Error upgrading Indico from v3.3.5 to v3.3.6

Hi,
I’ve found a problem upgrading Indico.
When I launch the command indico setup upgrade-python, I obtain this:

(indico) [indico@indico ~]$ indico setup upgrade-python
updating pyenv
Currently selected version 3.12.8 does not match preferred version 3.12.9
Installing python 3.12.9 (may take some time)
Setting global pyenv version to 3.12.9
Not executed via pyenv (probably inside virtualenv); re-executing with /opt/indico/.pyenv/shims/python
Python version: 3.12.9; wanted: 3.12.9
Venv path: /opt/indico/.venv
Venv found; python version 3.12.8 from /opt/indico/.pyenv/versions/3.12.8/bin
Updating symlink /opt/indico/.venv/bin/python -> /opt/indico/.pyenv/versions/3.12.9/bin/python
Requirement already satisfied: wheel in ./.venv/lib/python3.12/site-packages (0.45.1)
Rebuilding uWSGI for the current python version
Collecting uwsgi
  Downloading uwsgi-2.0.28.tar.gz (816 kB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 816.2/816.2 kB 32.1 MB/s eta 0:00:00
  Preparing metadata (setup.py) ... done
Building wheels for collected packages: uwsgi
  Building wheel for uwsgi (setup.py) ... error
  error: subprocess-exited-with-error
  
  × python setup.py bdist_wheel did not run successfully.
  │ exit code: 1
  ╰─> [372 lines of output]
      /opt/indico/.venv/lib/python3.12/site-packages/setuptools/_distutils/dist.py:265: UserWarning: Unknown distribution option: 'descriptions'
        warnings.warn(msg)
      running bdist_wheel
      running build
      running build_py
      creating build
      creating build/lib
      copying uwsgidecorators.py -> build/lib
      /opt/indico/.venv/lib/python3.12/site-packages/setuptools/_distutils/cmd.py:66: SetuptoolsDeprecationWarning: setup.py install is deprecated.
      !!
      
              ********************************************************************************
              Please avoid running ``setup.py`` directly.
              Instead, use pypa/build, pypa/installer or other
              standards-based tools.
      
              See https://blog.ganssle.io/articles/2021/10/setup-py-deprecated.html for details.
              ********************************************************************************
      
      !!
        self.initialize_options()
      installing to build/bdist.linux-x86_64/wheel
      running install
      using profile: buildconf/default.ini
      detected include path: ['/usr/lib/gcc/x86_64-redhat-linux/11/include', '/usr/local/include', '/usr/include']
      Patching "bin_name" to properly install_scripts dir
      detected CPU cores: 2
      configured CFLAGS: -O2 -I. -Wall -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -Wextra -Wno-unused-parameter -Wno-missing-field-initializers -Wformat-signedness -DUWSGI_HAS_IFADDRS -DUWSGI_ZLIB -DUWSGI_LOCK_USE_MUTEX -DUWSGI_EVENT_USE_EPOLL -DUWSGI_EVENT_TIMER_USE_TIMERFD -DUWSGI_EVENT_FILEMONITOR_USE_INOTIFY  -DUWSGI_PCRE -DUWSGI_ROUTING -DUWSGI_UUID -DUWSGI_VERSION="\"2.0.28\"" -DUWSGI_VERSION_BASE="2" -DUWSGI_VERSION_MAJOR="0" -DUWSGI_VERSION_MINOR="28" -DUWSGI_VERSION_REVISION="0" -DUWSGI_VERSION_CUSTOM="\"\"" -DUWSGI_YAML -DUWSGI_SSL -I/usr/include/libxml2 -DUWSGI_XML -DUWSGI_XML_LIBXML2 -DUWSGI_PLUGIN_DIR="\".\"" -DUWSGI_DECLARE_EMBEDDED_PLUGINS="UDEP(python);UDEP(gevent);UDEP(ping);UDEP(cache);UDEP(nagios);UDEP(rrdtool);UDEP(carbon);UDEP(rpc);UDEP(corerouter);UDEP(fastrouter);UDEP(http);UDEP(ugreen);UDEP(signal);UDEP(syslog);UDEP(rsyslog);UDEP(logsocket);UDEP(router_uwsgi);UDEP(router_redirect);UDEP(router_basicauth);UDEP(zergpool);UDEP(redislog);UDEP(mongodblog);UDEP(router_rewrite);UDEP(router_http);UDEP(logfile);UDEP(router_cache);UDEP(rawrouter);UDEP(router_static);UDEP(sslrouter);UDEP(spooler);UDEP(cheaper_busyness);UDEP(symcall);UDEP(transformation_tofile);UDEP(transformation_gzip);UDEP(transformation_chunked);UDEP(transformation_offload);UDEP(router_memcached);UDEP(router_redis);UDEP(router_hash);UDEP(router_expires);UDEP(router_metrics);UDEP(transformation_template);UDEP(stats_pusher_socket);" -DUWSGI_LOAD_EMBEDDED_PLUGINS="ULEP(python);ULEP(gevent);ULEP(ping);ULEP(cache);ULEP(nagios);ULEP(rrdtool);ULEP(carbon);ULEP(rpc);ULEP(corerouter);ULEP(fastrouter);ULEP(http);ULEP(ugreen);ULEP(signal);ULEP(syslog);ULEP(rsyslog);ULEP(logsocket);ULEP(router_uwsgi);ULEP(router_redirect);ULEP(router_basicauth);ULEP(zergpool);ULEP(redislog);ULEP(mongodblog);ULEP(router_rewrite);ULEP(router_http);ULEP(logfile);ULEP(router_cache);ULEP(rawrouter);ULEP(router_static);ULEP(sslrouter);ULEP(spooler);ULEP(cheaper_busyness);ULEP(symcall);ULEP(transformation_tofile);ULEP(transformation_gzip);ULEP(transformation_chunked);ULEP(transformation_offload);ULEP(router_memcached);ULEP(router_redis);ULEP(router_hash);ULEP(router_expires);ULEP(router_metrics);ULEP(transformation_template);ULEP(stats_pusher_socket);"
      *** uWSGI compiling server core ***
      [thread 0][gcc] core/protocol.o
      [thread 1][gcc] core/utils.o
      [thread 0][gcc] core/socket.o
      [thread 0][gcc] core/logging.o
      [thread 1][gcc] core/master.o
      [thread 0][gcc] core/master_utils.o
      [thread 1][gcc] core/emperor.o
      [thread 0][gcc] core/notify.o
      [thread 1][gcc] core/mule.o
      [thread 0][gcc] core/subscription.o
      [thread 1][gcc] core/stats.o
      [thread 0][gcc] core/sendfile.o
      [thread 0][gcc] core/async.o
      [thread 1][gcc] core/master_checks.o
      [thread 0][gcc] core/fifo.o
      [thread 1][gcc] core/offload.o
      [thread 0][gcc] core/io.o
      [thread 1][gcc] core/static.o
      [thread 1][gcc] core/websockets.o
      [thread 0][gcc] core/spooler.o
      [thread 1][gcc] core/snmp.o
      [thread 0][gcc] core/exceptions.o
      [thread 1][gcc] core/config.o
      [thread 0][gcc] core/setup_utils.o
      [thread 1][gcc] core/clock.o
      [thread 0][gcc] core/init.o
      [thread 1][gcc] core/buffer.o
      [thread 0][gcc] core/reader.o
      [thread 1][gcc] core/writer.o
      [thread 0][gcc] core/alarm.o
      [thread 1][gcc] core/cron.o
      [thread 0][gcc] core/hooks.o
      [thread 1][gcc] core/plugins.o
      [thread 1][gcc] core/lock.o
      [thread 0][gcc] core/cache.o
      [thread 1][gcc] core/daemons.o
      [thread 1][gcc] core/errors.o
      [thread 1][gcc] core/hash.o
      [thread 0][gcc] core/master_events.o
      [thread 1][gcc] core/chunked.o
      [thread 0][gcc] core/queue.o
      [thread 1][gcc] core/event.o
      [thread 0][gcc] core/signal.o
      [thread 1][gcc] core/strings.o
      [thread 0][gcc] core/progress.o
      [thread 0][gcc] core/timebomb.o
      [thread 1][gcc] core/ini.o
      [thread 0][gcc] core/fsmon.o
      [thread 1][gcc] core/mount.o
      [thread 0][gcc] core/metrics.o
      [thread 1][gcc] core/plugins_builder.o
      [thread 1][gcc] core/sharedarea.o
      [thread 1][gcc] core/rpc.o
      [thread 0][gcc] core/gateway.o
      [thread 1][gcc] core/loop.o
      [thread 0][gcc] core/cookie.o
      [thread 1][gcc] core/querystring.o
      [thread 0][gcc] core/rb_timers.o
      [thread 1][gcc] core/transformations.o
      [thread 0][gcc] core/uwsgi.o
      [thread 1][gcc] proto/base.o
      [thread 1][gcc] proto/uwsgi.o
      [thread 1][gcc] proto/http.o
      [thread 1][gcc] proto/fastcgi.o
      [thread 0][gcc] proto/scgi.o
      [thread 1][gcc] proto/puwsgi.o
      [thread 0][gcc] lib/linux_ns.o
      [thread 1][gcc] core/zlib.o
      [thread 0][gcc] core/regexp.o
      [thread 1][gcc] core/routing.o
      [thread 0][gcc] core/yaml.o
      [thread 0][gcc] core/ssl.o
      core/ssl.c: In function ‘uwsgi_ssl_new_server_context’:
      core/ssl.c:268:17: warning: ‘PEM_read_bio_DHparams’ is deprecated: Since OpenSSL 3.0 [-Wdeprecated-declarations]
        268 |                 DH *dh = PEM_read_bio_DHparams(bio, NULL, NULL, NULL);
            |                 ^~
