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Martinsos / edlib

Lightweight, super fast C/C++ (& Python) library for sequence alignment using edit (Levenshtein) distance.
http://martinsos.github.io/edlib
MIT License
492 stars 162 forks source link

Ubuntu 22.04, Python 3.12 => longintrepr.h: No such file or directory #222

Open nick-youngblut opened 6 days ago

nick-youngblut commented 6 days ago

Describe the bug

pip install edlib throws the error:

Collecting edlib
  Using cached edlib-1.3.9.tar.gz (91 kB)
  Preparing metadata (setup.py) ... done
Building wheels for collected packages: edlib
  Building wheel for edlib (setup.py) ... error
  error: subprocess-exited-with-error

  × python setup.py bdist_wheel did not run successfully.
  │ exit code: 1
  ╰─> [14 lines of output]
      running bdist_wheel
      running build
      running build_ext
      building 'edlib' extension
      creating build
      creating build/temp.linux-x86_64-cpython-312
      creating build/temp.linux-x86_64-cpython-312/edlib
      creating build/temp.linux-x86_64-cpython-312/edlib/src
      /home/nickyoungblut/miniforge3/envs/SQANTI3.env/bin/x86_64-conda-linux-gnu-cc -fno-strict-overflow -DNDEBUG -O2 -Wall -fPIC -O2 -isystem /home/nickyoungblut/miniforge3/envs/SQANTI3.env/include -fPIC -O2 -isystem /home/nickyoungblut/miniforge3/envs/SQANTI3.env/include -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem /home/nickyoungblut/miniforge3/envs/SQANTI3.env/include -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem /home/nickyoungblut/miniforge3/envs/SQANTI3.env/include -fPIC -Iedlib/include -I/home/nickyoungblut/miniforge3/envs/SQANTI3.env/include/python3.12 -c edlib.bycython.cpp -o build/temp.linux-x86_64-cpython-312/edlib.bycython.o -O3 -std=c++11
      edlib.bycython.cpp:198:12: fatal error: longintrepr.h: No such file or directory
        198 |   #include "longintrepr.h"
            |            ^~~~~~~~~~~~~~~
      compilation terminated.
      error: command '/home/nickyoungblut/miniforge3/envs/SQANTI3.env/bin/x86_64-conda-linux-gnu-cc' failed with exit code 1
      [end of output]

  note: This error originates from a subprocess, and is likely not a problem with pip.
  ERROR: Failed building wheel for edlib
  Running setup.py clean for edlib
Failed to build edlib
ERROR: Could not build wheels for edlib, which is required to install pyproject.toml-based projects

To Reproduce

See above

Expected behavior

Environment (please complete the following information):

