error.jl:33
│  [2] top-level scope at /home/chriselrod/.julia/packages/RCall/iojZI/deps/build.jl:49
│  [3] include at ./boot.jl:328 [inlined]
│  [4] include_relative(::Module, ::String) at ./loading.jl:1094
│  [5] include(::Module, ::String) at ./Base.jl:31
│  [6] include(::String) at ./client.jl:432
│  [7] top-level scope at none:5
│ in expression starting at /home/chriselrod/.julia/packages/RCall/iojZI/deps/build.jl:10
└ @ Pkg.Operations ~/Documents/languages/julia/usr/share/julia/stdlib/v1.3/Pkg/src/backwards_compatible_isolation.jl:647

shell> ls /usr/lib64/R/lib
haswell/  libRblas.so*  libRlapack.so*  libR.so*

Contents of /usr/lib64/R:

> ls /usr/lib64/R
bin/  COPYING  doc/  etc/  include/  lib/  library/  modules/  rstudio/  share/  SVN-REVISION
> ls /usr/lib64/R/lib
haswell/  libRblas.so*  libRlapack.so*  libR.so*

The official Julia 1.1 binary also fails to build RCall:

(v1.1) pkg> build RCall
  Building Conda → `~/.julia/packages/Conda/kLXeC/deps/build.log`
  Building RCall → `~/.julia/packages/RCall/iojZI/deps/build.log`
┌ Error: Error building `RCall`: 
│ ERROR: LoadError: R cannot be found. Set the "R_HOME" environment variable to re-run Pkg.build("RCall").
│ Stacktrace:
│  [1] error(::String) at ./error.jl:33
│  [2] top-level scope at /home/chriselrod/.julia/packages/RCall/iojZI/deps/build.jl:49
│  [3] include at ./boot.jl:326 [inlined]
│  [4] include_relative(::Module, ::String) at ./loading.jl:1038
│  [5] include(::Module, ::String) at ./sysimg.jl:29
│  [6] include(::String) at ./client.jl:403
│  [7] top-level scope at none:0
│ in expression starting at /home/chriselrod/.julia/packages/RCall/iojZI/deps/build.jl:10
└ @ Pkg.Operations /buildworker/worker/package_linux64/build/usr/share/julia/stdlib/v1.1/Pkg/src/Operations.jl:1075

julia> versioninfo()
Julia Version 1.1.0
Commit 80516ca202 (2019-01-21 21:24 UTC)
Platform Info:
  OS: Linux (x86_64-pc-linux-gnu)
  CPU: Intel(R) Core(TM) i9-7900X CPU @ 3.30GHz
  WORD_SIZE: 64
  LIBM: libopenlibm
  LLVM: libLLVM-6.0.1 (ORCJIT, skylake)

julia> ENV["R_HOME"]
"/usr/lib64/R"

The R version is:

> Rscript -e "R.version"
               _                           
platform       x86_64-generic-linux-gnu    
arch           x86_64                      
os             linux-gnu                   
system         x86_64, linux-gnu           
status                                     
major          3                           
minor          6.1                         
year           2019                        
month          07                          
day            05                          
svn rev        76782                       
language       R                           
version.string R version 3.6.1 (2019-07-05)
nickname       Action of the Toes         

[bbolker]

I'm having similar problems to this, with Julia 1.1.1/r-devel: see here

[bbolker]

ugh. managed to build RCall:

$ export LD_LIBRARY_PATH="$(R RHOME)/lib"
$ export R_HOME="/usr/local/lib/R"
$ julia -e "using Pkg; Pkg.build(\"RCall\")"

seems to work.

But then when I run julia and type using RCall, julia exits immediately. e.g. interactively, typing julia (in the same shell, so environment variables should still be set) produces the usual banner, then using RCall returns me to the shell prompt. Trying to capture any output via

julia -e "using RCall" 1>julia_out.tmp 2>&1

fails (i.e. produces an empty julia_out.tmp file)

Produces

I don't mean to hijack this issue, I'm happy to open a new one if this seems to be getting off-track.

[bbolker]

bump ... any suggestions for further experimentation/diagnosis?