      In file included from /usr/include/openssl/ssl.h:37,
                       from ./uwsgi.h:357,
                       from core/ssl.c:1:
      /usr/include/openssl/pem.h:473:1: note: declared here
        473 | DECLARE_PEM_rw_attr(OSSL_DEPRECATEDIN_3_0, DHparams, DH)
            | ^~~~~~~~~~~~~~~~~~~
      core/ssl.c:273:25: warning: ‘DH_free’ is deprecated: Since OpenSSL 3.0 [-Wdeprecated-declarations]
        273 |                         DH_free(dh);
            |                         ^~~~~~~
      In file included from /usr/include/openssl/dsa.h:31,
                       from /usr/include/openssl/x509.h:37,
                       from /usr/include/openssl/ssl.h:32,
                       from ./uwsgi.h:357,
                       from core/ssl.c:1:
      /usr/include/openssl/dh.h:207:28: note: declared here
        207 | OSSL_DEPRECATEDIN_3_0 void DH_free(DH *dh);
            |                            ^~~~~~~
      core/ssl.c:279:9: warning: ‘EC_KEY_new_by_curve_name’ is deprecated: Since OpenSSL 3.0 [-Wdeprecated-declarations]
        279 |         EC_KEY *ecdh = EC_KEY_new_by_curve_name(NID_X9_62_prime256v1);
            |         ^~~~~~
      In file included from /usr/include/openssl/x509.h:33,
                       from /usr/include/openssl/ssl.h:32,
                       from ./uwsgi.h:357,
                       from core/ssl.c:1:
      /usr/include/openssl/ec.h:1017:31: note: declared here
       1017 | OSSL_DEPRECATEDIN_3_0 EC_KEY *EC_KEY_new_by_curve_name(int nid);
            |                               ^~~~~~~~~~~~~~~~~~~~~~~~
      core/ssl.c:283:17: warning: ‘EC_KEY_free’ is deprecated: Since OpenSSL 3.0 [-Wdeprecated-declarations]
        283 |                 EC_KEY_free(ecdh);
            |                 ^~~~~~~~~~~
      In file included from /usr/include/openssl/x509.h:33,
                       from /usr/include/openssl/ssl.h:32,
                       from ./uwsgi.h:357,
                       from core/ssl.c:1:
      /usr/include/openssl/ec.h:1022:28: note: declared here
       1022 | OSSL_DEPRECATEDIN_3_0 void EC_KEY_free(EC_KEY *key);
            |                            ^~~~~~~~~~~
      core/ssl.c: In function ‘uwsgi_sha1’:
      core/ssl.c:563:9: warning: ‘SHA1_Init’ is deprecated: Since OpenSSL 3.0 [-Wdeprecated-declarations]
        563 |         SHA1_Init(&sha);
            |         ^~~~~~~~~
      In file included from /usr/include/openssl/x509.h:41,
                       from /usr/include/openssl/ssl.h:32,
                       from ./uwsgi.h:357,
                       from core/ssl.c:1:
      /usr/include/openssl/sha.h:49:27: note: declared here
         49 | OSSL_DEPRECATEDIN_3_0 int SHA1_Init(SHA_CTX *c);
            |                           ^~~~~~~~~
      core/ssl.c:564:9: warning: ‘SHA1_Update’ is deprecated: Since OpenSSL 3.0 [-Wdeprecated-declarations]
        564 |         SHA1_Update(&sha, src, len);
            |         ^~~~~~~~~~~
      In file included from /usr/include/openssl/x509.h:41,
                       from /usr/include/openssl/ssl.h:32,
                       from ./uwsgi.h:357,
                       from core/ssl.c:1:
      /usr/include/openssl/sha.h:50:27: note: declared here
         50 | OSSL_DEPRECATEDIN_3_0 int SHA1_Update(SHA_CTX *c, const void *data, size_t len);
            |                           ^~~~~~~~~~~
      core/ssl.c:565:9: warning: ‘SHA1_Final’ is deprecated: Since OpenSSL 3.0 [-Wdeprecated-declarations]
        565 |         SHA1_Final((unsigned char *)dst, &sha);
            |         ^~~~~~~~~~
      In file included from /usr/include/openssl/x509.h:41,
                       from /usr/include/openssl/ssl.h:32,
                       from ./uwsgi.h:357,
                       from core/ssl.c:1:
      /usr/include/openssl/sha.h:51:27: note: declared here
         51 | OSSL_DEPRECATEDIN_3_0 int SHA1_Final(unsigned char *md, SHA_CTX *c);
