gem install sqlite3 --platform=ruby fails to build starting at 2.6.0

[copiousfreetime]

Installing the ruby platform gem

Admittedly I'm doing this on an older linux -- rockylinux 8.6 -- which is linux kernel 5.19.11-1ep.el8.x86_64 and glibc 2.28.

But that shouldn't affect a working ruby 3.4.4, from building sqlite3.

It does look like this started with sqlite3 2.6.0 which is also when the autotools was changed to autosetup -- so I wonder if that is actually the issue.

Gem Environment

RubyGems Environment:
  - RUBYGEMS VERSION: 3.6.9
  - RUBY VERSION: 3.4.4 (2025-05-14 patchlevel 34) [x86_64-linux]
  - INSTALLATION DIRECTORY: /home/vagrant/.rbenv/versions/3.4.4/lib/ruby/gems/3.4.0
  - USER INSTALLATION DIRECTORY: /home/vagrant/.gem/ruby/3.4.0
  - CREDENTIALS FILE: /home/vagrant/.local/share/gem/credentials
  - RUBY EXECUTABLE: /home/vagrant/.rbenv/versions/3.4.4/bin/ruby
  - GIT EXECUTABLE: /usr/bin/git
  - EXECUTABLE DIRECTORY: /home/vagrant/.rbenv/versions/3.4.4/bin
  - SPEC CACHE DIRECTORY: /home/vagrant/.gem/specs
  - SYSTEM CONFIGURATION DIRECTORY: /home/vagrant/.rbenv/versions/3.4.4/etc
  - RUBYGEMS PLATFORMS:
     - ruby
     - x86_64-linux
  - GEM PATHS:
     - /home/vagrant/.rbenv/versions/3.4.4/lib/ruby/gems/3.4.0
     - /home/vagrant/.gem/ruby/3.4.0
  - GEM CONFIGURATION:
     - :update_sources => true
     - :verbose => true
     - :backtrace => false
     - :bulk_threshold => 1000
     - :sources => ["https://rubygems.org"]
     - :concurrent_downloads => 8
     - "benchmark" => false
     - "gem" => "--no-ri --no-rdoc"
  - REMOTE SOURCES:
     - https://rubygems.org

gem intall sqlite3 --platformr=ruby -v 2.6.0

• mkmf.log as a gist

Building native extensions. This could take a while...
ERROR:  Error installing sqlite3:
        ERROR: Failed to build gem native extension.

    current directory: /home/vagrant/.rbenv/versions/3.4.4/lib/ruby/gems/3.4.0/gems/sqlite3-2.6.0/ext/sqlite3
/home/vagrant/.rbenv/versions/3.4.4/bin/ruby extconf.rb
Building sqlite3-ruby using packaged sqlite3.
Extracting sqlite-autoconf-3490100.tar.gz into tmp/x86_64-redhat-linux/ports/sqlite3/3.49.1... OK
Running 'configure' for sqlite3 3.49.1... OK
Running 'compile' for sqlite3 3.49.1... OK
Running 'install' for sqlite3 3.49.1... OK
Activating sqlite3 3.49.1 (from /home/vagrant/.rbenv/versions/3.4.4/lib/ruby/gems/3.4.0/gems/sqlite3-2.6.0/ports/x86_64-redhat-linux/sqlite3/3.49.1)...
checking for pkg-config for /home/vagrant/.rbenv/versions/3.4.4/lib/ruby/gems/3.4.0/gems/sqlite3-2.6.0/ports/x86_64-redhat-linux/sqlite3/3.49.1/lib/pkgconfig/sqlite3.pc... ["-I/home/vagrant/.rbenv/versions/3.4.4/lib/ruby/gems/3.4.0/gems/sqlite3-2.6.0/ports/x86_64-redhat-linux/sqlite3/3.49.1/include ", "", "-lsqlite3"]
checking for whether -L/home/vagrant/.rbenv/versions/3.4.4/lib/ruby/gems/3.4.0/gems/sqlite3-2.6.0/ports/x86_64-redhat-linux/sqlite3/3.49.1/lib is accepted as LDFLAGS... yes
checking for whether -lsqlite3 is accepted as LDFLAGS... yes
checking for whether -lm is accepted as LDFLAGS... yes
checking for whether -lz is accepted as LDFLAGS... yes
checking for whether -DUSING_PACKAGED_LIBRARIES is accepted as CPPFLAGS... yes
checking for whether -fvisibility=hidden is accepted as CFLAGS... yes
checking for sqlite3.h... yes
checking for sqlite3_libversion_number() in -lsqlite3... no

