From stvchester at gmail.com  Thu Nov  3 01:45:19 2022
From: stvchester at gmail.com (Steve Chester)
Date: Thu Nov  3 09:23:35 2022
Subject: [odb-users] Error: auto_ptr is not a member of 'std'
Message-ID: <CAAFvKnNuz-AT7m0ZS5P5QLj9ZyNku=_3cHDUdTkq8bL=YzikkQ@mail.gmail.com>

Hello,

I am testing out the ODB using the libodb vcpkg, however I'm running into
an issue when I go to compile my project in visual studio 2022.  I am
specifying my C++ version as C++20 and am running into errors stating that
auto_ptr is not a member of std.  Looking at the documentation for
std::auto_ptr, it looks like it was removed in C++17.  I'm assuming it is a
configuration issue on my part, however I could not find anything online.
Is there a preprocessor definition I can define to replace the auto_ptr
with either shared_ptr or unique_ptr?

Any help would be appreciated.

Cheers,

-Steve Chester
From boris at codesynthesis.com  Thu Nov  3 09:37:42 2022
From: boris at codesynthesis.com (Boris Kolpackov)
Date: Thu Nov  3 09:31:42 2022
Subject: [odb-users] Error: auto_ptr is not a member of 'std'
In-Reply-To: <CAAFvKnNuz-AT7m0ZS5P5QLj9ZyNku=_3cHDUdTkq8bL=YzikkQ@mail.gmail.com>
References: <CAAFvKnNuz-AT7m0ZS5P5QLj9ZyNku=_3cHDUdTkq8bL=YzikkQ@mail.gmail.com>
Message-ID: <boris.20221103153019@codesynthesis.com>

Steve Chester <stvchester@gmail.com> writes:

> I am testing out the ODB using the libodb vcpkg, however I'm running into
> an issue when I go to compile my project in visual studio 2022.  I am
> specifying my C++ version as C++20 and am running into errors stating that
> auto_ptr is not a member of std.  Looking at the documentation for
> std::auto_ptr, it looks like it was removed in C++17.  Is there a
> preprocessor definition I can define to replace the auto_ptr with
> either shared_ptr or unique_ptr?

I am not sure how vcpkg builds ODB (or which version), but the first
thing to try would be to add `--std c++11` to your ODB compiler
invocation and see if that helps.

If that doesn't help, you can try to get ODB via build2[1], which is
known to build the runtimes[2] in the C++20 mode with Visual Studio
2022.

[1] https://codesynthesis.com/products/odb/doc/install-build2.xhtml

[2] https://cppget.org/?builds=libodb&cf=windows*-msvc_17**

From vavp12345 at yandex.ru  Mon Nov  7 02:40:11 2022
From: vavp12345 at yandex.ru (=?utf-8?B?0JDRgNGC0LXQvCDQkdCw0LHQsNC10LI=?=)
Date: Mon Nov  7 06:44:20 2022
Subject: [odb-users] the same SQL query is handled differently by odb and
	some DBManager
Message-ID: <19505101667805286@mail.yandex.ru>