            |                           ^~~~~~~~~~
      core/ssl.c: In function ‘uwsgi_md5’:
      core/ssl.c:571:9: warning: ‘MD5_Init’ is deprecated: Since OpenSSL 3.0 [-Wdeprecated-declarations]
        571 |         MD5_Init(&md5);
            |         ^~~~~~~~
      In file included from core/ssl.c:4:
      /usr/include/openssl/md5.h:49:27: note: declared here
         49 | OSSL_DEPRECATEDIN_3_0 int MD5_Init(MD5_CTX *c);
            |                           ^~~~~~~~
      core/ssl.c:572:9: warning: ‘MD5_Update’ is deprecated: Since OpenSSL 3.0 [-Wdeprecated-declarations]
        572 |         MD5_Update(&md5, src, len);
            |         ^~~~~~~~~~
      In file included from core/ssl.c:4:
      /usr/include/openssl/md5.h:50:27: note: declared here
         50 | OSSL_DEPRECATEDIN_3_0 int MD5_Update(MD5_CTX *c, const void *data, size_t len);
            |                           ^~~~~~~~~~
      core/ssl.c:573:9: warning: ‘MD5_Final’ is deprecated: Since OpenSSL 3.0 [-Wdeprecated-declarations]
        573 |         MD5_Final((unsigned char *)dst, &md5);
            |         ^~~~~~~~~
      In file included from core/ssl.c:4:
      /usr/include/openssl/md5.h:51:27: note: declared here
         51 | OSSL_DEPRECATEDIN_3_0 int MD5_Final(unsigned char *md, MD5_CTX *c);
            |                           ^~~~~~~~~
      core/ssl.c: In function ‘uwsgi_sha1_2n’:
      core/ssl.c:579:9: warning: ‘SHA1_Init’ is deprecated: Since OpenSSL 3.0 [-Wdeprecated-declarations]
        579 |         SHA1_Init(&sha);
            |         ^~~~~~~~~
      In file included from /usr/include/openssl/x509.h:41,
                       from /usr/include/openssl/ssl.h:32,
                       from ./uwsgi.h:357,
                       from core/ssl.c:1:
      /usr/include/openssl/sha.h:49:27: note: declared here
         49 | OSSL_DEPRECATEDIN_3_0 int SHA1_Init(SHA_CTX *c);
            |                           ^~~~~~~~~
      core/ssl.c:580:9: warning: ‘SHA1_Update’ is deprecated: Since OpenSSL 3.0 [-Wdeprecated-declarations]
        580 |         SHA1_Update(&sha, s1, len1);
            |         ^~~~~~~~~~~
      In file included from /usr/include/openssl/x509.h:41,
                       from /usr/include/openssl/ssl.h:32,
                       from ./uwsgi.h:357,
                       from core/ssl.c:1:
      /usr/include/openssl/sha.h:50:27: note: declared here
         50 | OSSL_DEPRECATEDIN_3_0 int SHA1_Update(SHA_CTX *c, const void *data, size_t len);
            |                           ^~~~~~~~~~~
      core/ssl.c:581:9: warning: ‘SHA1_Update’ is deprecated: Since OpenSSL 3.0 [-Wdeprecated-declarations]
        581 |         SHA1_Update(&sha, s2, len2);
            |         ^~~~~~~~~~~
      In file included from /usr/include/openssl/x509.h:41,
                       from /usr/include/openssl/ssl.h:32,
                       from ./uwsgi.h:357,
                       from core/ssl.c:1:
      /usr/include/openssl/sha.h:50:27: note: declared here
         50 | OSSL_DEPRECATEDIN_3_0 int SHA1_Update(SHA_CTX *c, const void *data, size_t len);
            |                           ^~~~~~~~~~~
      core/ssl.c:582:9: warning: ‘SHA1_Final’ is deprecated: Since OpenSSL 3.0 [-Wdeprecated-declarations]
        582 |         SHA1_Final((unsigned char *)dst, &sha);
            |         ^~~~~~~~~~
      In file included from /usr/include/openssl/x509.h:41,
                       from /usr/include/openssl/ssl.h:32,
                       from ./uwsgi.h:357,
                       from core/ssl.c:1:
      /usr/include/openssl/sha.h:51:27: note: declared here
         51 | OSSL_DEPRECATEDIN_3_0 int SHA1_Final(unsigned char *md, SHA_CTX *c);
            |                           ^~~~~~~~~~
      [thread 0][gcc] core/legion.o
      [thread 1][gcc] core/xmlconf.o
      [thread 1][gcc] core/dot_h.o
      Exception in thread Thread-2 (thread_compiler):
