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Error installing vt in conda environment #121

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jcasadogp opened this issue Oct 14, 2023 · 0 comments
Open

Error installing vt in conda environment #121

jcasadogp opened this issue Oct 14, 2023 · 0 comments

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@jcasadogp
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Hello!

I have this conda environment with the following packages:

     active environment : bioinformatics-env
    active env location : /Users/julia/miniconda3/envs/bioinformatics-env
            shell level : 1
       user config file : /Users/julia/.condarc
 populated config files : /Users/julia/.condarc
          conda version : 23.7.4
    conda-build version : not installed
         python version : 3.9.18.final.0
       virtual packages : __archspec=1=x86_64
                          __osx=10.16=0
                          __unix=0=0
       base environment : /Users/julia/miniconda3  (writable)
      conda av data dir : /Users/julia/miniconda3/etc/conda
  conda av metadata url : None
           channel URLs : https://conda.anaconda.org/conda-forge/osx-64
                          https://conda.anaconda.org/conda-forge/noarch
                          https://conda.anaconda.org/bioconda/osx-64
                          https://conda.anaconda.org/bioconda/noarch
                          https://repo.anaconda.com/pkgs/main/osx-64
                          https://repo.anaconda.com/pkgs/main/noarch
                          https://repo.anaconda.com/pkgs/r/osx-64
                          https://repo.anaconda.com/pkgs/r/noarch
          package cache : /Users/julia/miniconda3/pkgs
                          /Users/julia/.conda/pkgs
       envs directories : /Users/julia/miniconda3/envs
                          /Users/julia/.conda/envs
               platform : osx-64
             user-agent : conda/23.7.4 requests/2.31.0 CPython/3.9.18 Darwin/20.6.0 OSX/10.16
                UID:GID : 501:20
             netrc file : None
           offline mode : False

Packages:

