Use OS/system packaged sdsl library
kbipinkumar opened this issue · 10 comments
Platform
- SeqAn version: 3.2.0
- Operating system: Archlinux
- Compiler: gcc 13.1.1
Question
Is there a way to use sdsl library packaged in distribution repository?
we have managed to package sdsl as package for archlinux . the said package install sdsl library and headers as below
pacman -pQl sdsl-lite-2.3.1-2-x86_64.pkg.tar.zst
sdsl-lite /usr/
sdsl-lite /usr/include/
sdsl-lite /usr/include/sdsl/
sdsl-lite /usr/include/sdsl/bit_vector_il.hpp
sdsl-lite /usr/include/sdsl/bit_vectors.hpp
sdsl-lite /usr/include/sdsl/bits.hpp
sdsl-lite /usr/include/sdsl/bp_support.hpp
sdsl-lite /usr/include/sdsl/bp_support_algorithm.hpp
sdsl-lite /usr/include/sdsl/bp_support_g.hpp
sdsl-lite /usr/include/sdsl/bp_support_gg.hpp
sdsl-lite /usr/include/sdsl/bp_support_sada.hpp
sdsl-lite /usr/include/sdsl/coder.hpp
sdsl-lite /usr/include/sdsl/coder_comma.hpp
sdsl-lite /usr/include/sdsl/coder_elias_delta.hpp
sdsl-lite /usr/include/sdsl/coder_elias_gamma.hpp
sdsl-lite /usr/include/sdsl/coder_fibonacci.hpp
sdsl-lite /usr/include/sdsl/config.hpp
sdsl-lite /usr/include/sdsl/construct.hpp
sdsl-lite /usr/include/sdsl/construct_bwt.hpp
sdsl-lite /usr/include/sdsl/construct_config.hpp
sdsl-lite /usr/include/sdsl/construct_isa.hpp
sdsl-lite /usr/include/sdsl/construct_lcp.hpp
sdsl-lite /usr/include/sdsl/construct_lcp_helper.hpp
sdsl-lite /usr/include/sdsl/construct_sa.hpp
sdsl-lite /usr/include/sdsl/construct_sa_se.hpp
sdsl-lite /usr/include/sdsl/csa_alphabet_strategy.hpp
sdsl-lite /usr/include/sdsl/csa_bitcompressed.hpp
sdsl-lite /usr/include/sdsl/csa_sada.hpp
sdsl-lite /usr/include/sdsl/csa_sampling_strategy.hpp
sdsl-lite /usr/include/sdsl/csa_wt.hpp
sdsl-lite /usr/include/sdsl/cst_fully.hpp
sdsl-lite /usr/include/sdsl/cst_iterators.hpp
sdsl-lite /usr/include/sdsl/cst_sada.hpp
sdsl-lite /usr/include/sdsl/cst_sct3.hpp
sdsl-lite /usr/include/sdsl/dac_vector.hpp
sdsl-lite /usr/include/sdsl/enc_vector.hpp
sdsl-lite /usr/include/sdsl/fast_cache.hpp
sdsl-lite /usr/include/sdsl/hyb_vector.hpp
sdsl-lite /usr/include/sdsl/int_vector.hpp
sdsl-lite /usr/include/sdsl/int_vector_buffer.hpp
sdsl-lite /usr/include/sdsl/int_vector_io_wrappers.hpp
sdsl-lite /usr/include/sdsl/int_vector_mapper.hpp
sdsl-lite /usr/include/sdsl/inv_perm_support.hpp
sdsl-lite /usr/include/sdsl/io.hpp
sdsl-lite /usr/include/sdsl/iterators.hpp
sdsl-lite /usr/include/sdsl/k2_treap.hpp
sdsl-lite /usr/include/sdsl/k2_treap_algorithm.hpp
sdsl-lite /usr/include/sdsl/k2_treap_helper.hpp
sdsl-lite /usr/include/sdsl/k2_tree.hpp
sdsl-lite /usr/include/sdsl/k2_tree_helper.hpp
sdsl-lite /usr/include/sdsl/lcp.hpp
sdsl-lite /usr/include/sdsl/lcp_bitcompressed.hpp
sdsl-lite /usr/include/sdsl/lcp_byte.hpp
sdsl-lite /usr/include/sdsl/lcp_dac.hpp
sdsl-lite /usr/include/sdsl/lcp_support_sada.hpp
sdsl-lite /usr/include/sdsl/lcp_support_tree.hpp
sdsl-lite /usr/include/sdsl/lcp_support_tree2.hpp
sdsl-lite /usr/include/sdsl/lcp_vlc.hpp
sdsl-lite /usr/include/sdsl/lcp_wt.hpp
sdsl-lite /usr/include/sdsl/louds_tree.hpp
sdsl-lite /usr/include/sdsl/memory_management.hpp
sdsl-lite /usr/include/sdsl/nearest_neighbour_dictionary.hpp
sdsl-lite /usr/include/sdsl/nn_dict_dynamic.hpp
sdsl-lite /usr/include/sdsl/qsufsort.hpp
sdsl-lite /usr/include/sdsl/ram_filebuf.hpp
sdsl-lite /usr/include/sdsl/ram_fs.hpp