      Traceback (most recent call last):
        File "/opt/indico/.pyenv/versions/3.12.9/lib/python3.12/threading.py", line 1075, in _bootstrap_inner
          self.run()
        File "/opt/indico/.pyenv/versions/3.12.9/lib/python3.12/threading.py", line 1012, in run
          self._target(*self._args, **self._kwargs)
        File "/tmp/pip-install-euom9r14/uwsgi_11e727cab758445592bf02417f271a50/uwsgiconfig.py", line 116, in thread_compiler
          ret = subprocess.call(cmdline, shell=True)
                ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
        File "/opt/indico/.pyenv/versions/3.12.9/lib/python3.12/subprocess.py", line 391, in call
          with Popen(*popenargs, **kwargs) as p:
               ^^^^^^^^^^^^^^^^^^^^^^^^^^^
        File "/opt/indico/.pyenv/versions/3.12.9/lib/python3.12/subprocess.py", line 1028, in __init__
          self._execute_child(args, executable, preexec_fn, close_fds,
        File "/opt/indico/.pyenv/versions/3.12.9/lib/python3.12/subprocess.py", line 1963, in _execute_child
          raise child_exception_type(errno_num, err_msg, err_filename)
      OSError: [Errno 14] Bad address: '/bin/sh'
      [thread 0][gcc] core/config_py.o
      *** uWSGI compiling embedded plugins ***
      [thread 0][gcc] plugins/python/python_plugin.o
      plugins/python/python_plugin.c:138:9: warning: ‘Py_NoSiteFlag’ is deprecated [-Wdeprecated-declarations]
        138 |         {"no-site", no_argument, 0, "do not import site module", uwsgi_opt_true, &Py_NoSiteFlag, 0},
            |         ^
      In file included from /opt/indico/.pyenv/versions/3.12.9/include/python3.12/Python.h:48,
                       from plugins/python/uwsgi_python.h:4,
                       from plugins/python/python_plugin.c:1:
      /opt/indico/.pyenv/versions/3.12.9/include/python3.12/cpython/pydebug.h:14:37: note: declared here
         14 | Py_DEPRECATED(3.12) PyAPI_DATA(int) Py_NoSiteFlag;
            |                                     ^~~~~~~~~~~~~
      plugins/python/python_plugin.c: In function ‘uwsgi_python_init’:
      plugins/python/python_plugin.c:254:17: warning: ‘Py_SetPythonHome’ is deprecated [-Wdeprecated-declarations]
        254 |                 Py_SetPythonHome(wpyhome);
            |                 ^~~~~~~~~~~~~~~~
      In file included from /opt/indico/.pyenv/versions/3.12.9/include/python3.12/Python.h:94,
                       from plugins/python/uwsgi_python.h:4,
                       from plugins/python/python_plugin.c:1:
      /opt/indico/.pyenv/versions/3.12.9/include/python3.12/pylifecycle.h:40:38: note: declared here
         40 | Py_DEPRECATED(3.11) PyAPI_FUNC(void) Py_SetPythonHome(const wchar_t *);
            |                                      ^~~~~~~~~~~~~~~~
      plugins/python/python_plugin.c:278:9: warning: ‘Py_SetProgramName’ is deprecated [-Wdeprecated-declarations]
        278 |         Py_SetProgramName(pname);
            |         ^~~~~~~~~~~~~~~~~
      In file included from /opt/indico/.pyenv/versions/3.12.9/include/python3.12/Python.h:94,
                       from plugins/python/uwsgi_python.h:4,
                       from plugins/python/python_plugin.c:1:
      /opt/indico/.pyenv/versions/3.12.9/include/python3.12/pylifecycle.h:37:38: note: declared here
         37 | Py_DEPRECATED(3.11) PyAPI_FUNC(void) Py_SetProgramName(const wchar_t *);
            |                                      ^~~~~~~~~~~~~~~~~
      plugins/python/python_plugin.c:287:9: warning: ‘Py_OptimizeFlag’ is deprecated [-Wdeprecated-declarations]
        287 |         Py_OptimizeFlag = up.optimize;
            |         ^~~~~~~~~~~~~~~
      In file included from /opt/indico/.pyenv/versions/3.12.9/include/python3.12/Python.h:48,
                       from plugins/python/uwsgi_python.h:4,
                       from plugins/python/python_plugin.c:1:
      /opt/indico/.pyenv/versions/3.12.9/include/python3.12/cpython/pydebug.h:13:37: note: declared here