Name                    Version                   Build  Channel
_r-mutex                  1.0.1               anacondar_1    conda-forge
appnope                   0.1.3              pyhd8ed1ab_0    conda-forge
argon2-cffi               21.1.0           py36hfa26744_0    conda-forge
asttokens                 2.4.0              pyhd8ed1ab_0    conda-forge
backcall                  0.2.0              pyh9f0ad1d_0    conda-forge
backports                 1.0                pyhd8ed1ab_3    conda-forge
backports.functools_lru_cache 1.6.5              pyhd8ed1ab_0    conda-forge
bamtools                  2.5.2                hdf58011_2    bioconda
bash                      4.4.18            h1765d9f_1000    conda-forge
bash_kernel               0.9.0              pyh1a96a4e_0    conda-forge
bcftools                  1.5                           3    bioconda
bcrypt                    3.2.0            py36hfa26744_1    conda-forge
bedtools                  2.31.0               h6372da2_3    bioconda
biopython                 1.79             py36hfa26744_0    conda-forge
blas                      1.0                         mkl    conda-forge
bleach                    6.1.0              pyhd8ed1ab_0    conda-forge
blosc                     1.21.5               heccf04b_0    conda-forge
boost-cpp                 1.70.0               hd59e818_1    conda-forge
bowtie2                   2.5.1            py36hde6f128_1    bioconda
brotlipy                  0.7.0           py36hfa26744_1001    conda-forge
bwa                       0.7.17              h45fc8d7_11    bioconda
bwidget                   1.9.14               h694c41f_1    conda-forge
bzip2                     1.0.8                h0d85af4_4    conda-forge
ca-certificates           2023.7.22            h8857fd0_0    conda-forge
cairo                     1.16.0            h0ab9d94_1001    conda-forge
cctools_osx-64            949.0.1             hc7db93f_25  
certifi                   2021.5.30        py36h79c6626_0    conda-forge
cffi                      1.14.0           py36hb5b8e2f_0  
charset-normalizer        2.0.4              pyhd3eb1b0_0  
clang                     12.0.0               hecd8cb5_2  
clang-12                  12.0.0          default_hfcad0e5_2  
clang_osx-64              12.0.0               h7ad7729_2  
clangxx                   12.0.0          default_hfcad0e5_2  
clangxx_osx-64            12.0.0               he0c6f94_2  
compiler-rt               12.0.0               hd87ff74_2  
compiler-rt_osx-64        12.0.0               hfb26b64_2  
cryptography              3.4.8            py36h3d45be8_0    conda-forge
curl                      7.67.0               ha441bb4_0  
cycler                    0.11.0             pyhd8ed1ab_0    conda-forge
dbus                      1.13.6               h2f22bb5_0    conda-forge
decorator                 5.1.1              pyhd8ed1ab_0    conda-forge
defusedxml                0.7.1              pyhd8ed1ab_0    conda-forge
docutils                  0.13.1                   py36_0    conda-forge
dropbox                   11.36.2            pyhd8ed1ab_0    conda-forge
ecdsa                     0.18.0             pyhd8ed1ab_0    conda-forge
entrypoints               0.4                pyhd8ed1ab_0    conda-forge
executing                 1.2.0              pyhd8ed1ab_0    conda-forge
expat                     2.5.0                hf0c8a7f_1    conda-forge
fastqc                    0.12.1               hdfd78af_0    bioconda
filechunkio               1.8                        py_2    conda-forge
font-ttf-dejavu-sans-mono 2.37                 hab24e00_0    conda-forge
fontconfig                2.13.94              h10f422b_0    conda-forge
freetype                  2.12.1               h60636b9_2    conda-forge
fribidi                   1.0.10               hbcb3906_0    conda-forge
ftputil                   5.0.4              pyhd8ed1ab_0    conda-forge
gettext                   0.21.1               h8a4c099_0    conda-forge
gfortran_osx-64           4.8.5                h22b1bf0_8    conda-forge
glib                      2.63.1               hd977a24_0  
graphite2                 1.3.13            h2e338ed_1001    conda-forge
gsl                       2.6                  h71c5fe9_2    conda-forge
harfbuzz                  2.4.0                h831d699_0  
hdf5                      1.10.5          nompi_h0cbb7df_1103    conda-forge
icu                       58.2              h0a44026_1000    conda-forge
idna                      3.4                pyhd8ed1ab_0    conda-forge
importlib_metadata        1.5.0                    py36_0    conda-forge
importlib_resources       5.1.3            py36h79c6626_0    conda-forge
intel-openmp              2023.1.0         ha357a0b_43547  
ipykernel                 5.5.5            py36h495a4c6_0    conda-forge