[simonbyrne]

What is

• your OS?
• your version of Julia (and how did you install it)?
• your version of R (and how did you install it)?
• in your deps/deps.jl file in the RCall directory?

[bbolker]

• Ubuntu 16.04 (running in a VirtualBox)
• Julia 1.1.1; I believe I installed the generic binary, but I'm not sure
• R-devel (R Under development (unstable) (2019-08-07 r76933)), installed via ./configure; make; make install
• I don't seem to have a deps.jl file in my RCall directory: ~/.julia/packages/RCall/g7dhB/deps contains only build.jl , build.log, and setup.jl

[simonbyrne]

you may need to build R with the --enable-R-shlib option?

Unless you need cutting-edge R, I would suggest just installing from CRAN: see here for details
http://juliainterop.github.io/RCall.jl/stable/installation.html#Ubuntu-1

[bbolker]

I'll try --enable-R-shlib, thanks. I really do generally need cutting-edge R: I do a lot of R development and like to keep on top of all the latest tests that CRAN has added ...

[simonbyrne]

Fair enough.

If you do get this working, it would probably be good to add this to the .travis.yml.

[robsmith11]

I ran into this problem as well when using R installed with Ubuntu. The actuall error was hidden until I tried loading the shared library directly:

julia> using Libdl
julia> Libdl.dlopen("/usr/lib/R/lib/libR.so")
ERROR: could not load library "/usr/lib/R/lib/libR.so"
/lib/aarch64-linux-gnu/libblas.so.3: undefined symbol: gotoblas

I got it working by using Ubuntu's update-alternative and switching blas from openblas to the reference implementation. Obviously not ideal, but at least it works.

EDIT:
Oops.. spoke to soon. RCall builds now but crashes Julia with a nasty error when I try to use it:

julia> using RCall
[ Info: Precompiling RCall [6f49c342-dc21-5d91-9882-a32aef131414]
LLVM ERROR: Cannot select: 0x9a46c0: ch = init_trampoline 0x5f89e0, 0x1498f38, 0x9ab6a0, 0x87d938, SrcValue:ch<0x2484230>, SrcValue:ch<0x259efa8>
  0x1498f38: i64,ch = CopyFromReg 0x5f89e0, Register:i64 %0
    0x1498fa0: i64 = Register %0
  0x9ab6a0: i64 = AArch64ISD::WrapperLarge TargetGlobalAddress:i64<i64 (%jl_value_t addrspace(10)**, i64)* @"jlcapi_#28_16935"> 0 [TF=3], TargetGlobalAddress:i64<i64 (%jl_value_t addrspace(10)**, i64)* @"jlcapi_#28_16935"> 0 [TF=36], TargetGlobalAddress:i64<i64 (%jl_value_t addrspace(10)**, i64)* @"jlcapi_#28_16935"> 0 [TF=37], TargetGlobalAddress:i64<i64 (%jl_value_t addrspace(10)**, i64)* @"jlcapi_#28_16935"> 0 [TF=38]
    0x9ab638: i64 = TargetGlobalAddress<i64 (%jl_value_t addrspace(10)**, i64)* @"jlcapi_#28_16935"> 0 [TF=3]
    0xb17cf0: i64 = TargetGlobalAddress<i64 (%jl_value_t addrspace(10)**, i64)* @"jlcapi_#28_16935"> 0 [TF=36]
    0x87cf78: i64 = TargetGlobalAddress<i64 (%jl_value_t addrspace(10)**, i64)* @"jlcapi_#28_16935"> 0 [TF=37]
    0x1498cc8: i64 = TargetGlobalAddress<i64 (%jl_value_t addrspace(10)**, i64)* @"jlcapi_#28_16935"> 0 [TF=38]
  0x87d938: i64,ch = CopyFromReg 0x5f89e0, Register:i64 %1
    0x149efb8: i64 = Register %1
In function: jlcapi_#28_16935_gfthunkmake

[chriselrod]