conda env

# Name                    Version                   Build  Channel
_libgcc_mutex             0.1                 conda_forge    conda-forge
_openmp_mutex             4.5                       2_gnu    conda-forge
_r-mutex                  1.0.1               anacondar_1    conda-forge
argcomplete               3.4.0              pyhd8ed1ab_0    conda-forge
bcbio-gff                 0.7.1              pyh7cba7a3_1    bioconda
bedtools                  2.31.1               hf5e1c6e_1    bioconda
binutils                  2.40                 h4852527_7    conda-forge
binutils_impl_linux-64    2.40                 ha1999f0_7    conda-forge
binutils_linux-64         2.40                 hb3c18ed_9    conda-forge
bioconductor-annotationdbi 1.64.1            r43hdfd78af_0    bioconda
bioconductor-annotationfilter 1.26.0            r43hdfd78af_0    bioconda
bioconductor-biobase      2.62.0            r43ha9d7317_2    bioconda
bioconductor-biocfilecache 2.10.1            r43hdfd78af_0    bioconda
bioconductor-biocgenerics 0.48.1            r43hdfd78af_2    bioconda
bioconductor-biocio       1.12.0            r43hdfd78af_0    bioconda
bioconductor-biocparallel 1.36.0            r43hf17093f_2    bioconda
bioconductor-biomart      2.58.0            r43hdfd78af_0    bioconda
bioconductor-biostrings   2.70.1            r43ha9d7317_2    bioconda
bioconductor-bsgenome     1.70.1            r43hdfd78af_0    bioconda
bioconductor-busparse     1.16.0            r43hf17093f_0    bioconda
bioconductor-data-packages 20231203             hdfd78af_0    bioconda
bioconductor-delayedarray 0.28.0            r43ha9d7317_2    bioconda
bioconductor-ensembldb    2.26.0            r43hdfd78af_0    bioconda
bioconductor-genomeinfodb 1.38.1            r43hdfd78af_1    bioconda
bioconductor-genomeinfodbdata 1.2.11            r43hdfd78af_1    bioconda
bioconductor-genomicalignments 1.38.0            r43ha9d7317_1    bioconda
bioconductor-genomicfeatures 1.54.1            r43hdfd78af_0    bioconda
bioconductor-genomicranges 1.54.1            r43ha9d7317_2    bioconda
bioconductor-iranges      2.36.0            r43ha9d7317_2    bioconda
bioconductor-keggrest     1.42.0            r43hdfd78af_0    bioconda
bioconductor-matrixgenerics 1.14.0            r43hdfd78af_3    bioconda
bioconductor-noiseq       2.46.0            r43hdfd78af_0    bioconda
bioconductor-plyranges    1.22.0            r43hdfd78af_0    bioconda
bioconductor-protgenerics 1.34.0            r43hdfd78af_0    bioconda
bioconductor-rhtslib      2.4.0             r43ha9d7317_2    bioconda
bioconductor-rsamtools    2.18.0            r43hf17093f_2    bioconda
bioconductor-rtracklayer  1.62.0            r43ha9d7317_1    bioconda
bioconductor-s4arrays     1.2.0             r43ha9d7317_2    bioconda
bioconductor-s4vectors    0.40.2            r43ha9d7317_2    bioconda
bioconductor-sparsearray  1.2.2             r43ha9d7317_2    bioconda
bioconductor-summarizedexperiment 1.32.0            r43hdfd78af_0    bioconda
bioconductor-xvector      0.42.0            r43ha9d7317_2    bioconda
bioconductor-zlibbioc     1.48.0            r43ha9d7317_2    bioconda
biopython                 1.81            py312h98912ed_1    conda-forge
bwidget                   1.9.14               ha770c72_1    conda-forge
bx-python                 0.11.0          py312hf0ab922_2    bioconda
bzip2                     1.0.8                hd590300_5    conda-forge
c-ares                    1.28.1               hd590300_0    conda-forge
c-compiler                1.7.0                hd590300_1    conda-forge
ca-certificates           2024.6.2             hbcca054_0    conda-forge
cairo                     1.18.0               h3faef2a_0    conda-forge
compilers                 1.7.0                ha770c72_1    conda-forge
curl                      8.8.0                he654da7_0    conda-forge
cxx-compiler              1.7.0                h00ab1b0_1    conda-forge
cython                    3.0.10          py312h30efb56_0    conda-forge
desalt                    1.5.6                he4a0461_4    bioconda