Could not find sqlite3.
Please visit https://github.com/sparklemotion/sqlite3-ruby for installation instructions.


*** 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=${opt-dir}/include
        --without-make-prog
        --srcdir=.
        --curdir
        --ruby=/home/vagrant/.rbenv/versions/3.4.4/bin/$(RUBY_BASE_NAME)
        --help
        --download-dependencies
        --with-sqlcipher
        --without-sqlcipher
        --with-sqlcipher-dir
        --without-sqlcipher-dir
        --with-sqlcipher-include
        --without-sqlcipher-include
        --with-sqlcipher-lib
        --without-sqlcipher-lib
        --enable-system-libraries
        --disable-system-libraries
        --with-sqlcipher
        --without-sqlcipher
        --with-sqlcipher-dir
        --without-sqlcipher-dir
        --with-sqlcipher-include
        --without-sqlcipher-include
        --with-sqlcipher-lib
        --without-sqlcipher-lib
        --with-sqlite-source-dir
        --with-sqlite-cflags
        --without-sqlite-cflags
        --with-/home/vagrant/.rbenv/versions/3.4.4/lib/ruby/gems/3.4.0/gems/sqlite3-2.6.0/ports/x86_64-redhat-linux/sqlite3/3.49.1/lib/pkgconfig/sqlite3.pc-dir
        --without-/home/vagrant/.rbenv/versions/3.4.4/lib/ruby/gems/3.4.0/gems/sqlite3-2.6.0/ports/x86_64-redhat-linux/sqlite3/3.49.1/lib/pkgconfig/sqlite3.pc-dir
        --with-/home/vagrant/.rbenv/versions/3.4.4/lib/ruby/gems/3.4.0/gems/sqlite3-2.6.0/ports/x86_64-redhat-linux/sqlite3/3.49.1/lib/pkgconfig/sqlite3.pc-include=${/home/vagrant/.rbenv/versions/3.4.4/lib/ruby/gems/3.4.0/gems/sqlite3-2.6.0/ports/x86_64-redhat-linux/sqlite3/3.49.1/lib/pkgconfig/sqlite3.pc-dir}/include
        --without-/home/vagrant/.rbenv/versions/3.4.4/lib/ruby/gems/3.4.0/gems/sqlite3-2.6.0/ports/x86_64-redhat-linux/sqlite3/3.49.1/lib/pkgconfig/sqlite3.pc-include
        --with-/home/vagrant/.rbenv/versions/3.4.4/lib/ruby/gems/3.4.0/gems/sqlite3-2.6.0/ports/x86_64-redhat-linux/sqlite3/3.49.1/lib/pkgconfig/sqlite3.pc-lib=${/home/vagrant/.rbenv/versions/3.4.4/lib/ruby/gems/3.4.0/gems/sqlite3-2.6.0/ports/x86_64-redhat-linux/sqlite3/3.49.1/lib/pkgconfig/sqlite3.pc-dir}/lib
        --without-/home/vagrant/.rbenv/versions/3.4.4/lib/ruby/gems/3.4.0/gems/sqlite3-2.6.0/ports/x86_64-redhat-linux/sqlite3/3.49.1/lib/pkgconfig/sqlite3.pc-lib
        --with-/home/vagrant/.rbenv/versions/3.4.4/lib/ruby/gems/3.4.0/gems/sqlite3-2.6.0/ports/x86_64-redhat-linux/sqlite3/3.49.1/lib/pkgconfig/sqlite3.pc-config
        --without-/home/vagrant/.rbenv/versions/3.4.4/lib/ruby/gems/3.4.0/gems/sqlite3-2.6.0/ports/x86_64-redhat-linux/sqlite3/3.49.1/lib/pkgconfig/sqlite3.pc-config
        --with-pkg-config
        --without-pkg-config
        --enable-cross-build
        --disable-cross-build
        --with-sqlcipher
        --without-sqlcipher
        --with-sqlcipher-dir
        --without-sqlcipher-dir
        --with-sqlcipher-include
        --without-sqlcipher-include
        --with-sqlcipher-lib
        --without-sqlcipher-lib
        --with-sqlite3-dir
        --without-sqlite3-dir
        --with-sqlite3-include=${sqlite3-dir}/include
        --without-sqlite3-include
        --with-sqlite3-lib=${sqlite3-dir}/lib
        --without-sqlite3-lib
        --with-sqlite3lib
        --without-sqlite3lib
        --with-sqlcipher
        --without-sqlcipher
        --with-sqlcipher-dir
        --without-sqlcipher-dir
        --with-sqlcipher-include
        --without-sqlcipher-include
        --with-sqlcipher-lib
        --without-sqlcipher-lib

