Use OS/system packaged sdsl library

[kbipinkumar]

Use OS/system packaged sdsl library

[eseiler]

Dear @kbipinkumar,

Thanks for reaching out!

It is possible to use a packaged version, but the version needs to be 3.0.1, which is available here: https://github.com/xxsds/sdsl-lite

The packaged debian version (https://packages.debian.org/sid/libseqan3-dev, https://salsa.debian.org/med-team/seqan3) doesn't package sdsl-lite v3, but uses the submodule.

Please let us know if you have any further questions.

[kbipinkumar]

Thanks for the input. We will attempt to build with submodule approach then.

[kbipinkumar]

hi i am attempting to build from sources as below

$ git clone https://github.com/seqan/seqan3.git
$ cd seqan3
$ git submodule update --init --recursive
Submodule 'cereal' (https://github.com/USCiLab/cereal) registered for path 'submodules/cereal'
Submodule 'sdsl-lite' (https://github.com/xxsds/sdsl-lite) registered for path 'submodules/sdsl-lite'
Cloning into '/build/seqan3/src/seqan3/submodules/cereal'...
Cloning into '/build/seqan3/src/seqan3/submodules/sdsl-lite'...
Submodule path 'submodules/cereal': checked out 'ebef1e929807629befafbb2918ea1a08c7194554'
Submodule path 'submodules/sdsl-lite': checked out '549721d74f346f540b0e7c2e276dba643405c16e'
Submodule 'external/cereal' (https://github.com/USCiLab/cereal.git) registered for path 'submodules/sdsl-lite/external/cereal'
Submodule 'external/googletest' (https://github.com/google/googletest.git) registered for path 'submodules/sdsl-lite/external/googletest'
Cloning into '/build/seqan3/src/seqan3/submodules/sdsl-lite/external/cereal'...
Cloning into '/build/seqan3/src/seqan3/submodules/sdsl-lite/external/googletest'...
Submodule path 'submodules/sdsl-lite/external/cereal': checked out '02eace19a99ce3cd564ca4e379753d69af08c2c8'
Submodule path 'submodules/sdsl-lite/external/googletest': checked out 'e2239ee6043f73722e7aa812a459f54a28552929'
$ cmake -B build  \
        -DCMAKE_BUILD_TYPE='None' \
        -DCMAKE_INSTALL_PREFIX='/usr' \
        -DCMAKE_SKIP_RPATH=true \
        -Wno-dev
$  cmake --build build

the build process errors out as below

-- Finding SeqAn3 and checking requirements:
--   SeqAn3 include dir found:   /build/seqan3/src/seqan3/include
--   Detected as running from a repository checkout…
--     …adding submodule include:  /build/seqan3/src/seqan3/submodules/cereal/include
--     …adding submodule include:  /build/seqan3/src/seqan3/submodules/sdsl-lite/include
--   C++ Standard-20 support:    via -std=c++20
--   C++ Concepts support:       via -std=c++20
--   Thread support:             builtin.
CMake Error at build_system/seqan3-config.cmake:113 (message):
  The SDSL library is required, but wasn't found.  Get it from
  https://github.com/xxsds/sdsl-lite
Call Stack (most recent call first):
  build_system/seqan3-config.cmake:319 (seqan3_config_error)
  CMakeLists.txt:32 (find_package)


-- Configuring incomplete, errors occurred!

i am sure git submodule update --init --recursive did fetch sdsl-lite but it seems to be not detected by cmake.

[SGSSGene]

Hey, I couldn't reproduce this on my arch linux machine.
Can you tell me the exact git commit version, you are using?
The line C++ Concepts support: via -std=c++20 is suspicious. It was removed 24th Oct 2022 ( #771c10e108c ) . We require c++20 now in any case.