expat                     2.6.2                h59595ed_0    conda-forge
font-ttf-dejavu-sans-mono 2.37                 hab24e00_0    conda-forge
font-ttf-inconsolata      3.000                h77eed37_0    conda-forge
font-ttf-source-code-pro  2.038                h77eed37_0    conda-forge
font-ttf-ubuntu           0.83                 h77eed37_2    conda-forge
fontconfig                2.14.2               h14ed4e7_0    conda-forge
fonts-conda-ecosystem     1                             0    conda-forge
fonts-conda-forge         1                             0    conda-forge
fortran-compiler          1.7.0                heb67821_1    conda-forge
freetype                  2.12.1               h267a509_2    conda-forge
fribidi                   1.0.10               h36c2ea0_0    conda-forge
gcc                       12.3.0              h915e2ae_13    conda-forge
gcc_impl_linux-64         12.3.0              h58ffeeb_13    conda-forge
gcc_linux-64              12.3.0               h9528a6a_9    conda-forge
gffread                   0.12.7               hdcf5f25_4    bioconda
gfortran                  12.3.0              h915e2ae_13    conda-forge
gfortran_impl_linux-64    12.3.0              h8f2110c_13    conda-forge
gfortran_linux-64         12.3.0               h5877db1_9    conda-forge
gmap                      2024.05.20      pl5321h9d449c0_0    bioconda
graphite2                 1.3.13            h59595ed_1003    conda-forge
gxx                       12.3.0              h915e2ae_13    conda-forge
gxx_impl_linux-64         12.3.0              h2a574ab_13    conda-forge
gxx_linux-64              12.3.0               ha28b414_9    conda-forge
harfbuzz                  8.5.0                hfac3d4d_0    conda-forge
hdf5                      1.12.1          nompi_h4df4325_104    conda-forge
htslib                    1.20                 h5efdd21_1    bioconda
icu                       73.2                 h59595ed_0    conda-forge
jq                        1.7.1                hd590300_0    conda-forge
k8                        0.2.5                hdcf5f25_4    bioconda
kallisto                  0.48.0               h15996b6_2    bioconda
kernel-headers_linux-64   2.6.32              he073ed8_17    conda-forge
keyutils                  1.6.1                h166bdaf_0    conda-forge
krb5                      1.21.2               h659d440_0    conda-forge
ld_impl_linux-64          2.40                 hf3520f5_7    conda-forge
lerc                      4.0.0                h27087fc_0    conda-forge
libblas                   3.9.0           20_linux64_openblas    conda-forge
libcblas                  3.9.0           20_linux64_openblas    conda-forge
libcurl                   8.8.0                hca28451_0    conda-forge
libdeflate                1.20                 hd590300_0    conda-forge
libedit                   3.1.20191231         he28a2e2_2    conda-forge
libev                     4.33                 hd590300_2    conda-forge
libexpat                  2.6.2                h59595ed_0    conda-forge
libffi                    3.4.2                h7f98852_5    conda-forge
libgcc-devel_linux-64     12.3.0             h6b66f73_113    conda-forge
libgcc-ng                 13.2.0              h77fa898_13    conda-forge
libgfortran-ng            13.2.0              h69a702a_13    conda-forge
libgfortran5              13.2.0              h3d2ce59_13    conda-forge
libgit2                   1.8.1                ha5f426f_0    conda-forge
libglib                   2.80.2               hf974151_0    conda-forge
libgomp                   13.2.0              h77fa898_13    conda-forge
libiconv                  1.17                 hd590300_2    conda-forge
libjpeg-turbo             3.0.0                hd590300_1    conda-forge
liblapack                 3.9.0           20_linux64_openblas    conda-forge
libnghttp2                1.58.0               h47da74e_1    conda-forge
libnsl                    2.0.1                hd590300_0    conda-forge