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

  /home/vagrant/.rbenv/versions/3.4.4/lib/ruby/gems/3.4.0/extensions/x86_64-linux/3.4.0/sqlite3-2.6.0/mkmf.log

extconf failed, exit code 1

Gem files will remain installed in /home/vagrant/.rbenv/versions/3.4.4/lib/ruby/gems/3.4.0/gems/sqlite3-2.6.0 for inspection.
Results logged to /home/vagrant/.rbenv/versions/3.4.4/lib/ruby/gems/3.4.0/extensions/x86_64-linux/3.4.0/sqlite3-2.6.0/gem_make.out

Last working version 2.5.0

% gem install sqlite3 --platform=ruby  -v 2.5.0
Building native extensions. This could take a while...
Successfully installed sqlite3-2.5.0
Parsing documentation for sqlite3-2.5.0
Done installing documentation for sqlite3 after 3 seconds
1 gem installed

[copiousfreetime]

I did decide to attempt to build from the sqlite3-ruby release tarball using the source release, and this also failed.

vagrant@podman:~/tmp/sqlite3-ruby-2.6.0 3.4.3 % bundle exec rake compile
mkdir -p tmp/x86_64-linux/sqlite3_native/3.4.3
cd tmp/x86_64-linux/sqlite3_native/3.4.3
/home/vagrant/.rbenv/versions/3.4.3/bin/ruby -I. ../../../../ext/sqlite3/extconf.rb
Building sqlite3-ruby using packaged sqlite3.
Downloading sqlite-autoconf-3490100.tar.gz (100%)
Extracting sqlite-autoconf-3490100.tar.gz into tmp/x86_64-redhat-linux/ports/sqlite3/3.49.1... OK
Running 'configure' for sqlite3 3.49.1... OK
Running 'compile' for sqlite3 3.49.1... OK
Running 'install' for sqlite3 3.49.1... OK
Activating sqlite3 3.49.1 (from /home/vagrant/tmp/sqlite3-ruby-2.6.0/ports/x86_64-redhat-linux/sqlite3/3.49.1)...
checking for pkg-config for /home/vagrant/tmp/sqlite3-ruby-2.6.0/ports/x86_64-redhat-linux/sqlite3/3.49.1/lib/pkgconfig/sqlite3.pc... ["-I/home/vagrant/tmp/sqlite3-ruby-2.6.0/ports/x86_64-redhat-linux/sqlite3/3.49.1/include ", "", "-lsqlite3"]
checking for whether -L/home/vagrant/tmp/sqlite3-ruby-2.6.0/ports/x86_64-redhat-linux/sqlite3/3.49.1/lib is accepted as LDFLAGS... yes
checking for whether -lsqlite3 is accepted as LDFLAGS... yes
checking for whether -lm is accepted as LDFLAGS... yes
checking for whether -lz is accepted as LDFLAGS... yes
checking for whether -DUSING_PACKAGED_LIBRARIES is accepted as CPPFLAGS... yes
checking for whether -fvisibility=hidden is accepted as CFLAGS... yes
checking for sqlite3.h... yes
checking for sqlite3_libversion_number() in -lsqlite3... no

Could not find sqlite3.

