dbConnect works in RStudio but fails in R on macOS

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This is now resolved. The main clue from from the "Understanding R's Startup" article linked above, where @slopp mentions that RStudio "doesn’t 'start' R, it uses R as a library, either as a DLL on Windows or as a shared object on Mac and Linux." This is intriguing, because it suggests that there may be different binaries involved for each environment. This seems to matter for run-path dependent libraries.

It turns that that the Oracle ODBC driver does use @rpath, here is the (partial) output from otool -l libsqora.dylib.12.1:

Load command 3
          cmd LC_ID_DYLIB
      cmdsize 56
         name @rpath/libsqora.dylib.12.1 (offset 24)
   time stamp 1 Wed Dec 31 19:00:01 1969
      current version 0.0.0
compatibility version 0.0.0
...
Load command 12
          cmd LC_LOAD_DYLIB
      cmdsize 56
         name @rpath/libclntsh.dylib.12.1 (offset 24)
   time stamp 2 Wed Dec 31 19:00:02 1969
      current version 0.0.0
compatibility version 0.0.0
Load command 13
          cmd LC_LOAD_DYLIB
      cmdsize 56
         name @rpath/libodbcinst.2.dylib (offset 24)
   time stamp 2 Wed Dec 31 19:00:02 1969
      current version 3.0.0
compatibility version 3.0.0
Load command 14
          cmd LC_RPATH
      cmdsize 48
         path @executable_path/../../oracle/lib (offset 12)

My understanding is that the value of @rpath at the time libsqora.dylib.12.1 is loaded will determine whether these libraries can be found. I made the following changes:

install_name_tool -id "/usr/local/opt/instantclient-basic/lib/libsqora.dylib.12.1" libsqora.dylib.12.1
install_name_tool -change "@rpath/libodbcinst.2.dylib" "/usr/local/lib/libodbcinst.2.dylib" libsqora.dylib.12.1
install_name_tool -change "@rpath/libclntsh.dylib.12.1" "/usr/local/lib/libclntsh.dylib.12.1" libsqora.dylib.12.1
install_name_tool -rpath "@executable_path/../../oracle/lib" "/usr/local/lib" libsqora.dylib.12.1

where /usr/local/opt/instantclient-basic/lib is the location of libsqora.dylib.12.1.

So, I turned all the run-paths into absolute paths, and that seems to have fixed it. Everything is now working in (command-line) R, as well as RStudio, including knitting R Markdown.

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