<div style="background-color:rgb( 255 , 255 , 255 );color:rgb( 0 , 0 , 0 );font-family:'ys text' , 'arial' , sans-serif;font-size:16px;font-style:normal;font-weight:400;text-decoration-style:initial;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px">OS: Ubuntu 20.04.4 LTS</div><div style="background-color:rgb( 255 , 255 , 255 );color:rgb( 0 , 0 , 0 );font-family:'ys text' , 'arial' , sans-serif;font-size:16px;font-style:normal;font-weight:400;text-decoration-style:initial;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px">package: libodb-sqlite-2.5.0</div><div style="background-color:rgb( 255 , 255 , 255 );color:rgb( 0 , 0 , 0 );font-family:'ys text' , 'arial' , sans-serif;font-size:16px;font-style:normal;font-weight:400;text-decoration-style:initial;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px">compiler: gcc 9.4.0</div><div style="background-color:rgb( 255 , 255 , 255 );color:rgb( 0 , 0 , 0 );font-family:'ys text' , 'arial' , sans-serif;font-size:16px;font-style:normal;font-weight:400;text-decoration-style:initial;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px">SQlite DB</div><div style="background-color:rgb( 255 , 255 , 255 );color:rgb( 0 , 0 , 0 );font-family:'ys text' , 'arial' , sans-serif;font-size:16px;font-style:normal;font-weight:400;text-decoration-style:initial;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px">?</div><div style="background-color:rgb( 255 , 255 , 255 );color:rgb( 0 , 0 , 0 );font-family:'ys text' , 'arial' , sans-serif;font-size:16px;font-style:normal;font-weight:400;text-decoration-style:initial;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px">this SQL query works from some dbManager (DBeaver 21.3.4)<br />But doesnt works from odb::database (column and table names changed to simple little names)</div><div style="background-color:rgb( 255 , 255 , 255 );color:rgb( 0 , 0 , 0 );font-family:'ys text' , 'arial' , sans-serif;font-size:16px;font-style:normal;font-weight:400;text-decoration-style:initial;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px">?</div><div style="background-color:rgb( 255 , 255 , 255 );color:rgb( 0 , 0 , 0 );font-family:'ys text' , 'arial' , sans-serif;font-size:16px;font-style:normal;font-weight:400;text-decoration-style:initial;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px"><pre style="margin:0px;text-indent:0px"><span style="color:#c0c0c0"> ? ?</span><span style="color:#800080">QString</span><span style="color:#c0c0c0"> </span><span style="color:#092e64">s</span><span style="color:#c0c0c0"> </span>=<span style="color:#c0c0c0"> </span><span style="color:#808000">R"(</span></pre><pre style="margin:0px;text-indent:0px"><span style="color:#008000"> ? ?UPDATE "T1" SET "c1"="2"</span></pre><pre style="margin:0px;text-indent:0px"><span style="color:#008000"> ? ?FROM (SELECT rowid, "c2" FROM "T2" WHERE "c2" IN (51,52) AND "c3" = 59) AS t2</span></pre><pre style="margin:0px;text-indent:0px"><span style="color:#008000"> ? ?WHERE "c4" = t2.rowid</span></pre><pre style="margin:0px;text-indent:0px"><span style="color:#008000"> ? ?</span><span style="color:#808000">)"</span>;</pre><pre style="margin:0px;text-indent:0px">
?</pre><pre style="margin:0px;text-indent:0px"><span style="color:#c0c0c0"> ? ?</span><span style="color:#092e64">dbConn</span>.<span style="color:#00677c">execute</span>(<span style="color:#092e64">s</span>.<span style="color:#00677c">toStdString</span>());</pre><div>?</div><div>i can do this query and it works:<pre style="margin:0px;text-indent:0px"><span style="color:#008000">WITH</span><span style="color:#c0c0c0"> </span><span style="color:#008000">t2</span><span style="color:#c0c0c0"> </span><span style="color:#008000">AS</span><span style="color:#c0c0c0"> </span><span style="color:#008000">(SELECT</span><span style="color:#c0c0c0"> </span><span style="color:#008000">rowid</span><span style="color:#c0c0c0"> </span><span style="color:#008000">FROM</span><span style="color:#c0c0c0"> </span><span style="color:#008000">"T2"</span><span style="color:#c0c0c0"> </span><span style="color:#008000">WHERE</span><span style="color:#c0c0c0"> </span><span style="color:#008000">"c2"</span><span style="color:#c0c0c0"> </span><span style="color:#008000">IN</span><span style="color:#c0c0c0"> </span><span style="color:#008000">(51,52)</span><span style="color:#c0c0c0"> </span><span style="color:#008000">AND</span><span style="color:#c0c0c0"> </span><span style="color:#008000">"c3"</span><span style="color:#c0c0c0"> </span><span style="color:#008000">=</span><span style="color:#c0c0c0"> </span><span style="color:#008000">59)</span></pre><div><span style="color:#008000">UPDATE "T1" SET "c1"="2"</span></div><div><span style="color:#008000">WHERE "c4" IN?t2</span></div><div>?</div><div>but?eventually i need somethink like this, so i need to get reference to foreign table.</div><div>?</div><div><pre style="margin:0px;text-indent:0px"><span style="color:#008000">UPDATE "T1"</span></pre><pre style="margin:0px;text-indent:0px"><span style="color:#008000">SET "c1"=CASE t2.c2 WHEN 51 THEN 2 WHEN 52 THEN 3 END</span></pre><pre style="margin:0px;text-indent:0px"><span style="color:#008000">FROM (SELECT rowid, "c2" FROM "T2" WHERE "c2" IN (51,52) AND "c3" = 59) AS t2</span></pre><pre style="margin:0px;text-indent:0px"><span style="color:#008000">WHERE "c4" = t2.rowid</span></pre></div><div>?</div><div>i get an error on all of this attempts (keyword FROM in UPDATE query)</div><div><blockquote><div>odb::sqlite::database_exception 1: near "FROM": syntax error</div></blockquote></div></div></div><div>looks like there is some difference in the processing of SQL queries in odb and dbmanager</div><div>?</div><div>The question is:<br />How to ensure that you can use SQL queries that work from the database manager?</div>
From javier.gutierrez at web.de  Thu Nov 17 06:57:19 2022
From: javier.gutierrez at web.de (Javier Gutierrez)
Date: Thu Nov 17 06:51:16 2022
Subject: [odb-users] libsqlite3-1.so => not found
Message-ID: <002701d8fa7b$bf31c120$3d954360$@web.de>