In order to double check that this is an issue in the ruby extension, I also downloaded the same sqlite3 tarball above from sqlite and ran its build:

Line-editing support for the sqlite3 shell: none
Checking libs for dlopen...-ldl
Loadable extension support enabled.
Checking libs for ceil...-lm
Enabling math SQL functions -lm
ICU support is disabled.
Feature flags...
  - fts4
  + fts5
  - geopoly
  - rtree
  - session
  - update-limit
  - memsys5
  - memsys3
  - scanstatus
  + json
Library feature flags: -DSQLITE_ENABLE_FTS5 -DSQLITE_ENABLE_MATH_FUNCTIONS -DSQLITE_THREADSAFE=1
Shell options: -DSQLITE_HAVE_ZLIB=1
Makefile is unchanged
sqlite3.pc is unchanged
sqlite_cfg.h is unchanged

vagrant@podman:~/tmp/sqlite-autoconf-3490100 3.4.3 % ./configure  "--enable-static" "--disable-shared" "--disable-shared" "--enable-static" "--enable-fts5" "CC=gcc" "CFLAGS=-fPIC -O2 -fvisibility=hidden -DSQLITE_DEFAULT_WAL_SYNCHRONOUS=1 -DSQLITE_USE_URI=1 -DSQLITE_ENABLE_DBPAGE_VTAB=1 -DSQLITE_ENABLE_DBSTAT_VTAB=1"
Host System...x86_64-pc-linux-gnu
Build System...x86_64-pc-linux-gnu
C compiler... gcc -fPIC -O2 -fvisibility=hidden -DSQLITE_DEFAULT_WAL_SYNCHRONOUS=1 -DSQLITE_USE_URI=1 -DSQLITE_ENABLE_DBPAGE_VTAB=1 -DSQLITE_ENABLE_DBSTAT_VTAB=1
C++ compiler... c++ -fPIC -O2 -fvisibility=hidden -DSQLITE_DEFAULT_WAL_SYNCHRONOUS=1 -DSQLITE_USE_URI=1 -DSQLITE_ENABLE_DBPAGE_VTAB=1 -DSQLITE_ENABLE_DBSTAT_VTAB=1
Build C compiler...cc
Checking for stdlib.h...ok
Source dir = /home/vagrant/tmp/sqlite-autoconf-3490100
Build dir  = /home/vagrant/tmp/sqlite-autoconf-3490100
Configuring SQLite version 3.49.1
Looking for install ... /usr/bin/install
Checking for int8_t...ok
Checking for int16_t...ok
Checking for int32_t...ok
Checking for int64_t...ok
Checking for intptr_t...ok
Checking for uint8_t...ok
Checking for uint16_t...ok
Checking for uint32_t...ok
Checking for uint64_t...ok
Checking for uintptr_t...ok
Checking for gmtime_r...ok
Checking for isnan...ok
Checking for localtime_r...ok
Checking for localtime_s...not found
Checking for malloc_usable_size...ok
Checking for strchrnul...ok
Checking for usleep...ok
Checking for utime...ok
Checking for pread...ok
Checking for pread64...ok
Checking for pwrite...ok
Checking for pwrite64...ok
Checking libs for fdatasync...none needed
Checking libs for nanosleep...none needed
Checking for sys/types.h...ok
Checking for sys/stat.h...ok
Checking for dlfcn.h...ok
Checking for unistd.h...ok
Checking for stdlib.h...(cached) ok
Checking for malloc.h...ok
Checking for memory.h...ok
Checking for string.h...ok
Checking for strings.h...ok
Checking for inttypes.h...ok
Checking for zlib.h...ok
Checking libs for deflate...-lz
Checking whether the C compiler accepts -rpath /usr/local/lib...no
Checking whether the C compiler accepts -Wl,-rpath,/usr/local/lib...yes
SQLITE_DEBUG build? no
Support threadsafe operation? Checking for libs...
Checking libs for pthread_create...-lpthread
Checking libs for pthread_mutexattr_init...-lpthread
Checking for line-editing capability...
Line-editing support for the sqlite3 shell: none
Checking libs for dlopen...-ldl
Loadable extension support enabled.
Checking libs for ceil...-lm
Enabling math SQL functions -lm
ICU support is disabled.
Feature flags...
  - fts4
  + fts5
  - geopoly
  - rtree
  - session
  - update-limit
  - memsys5
  - memsys3
  - scanstatus
  + json
Library feature flags: -DSQLITE_ENABLE_DBPAGE_VTAB=1 -DSQLITE_ENABLE_DBSTAT_VTAB=1 -DSQLITE_ENABLE_FTS5 -DSQLITE_ENABLE_MATH_FUNCTIONS -DSQLITE_THREADSAFE=1
Shell options: -DSQLITE_HAVE_ZLIB=1
Makefile is unchanged
sqlite3.pc is unchanged
sqlite_cfg.h is unchanged
vagrant@podman:~/tmp/sqlite-autoconf-3490100 3.4.3 % make
gcc -c /home/vagrant/tmp/sqlite-autoconf-3490100/sqlite3.c -o sqlite3.o -fPIC -O2 -fvisibility=hidden -DSQLITE_DEFAULT_WAL_SYNCHRONOUS=1 -DSQLITE_USE_URI=1  -I. -fPIC  -DSQLITE_ENABLE_DBPAGE_VTAB=1 -DSQLITE_ENABLE_DBSTAT_VTAB=1 -DSQLITE_ENABLE_FTS5 -DSQLITE_ENABLE_MATH_FUNCTIONS -DSQLITE_THREADSAFE=1
gcc -o libsqlite3.so  sqlite3.o -shared \
	 -Wl,-rpath,/usr/local/lib -lpthread -lm -ldl -lz    \