Great lead. On Clear Linux, I seem to have had a similar, but slightly different, problem:

julia> using Libdl

julia> Libdl.dlopen("/usr/lib64/R/lib/libR.so")
ERROR: could not load library "/usr/lib64/R/lib/libR.so"
libRblas.so: cannot open shared object file: No such file or directory
Stacktrace:
 [1] dlopen(::String, ::UInt32; throw_error::Bool) at /home/chriselrod/Documents/languages/julia/usr/share/julia/stdlib/v1.4/Libdl/src/Libdl.jl:109
 [2] dlopen [inlined]
 [3] dlopen(::String) at /home/chriselrod/Documents/languages/julia/usr/share/julia/stdlib/v1.4/Libdl/src/Libdl.jl:109
 [4] top-level scope at REPL[2]:1

shell> ls /usr/lib64/R/lib
haswell/  libRblas.so*  libRlapack.so*  libR.so*

It couldn't find libRblas.so, so I added /usr/lib64/R/lib to the LD_LIBRARY_PATH.
Now, after rebuilding RCall:

julia> using RCall

signal (11): Segmentation fault
in expression starting at REPL[1]:1
Rf_install at /usr/lib64/R/lib/haswell/avx512_1/libR.so (unknown line)
unknown function (ip: 0x7ff3fb6485b5)
unknown function (ip: 0x7ff3fb648ccb)
unknown function (ip: 0x7ff3e1793e8e)
Rf_eval at /usr/lib64/R/lib/libR.so (unknown line)
unknown function (ip: 0x7ff3e17b2971)
Rf_applyClosure at /usr/lib64/R/lib/libR.so (unknown line)
unknown function (ip: 0x7ff3e1797cb7)
Rf_eval at /usr/lib64/R/lib/libR.so (unknown line)
unknown function (ip: 0x7ff3e17b2971)
Rf_applyClosure at /usr/lib64/R/lib/libR.so (unknown line)
unknown function (ip: 0x7ff3e1797cb7)
Rf_eval at /usr/lib64/R/lib/libR.so (unknown line)
unknown function (ip: 0x7ff3e17add86)
unknown function (ip: 0x7ff3e17a5bce)
unknown function (ip: 0x7ff3e17931b2)
Rf_eval at /usr/lib64/R/lib/libR.so (unknown line)
unknown function (ip: 0x7ff3e17add86)
unknown function (ip: 0x7ff3e17a5bce)
unknown function (ip: 0x7ff3e17931b2)
Rf_eval at /usr/lib64/R/lib/libR.so (unknown line)
unknown function (ip: 0x7ff3e17add86)
unknown function (ip: 0x7ff3e17a5bce)
unknown function (ip: 0x7ff3e17931b2)
Rf_eval at /usr/lib64/R/lib/libR.so (unknown line)
unknown function (ip: 0x7ff3e17add86)
unknown function (ip: 0x7ff3e17a5bce)
unknown function (ip: 0x7ff3e17931b2)
Rf_eval at /usr/lib64/R/lib/libR.so (unknown line)
unknown function (ip: 0x7ff3e17b2971)
Rf_applyClosure at /usr/lib64/R/lib/libR.so (unknown line)
unknown function (ip: 0x7ff3e1797cb7)
Rf_eval at /usr/lib64/R/lib/libR.so (unknown line)
unknown function (ip: 0x7ff3e17b2971)
Rf_applyClosure at /usr/lib64/R/lib/libR.so (unknown line)
unknown function (ip: 0x7ff3e1797cb7)
Rf_eval at /usr/lib64/R/lib/libR.so (unknown line)
unknown function (ip: 0x7ff3e17b2971)
Rf_applyClosure at /usr/lib64/R/lib/libR.so (unknown line)
unknown function (ip: 0x7ff3e1797cb7)
Rf_eval at /usr/lib64/R/lib/libR.so (unknown line)
unknown function (ip: 0x7ff3e17b2971)
Rf_applyClosure at /usr/lib64/R/lib/libR.so (unknown line)
unknown function (ip: 0x7ff3e1797cb7)
Rf_eval at /usr/lib64/R/lib/libR.so (unknown line)
unknown function (ip: 0x7ff3e17b2971)
Rf_applyClosure at /usr/lib64/R/lib/libR.so (unknown line)
unknown function (ip: 0x7ff3e1797cb7)
Rf_eval at /usr/lib64/R/lib/libR.so (unknown line)
unknown function (ip: 0x7ff3e17b2971)