         13 | Py_DEPRECATED(3.12) PyAPI_DATA(int) Py_OptimizeFlag;
            |                                     ^~~~~~~~~~~~~~~
      [thread 0][gcc] plugins/python/pyutils.o
      plugins/python/pyutils.c: In function ‘init_pyargv’:
      plugins/python/pyutils.c:391:9: warning: ‘PySys_SetArgv’ is deprecated [-Wdeprecated-declarations]
        391 |         PySys_SetArgv(up.argc, up.py_argv);
            |         ^~~~~~~~~~~~~
      In file included from /opt/indico/.pyenv/versions/3.12.9/include/python3.12/Python.h:96,
                       from plugins/python/uwsgi_python.h:4,
                       from plugins/python/pyutils.c:1:
      /opt/indico/.pyenv/versions/3.12.9/include/python3.12/sysmodule.h:13:38: note: declared here
         13 | Py_DEPRECATED(3.11) PyAPI_FUNC(void) PySys_SetArgv(int, wchar_t **);
            |                                      ^~~~~~~~~~~~~
      [thread 0][gcc] plugins/python/pyloader.o
      [thread 0][gcc] plugins/python/wsgi_handlers.o
      [thread 0][gcc] plugins/python/wsgi_headers.o
      [thread 0][gcc] plugins/python/wsgi_subhandler.o
      [thread 0][gcc] plugins/python/web3_subhandler.o
      [thread 0][gcc] plugins/python/pump_subhandler.o
      [thread 0][gcc] plugins/python/gil.o
      [thread 0][gcc] plugins/python/uwsgi_pymodule.o
      [thread 0][gcc] plugins/python/profiler.o
      [thread 0][gcc] plugins/python/symimporter.o
      [thread 0][gcc] plugins/python/tracebacker.o
      [thread 0][gcc] plugins/python/raw.o
      [thread 0][gcc] plugins/gevent/gevent.o
      [thread 0][gcc] plugins/gevent/hooks.o
      [thread 0][gcc] plugins/ping/ping_plugin.o
      [thread 0][gcc] plugins/cache/cache.o
      [thread 0][gcc] plugins/nagios/nagios.o
      [thread 0][gcc] plugins/rrdtool/rrdtool.o
      [thread 0][gcc] plugins/carbon/carbon.o
      [thread 0][gcc] plugins/rpc/rpc_plugin.o
      [thread 0][gcc] plugins/corerouter/cr_common.o
      [thread 0][gcc] plugins/corerouter/cr_map.o
      [thread 0][gcc] plugins/corerouter/corerouter.o
      [thread 0][gcc] plugins/fastrouter/fastrouter.o
      [thread 0][gcc] plugins/http/http.o
      [thread 0][gcc] plugins/http/keepalive.o
      [thread 0][gcc] plugins/http/https.o
      [thread 0][gcc] plugins/http/spdy3.o
      [thread 0][gcc] plugins/ugreen/ugreen.o
      [thread 0][gcc] plugins/signal/signal_plugin.o
      [thread 0][gcc] plugins/syslog/syslog_plugin.o
      [thread 0][gcc] plugins/rsyslog/rsyslog_plugin.o
      [thread 0][gcc] plugins/logsocket/logsocket_plugin.o
      [thread 0][gcc] plugins/router_uwsgi/router_uwsgi.o
      [thread 0][gcc] plugins/router_redirect/router_redirect.o
      [thread 0][gcc] plugins/router_basicauth/router_basicauth.o
      [thread 0][gcc] plugins/zergpool/zergpool.o
      [thread 0][gcc] plugins/redislog/redislog_plugin.o
      [thread 0][gcc] plugins/mongodblog/mongodblog_plugin.o
      [thread 0][gcc] plugins/router_rewrite/router_rewrite.o
      [thread 0][gcc] plugins/router_http/router_http.o
      [thread 0][gcc] plugins/logfile/logfile.o
      [thread 0][gcc] plugins/router_cache/router_cache.o
      [thread 0][gcc] plugins/rawrouter/rawrouter.o
      [thread 0][gcc] plugins/router_static/router_static.o
      [thread 0][gcc] plugins/sslrouter/sslrouter.o
      [thread 0][gcc] plugins/spooler/spooler_plugin.o
      [thread 0][gcc] plugins/cheaper_busyness/cheaper_busyness.o
      [thread 0][gcc] plugins/symcall/symcall_plugin.o
      [thread 0][gcc] plugins/transformation_tofile/tofile.o
      [thread 0][gcc] plugins/transformation_gzip/gzip.o
      [thread 0][gcc] plugins/transformation_chunked/chunked.o
      [thread 0][gcc] plugins/transformation_offload/offload.o
      [thread 0][gcc] plugins/router_memcached/router_memcached.o
      [thread 0][gcc] plugins/router_redis/router_redis.o
      [thread 0][gcc] plugins/router_hash/router_hash.o
