Workaround for Non-Contradiction#99 (could not load library on multia…

…rch installs)

Julia's embedding fails in jl_init if Julia is built and installed with
MULTIARCH_INSTALL=1, which it is in Debian and Ubuntu. It fails with:

    > julia_setup()
    Julia version 1.5.2 at location /usr/bin will be used.
    ERROR: could not load library "/usr/lib/x86_64-linux-gnu/../bin/../lib/x86_64-linux-gnu/julia/sys.so"
    /usr/lib/x86_64-linux-gnu/../bin/../lib/x86_64-linux-gnu/julia/sys.so: cannot open shared object file: No such file or directory

The problem is described at JuliaLang/julia#32614 (comment).

As a workaround, let's allow overriding the bindir by setting
JULIA_BINDIR environment variable (`/usr/bin` to fix this on Debian).

Fixes: Non-Contradiction#99

NEWS.md

@@ -1,6 +1,8 @@
 # 0.17.1.9000
 
 * Fix bug for Julia plot in RMarkdown document caused by change of knitr #1717.
+* Workaround for #99: `ERROR: could not load library` on Debian/Ubuntu and
+  other systems which build Julia with `MULTIARCH_INSTALL=1` (#143 by @liskin).
 
 # JuliaCall 0.17.1
 

README.Rmd

@@ -122,6 +122,13 @@ The issue is usually caused by updates in R, and it can be typically solved by s
 JuliaCall::julia_setup(rebuild = TRUE)
 ```
 
+### `ERROR: could not load library "/usr/lib/x86_64-linux-gnu/../bin/../lib/x86_64-linux-gnu/julia/sys.so"`
+
+This error happens when Julia is built/installed with `MULTIARCH_INSTALL=1`, as
+it is on e.g. Debian. It is caused by [the bindir-locating code in jl\_init not
+being multiarch-aware](https://github.com/JuliaLang/julia/issues/32614#issuecomment-656787386).
+To work around it, try setting `JULIA_BINDIR=/usr/bin` in your environment.
+
 ### How to Get Help
 
 - One way to get help for Julia functions is just using `julia$help` as the following example:

README.md

@@ -145,6 +145,15 @@ follows.
 JuliaCall::julia_setup(rebuild = TRUE)
 ```
 
+### `ERROR: could not load library "/usr/lib/x86_64-linux-gnu/../bin/../lib/x86_64-linux-gnu/julia/sys.so"`
+
+This error happens when Julia is built/installed with
+`MULTIARCH_INSTALL=1`, as it is on e.g. Debian. It is caused by [the
+bindir-locating code in jl\_init not being
+multiarch-aware](https://github.com/JuliaLang/julia/issues/32614#issuecomment-656787386).
+To work around it, try setting `JULIA_BINDIR=/usr/bin` in your
+environment.
+
 ### How to Get Help
 
   - One way to get help for Julia functions is just using `julia$help`

src/JuliaCall.cpp

@@ -1,3 +1,4 @@
+#include <stdlib.h>
 #include <Rcpp.h>
 #include "libjulia.h"
 
@@ -17,7 +18,11 @@ bool juliacall_initialize(const std::string& libpath) {
         stop(get_last_loaded_symbol() + " - " + get_last_dl_error_message());
     }
 
-    jl_init();
+    const char *julia_bindir = getenv("JULIA_BINDIR");
+    if (julia_bindir)
+        jl_init_with_image(julia_bindir, NULL);
+    else
+        jl_init();
 
     if (!load_libjulia_modules()) {
         stop(get_last_dl_error_message());

src/libjulia.cpp

@@ -119,6 +119,8 @@ bool load_libjulia_symbols() {
     // load jl_init
     if (!(load_symbol(libjulia_t, "jl_init", (void**) &jl_init) || load_symbol(libjulia_t, "jl_init__threading", (void**) &jl_init)))
         return false;
+    if (!(load_symbol(libjulia_t, "jl_init_with_image", (void**) &jl_init_with_image) || load_symbol(libjulia_t, "jl_init_with_image__threading", (void**) &jl_init_with_image)))
+        return false;
     LOAD_JULIA_SYMBOL(jl_atexit_hook);
     LOAD_JULIA_SYMBOL(jl_eval_string);
 

src/libjulia.h

@@ -87,6 +87,8 @@ STATIC_INLINE jl_function_t *jl_get_function(jl_module_t *m, const char *name)
 // initialization functions
 JL_EXTERN int (*jl_is_initialized)(void);
 JL_EXTERN void (*jl_init)(void);
+JL_EXTERN void (*jl_init_with_image)(const char *julia_bindir,
+                                     const char *image_relative_path);
 JL_EXTERN void (*jl_atexit_hook)(int status);
 
 // front end interface