libopenblas               0.3.25          pthreads_h413a1c8_0    conda-forge
libpng                    1.6.43               h2797004_0    conda-forge
libsanitizer              12.3.0              hb8811af_13    conda-forge
libsqlite                 3.46.0               hde9e2c9_0    conda-forge
libssh2                   1.11.0               h0841786_0    conda-forge
libstdcxx-devel_linux-64  12.3.0             h6b66f73_113    conda-forge
libstdcxx-ng              13.2.0              hc0a3c3a_13    conda-forge
libtiff                   4.6.0                h1dd3fc0_3    conda-forge
libuuid                   2.38.1               h0b41bf4_0    conda-forge
libwebp-base              1.4.0                hd590300_0    conda-forge
libxcb                    1.15                 h0b41bf4_0    conda-forge
libxcrypt                 4.4.36               hd590300_1    conda-forge
libxml2                   2.12.7               hc051c1a_1    conda-forge
libzlib                   1.2.13               h4ab18f5_6    conda-forge
make                      4.3                  hd18ef5c_1    conda-forge
minimap2                  2.28                 he4a0461_1    bioconda
ncurses                   6.5                  h59595ed_0    conda-forge
numpy                     1.26.4          py312heda63a1_0    conda-forge
oniguruma                 6.9.9                hd590300_0    conda-forge
openssl                   3.3.1                h4ab18f5_0    conda-forge
pandoc                    3.2.1                ha770c72_0    conda-forge
pango                     1.54.0               h84a9a3c_0    conda-forge
pcre2                     10.43                hcad00b1_0    conda-forge
perl                      5.32.1          7_hd590300_perl5    conda-forge
perl-constant             1.33            pl5321hd8ed1ab_0    conda-forge
perl-exporter             5.74            pl5321hd8ed1ab_0    conda-forge
perl-file-util            4.201720        pl5321hdfd78af_0    bioconda
perl-lib                  0.63            pl5321hd8ed1ab_0    conda-forge
pip                       24.0               pyhd8ed1ab_0    conda-forge
pixman                    0.43.2               h59595ed_0    conda-forge
psutil                    6.0.0           py312h9a8786e_0    conda-forge
pthread-stubs             0.4               h36c2ea0_1001    conda-forge
pybedtools                0.10.0          py312ha1f7cf2_1    bioconda
pysam                     0.22.1          py312hcfdcdd7_1    bioconda
python                    3.12.3          hab00c5b_0_cpython    conda-forge
python_abi                3.12                    4_cp312    conda-forge
pyyaml                    6.0.1           py312h98912ed_1    conda-forge
r                         4.3             r43hd8ed1ab_1007    conda-forge
r-abind                   1.4_5           r43hc72bb7e_1005    conda-forge
r-askpass                 1.2.0             r43h57805ef_0    conda-forge
r-assertthat              0.2.1             r43hc72bb7e_4    conda-forge
r-base                    4.3.3                hf0d99cb_1    conda-forge
r-base64enc               0.1_3           r43h57805ef_1006    conda-forge
r-bh                      1.84.0_0          r43hc72bb7e_0    conda-forge
r-biocmanager             1.30.23           r43hc72bb7e_0    conda-forge
r-bit                     4.0.5             r43h57805ef_1    conda-forge
r-bit64                   4.0.5             r43h57805ef_2    conda-forge
r-bitops                  1.0_7             r43h57805ef_2    conda-forge
r-blob                    1.2.4             r43hc72bb7e_1    conda-forge
r-boot                    1.3_30            r43hc72bb7e_0    conda-forge
r-brew                    1.0_10            r43hc72bb7e_0    conda-forge
r-brio                    1.1.5             r43hb1dbf0f_0    conda-forge
r-bslib                   0.7.0             r43hc72bb7e_0    conda-forge
r-cachem                  1.1.0             r43hb1dbf0f_0    conda-forge
r-callr                   3.7.6             r43hc72bb7e_0    conda-forge
r-caret                   6.0_94            r43h57805ef_1    conda-forge
