# Possible to define a module where one dependency is built after running other stuff first?

**URL:** <https://discourse.julialang.org/t/possible-to-define-a-module-where-one-dependency-is-built-after-running-other-stuff-first/49384>\
**Category:** New to Julia\
**Tags:** question, package, pkg\
**Created:** [October 31, 2020, 8:12pm UTC](https://discourse.julialang.org/t/possible-to-define-a-module-where-one-dependency-is-built-after-running-other-stuff-first/49384 "2020-10-31T20:12:42Z")\
**Posts on this page:** 7\
**Page:** 1

<div class="post-metadata">

**Author:** ![mkarikom](https://sea2.discourse-cdn.com/julialang/user_avatar/discourse.julialang.org/mkarikom/32/7096_2.png) [@mkarikom](https://discourse.julialang.org/u/mkarikom)\
**Post date:** [October 31, 2020, 8:12pm UTC](https://discourse.julialang.org/t/possible-to-define-a-module-where-one-dependency-is-built-after-running-other-stuff-first/49384/1 "2020-10-31T20:12:43Z")

</div>

I need this module to create a Conda environment whose full path is required by Pkg.build() for another dependency.

```julia
tmpdir = "/home/me/Desktop/tmp"
mkdir(tmpdir)
cd(tmpdir)
using Pkg
Pkg.activate("./")
Pkg.add(["RCall","Conda","Dates"])

module BuildDepsSeparately

using Pkg
using Conda,Dates
using RCall

# install r to a temp path and return the path
function initR()
    # make a new temporary conda environment for r
    ts = Dates.time()
    tdir = joinpath(tmpdir,"r$ts")
    mkpath(tdir)
    run(`conda create -p $tdir -y`)

    # install r in the temp environment
    Conda.add_channel("r",tdir)
    Conda.add("r-base>=3.4.0,<4",tdir) # greater than or equal to 3.4.0 AND strictly less than 4.0

    ENV["R_HOME"] = joinpath(tdir,"lib","R")
    Pkg.build("RCall")
    return(tdir)
end
end

```

Running this code causes the REPL to crash with the following errors:

> **full error output**
>
> ```julia
> [Info: Precompiling RCall [6f49c342-dc21-5d91-9882-a32aef131414]
> FATAL ERROR: Symbol "ccalllib_libR.so4725"not found
> signal (6): Aborted
> in expression starting at /home/me/Desktop/scratch3.jl:12
> gsignal at /lib/x86_64-linux-gnu/libc.so.6 (unknown line)
> abort at /lib/x86_64-linux-gnu/libc.so.6 (unknown line)
> addModule at /buildworker/worker/package_linux64/build/src/jitlayers.cpp:640
> jl_add_to_ee at /buildworker/worker/package_linux64/build/src/jitlayers.cpp:893 [inlined]
> jl_add_to_ee at /buildworker/worker/package_linux64/build/src/jitlayers.cpp:955
> jl_add_to_ee at /buildworker/worker/package_linux64/build/src/jitlayers.cpp:977 [inlined]
> _jl_compile_codeinst at /buildworker/worker/package_linux64/build/src/jitlayers.cpp:126
> jl_generate_fptr at /buildworker/worker/package_linux64/build/src/jitlayers.cpp:302
> jl_compile_method_internal at /buildworker/worker/package_linux64/build/src/gf.c:1964
> gen_cfun_wrapper at /buildworker/worker/package_linux64/build/src/codegen.cpp:4068
> emit_cfunction at /buildworker/worker/package_linux64/build/src/codegen.cpp:4654 [inlined]
> emit_expr at /buildworker/worker/package_linux64/build/src/codegen.cpp:3694
> emit_ssaval_assign at /buildworker/worker/package_linux64/build/src/codegen.cpp:3339
> emit_stmtpos at /buildworker/worker/package_linux64/build/src/codegen.cpp:3576 [inlined]
> emit_function at /buildworker/worker/package_linux64/build/src/codegen.cpp:6110
> jl_emit_code at /buildworker/worker/package_linux64/build/src/codegen.cpp:6463
> jl_emit_codeinst at /buildworker/worker/package_linux64/build/src/codegen.cpp:6497
> _jl_compile_codeinst at /buildworker/worker/package_linux64/build/src/jitlayers.cpp:97
> jl_generate_fptr at /buildworker/worker/package_linux64/build/src/jitlayers.cpp:302
> jl_compile_method_internal at /buildworker/worker/package_linux64/build/src/gf.c:1964
> jl_compile_method_internal at /buildworker/worker/package_linux64/build/src/gf.c:1919 [inlined]
> _jl_invoke at /buildworker/worker/package_linux64/build/src/gf.c:2224 [inlined]
> jl_apply_generic at /buildworker/worker/package_linux64/build/src/gf.c:2398
> jl_apply at /buildworker/worker/package_linux64/build/src/julia.h:1690 [inlined]
> jl_module_run_initializer at /buildworker/worker/package_linux64/build/src/toplevel.c:74
> jl_init_restored_modules at /buildworker/worker/package_linux64/build/src/dump.c:2544
> _include_from_serialized at ./loading.jl:697
> _require_from_serialized at ./loading.jl:749
> _require at ./loading.jl:1040
> require at ./loading.jl:928
> require at ./loading.jl:923
> _jl_invoke at /buildworker/worker/package_linux64/build/src/gf.c:2214 [inlined]
> jl_apply_generic at /buildworker/worker/package_linux64/build/src/gf.c:2398
> jl_apply at /buildworker/worker/package_linux64/build/src/julia.h:1690 [inlined]
> call_require at /buildworker/worker/package_linux64/build/src/toplevel.c:425 [inlined]
> eval_import_path at /buildworker/worker/package_linux64/build/src/toplevel.c:462
> jl_toplevel_eval_flex at /buildworker/worker/package_linux64/build/src/toplevel.c:682
> jl_eval_module_expr at /buildworker/worker/package_linux64/build/src/toplevel.c:197
> jl_toplevel_eval_flex at /buildworker/worker/package_linux64/build/src/toplevel.c:666
> jl_parse_eval_all at /buildworker/worker/package_linux64/build/src/ast.c:913
> include_string at ./loading.jl:1091
> include_string at /home/me/.julia/packages/Atom/9OFfu/src/utils.jl:280
> unknown function (ip: 0x7f3ca67f5b26)
> _jl_invoke at /buildworker/worker/package_linux64/build/src/gf.c:2214 [inlined]
> jl_apply_generic at /buildworker/worker/package_linux64/build/src/gf.c:2398
> #190 at /home/me/.julia/packages/Atom/9OFfu/src/eval.jl:76
> withpath at /home/me/.julia/packages/CodeTools/VsjEq/src/utils.jl:30
> unknown function (ip: 0x7f3ca67f59f5)
> _jl_invoke at /buildworker/worker/package_linux64/build/src/gf.c:2214 [inlined]
> jl_apply_generic at /buildworker/worker/package_linux64/build/src/gf.c:2398
> withpath at /home/me/.julia/packages/Atom/9OFfu/src/eval.jl:9
> #189 at /home/me/.julia/packages/Atom/9OFfu/src/eval.jl:74
> unknown function (ip: 0x7f3ca67f51ac)
> _jl_invoke at /buildworker/worker/package_linux64/build/src/gf.c:2214 [inlined]
> jl_apply_generic at /buildworker/worker/package_linux64/build/src/gf.c:2398
> with_logstate at ./logging.jl:408
> with_logger at ./logging.jl:514 [inlined]
> #188 at /home/me/.julia/packages/Atom/9OFfu/src/eval.jl:73 [inlined]
> hideprompt at /home/me/.julia/packages/Atom/9OFfu/src/repl.jl:127
> macro expansion at /home/me/.julia/packages/Atom/9OFfu/src/eval.jl:72 [inlined]
> macro expansion at /home/me/.julia/packages/Media/ItEPc/src/dynamic.jl:24 [inlined]
> evalshow at /home/me/.julia/packages/Atom/9OFfu/src/eval.jl:69
> unknown function (ip: 0x7f3ca67e55e2)
> _jl_invoke at /buildworker/worker/package_linux64/build/src/gf.c:2214 [inlined]
> jl_apply_generic at /buildworker/worker/package_linux64/build/src/gf.c:2398
> jl_apply at /buildworker/worker/package_linux64/build/src/julia.h:1690 [inlined]
> do_apply at /buildworker/worker/package_linux64/build/src/builtins.c:655
> jl_f__apply_latest at /buildworker/worker/package_linux64/build/src/builtins.c:705
> #invokelatest#1 at ./essentials.jl:710
> _jl_invoke at /buildworker/worker/package_linux64/build/src/gf.c:2214 [inlined]
> jl_apply_generic at /buildworker/worker/package_linux64/build/src/gf.c:2398
> jl_apply at /buildworker/worker/package_linux64/build/src/julia.h:1690 [inlined]
> do_apply at /buildworker/worker/package_linux64/build/src/builtins.c:655
> invokelatest at ./essentials.jl:709
> _jl_invoke at /buildworker/worker/package_linux64/build/src/gf.c:2214 [inlined]
> jl_apply_generic at /buildworker/worker/package_linux64/build/src/gf.c:2398
> jl_apply at /buildworker/worker/package_linux64/build/src/julia.h:1690 [inlined]
> do_apply at /buildworker/worker/package_linux64/build/src/builtins.c:655
> macro expansion at /home/me/.julia/packages/Atom/9OFfu/src/eval.jl:41 [inlined]
> #184 at ./task.jl:356
> unknown function (ip: 0x7f3ca670458c)
> _jl_invoke at /buildworker/worker/package_linux64/build/src/gf.c:2231 [inlined]
> jl_apply_generic at /buildworker/worker/package_linux64/build/src/gf.c:2398
> jl_apply at /buildworker/worker/package_linux64/build/src/julia.h:1690 [inlined]
> start_task at /buildworker/worker/package_linux64/build/src/task.c:707
> unknown function (ip: (nil))
> Allocations: 50354887 (Pool: 50338039; Big: 16848); GC: 53
> 
> Julia has exited.
> 
> ```