Hello Boris,



Hope this mail finds you well.



I am trying to install odb on a brand new Ubuntu 22.04 box. But after
installation I see the libraries somehow "lose" their dependencies. Here is
what I mean:



For the installation I follow Installing ODB with build2 (codesynthesis.com)
<https://www.codesynthesis.com/products/odb/doc/install-build2.xhtml#linux-b
uild2>



In the section 1.3  Building ODB Runtime Libraries, in my folder
"/home/user1/odb/odb-build/libodb-gcc-11" I run the following:



# bpkg build libodb-sqlite

.

# ldd ./libodb-sqlite-2.5.0-b.23/odb/sqlite/libodb-sqlite-2.5.0-b.23.so

        linux-vdso.so.1 (0x00007ffef9d66000)

        libodb-2.5.0-b.23.so => /home/user1/
odb/odb-build/libodb-gcc-11/libodb-2.5.0-b.23/odb/libodb-2.5.0-b.23.so
(0x00007f6bd67d2000)

        libsqlite3-1.so =>
/home/user1/odb/odb-build/libodb-gcc-11/libsqlite3-3.35.5/libsqlite3/libsqli
te3-1.so (0x00007f6bd661e000)

        libstdc++.so.6 => /lib/x86_64-linux-gnu/libstdc++.so.6
(0x00007f6bd63e3000)

        libgcc_s.so.1 => /lib/x86_64-linux-gnu/libgcc_s.so.1
(0x00007f6bd63c3000)

        libc.so.6 => /lib/x86_64-linux-gnu/libc.so.6 (0x00007f6bd6199000)

        /lib64/ld-linux-x86-64.so.2 (0x00007f6bd6832000)

        libm.so.6 => /lib/x86_64-linux-gnu/libm.so.6 (0x00007f6bd60b2000)



Then I install:



# bpkg uninstall --all -recursive



After installation when I run ldd on
"/home/user1/odb/odb-build/libodb-gcc-11" I see following:



# ldd ./libodb-sqlite-2.5.0-b.23/odb/sqlite/libodb-sqlite-2.5.0-b.23.so


        linux-vdso.so.1 (0x00007ffec59a7000)


        libodb-2.5.0-b.23.so => not found  <----------

        libsqlite3-1.so => not found       <----------

        libstdc++.so.6 => /lib/x86_64-linux-gnu/libstdc++.so.6
(0x00007f1c49194000)

        libgcc_s.so.1 => /lib/x86_64-linux-gnu/libgcc_s.so.1
(0x00007f1c49174000)

        libc.so.6 => /lib/x86_64-linux-gnu/libc.so.6 (0x00007f1c48f4c000)


        libm.so.6 => /lib/x86_64-linux-gnu/libm.so.6 (0x00007f1c48e63000)


        /lib64/ld-linux-x86-64.so.2 (0x00007f1c49407000)



Any idea why these libraries are not found any more after running the
installation?

How to make bpkg download other versions, e.g.: 2.5.0-b.19?



NOTE: If I run "bpkg build libodb-sqlite ?sys:libsqlite3" using my
installation of sqlite3 libraries, then that dependency is not "lost" but
libodb-2.5.0-b.23.so is.