ar cr libsqlite3.a sqlite3.o
gcc -o sqlite3 \
	/home/vagrant/tmp/sqlite-autoconf-3490100/shell.c /home/vagrant/tmp/sqlite-autoconf-3490100/sqlite3.c -Wl,-rpath,/usr/local/lib -lpthread -lm -ldl -lz    \
	-I. -DSQLITE_ENABLE_DBPAGE_VTAB=1 -DSQLITE_ENABLE_DBSTAT_VTAB=1 -DSQLITE_ENABLE_FTS5 -DSQLITE_ENABLE_MATH_FUNCTIONS -DSQLITE_THREADSAFE=1 -DSQLITE_HAVE_ZLIB=1 \
	-fPIC -O2 -fvisibility=hidden -DSQLITE_DEFAULT_WAL_SYNCHRONOUS=1 -DSQLITE_USE_URI=1    \

vagrant@podman:~/tmp/sqlite-autoconf-3490100 3.4.3 % ./sqlite3
SQLite version 3.49.1 2025-02-18 13:38:58
Enter ".help" for usage hints.
Connected to a transient in-memory database.
Use ".open FILENAME" to reopen on a persistent database.
sqlite> .quit

And this runs fine.

[flavorjones]

Digging in now, thanks for providing enough detail to get started. Agree it seems likely to be related to the autoconf/autosetup change upstream.

[flavorjones]

Building a rockylinux:8.6 OCI image to try to reproduce.