r-class                   7.3_22            r43h57805ef_1    conda-forge
r-cli                     3.6.3             r43ha18555a_0    conda-forge
r-clipr                   0.8.0             r43hc72bb7e_2    conda-forge
r-clock                   0.7.0             r43ha503ecb_1    conda-forge
r-cluster                 2.1.6             r43h61816a4_0    conda-forge
r-codetools               0.2_20            r43hc72bb7e_0    conda-forge
r-colorspace              2.1_0             r43h57805ef_1    conda-forge
r-commonmark              1.9.1             r43h57805ef_0    conda-forge
r-cpp11                   0.4.7             r43hc72bb7e_0    conda-forge
r-crayon                  1.5.3             r43hc72bb7e_0    conda-forge
r-credentials             2.0.1             r43hc72bb7e_0    conda-forge
r-crosstalk               1.2.1             r43hc72bb7e_0    conda-forge
r-curl                    5.1.0             r43hf9611b0_0    conda-forge
r-data.table              1.15.2            r43h029312a_0    conda-forge
r-dbi                     1.2.3             r43hc72bb7e_0    conda-forge
r-dbplyr                  2.5.0             r43hc72bb7e_0    conda-forge
r-desc                    1.4.3             r43hc72bb7e_0    conda-forge
r-devtools                2.4.5             r43hc72bb7e_2    conda-forge
r-diagram                 1.6.5             r43ha770c72_2    conda-forge
r-diffobj                 0.3.5             r43h57805ef_2    conda-forge
r-digest                  0.6.36            r43ha18555a_0    conda-forge
r-downlit                 0.4.4             r43hc72bb7e_0    conda-forge
r-dplyr                   1.1.4             r43ha503ecb_0    conda-forge
r-dt                      0.33              r43hc72bb7e_0    conda-forge
r-e1071                   1.7_14            r43ha503ecb_0    conda-forge
r-ellipsis                0.3.2             r43h57805ef_2    conda-forge
r-evaluate                0.24.0            r43hc72bb7e_0    conda-forge
r-fansi                   1.0.6             r43h57805ef_0    conda-forge
r-farver                  2.1.2             r43ha18555a_0    conda-forge
r-fastmap                 1.2.0             r43ha18555a_0    conda-forge
r-filelock                1.0.3             r43h57805ef_0    conda-forge
r-fontawesome             0.5.2             r43hc72bb7e_0    conda-forge
r-forcats                 1.0.0             r43hc72bb7e_1    conda-forge
r-foreach                 1.5.2             r43hc72bb7e_2    conda-forge
r-foreign                 0.8_86            r43h57805ef_0    conda-forge
r-formatr                 1.14              r43hc72bb7e_1    conda-forge
r-fs                      1.6.4             r43ha18555a_0    conda-forge
r-futile.logger           1.4.3           r43hc72bb7e_1005    conda-forge
r-futile.options          1.0.1           r43hc72bb7e_1004    conda-forge
r-future                  1.33.2            r43h785f33e_0    conda-forge
r-future.apply            1.11.2            r43hc72bb7e_0    conda-forge
r-generics                0.1.3             r43hc72bb7e_2    conda-forge
r-gert                    2.0.1             r43h9b95477_1    conda-forge
r-getopt                  1.20.4            r43ha770c72_0    conda-forge
r-ggplot2                 3.5.1             r43hc72bb7e_0    conda-forge
r-ggplotify               0.1.2             r43hc72bb7e_0    conda-forge
r-gh                      1.4.1             r43hc72bb7e_0    conda-forge
r-gitcreds                0.1.2             r43hc72bb7e_2    conda-forge
r-globals                 0.16.3            r43hc72bb7e_0    conda-forge
r-glue                    1.7.0             r43h57805ef_0    conda-forge
r-gower                   1.0.1             r43h57805ef_1    conda-forge
r-gridbase                0.4_7           r43hc72bb7e_1005    conda-forge
r-gridextra               2.3             r43hc72bb7e_1005    conda-forge
r-gridgraphics            0.5_1             r43hc72bb7e_2    conda-forge
r-gtable                  0.3.5             r43hc72bb7e_0    conda-forge