ipython                   6.5.0                    py36_0    conda-forge
ipython_genutils          0.2.0                      py_1    conda-forge
ipywidgets                7.3.0                    py36_0    conda-forge
jedi                      0.10.2                   py36_0    conda-forge
jinja2                    2.11.3             pyhd8ed1ab_2    conda-forge
jpeg                      9e                   hb7f2c08_3    conda-forge
json5                     0.9.6              pyhd3eb1b0_0  
jsonschema                2.6.0                 py36_1002    conda-forge
jupyter_client            7.1.2              pyhd8ed1ab_0    conda-forge
jupyter_core              4.8.1            py36h79c6626_0    conda-forge
kiwisolver                1.3.1            py36hc61eee1_1    conda-forge
krb5                      1.16.4               h1752a42_0    conda-forge
lcms2                     2.12                 h577c468_0    conda-forge
ld64_osx-64               530                 h70f3046_23  
ldid                      2.1.2                h6a69015_3    conda-forge
lerc                      4.0.0                hb486fe8_0    conda-forge
libblas                   3.9.0              12_osx64_mkl    conda-forge
libcblas                  3.9.0              12_osx64_mkl    conda-forge
libclang-cpp12            12.0.0          default_hfcad0e5_2  
libcurl                   7.67.0               h051b688_0  
libcxx                    16.0.6               hd57cbcb_0    conda-forge
libdeflate                1.18                 hac1461d_0    conda-forge
libedit                   3.1.20191231         h0678c8f_2    conda-forge
libexpat                  2.5.0                hf0c8a7f_1    conda-forge
libffi                    3.2.1             hb1e8313_1007    conda-forge
libgfortran               3.0.1                         0    conda-forge
libiconv                  1.17                 hac89ed1_0    conda-forge
liblapack                 3.9.0              12_osx64_mkl    conda-forge
libllvm12                 12.0.0               h9b2ccf5_3  
libllvm14                 14.0.6               hc8e404f_4    conda-forge
libpng                    1.6.39               ha978bb4_0    conda-forge
libsodium                 1.0.18               hbcb3906_1    conda-forge
libssh2                   1.10.0               hdb2fb19_2  
libtiff                   4.2.0                h1167814_3    conda-forge
libwebp-base              1.3.2                h0dc2134_0    conda-forge
libxml2                   2.10.4               h930c0e2_0  
libxslt                   1.1.37               h5d22bc9_0    conda-forge
libzlib                   1.2.13               h8a1eda9_5    conda-forge
llvm-openmp               17.0.2               hff08bdf_0    conda-forge
llvm-tools                12.0.0               h9b2ccf5_3  
lxml                      4.6.3            py36habcf893_0    conda-forge
lz4-c                     1.9.4                hf0c8a7f_0    conda-forge
make                      4.3                  h22f3db7_1    conda-forge
markupsafe                1.1.1            py36hfa26744_3    conda-forge
matplotlib                3.3.4            py36h79c6626_0    conda-forge
matplotlib-base           3.3.4            py36h4ea959b_0    conda-forge
mistune                   0.8.4           pyh1a96a4e_1006    conda-forge
mkl                       2021.4.0           h89fa619_689    conda-forge
mkl-service               2.4.0            py36hfa26744_0    conda-forge
mkl_fft                   1.3.0            py36h4a7008c_2  
mkl_random                1.2.2            py36hb2f4e1b_0  
mock                      5.1.0              pyhd8ed1ab_0    conda-forge
nbconvert                 5.6.1            py36h9f0ad1d_1    conda-forge
nbformat                  5.1.3              pyhd8ed1ab_0    conda-forge
ncurses                   6.4                  hf0c8a7f_0    conda-forge
nest-asyncio              1.5.8              pyhd8ed1ab_0    conda-forge
notebook                  6.3.0            py36h79c6626_0    conda-forge
numexpr                   2.7.3            py36h7083def_0    conda-forge
numpy                     1.16.6           py36h300780c_3  
numpy-base                1.16.6           py36h4850c68_3  
olefile                   0.46               pyh9f0ad1d_1    conda-forge
openjdk                   20.0.2               h7d26f99_2    conda-forge
openssl                   1.1.1w               h8a1eda9_0    conda-forge
packaging                 21.3               pyhd8ed1ab_0    conda-forge
pandas                    1.1.5            py36h2be6da3_0    conda-forge
pandoc                    2.19.2               h694c41f_2    conda-forge
pandocfilters             1.5.0              pyhd8ed1ab_0    conda-forge
pango                     1.42.4               haa940fe_4    conda-forge
paramiko                  1.18.2                   py36_0    conda-forge
