Funnannotate

[laraPPr]

• link to support ticket: #2024093060001064
• website: https://funannotate.readthedocs.io
• installation docs: https://funannotate.readthedocs.io/en/latest/install.html
• toolchain: foss/2023a
• easyblock to use: PythonBundle
• required dependencies:
  • also include EVidenceModeler
  • DBD-mysql
  • funannotate check to see missing dependencies
• optional dependencies:
  • ...
• notes:
  • ...
• effort: (TBD)
• other install methods
  • conda: yes (link?) / no
  • container image: yes (link?) / no
  • pre-built binaries (RHEL8 Linux x86_64): yes (link?) / no
  • easyconfig outside EasyBuild: yes / no

[laraPPr]

Firs looking at DBD-mysql a depency and got stuck here. See WIP for the easyconfigs.

# output for command: perl Makefile.PL PREFIX=/data/gent/vo/000/gvo00002/vsc    46128/easybuild/RHEL8/cascadelake-ampere-ib/software/DBD-mysql/5.009-GCC-12.3.0


PLEASE NOTE:
For 'make test' to run properly, you must ensure that the
 database user 'vsc46128' can connect to your MySQL server
and has the proper privileges that these tests require such
as 'drop table', 'create table', 'drop procedure', 'create procedure'
 as well as others.
mysql> CREATE USER 'vsc46128'@'localhost' IDENTIFIED BY 's3kr1t';
mysql> GRANT ALL PRIVILEGES ON test.* TO 'vsc46128'@'localhost';
 You can also optionally set the user to run 'make test' with:
perl Makefile.PL --testuser=username
DBD::mysql requires MySQL 8.x or newer for building. Version reported by mys    ql_config --version: 11.6.0 at Makefile.PL line 451, <PIPE> line 3.

[boegel]

That looks like an incorrect check for the MySQL (MariaDB) version to me...

See https://github.com/perl5-dbi/DBD-mysql/blob/3f82c9a4658073d3e6acf5c3e81b2934edd98400/Makefile.PL#L449-L451

It requires that the version starts with 8 or 9... 🤦

[boegel]

Maybe we should be using https://metacpan.org/dist/DBD-MariaDB instead?

[laraPPr]

I just discovered that this exhists so did some double work https://github.com/easybuilders/easybuild-easyconfigs/blob/fdac40400e478c5bb4da1c7b6ef28376f8408f65/easybuild/easyconfigs/p/Perl-bundle-CPAN/Perl-bundle-CPAN-5.36.1-GCCcore-12.3.0.eb

[laraPPr]

Maybe we should be using https://metacpan.org/dist/DBD-MariaDB instead?

The documentation says that you have to install the actual MariaDB or MySQL as well

[laraPPr]

with the previous version of DBD-mysql we also build with 10. But the check was not added in that version

[boegel]

@laraPPr I guess we can patch the version check and see if that works?

[laraPPr]

Yes I can try that

[laraPPr]

I got that hook working but now it got stuck in the make step

564 dbdimp.c: In function mysql_dr_connect:

565 dbdimp.c:1244:31: error: MYSQL_OPT_COMPRESSION_ALGORITHMS undeclared (first use in this function)

566  1244 |           mysql_options(sock, MYSQL_OPT_COMPRESSION_ALGORITHMS, calg);

567       |                               ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

568 dbdimp.c:1244:31: note: each undeclared identifier is reported only once for each function it appears in

569 dbdimp.c:1415:31: error: MYSQL_OPT_GET_SERVER_PUBLIC_KEY undeclared (first use in this function); did you mean MYSQL_SERVER_PUBLIC_KEY?

570  1415 |           mysql_options(sock, MYSQL_OPT_GET_SERVER_PUBLIC_KEY, &server_get_pubkey);
571       |                               ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

572       |                               MYSQL_SERVER_PUBLIC_KEY

573 dbdimp.c:1479:22: error: SSL_MODE_PREFERRED undeclared (first use in this function)

574  1479 |           ssl_mode = SSL_MODE_PREFERRED;

575       |                      ^~~~~~~~~~~~~~~~~~

576 dbdimp.c:1481:26: error: SSL_MODE_VERIFY_IDENTITY undeclared (first use in this function)

577  1481 |               ssl_mode = SSL_MODE_VERIFY_IDENTITY;

578       |                          ^~~~~~~~~~~~~~~~~~~~~~~~

579 dbdimp.c:1483:26: error: SSL_MODE_VERIFY_CA undeclared (first use in this function)

580  1483 |               ssl_mode = SSL_MODE_VERIFY_CA;

581       |                          ^~~~~~~~~~~~~~~~~~

582 dbdimp.c:1485:26: error: SSL_MODE_REQUIRED undeclared (first use in this function)

583  1485 |               ssl_mode = SSL_MODE_REQUIRED;

584       |                          ^~~~~~~~~~~~~~~~~


585 dbdimp.c:1486:37: error: MYSQL_OPT_SSL_MODE undeclared (first use in this function); did you mean MYSQL_OPT_SSL_CRL?

586  1486 |             if (mysql_options(sock, MYSQL_OPT_SSL_MODE, &ssl_mode) != 0) {

587       |                                     ^~~~~~~~~~~~~~~~~~

588       |                                     MYSQL_OPT_SSL_CRL

589 dbdimp.c:1495:37: error: SSL_MODE_DISABLED undeclared (first use in this function)

590  1495 |             unsigned int ssl_mode = SSL_MODE_DISABLED;

591       |                                     ^~~~~~~~~~~~~~~~~

592 dbdimp.c: In function mysql_st_prepare:

593 dbdimp.c:2419:24: warning: assignment to my_bool * {aka char *} from incompatible pointer type _Bool * [-Wincompatible-pointer-types]

594  2419 |           bind->is_null=  &(fbind->is_null);

595       |                        ^

596 dbdimp.c: In function mysql_st_internal_execute41:

597 dbdimp.c:2856:9: warning: implicit declaration of function mysql_stmt_bind_named_param; did you mean mysql_stmt_bind_param? [-Wimplicit-function-declara    tion]

598  2856 |     if (mysql_stmt_bind_named_param(stmt,bind,num_params, NULL))

599       |         ^~~~~~~~~~~~~~~~~~~~~~~~~~~
600       |         mysql_stmt_bind_param

601 dbdimp.c: In function mysql_describe:

602 dbdimp.c:3170:22: warning: assignment to my_bool * {aka char *} from incompatible pointer type _Bool * [-Wincompatible-pointer-types]

603  3170 |       buffer->is_null= &(fbh->is_null);

604       |                      ^

605 dbdimp.c:3171:20: warning: assignment to my_bool * {aka char *} from incompatible pointer type _Bool * [-Wincompatible-pointer-types]

606  3171 |       buffer->error= (bool*) &(fbh->error);

607       |                    ^

608 dbdimp.c: In function mysql_db_quote:

609 dbdimp.c:4626:12: warning: implicit declaration of function mysql_real_escape_string_quote; did you mean mysql_real_escape_string? [-Wimplicit-function-declaration]

610  4626 |     sptr+= mysql_real_escape_string_quote(imp_dbh->pmysql, sptr,

611       |            ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

612       |            mysql_real_escape_string

613 make: *** [Makefile:356: dbdimp.o] Error 1

614 make: *** Waiting for unfinished jobs....