Building the CLI in WSL2 (Ububtu 2204.2.33.0)

[magnuspalmblad]

I get the following error when trying to build the CLI in WSL2:

$ sudo gem install unipept
Building native extensions. This could take a while...
ERROR:  Error installing unipept:
        ERROR: Failed to build gem native extension.

    current directory: /var/lib/gems/3.0.0/gems/ffi-1.15.5/ext/ffi_c
/usr/bin/ruby3.0 -I /usr/lib/ruby/vendor_ruby -r ./siteconf20230831-9902-z89lod.rb extconf.rb
checking for ffi.h... *** extconf.rb failed ***
Could not create Makefile due to some reason, probably lack of necessary
libraries and/or headers.  Check the mkmf.log file for more details.  You may
need configuration options.

Provided configuration options:
        --with-opt-dir
        --without-opt-dir
        --with-opt-include
        --without-opt-include=${opt-dir}/include
        --with-opt-lib
        --without-opt-lib=${opt-dir}/lib
        --with-make-prog
        --without-make-prog
        --srcdir=.
        --curdir
        --ruby=/usr/bin/$(RUBY_BASE_NAME)3.0
        --with-ffi_c-dir
        --without-ffi_c-dir
        --with-ffi_c-include
        --without-ffi_c-include=${ffi_c-dir}/include
        --with-ffi_c-lib
        --without-ffi_c-lib=${ffi_c-dir}/lib
        --enable-system-libffi
        --disable-system-libffi
        --with-libffi-config
        --without-libffi-config
        --with-pkg-config
        --without-pkg-config
        --with-ffi-dir
        --without-ffi-dir
        --with-ffi-include
        --without-ffi-include=${ffi-dir}/include
        --with-ffi-lib
        --without-ffi-lib=${ffi-dir}/lib
/usr/lib/ruby/3.0.0/mkmf.rb:471:in `try_do': The compiler failed to generate an executable file. (RuntimeError)
You have to install development tools first.
        from /usr/lib/ruby/3.0.0/mkmf.rb:613:in `try_cpp'
        from /usr/lib/ruby/3.0.0/mkmf.rb:1124:in `block in have_header'
        from /usr/lib/ruby/3.0.0/mkmf.rb:971:in `block in checking_for'
        from /usr/lib/ruby/3.0.0/mkmf.rb:361:in `block (2 levels) in postpone'
        from /usr/lib/ruby/3.0.0/mkmf.rb:331:in `open'
        from /usr/lib/ruby/3.0.0/mkmf.rb:361:in `block in postpone'
        from /usr/lib/ruby/3.0.0/mkmf.rb:331:in `open'
        from /usr/lib/ruby/3.0.0/mkmf.rb:357:in `postpone'
        from /usr/lib/ruby/3.0.0/mkmf.rb:970:in `checking_for'
        from /usr/lib/ruby/3.0.0/mkmf.rb:1123:in `have_header'
        from extconf.rb:10:in `system_libffi_usable?'
        from extconf.rb:42:in `<main>'

To see why this extension failed to compile, please check the mkmf.log which can be found here:

  /var/lib/gems/3.0.0/extensions/x86_64-linux/3.0.0/ffi-1.15.5/mkmf.log

extconf failed, exit code 1

Gem files will remain installed in /var/lib/gems/3.0.0/gems/ffi-1.15.5 for inspection.
Results logged to /var/lib/gems/3.0.0/extensions/x86_64-linux/3.0.0/ffi-1.15.5/gem_make.out

where the log file contains the following:

$ cat  /var/lib/gems/3.0.0/extensions/x86_64-linux/3.0.0/ffi-1.15.5/mkmf.log
package configuration for libffi is not found
"x86_64-linux-gnu-gcc -o conftest -I/usr/include/x86_64-linux-gnu/ruby-3.0.0 -I/usr/include/ruby-3.0.0/ruby/backward -I/usr/include/ruby-3.0.0 -I. -Wdate-time -D_FORTIFY_SOURCE=2   -g -O2 -ffile-prefix-map=/build/ruby3.0-ohOwi0/ruby3.0-3.0.2=. -fstack-protector-strong -Wformat -Werror=format-security -fPIC conftest.c  -L. -L/usr/lib/x86_64-linux-gnu -L. -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -fstack-protector-strong -rdynamic -Wl,-export-dynamic     -lruby-3.0  -lm   -lc"
checked program was:
/* begin */
1: #include "ruby.h"
2:
3: int main(int argc, char **argv)
4: {
5:   return !!argv[argc];
6: }
/* end */

I have the following versions of ruby and gem installed:

$ ruby -v
ruby 3.0.2p107 (2021-07-07 revision 0db68f0233) [x86_64-linux-gnu]

and

$ gem -v
3.3.5

and I have the latest ruby-dev installed as well (1:3.0~exp1).

Any ideas? Has anyone installed unipept in Ubuntu in WSL2 before?

[pverscha]

@magnuspalmblad Thank you for reporting this issue. This is probably the result of a Ruby dependency that is not installed on WSL by default. Can you try to perform the following 2 commands?

1. Install the required dev dependencies for Ruby apt install clang make ruby-dev libffi-dev
2. Install FFI (which is causing the error): gem install ffi

I don't have a Windows system at my disposal at this time, but I will try this out myself tonight.