Rf_applyClosure at /usr/lib64/R/lib/libR.so (unknown line)
unknown function (ip: 0x7ff3e1797cb7)
Rf_eval at /usr/lib64/R/lib/libR.so (unknown line)
unknown function (ip: 0x7ff3e17add86)
unknown function (ip: 0x7ff3e17a5bce)
unknown function (ip: 0x7ff3e17931b2)
Rf_eval at /usr/lib64/R/lib/libR.so (unknown line)
unknown function (ip: 0x7ff3e17add86)
unknown function (ip: 0x7ff3e17a5bce)
unknown function (ip: 0x7ff3e17931b2)
Rf_eval at /usr/lib64/R/lib/libR.so (unknown line)
unknown function (ip: 0x7ff3e17add86)
unknown function (ip: 0x7ff3e17a5bce)
unknown function (ip: 0x7ff3e17931b2)
Rf_eval at /usr/lib64/R/lib/libR.so (unknown line)
unknown function (ip: 0x7ff3e17add86)
unknown function (ip: 0x7ff3e17a5bce)
unknown function (ip: 0x7ff3e17931b2)
Rf_eval at /usr/lib64/R/lib/libR.so (unknown line)
unknown function (ip: 0x7ff3e17b2971)
Rf_applyClosure at /usr/lib64/R/lib/libR.so (unknown line)
unknown function (ip: 0x7ff3e1797cb7)
Rf_eval at /usr/lib64/R/lib/libR.so (unknown line)
unknown function (ip: 0x7ff3e17b2971)
Rf_applyClosure at /usr/lib64/R/lib/libR.so (unknown line)
unknown function (ip: 0x7ff3e1797cb7)
Rf_eval at /usr/lib64/R/lib/libR.so (unknown line)
unknown function (ip: 0x7ff3e17b2971)
Rf_applyClosure at /usr/lib64/R/lib/libR.so (unknown line)
unknown function (ip: 0x7ff3e1797cb7)
Rf_eval at /usr/lib64/R/lib/libR.so (unknown line)
unknown function (ip: 0x7ff3e17b2971)
Rf_applyClosure at /usr/lib64/R/lib/libR.so (unknown line)
unknown function (ip: 0x7ff3e1797cb7)
Rf_eval at /usr/lib64/R/lib/libR.so (unknown line)
unknown function (ip: 0x7ff3e17b2971)
Rf_applyClosure at /usr/lib64/R/lib/libR.so (unknown line)
unknown function (ip: 0x7ff3e1797cb7)
Rf_eval at /usr/lib64/R/lib/libR.so (unknown line)
unknown function (ip: 0x7ff3e17add86)
unknown function (ip: 0x7ff3e17a5bce)
unknown function (ip: 0x7ff3e17931b2)
Rf_eval at /usr/lib64/R/lib/libR.so (unknown line)
unknown function (ip: 0x7ff3e17add86)
unknown function (ip: 0x7ff3e17a5bce)
unknown function (ip: 0x7ff3e17931b2)
Rf_eval at /usr/lib64/R/lib/libR.so (unknown line)
unknown function (ip: 0x7ff3e17add86)
unknown function (ip: 0x7ff3e17a5bce)
unknown function (ip: 0x7ff3e17931b2)
Rf_eval at /usr/lib64/R/lib/libR.so (unknown line)
unknown function (ip: 0x7ff3e17add86)
unknown function (ip: 0x7ff3e17a5bce)
unknown function (ip: 0x7ff3e17931b2)
Rf_eval at /usr/lib64/R/lib/libR.so (unknown line)
unknown function (ip: 0x7ff3e17b2971)
Rf_applyClosure at /usr/lib64/R/lib/libR.so (unknown line)
unknown function (ip: 0x7ff3e1797cb7)
Rf_eval at /usr/lib64/R/lib/libR.so (unknown line)
unknown function (ip: 0x7ff3e17b2971)
Rf_applyClosure at /usr/lib64/R/lib/libR.so (unknown line)
unknown function (ip: 0x7ff3e1797cb7)
Rf_eval at /usr/lib64/R/lib/libR.so (unknown line)
unknown function (ip: 0x7ff3e17b2971)
Rf_applyClosure at /usr/lib64/R/lib/libR.so (unknown line)
unknown function (ip: 0x7ff3e1797cb7)
Rf_eval at /usr/lib64/R/lib/libR.so (unknown line)
unknown function (ip: 0x7ff3e17b2971)
Rf_applyClosure at /usr/lib64/R/lib/libR.so (unknown line)
unknown function (ip: 0x7ff3e1797cb7)
Rf_eval at /usr/lib64/R/lib/libR.so (unknown line)