r-hardhat                 1.4.0             r43hc72bb7e_0    conda-forge
r-hexbin                  1.28.3            r43h61816a4_1    conda-forge
r-highr                   0.11              r43hc72bb7e_0    conda-forge
r-hms                     1.1.3             r43hc72bb7e_1    conda-forge
r-htmltools               0.5.8.1           r43ha503ecb_0    conda-forge
r-htmlwidgets             1.6.4             r43hc72bb7e_1    conda-forge
r-httpuv                  1.6.15            r43ha503ecb_0    conda-forge
r-httr                    1.4.7             r43hc72bb7e_0    conda-forge
r-httr2                   1.0.1             r43hc72bb7e_0    conda-forge
r-ini                     0.3.1           r43hc72bb7e_1005    conda-forge
r-ipred                   0.9_14            r43h57805ef_1    conda-forge
r-isoband                 0.2.7             r43ha503ecb_2    conda-forge
r-iterators               1.0.14            r43hc72bb7e_2    conda-forge
r-jquerylib               0.1.4             r43hc72bb7e_2    conda-forge
r-jsonlite                1.8.8             r43h57805ef_0    conda-forge
r-kernsmooth              2.23_24           r43hc2011d3_0    conda-forge
r-knitr                   1.47              r43hc72bb7e_0    conda-forge
r-labeling                0.4.3             r43hc72bb7e_0    conda-forge
r-lambda.r                1.2.4             r43hc72bb7e_3    conda-forge
r-later                   1.3.2             r43ha503ecb_0    conda-forge
r-lattice                 0.22_6            r43h57805ef_0    conda-forge
r-lava                    1.7.3             r43hc72bb7e_0    conda-forge
r-lazyeval                0.2.2             r43h57805ef_4    conda-forge
r-lifecycle               1.0.4             r43hc72bb7e_0    conda-forge
r-listenv                 0.9.1             r43hc72bb7e_0    conda-forge
r-lubridate               1.9.3             r43h57805ef_0    conda-forge
r-magrittr                2.0.3             r43h57805ef_2    conda-forge
r-mass                    7.3_60            r43h57805ef_1    conda-forge
r-matrix                  1.6_5             r43h316c678_0    conda-forge
r-matrixstats             1.3.0             r43h57805ef_0    conda-forge
r-memoise                 2.0.1             r43hc72bb7e_2    conda-forge
r-mgcv                    1.9_1             r43h316c678_0    conda-forge
r-mime                    0.12              r43h57805ef_2    conda-forge
r-miniui                  0.1.1.1         r43hc72bb7e_1004    conda-forge
r-modelmetrics            1.2.2.2           r43ha503ecb_3    conda-forge
r-munsell                 0.5.1             r43hc72bb7e_0    conda-forge
r-nlme                    3.1_165           r43hbcb9c34_0    conda-forge
r-nnet                    7.3_19            r43h57805ef_1    conda-forge
r-numderiv                2016.8_1.1        r43hc72bb7e_5    conda-forge
r-openssl                 2.2.0             r43hd7d0243_0    conda-forge
r-optparse                1.7.5             r43hc72bb7e_0    conda-forge
r-parallelly              1.37.1            r43h57805ef_0    conda-forge
r-pillar                  1.9.0             r43hc72bb7e_1    conda-forge
r-pkgbuild                1.4.4             r43hc72bb7e_0    conda-forge
r-pkgconfig               2.0.3             r43hc72bb7e_3    conda-forge
r-pkgdown                 2.0.9             r43hc72bb7e_0    conda-forge
r-pkgload                 1.3.4             r43hc72bb7e_0    conda-forge
r-plogr                   0.2.0           r43hc72bb7e_1005    conda-forge
r-plotly                  4.10.4            r43hc72bb7e_0    conda-forge
r-plyr                    1.8.9             r43ha503ecb_0    conda-forge
r-png                     0.1_8             r43h81d01c5_1    conda-forge
r-praise                  1.0.0           r43hc72bb7e_1007    conda-forge
r-prettyunits             1.2.0             r43hc72bb7e_0    conda-forge
r-proc                    1.18.5            r43ha503ecb_0    conda-forge
r-processx                3.8.4             r43h57805ef_0    conda-forge