This appears to be a result of some issue with the module declaration because the following test passes:

```julia
tmpdir = "/home/me/Desktop/tmp"
mkpath(tmpdir)
cd(tmpdir)
using Pkg
Pkg.activate("./")
Pkg.add(["RCall","Conda","Dates"])
using Conda,Dates

ts = Dates.time()
tdir = joinpath(tmpdir,"r$ts")
mkpath(tdir)
run(`conda create -p $tdir -y`)

# install r in the temp environment
Conda.add_channel("r",tdir)
Conda.add("r-base>=3.4.0,<4",tdir) # greater than or equal to 3.4.0 AND strictly less than 4.0

ENV["R_HOME"] = joinpath(tdir,"lib","R")
Pkg.build("RCall")

using RCall

R"wd = getwd()"
dat = rcopy(R"wd")
run(`conda env remove -p $tdir`)

using Test
@test dat == tmpdir

Test Passed

```

–edit updated for clarity  
–edit fix example bug (not related to error)  
–edit new examples and update crash output

---

<div class="post-metadata">

**Author:** ![Henrique\_Becker](https://sea2.discourse-cdn.com/julialang/user_avatar/discourse.julialang.org/henrique_becker/32/15443_2.png) [@Henrique\_Becker](https://discourse.julialang.org/u/Henrique_Becker)\
**Post date:** [October 31, 2020, 8:15pm UTC](https://discourse.julialang.org/t/possible-to-define-a-module-where-one-dependency-is-built-after-running-other-stuff-first/49384/2 "2020-10-31T20:15:20Z")

</div>

What exactly you want to know if it is possible? I understand you already have a package that does that, so what exactly is the doubt?

---

<div class="post-metadata">

**Author:** ![mkarikom](https://sea2.discourse-cdn.com/julialang/user_avatar/discourse.julialang.org/mkarikom/32/7096_2.png) [@mkarikom](https://discourse.julialang.org/u/mkarikom)\
**Post date:** [October 31, 2020, 8:25pm UTC](https://discourse.julialang.org/t/possible-to-define-a-module-where-one-dependency-is-built-after-running-other-stuff-first/49384/3 "2020-10-31T20:25:29Z")

</div>

@Henrique_Becker sorry the post was unclear, I have updated to explain what I need

---

<div class="post-metadata">

**Author:** ![Henrique\_Becker](https://sea2.discourse-cdn.com/julialang/user_avatar/discourse.julialang.org/henrique_becker/32/15443_2.png) [@Henrique\_Becker](https://discourse.julialang.org/u/Henrique_Becker)\
**Post date:** [October 31, 2020, 8:31pm UTC](https://discourse.julialang.org/t/possible-to-define-a-module-where-one-dependency-is-built-after-running-other-stuff-first/49384/4 "2020-10-31T20:31:08Z")

</div>

The error seems related to building `RCall`, no? Did you try write some code that just try to build `RCall` with a `ENV["R_HOME"]` you created manually and are sure it is alright? This `ccalllib_libR.so4630` is somewhere in the folder Conda created?

---

<div class="post-metadata">

**Author:** ![mkarikom](https://sea2.discourse-cdn.com/julialang/user_avatar/discourse.julialang.org/mkarikom/32/7096_2.png) [@mkarikom](https://discourse.julialang.org/u/mkarikom)\
**Post date:** [October 31, 2020, 8:33pm UTC](https://discourse.julialang.org/t/possible-to-define-a-module-where-one-dependency-is-built-after-running-other-stuff-first/49384/5 "2020-10-31T20:33:53Z")

</div>

Yes it works if I force RCall to [create its own Conda environment by defining](https://juliainterop.github.io/RCall.jl/stable/installation/):

```julia
ENV[R_HOME] = "*"
Pkg.build("RCall")

```

---

<div class="post-metadata">

**Author:** ![Henrique\_Becker](https://sea2.discourse-cdn.com/julialang/user_avatar/discourse.julialang.org/henrique_becker/32/15443_2.png) [@Henrique\_Becker](https://discourse.julialang.org/u/Henrique_Becker)\
**Post date:** [October 31, 2020, 8:45pm UTC](https://discourse.julialang.org/t/possible-to-define-a-module-where-one-dependency-is-built-after-running-other-stuff-first/49384/6 "2020-10-31T20:45:14Z")

</div>

Can you run `diff -R <your_folder> <auto_rcall_folder>` to check the differences between the environment you created by hand and the one `RCall` creates automatically? Also, maybe you can check how `Rcall` does so (by checking its source).

---

<div class="post-metadata">

**Author:** ![mkarikom](https://sea2.discourse-cdn.com/julialang/user_avatar/discourse.julialang.org/mkarikom/32/7096_2.png) [@mkarikom](https://discourse.julialang.org/u/mkarikom)\
**Post date:** [October 31, 2020, 9:15pm UTC](https://discourse.julialang.org/t/possible-to-define-a-module-where-one-dependency-is-built-after-running-other-stuff-first/49384/7 "2020-10-31T21:15:00Z")

</div>

Hi @Henrique_Becker, I’ve updated the example, the error, and added an MWE unit test for the code the module attempts to run to clarify what is happening.