      [thread 0][gcc] plugins/router_expires/expires.o
      [thread 0][gcc] plugins/router_metrics/plugin.o
      [thread 0][gcc] plugins/transformation_template/tt.o
      [thread 0][gcc] plugins/stats_pusher_socket/plugin.o
      *** uWSGI linking ***
      gcc -o build/bdist.linux-x86_64/wheel/uWSGI-2.0.28.data/scripts/uwsgi -L/opt/indico/.pyenv/versions/3.12.9/lib -Wl,-rpath,/opt/indico/.pyenv/versions/3.12.9/lib core/utils.o core/protocol.o core/socket.o core/logging.o core/master.o core/master_utils.o core/emperor.o core/notify.o core/mule.o core/subscription.o core/stats.o core/sendfile.o core/async.o core/master_checks.o core/fifo.o core/offload.o core/io.o core/static.o core/websockets.o core/spooler.o core/snmp.o core/exceptions.o core/config.o core/setup_utils.o core/clock.o core/init.o core/buffer.o core/reader.o core/writer.o core/alarm.o core/cron.o core/hooks.o core/plugins.o core/lock.o core/cache.o core/daemons.o core/errors.o core/hash.o core/master_events.o core/chunked.o core/queue.o core/event.o core/signal.o core/strings.o core/progress.o core/timebomb.o core/ini.o core/fsmon.o core/mount.o core/metrics.o core/plugins_builder.o core/sharedarea.o core/rpc.o core/gateway.o core/loop.o core/cookie.o core/querystring.o core/rb_timers.o core/transformations.o core/uwsgi.o proto/base.o proto/uwsgi.o proto/http.o proto/fastcgi.o proto/scgi.o proto/puwsgi.o lib/linux_ns.o core/zlib.o core/regexp.o core/routing.o core/yaml.o core/ssl.o core/legion.o core/xmlconf.o core/dot_h.o core/config_py.o plugins/python/python_plugin.o plugins/python/pyutils.o plugins/python/pyloader.o plugins/python/wsgi_handlers.o plugins/python/wsgi_headers.o plugins/python/wsgi_subhandler.o plugins/python/web3_subhandler.o plugins/python/pump_subhandler.o plugins/python/gil.o plugins/python/uwsgi_pymodule.o plugins/python/profiler.o plugins/python/symimporter.o plugins/python/tracebacker.o plugins/python/raw.o plugins/gevent/gevent.o plugins/gevent/hooks.o plugins/ping/ping_plugin.o plugins/cache/cache.o plugins/nagios/nagios.o plugins/rrdtool/rrdtool.o plugins/carbon/carbon.o plugins/rpc/rpc_plugin.o plugins/corerouter/cr_common.o plugins/corerouter/cr_map.o plugins/corerouter/corerouter.o plugins/fastrouter/fastrouter.o plugins/http/http.o plugins/http/keepalive.o plugins/http/https.o plugins/http/spdy3.o plugins/ugreen/ugreen.o plugins/signal/signal_plugin.o plugins/syslog/syslog_plugin.o plugins/rsyslog/rsyslog_plugin.o plugins/logsocket/logsocket_plugin.o plugins/router_uwsgi/router_uwsgi.o plugins/router_redirect/router_redirect.o plugins/router_basicauth/router_basicauth.o plugins/zergpool/zergpool.o plugins/redislog/redislog_plugin.o plugins/mongodblog/mongodblog_plugin.o plugins/router_rewrite/router_rewrite.o plugins/router_http/router_http.o plugins/logfile/logfile.o plugins/router_cache/router_cache.o plugins/rawrouter/rawrouter.o plugins/router_static/router_static.o plugins/sslrouter/sslrouter.o plugins/spooler/spooler_plugin.o plugins/cheaper_busyness/cheaper_busyness.o plugins/symcall/symcall_plugin.o plugins/transformation_tofile/tofile.o plugins/transformation_gzip/gzip.o plugins/transformation_chunked/chunked.o plugins/transformation_offload/offload.o plugins/router_memcached/router_memcached.o plugins/router_redis/router_redis.o plugins/router_hash/router_hash.o plugins/router_expires/expires.o plugins/router_metrics/plugin.o plugins/transformation_template/tt.o plugins/stats_pusher_socket/plugin.o -lpthread -lm -rdynamic -ldl -lz -lpcre -luuid -lssl -lcrypto -lxml2 -lz -llzma -lm -ldl -L/opt/indico/.pyenv/versions/3.12.9/lib -Wl,-rpath,/opt/indico/.pyenv/versions/3.12.9/lib -lm -lpython3.12 -lcrypt
      /usr/bin/ld: cannot find core/dot_h.o: No such file or directory
      collect2: error: ld returned 1 exit status
      *** error linking uWSGI ***
      [end of output]
  
  note: This error originates from a subprocess, and is likely not a problem with pip.