r-prodlim                 2024.06.25        r43ha18555a_0    conda-forge
r-profvis                 0.3.8             r43h57805ef_3    conda-forge
r-progress                1.2.3             r43hc72bb7e_0    conda-forge
r-progressr               0.14.0            r43hc72bb7e_0    conda-forge
r-promises                1.3.0             r43ha503ecb_0    conda-forge
r-proxy                   0.4_27            r43h57805ef_2    conda-forge
r-ps                      1.7.6             r43h57805ef_0    conda-forge
r-purrr                   1.0.2             r43h57805ef_0    conda-forge
r-r6                      2.5.1             r43hc72bb7e_2    conda-forge
r-ragg                    1.3.2             r43hffa04bc_0    conda-forge
r-randomforest            4.7_1.1           r43h61816a4_2    conda-forge
r-rappdirs                0.3.3             r43h57805ef_2    conda-forge
r-rcmdcheck               1.4.0             r43h785f33e_2    conda-forge
r-rcolorbrewer            1.1_3             r43h785f33e_2    conda-forge
r-rcpp                    1.0.12            r43h7df8631_0    conda-forge
r-rcpparmadillo           0.12.8.4.0        r43h58a4165_0    conda-forge
r-rcppprogress            0.4.2             r43hc72bb7e_3    conda-forge
r-rcurl                   1.98_1.14         r43hf9611b0_0    conda-forge
r-readr                   2.1.5             r43ha503ecb_0    conda-forge
r-recipes                 1.0.10            r43hc72bb7e_0    conda-forge
r-recommended             4.3             r43hd8ed1ab_1006    conda-forge
r-rematch2                2.1.2             r43hc72bb7e_3    conda-forge
r-remotes                 2.5.0             r43hc72bb7e_0    conda-forge
r-reshape                 0.8.9             r43hc72bb7e_2    conda-forge
r-reshape2                1.4.4             r43ha503ecb_3    conda-forge
r-restfulr                0.0.15            r43h56115f1_4    bioconda
r-rjson                   0.2.21            r43ha503ecb_3    conda-forge
r-rlang                   1.1.4             r43ha18555a_0    conda-forge
r-rmarkdown               2.27              r43hc72bb7e_1    conda-forge
r-roxygen2                7.3.1             r43ha503ecb_0    conda-forge
r-rpart                   4.1.23            r43h57805ef_0    conda-forge
r-rprojroot               2.0.4             r43hc72bb7e_0    conda-forge
r-rsqlite                 2.3.4             r43ha503ecb_0    conda-forge
r-rstudioapi              0.16.0            r43hc72bb7e_0    conda-forge
r-rversions               2.1.2             r43hc72bb7e_2    conda-forge
r-sass                    0.4.9             r43ha503ecb_0    conda-forge
r-scales                  1.3.0             r43hc72bb7e_0    conda-forge
r-sessioninfo             1.2.2             r43hc72bb7e_2    conda-forge
r-shape                   1.4.6.1           r43ha770c72_0    conda-forge
r-shiny                   1.8.1.1           r43h785f33e_0    conda-forge
r-snow                    0.4_4             r43hc72bb7e_2    conda-forge
r-sourcetools             0.1.7_1           r43ha503ecb_1    conda-forge
r-spatial                 7.3_17            r43h57805ef_0    conda-forge
r-squarem                 2021.1            r43hc72bb7e_2    conda-forge
r-stringi                 1.8.4             r43hbd1cc82_0    conda-forge
r-stringr                 1.5.1             r43h785f33e_0    conda-forge
r-survival                3.7_0             r43hb1dbf0f_0    conda-forge
r-sys                     3.4.2             r43h57805ef_1    conda-forge
r-systemfonts             1.1.0             r43h6e55c91_0    conda-forge
r-testthat                3.2.1.1           r43ha503ecb_0    conda-forge
r-textshaping             0.4.0             r43h024d615_0    conda-forge
r-tibble                  3.2.1             r43h57805ef_2    conda-forge
r-tidyr                   1.3.1             r43ha503ecb_0    conda-forge
r-tidyselect              1.2.1             r43hc72bb7e_0    conda-forge
r-timechange              0.3.0             r43ha503ecb_0    conda-forge
r-timedate                4032.109          r43hc72bb7e_0    conda-forge