[starsareintherose]

hi i am attempting to build from sources as below

$ git clone https://github.com/seqan/seqan3.git
$ cd seqan3
$ git submodule update --init --recursive
Submodule 'cereal' (https://github.com/USCiLab/cereal) registered for path 'submodules/cereal'
Submodule 'sdsl-lite' (https://github.com/xxsds/sdsl-lite) registered for path 'submodules/sdsl-lite'
Cloning into '/build/seqan3/src/seqan3/submodules/cereal'...
Cloning into '/build/seqan3/src/seqan3/submodules/sdsl-lite'...
Submodule path 'submodules/cereal': checked out 'ebef1e929807629befafbb2918ea1a08c7194554'
Submodule path 'submodules/sdsl-lite': checked out '549721d74f346f540b0e7c2e276dba643405c16e'
Submodule 'external/cereal' (https://github.com/USCiLab/cereal.git) registered for path 'submodules/sdsl-lite/external/cereal'
Submodule 'external/googletest' (https://github.com/google/googletest.git) registered for path 'submodules/sdsl-lite/external/googletest'
Cloning into '/build/seqan3/src/seqan3/submodules/sdsl-lite/external/cereal'...
Cloning into '/build/seqan3/src/seqan3/submodules/sdsl-lite/external/googletest'...
Submodule path 'submodules/sdsl-lite/external/cereal': checked out '02eace19a99ce3cd564ca4e379753d69af08c2c8'
Submodule path 'submodules/sdsl-lite/external/googletest': checked out 'e2239ee6043f73722e7aa812a459f54a28552929'
$ cmake -B build  \
        -DCMAKE_BUILD_TYPE='None' \
        -DCMAKE_INSTALL_PREFIX='/usr' \
        -DCMAKE_SKIP_RPATH=true \
        -Wno-dev
$  cmake --build build

the build process errors out as below

-- Finding SeqAn3 and checking requirements:
--   SeqAn3 include dir found:   /build/seqan3/src/seqan3/include
--   Detected as running from a repository checkout…
--     …adding submodule include:  /build/seqan3/src/seqan3/submodules/cereal/include
--     …adding submodule include:  /build/seqan3/src/seqan3/submodules/sdsl-lite/include
--   C++ Standard-20 support:    via -std=c++20
--   C++ Concepts support:       via -std=c++20
--   Thread support:             builtin.
CMake Error at build_system/seqan3-config.cmake:113 (message):
  The SDSL library is required, but wasn't found.  Get it from
  https://github.com/xxsds/sdsl-lite
Call Stack (most recent call first):
  build_system/seqan3-config.cmake:319 (seqan3_config_error)
  CMakeLists.txt:32 (find_package)


-- Configuring incomplete, errors occurred!

i am sure git submodule update --init --recursive did fetch sdsl-lite but it seems to be not detected by cmake.

Sorry for the late, I found this issue but already Merged the PR, therefore the error log can be found here. You can commit this pkg on our repo directly.

Full log is here
https://build.bioarchlinux.org/api/pkg/seqan3/log/1688923248

[SGSSGene]

I can reproduce this. There seems to be an error with seqan3 3.2.0 release. Looking at the cmake documentation, I am not sure why it is working on the current main branch. We will investigate.

[eseiler]

I can reproduce this. There seems to be an error with seqan3 3.2.0 release. Looking at the cmake documentation, I am not sure why it is working on the current main branch. We will investigate.

It's because of ceb2f32. The sdsl was missing a header (for gcc>=13). Hence, the include check failed. gcc13 was not available when 3.2.0 was released.

SDSL commit: xxsds/sdsl-lite@607019d

[starsareintherose]

Now I fix it at BioArchLinux/Packages@ad3a292

@kbipinkumar Could you help me check it if it's okay

[kbipinkumar]

Now I fix it at BioArchLinux/Packages@ad3a292

@kbipinkumar Could you help me check it if it's okay

yeas. the package is being built just fine.

[starsareintherose]

okay, you can close it now.

Thanks for the repo programmer.