[flavorjones]

I've reproduced using an image built with this Dockerfile:

FROM rockylinux:8.6

# build essentials
RUN dnf update -y 
RUN dnf install -y epel-release && dnf update -y
RUN dnf config-manager --set-enabled powertools
RUN dnf group install -y "Development Tools"
RUN dnf install -y openssl-devel readline-devel zlib-devel libyaml-devel libffi-devel wget curl

# mise and ruby
RUN dnf install -y dnf-plugins-core && \
    dnf config-manager --add-repo https://mise.jdx.dev/rpm/mise.repo && \
    dnf install -y mise
RUN mise install ruby@3.4.4

# now run `mise exec ruby@3.4.4 -- gem install sqlite3 --platform=ruby`

[flavorjones]

OK, the mkmf.log you provided matches what I'm seeing locally:

/usr/bin/ld: /root/.local/share/mise/installs/ruby/3.4.4/lib/ruby/gems/3.4.0/gems/sqlite3-2.7.1/ports/x86_64-redhat-linux/sqlite3/3.50.2/lib/libsqlite3.a(sqlite3.o): undefined reference to symbol 'dlclose@@GLIBC_2.2.5'
//usr/lib64/libdl.so.2: error adding symbols: DSO missing from command line
collect2: error: ld returned 1 exit status

[flavorjones]

OK, SQLite is getting built just fine, the issue is in linking the Ruby extension against it.

Here's my diagnosis:

1. on rockylinux, the symbol dlclose is in libdl.so

   /usr/lib64/libdl.so.2
   0000000000001090 g    DF .text  000000000000004a  GLIBC_2.2.5 dlclose
   

2. while on debian/ubuntu it is in libc.so

   /usr/lib/x86_64-linux-gnu/libc.so.6
   000000000009e580 g    DF .text  000000000000003c (GLIBC_2.2.5) dlclose
   000000000009e580 g    DF .text  000000000000003c  GLIBC_2.34  dlclose
   

3. the pkgconf file generated by SQLite in 3.48.0+, which is used to determine the linker flags used while building the extension, emits something like this on both rockylinux and debian:

   pkg-config --libs --static ./ports/x86_64-redhat-linux/sqlite3/3.50.2/lib/pkgconfig/sqlite3.pc
   -L/path/to/sqlite3/3.50.2/lib -lsqlite3 -lm -lz
   

   The thing to note is that -ldl is not present.
4. the pkgconf file generate by SQLite 3.47.2 emits this on rockylinux:

   pkg-config --libs --static path/to/sqlite3.pc
   -L/path/to/sqlite3/3.47.2/lib -lsqlite3 -lz -lm -ldl -lpthread
   

   while on debian it emits the same as noted above, -lsqlite3 -lz -lm

So I think what we're seeing is: on debian platforms, the dlclose symbol is found at linktime by its presence in libc; but on rockylinux, dlclose must be resolved by an explicit -ldl on the link line, which isn't present in the pkgconf file.

In previous versions of SQLite, the -ldl (and -lpthread, though that's less of an issue because it's always present in Ruby's LIBS) were included in the pkgconf output, and so were linked against. In the current version (which as you noted was a change from autosetup) it's not present, and so you see these linker failures.

Make sense?

A couple of things we should do:

• post about this upstream in the forum (which I'll do now) to see if they'll fix it
• and then to work around this, one of:
  • add special handling for rockylinux (and, I'm assuming, possibly other redhat-derived distros?) to add this to the link line
  • add the general ability to inject linker flags through an environment variable or config option, and then you set those yourself at build time
  • always tack on -ldl on *nix systems (since Ruby needs those anyway, it shouldn't cause any problems) *

Let's start by opening a forum post upstream and see what they say.

* Edit: ah, can't add this library on Musl Linux platforms.

[flavorjones]

Upstream forum post: https://sqlite.org/forum/forumpost/44a58c8073

[flavorjones]

Potential fix at #635

[flavorjones]

Upstream has fixed the issue on trunk, in response to the forum post: https://sqlite.org/src/info/64f5f14322, and so I've rewritten #635 to just apply that patch.