r-tinytex                 0.51              r43hc72bb7e_0    conda-forge
r-tzdb                    0.4.0             r43ha503ecb_1    conda-forge
r-urlchecker              1.0.1             r43hc72bb7e_2    conda-forge
r-usethis                 2.2.3             r43hc72bb7e_0    conda-forge
r-utf8                    1.2.4             r43h57805ef_0    conda-forge
r-vctrs                   0.6.5             r43ha503ecb_0    conda-forge
r-viridislite             0.4.2             r43hc72bb7e_1    conda-forge
r-vroom                   1.6.5             r43ha503ecb_0    conda-forge
r-waldo                   0.5.2             r43hc72bb7e_0    conda-forge
r-whisker                 0.4.1             r43hc72bb7e_1    conda-forge
r-withr                   3.0.0             r43hc72bb7e_0    conda-forge
r-xfun                    0.45              r43ha18555a_0    conda-forge
r-xml                     3.99_0.16.1       r43hc6530ce_0    conda-forge
r-xml2                    1.3.6             r43hbfba7a4_1    conda-forge
r-xopen                   1.0.1             r43hc72bb7e_0    conda-forge
r-xtable                  1.8_4             r43hc72bb7e_5    conda-forge
r-yaml                    2.3.8             r43h57805ef_0    conda-forge
r-yulab.utils             0.1.4             r43hc72bb7e_0    conda-forge
r-zeallot                 0.1.0           r43hc72bb7e_1005    conda-forge
r-zip                     2.3.1             r43h57805ef_0    conda-forge
readline                  8.2                  h8228510_1    conda-forge
samtools                  1.20                 h50ea8bc_0    bioconda
scipy                     1.11.4          py312heda63a1_0    conda-forge
sed                       4.8                  he412f7d_0    conda-forge
seqtk                     1.4                  he4a0461_2    bioconda
setuptools                70.1.1             pyhd8ed1ab_0    conda-forge
six                       1.16.0             pyh6c4a22f_0    conda-forge
slamem                    0.8.5                h031d066_3    bioconda
star                      2.7.11b              h43eeafb_1    bioconda
sysroot_linux-64          2.12                he073ed8_17    conda-forge
tk                        8.6.13          noxft_h4845f30_101    conda-forge
tktable                   2.10                 h8bc8fbc_6    conda-forge
toml                      0.10.2             pyhd8ed1ab_0    conda-forge
tomlkit                   0.12.5             pyha770c72_0    conda-forge
tzdata                    2024a                h0c530f3_0    conda-forge
wheel                     0.43.0             pyhd8ed1ab_1    conda-forge
xmltodict                 0.13.0             pyhd8ed1ab_0    conda-forge
xorg-kbproto              1.0.7             h7f98852_1002    conda-forge
xorg-libice               1.1.1                hd590300_0    conda-forge
xorg-libsm                1.2.4                h7391055_0    conda-forge
xorg-libx11               1.8.9                h8ee46fc_0    conda-forge
xorg-libxau               1.0.11               hd590300_0    conda-forge
xorg-libxdmcp             1.1.3                h7f98852_0    conda-forge
xorg-libxext              1.3.4                h0b41bf4_2    conda-forge
xorg-libxrender           0.9.11               hd590300_0    conda-forge
xorg-libxt                1.3.0                hd590300_1    conda-forge
xorg-renderproto          0.11.1            h7f98852_1002    conda-forge
xorg-xextproto            7.3.0             h0b41bf4_1003    conda-forge
xorg-xproto               7.0.31            h7f98852_1007    conda-forge
xz                        5.2.6                h166bdaf_0    conda-forge
yaml                      0.2.5                h7f98852_2    conda-forge
yq                        3.4.3              pyhd8ed1ab_0    conda-forge
zlib                      1.2.13               h4ab18f5_6    conda-forge
zstd                      1.5.6                ha6fb4c9_0    conda-forge

Additional context

For me, edlib is a dependency, within in a dependency: SQUATI3 => ultra-bioinformatics => edlib