  ERROR: Failed building wheel for uwsgi
  Running setup.py clean for uwsgi
Failed to build uwsgi
ERROR: Failed to build installable wheels for some pyproject.toml based projects (uwsgi)
Traceback (most recent call last):
  File "/opt/indico/.venv/lib/python3.12/site-packages/indico/cli/python_upgrader.py", line 141, in <module>
    main()
  File "/opt/indico/.venv/lib/python3.12/site-packages/indico/cli/python_upgrader.py", line 137, in main
    upgrader.reinstall_uwsgi()
  File "/opt/indico/.venv/lib/python3.12/site-packages/indico/cli/python_upgrader.py", line 53, in reinstall_uwsgi
    subprocess.run([str(self.venv_path / 'bin' / 'pip'), 'install', '--force-reinstall', '--no-cache', 'uwsgi'],
  File "/opt/indico/.pyenv/versions/3.12.9/lib/python3.12/subprocess.py", line 573, in run
    raise CalledProcessError(retcode, process.args,
subprocess.CalledProcessError: Command '['/opt/indico/.venv/bin/pip', 'install', '--force-reinstall', '--no-cache', 'uwsgi']' returned non-zero exit status 1.
Traceback (most recent call last):
  File "/opt/indico/.venv/bin/indico", line 8, in <module>
    sys.exit(cli())
             ^^^^^
  File "/opt/indico/.venv/lib/python3.12/site-packages/click/core.py", line 1157, in __call__
    return self.main(*args, **kwargs)
           ^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/opt/indico/.venv/lib/python3.12/site-packages/click/core.py", line 1078, in main
    rv = self.invoke(ctx)
         ^^^^^^^^^^^^^^^^
  File "/opt/indico/.venv/lib/python3.12/site-packages/click/core.py", line 1688, in invoke
    return _process_result(sub_ctx.command.invoke(sub_ctx))
                           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/opt/indico/.venv/lib/python3.12/site-packages/indico/cli/util.py", line 108, in invoke
    return self._impl.invoke(ctx)
           ^^^^^^^^^^^^^^^^^^^^^^
  File "/opt/indico/.venv/lib/python3.12/site-packages/click/core.py", line 1688, in invoke
    return _process_result(sub_ctx.command.invoke(sub_ctx))
                           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/opt/indico/.venv/lib/python3.12/site-packages/click/core.py", line 1434, in invoke
    return ctx.invoke(self.callback, **ctx.params)
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/opt/indico/.venv/lib/python3.12/site-packages/click/core.py", line 783, in invoke
    return __callback(*args, **kwargs)
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/opt/indico/.venv/lib/python3.12/site-packages/indico/cli/setup.py", line 305, in upgrade_python
    subprocess.run([sys.executable, '-I', python_upgrader.__file__, *args], check=True)
  File "/opt/indico/.pyenv/versions/3.12.8/lib/python3.12/subprocess.py", line 571, in run
    raise CalledProcessError(retcode, process.args,
subprocess.CalledProcessError: Command '['/opt/indico/.venv/bin/python', '-I', '/opt/indico/.venv/lib/python3.12/site-packages/indico/cli/python_upgrader.py', '/opt/indico/.venv']' returned non-zero exit status 1.
(indico) [indico@indico ~]$ indico setup upgrade-python
updating pyenv
Already running on preferred version (3.12.9)
(indico) [indico@indico ~]$ 

Indico is running on a Rocky Linux 9, updated just before starting the Indico update.

Is there anything I’m missing?

Thank you very much.

All the best,
Cristiano.

Ok,
I think I’ve solved by upgrading pip before installing Indico:

pip install --upgrade pip

Cheers,
Cristiano.