sdsl-lite /usr/include/sdsl/rank_support.hpp
sdsl-lite /usr/include/sdsl/rank_support_scan.hpp
sdsl-lite /usr/include/sdsl/rank_support_v.hpp
sdsl-lite /usr/include/sdsl/rank_support_v5.hpp
sdsl-lite /usr/include/sdsl/raster_img.hpp
sdsl-lite /usr/include/sdsl/rle_vector.hpp
sdsl-lite /usr/include/sdsl/rmq_succinct_sada.hpp
sdsl-lite /usr/include/sdsl/rmq_succinct_sct.hpp
sdsl-lite /usr/include/sdsl/rmq_support.hpp
sdsl-lite /usr/include/sdsl/rmq_support_sparse_table.hpp
sdsl-lite /usr/include/sdsl/rrr_helper.hpp
sdsl-lite /usr/include/sdsl/rrr_vector.hpp
sdsl-lite /usr/include/sdsl/rrr_vector_15.hpp
sdsl-lite /usr/include/sdsl/sd_vector.hpp
sdsl-lite /usr/include/sdsl/sdsl_concepts.hpp
sdsl-lite /usr/include/sdsl/select_support.hpp
sdsl-lite /usr/include/sdsl/select_support_mcl.hpp
sdsl-lite /usr/include/sdsl/select_support_scan.hpp
sdsl-lite /usr/include/sdsl/sfstream.hpp
sdsl-lite /usr/include/sdsl/simple_sds.hpp
sdsl-lite /usr/include/sdsl/sorted_int_stack.hpp
sdsl-lite /usr/include/sdsl/sorted_multi_stack_support.hpp
sdsl-lite /usr/include/sdsl/sorted_stack_support.hpp
sdsl-lite /usr/include/sdsl/structure_tree.hpp
sdsl-lite /usr/include/sdsl/suffix_array_algorithm.hpp
sdsl-lite /usr/include/sdsl/suffix_array_helper.hpp
sdsl-lite /usr/include/sdsl/suffix_arrays.hpp
sdsl-lite /usr/include/sdsl/suffix_tree_algorithm.hpp
sdsl-lite /usr/include/sdsl/suffix_tree_helper.hpp
sdsl-lite /usr/include/sdsl/suffix_trees.hpp
sdsl-lite /usr/include/sdsl/uint128_t.hpp
sdsl-lite /usr/include/sdsl/uint256_t.hpp
sdsl-lite /usr/include/sdsl/uintx_t.hpp
sdsl-lite /usr/include/sdsl/util.hpp
sdsl-lite /usr/include/sdsl/vectors.hpp
sdsl-lite /usr/include/sdsl/vlc_vector.hpp
sdsl-lite /usr/include/sdsl/wavelet_trees.hpp
sdsl-lite /usr/include/sdsl/wm_int.hpp
sdsl-lite /usr/include/sdsl/wt_algorithm.hpp
sdsl-lite /usr/include/sdsl/wt_ap.hpp
sdsl-lite /usr/include/sdsl/wt_blcd.hpp
sdsl-lite /usr/include/sdsl/wt_gmr.hpp
sdsl-lite /usr/include/sdsl/wt_helper.hpp
sdsl-lite /usr/include/sdsl/wt_huff.hpp
sdsl-lite /usr/include/sdsl/wt_hutu.hpp
sdsl-lite /usr/include/sdsl/wt_int.hpp
sdsl-lite /usr/include/sdsl/wt_pc.hpp
sdsl-lite /usr/include/sdsl/wt_rlmn.hpp
sdsl-lite /usr/lib/
sdsl-lite /usr/lib/libsdsl.so
sdsl-lite /usr/lib/libsdsl.so.2.3.1
sdsl-lite /usr/lib/libsdsl.so.3
sdsl-lite /usr/lib/pkgconfig/
sdsl-lite /usr/lib/pkgconfig/sdsl-lite.pc
my query is whether it is possible to use the sdsl library from OS repo instead of checking out sdsl repo into submodules folder?
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.
Thanks for the input. We will attempt to build with submodule approach then.
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.
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.
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 buildthe 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 --recursivedid 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
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.
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
mainbranch. 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
Now I fix it at BioArchLinux/Packages@ad3a292
@kbipinkumar Could you help me check it if it's okay
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.
okay, you can close it now.
Thanks for the repo programmer.