unknown function (ip: 0x7ff3e17b2971)
Rf_applyClosure at /usr/lib64/R/lib/libR.so (unknown line)
Rf_eval at /usr/lib64/R/lib/libR.so (unknown line)
unknown function (ip: 0x7ff3e17a9b8e)
Rf_eval at /usr/lib64/R/lib/libR.so (unknown line)
unknown function (ip: 0x7ff3e17b64f6)
Rf_eval at /usr/lib64/R/lib/libR.so (unknown line)
Rf_eval at /usr/lib64/R/lib/libR.so (unknown line)
unknown function (ip: 0x7ff3e17a52fc)
Rf_eval at /usr/lib64/R/lib/libR.so (unknown line)
unknown function (ip: 0x7ff3e17b2971)
Rf_applyClosure at /usr/lib64/R/lib/libR.so (unknown line)
Rf_eval at /usr/lib64/R/lib/libR.so (unknown line)
setup_Rmainloop at /usr/lib64/R/lib/libR.so (unknown line)
initEmbeddedR at (null):0
__init__ at (null):0
unknown function (ip: 0x7ff3ecbfae90)
jl_apply at /home/chriselrod/Documents/languages/julia/src/julia.h:1640 [inlined]
jl_module_run_initializer at /home/chriselrod/Documents/languages/julia/src/toplevel.c:74
jl_init_restored_modules at /home/chriselrod/Documents/languages/julia/src/dump.c:2483
_include_from_serialized at (null):0
_require_search_from_serialized at (null):0
_require at (null):0
require at (null):0
require at (null):0
jl_apply at /home/chriselrod/Documents/languages/julia/src/julia.h:1640 [inlined]
call_require at /home/chriselrod/Documents/languages/julia/src/toplevel.c:399 [inlined]
eval_import_path at /home/chriselrod/Documents/languages/julia/src/toplevel.c:436
jl_toplevel_eval_flex at /home/chriselrod/Documents/languages/julia/src/toplevel.c:656
jl_toplevel_eval_flex at /home/chriselrod/Documents/languages/julia/src/toplevel.c:764
jl_toplevel_eval at /home/chriselrod/Documents/languages/julia/src/toplevel.c:823 [inlined]
jl_toplevel_eval_in at /home/chriselrod/Documents/languages/julia/src/toplevel.c:843
eval at ./boot.jl:330
eval_user_input at /home/chriselrod/Documents/languages/julia/usr/share/julia/stdlib/v1.4/REPL/src/REPL.jl:86
run_backend at (null):0
#79 at (null):0
jl_apply at /home/chriselrod/Documents/languages/julia/src/julia.h:1640 [inlined]
start_task at /home/chriselrod/Documents/languages/julia/src/task.c:687
unknown function (ip: 0xffffffffffffffff)
Allocations: 32522069 (Pool: 32518540; Big: 3529); GC: 45
fish: “/home/chriselrod/Documents/lang…” terminated by signal SIGSEGV (Address boundary error)

A different linking error, and then upon solving it, a different crash.

Thankfully RCall seems to work on the Redhat cluster at work, but it doesn't work on any of my personal computers. Eventually I'm supposed to make some of my Julia code callable from R, and RCall is a dependency of JuliaCall.
There is also XRJulia. It has extremely high overhead on the Julia-R interface, but it works.

[IanButterworth]

@chriselrod did you get to the bottom of this? I see it in #433

[chriselrod]

@chriselrod did you get to the bottom of this? I see it in #433

No. As of my last update here, it worked at work but not at home.
My update since then is that at that (former) place of work, they started building R to use MKL so it started crashing there, too.

EDIT:
I just tried again locally to confirm that using RCall still segfaults.