Thanks in advance.



Best regards,

Javier Gutierrez



From boris at codesynthesis.com  Fri Nov 18 02:48:46 2022
From: boris at codesynthesis.com (Boris Kolpackov)
Date: Fri Nov 18 02:42:36 2022
Subject: [odb-users] libsqlite3-1.so => not found
In-Reply-To: <002701d8fa7b$bf31c120$3d954360$@web.de>
References: <002701d8fa7b$bf31c120$3d954360$@web.de>
Message-ID: <boris.20221118093456@codesynthesis.com>

Javier Gutierrez <javier.gutierrez@web.de> writes:

> # bpkg uninstall --all -recursive
> 
> After installation when I run ldd on
> "/home/user1/odb/odb-build/libodb-gcc-11" I see following:
> 
> # ldd ./libodb-sqlite-2.5.0-b.23/odb/sqlite/libodb-sqlite-2.5.0-b.23.so
>  
>         libodb-2.5.0-b.23.so => not found  <----------
>
> Any idea why these libraries are not found any more after running the
> installation?

When build2 builds executables and shared libraries, it automatically
adds rpath so that you can run things in place. However, when
installing, build2 automatically re-links them to get rid of rpath
(since we don't want the installed binaries to contain rpath pointing
to build directories). One side effect of this is that binaries that
are left after the installation do not have rpath and are thus not
runnable. But this can be easily corrected with an update (which will
again re-link them but now with rpath):

$ bpkg update --all -recursive


> How to make bpkg download other versions, e.g.: 2.5.0-b.19?

You can specify the version to build, for example:

$ bpkg build libodb-sqlite/2.5.0-b.19

For details, see: https://build2.org/bpkg/doc/bpkg-pkg-build.xhtml

From doug at donohoe.info  Sun Nov 27 13:04:11 2022
From: doug at donohoe.info (Doug Donohoe)
Date: Mon Nov 28 08:40:50 2022
Subject: [odb-users] Dockerized odb build
Message-ID: <CADm_sO-YQ9RVBdRMGzuGV1UhXAhmaX0f_b1kQtmjNztquJwi4A@mail.gmail.com>

Hi odb community:

In an effort to get a multi-architecture Docker image of vcf-validator
<https://github.com/EBIvariation/vcf-validator> working so I could use it
on my M1 Mac, I ended up building the latest odb in Docker.  I thought it
might be useful for this community.

This is the PR:  https://github.com/EBIvariation/vcf-validator/pull/221
(checkout the Dockerfile and related Makefile commands).

For the purposes of this email, I created an odb branch
<https://github.com/dougdonohoe/vcf-validator/tree/odb> which has an
odb-only Dockerfile.  Here's how to test it out.

git clone git@github.com:dougdonohoe/vcf-validator.git
cd vcf-validator
git checkout odb
REPO_NAME=my-odb make build-odb
docker run -it --rm my-odb/odb:2.5.0-b.23 odb --version


This should work on amd64 and arm64 architectures (e.g., old and new Macs).

Thanks and hopefully this helps someone.

Doug Donohoe
From boris at codesynthesis.com  Tue Nov 29 08:18:13 2022
From: boris at codesynthesis.com (Boris Kolpackov)
Date: Tue Nov 29 08:11:56 2022
Subject: [odb-users] Dockerized odb build
In-Reply-To: <CADm_sO-YQ9RVBdRMGzuGV1UhXAhmaX0f_b1kQtmjNztquJwi4A@mail.gmail.com>
References: <CADm_sO-YQ9RVBdRMGzuGV1UhXAhmaX0f_b1kQtmjNztquJwi4A@mail.gmail.com>
Message-ID: <boris.20221129151703@codesynthesis.com>

Doug Donohoe <doug@donohoe.info> writes:

> For the purposes of this email, I created an odb branch
> <https://github.com/dougdonohoe/vcf-validator/tree/odb> which has an
> odb-only Dockerfile.  Here's how to test it out.
> 
> git clone git@github.com:dougdonohoe/vcf-validator.git
> cd vcf-validator
> git checkout odb
> REPO_NAME=my-odb make build-odb
> docker run -it --rm my-odb/odb:2.5.0-b.23 odb --version

Sounds nice, thanks for sharing!