[magnuspalmblad]

Step 1 worked without errors. However, step 2 generates a similar error as when trying to install unipept:

$ sudo gem install ffi
Building native extensions. This could take a while...
ERROR:  Error installing ffi:
        ERROR: Failed to build gem native extension.

    current directory: /var/lib/gems/3.0.0/gems/ffi-1.15.5/ext/ffi_c
/usr/bin/ruby3.0 -I /usr/lib/ruby/vendor_ruby -r ./siteconf20230904-10844-j3v4jg.rb extconf.rb
checking for ffi.h... *** extconf.rb failed ***
Could not create Makefile due to some reason, probably lack of necessary
libraries and/or headers.  Check the mkmf.log file for more details.  You may
need configuration options.

Provided configuration options:
        --with-opt-dir
        --without-opt-dir
        --with-opt-include
        --without-opt-include=${opt-dir}/include
        --with-opt-lib
        --without-opt-lib=${opt-dir}/lib
        --with-make-prog
        --without-make-prog
        --srcdir=.
        --curdir
        --ruby=/usr/bin/$(RUBY_BASE_NAME)3.0
        --with-ffi_c-dir
        --without-ffi_c-dir
        --with-ffi_c-include
        --without-ffi_c-include=${ffi_c-dir}/include
        --with-ffi_c-lib
        --without-ffi_c-lib=${ffi_c-dir}/lib
        --enable-system-libffi
        --disable-system-libffi
        --with-libffi-config
        --without-libffi-config
        --with-pkg-config
        --without-pkg-config
        --with-ffi-dir
        --without-ffi-dir
        --with-ffi-include
        --without-ffi-include=${ffi-dir}/include
        --with-ffi-lib
        --without-ffi-lib=${ffi-dir}/lib
/usr/lib/ruby/3.0.0/mkmf.rb:471:in `try_do': The compiler failed to generate an executable file. (RuntimeError)
You have to install development tools first.
        from /usr/lib/ruby/3.0.0/mkmf.rb:613:in `try_cpp'
        from /usr/lib/ruby/3.0.0/mkmf.rb:1124:in `block in have_header'
        from /usr/lib/ruby/3.0.0/mkmf.rb:971:in `block in checking_for'
        from /usr/lib/ruby/3.0.0/mkmf.rb:361:in `block (2 levels) in postpone'
        from /usr/lib/ruby/3.0.0/mkmf.rb:331:in `open'
        from /usr/lib/ruby/3.0.0/mkmf.rb:361:in `block in postpone'
        from /usr/lib/ruby/3.0.0/mkmf.rb:331:in `open'
        from /usr/lib/ruby/3.0.0/mkmf.rb:357:in `postpone'
        from /usr/lib/ruby/3.0.0/mkmf.rb:970:in `checking_for'
        from /usr/lib/ruby/3.0.0/mkmf.rb:1123:in `have_header'
        from extconf.rb:10:in `system_libffi_usable?'
        from extconf.rb:42:in `<main>'

To see why this extension failed to compile, please check the mkmf.log which can be found here:

  /var/lib/gems/3.0.0/extensions/x86_64-linux/3.0.0/ffi-1.15.5/mkmf.log

extconf failed, exit code 1

Gem files will remain installed in /var/lib/gems/3.0.0/gems/ffi-1.15.5 for inspection.
Results logged to /var/lib/gems/3.0.0/extensions/x86_64-linux/3.0.0/ffi-1.15.5/gem_make.out

The log file has a bit more info:

$ cat /var/lib/gems/3.0.0/extensions/x86_64-linux/3.0.0/ffi-1.15.5/mkmf.log
package configuration for libffi is not found
"x86_64-linux-gnu-gcc -o conftest -I/usr/include/x86_64-linux-gnu/ruby-3.0.0 -I/usr/include/ruby-3.0.0/ruby/backward -I/usr/include/ruby-3.0.0 -I. -Wdate-time -D_FORTIFY_SOURCE=2   -g -O2 -ffile-prefix-map=/build/ruby3.0-ohOwi0/ruby3.0-3.0.2=. -fstack-protector-strong -Wformat -Werror=format-security -fPIC conftest.c  -L. -L/usr/lib/x86_64-linux-gnu -L. -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -fstack-protector-strong -rdynamic -Wl,-export-dynamic     -lruby-3.0  -lm   -lc"
checked program was:
/* begin */
1: #include "ruby.h"
2:
3: int main(int argc, char **argv)
4: {
5:   return !!argv[argc];
6: }
/* end */

I checked, and libffi-dev is installed (the newest version 3.4.2-4).

[pverscha]

@magnuspalmblad Thank you for trying this out. I will check this myself tonight and I will get back to you with (hopefully) a solution.

[pverscha]

I'm sorry for the delay in looking into this issue. I have now had similar reports coming in from other users and found a workaround for using Unipept in WSL (Windows Subsystem for Linux):

1. Deinstall ruby: sudo apt purge ruby
2. Install Ruby Version Manager (RVM)
   • gpg --keyserver keyserver.ubuntu.com --recv-keys 409B6B1796C275462A1703113804BB82D39DC0E3 7D2BAF1CF37B13E2069D6956105BD0E739499BDB
   • \curl -sSL https://get.rvm.io | bash
   • source /home/<linux_username>/.rvm/scripts/rvm (replace <linux_username> with your username in WSL)
3. Install Ruby 3.0 using RVM: rvm install ruby-3.0
4. rvm use ruby-3.0
5. Finally, install gem install unipept