parso                     0.8.3              pyhd8ed1ab_0    conda-forge
patsy                     0.5.3              pyhd8ed1ab_0    conda-forge
pcre                      8.45                 he49afe7_0    conda-forge
perl                      5.32.1          4_h0dc2134_perl5    conda-forge
pexpect                   4.8.0              pyh1a96a4e_2    conda-forge
pickleshare               0.7.5                   py_1003    conda-forge
pillow                    7.2.0            py36h79df3f4_2    conda-forge
pip                       20.0.2                   py36_1    conda-forge
pixman                    0.38.0            h01d97ff_1003    conda-forge
ply                       3.11                       py_1    conda-forge
prometheus_client         0.17.1             pyhd8ed1ab_0    conda-forge
prompt_toolkit            1.0.15                     py_1    conda-forge
psutil                    4.4.2                    py36_0    conda-forge
ptyprocess                0.7.0              pyhd3deb0d_0    conda-forge
pure_eval                 0.2.2              pyhd8ed1ab_0    conda-forge
pycparser                 2.21               pyhd8ed1ab_0    conda-forge
pycrypto                  2.6.1           py36ha3de816_1005    conda-forge
pycurl                    7.43.0.5         py36h16304de_2    conda-forge
pygments                  2.12.0             pyhd8ed1ab_0    conda-forge
pynacl                    0.3.0                    py36_0    bioconda
pyobjc-core               7.3              py36hfa26744_2    conda-forge
pyobjc-framework-cocoa    6.2              py36h9f0ad1d_1    conda-forge
pyopenssl                 20.0.1             pyhd8ed1ab_0    conda-forge
pyparsing                 3.1.1              pyhd8ed1ab_0    conda-forge
pyqt                      5.9.2            py36h2a560b1_4    conda-forge
pysftp                    0.2.9                      py_1    conda-forge
pysocks                   1.7.1            py36h79c6626_3    conda-forge
pytables                  3.6.1            py36h6f8395a_1    conda-forge
python                    3.6.7             h8dc6b48_1004    conda-forge
python-dateutil           2.8.2              pyhd8ed1ab_0    conda-forge
python_abi                3.6                     2_cp36m    conda-forge
pytz                      2023.3.post1       pyhd8ed1ab_0    conda-forge
pyyaml                    5.4.1            py36hfa26744_1    conda-forge
pyzmq                     19.0.2           py36hd529914_2    conda-forge
qt                        5.9.7                h93ee506_2    conda-forge
qtconsole                 4.4.2                    py36_0    conda-forge
r                         3.6.0                     r36_0  
r-assertthat              0.2.1             r36h6115d3f_2    conda-forge
r-base                    3.6.0                hcb44179_0  
r-base64enc               0.1_3           r36h28b5c78_1004    conda-forge
r-boot                    1.3_20            r36h6115d3f_0  
r-class                   7.3_15            r36h46e59ec_0  
r-cli                     2.5.0             r36hc72bb7e_0    conda-forge
r-cluster                 2.0.8             r36hfffe0aa_0  
r-codetools               0.2_16            r36h6115d3f_0  
r-crayon                  1.4.1             r36hc72bb7e_0    conda-forge
r-digest                  0.6.27            r36h9951f98_0    conda-forge
r-ellipsis                0.3.2             r36h28b5c78_0    conda-forge
r-evaluate                0.14              r36h6115d3f_2    conda-forge
r-fansi                   0.4.2             r36h28b5c78_0    conda-forge
r-foreign                 0.8_71            r36h46e59ec_0  
r-glue                    1.4.2             r36h066c5db_0    conda-forge
r-htmltools               0.5.1.1           r36h9951f98_0    conda-forge
r-irdisplay               1.0               r36hd8ed1ab_0    conda-forge
r-irkernel                1.2               r36hc72bb7e_0    conda-forge
r-jsonlite                1.7.2             r36h066c5db_0    conda-forge
r-kernsmooth              2.23_15           r36hfffe0aa_4  
r-lattice                 0.20_38           r36h46e59ec_0  
r-lifecycle               1.0.0             r36hc72bb7e_0    conda-forge
r-mass                    7.3_51.3          r36h46e59ec_0  
r-matrix                  1.2_17            r36h46e59ec_0  
r-mgcv                    1.8_28            r36h46e59ec_0  
r-nlme                    3.1_139           r36hfffe0aa_0  
r-nnet                    7.3_12            r36h46e59ec_0  
r-pbdzmq                  0.3_5             r36h5cc58b7_1    conda-forge
r-pillar                  1.6.1             r36hc72bb7e_0    conda-forge
r-recommended             3.6.0                     r36_0  
r-repr                    1.1.3             r36h785f33e_0    conda-forge
r-rlang                   0.4.11            r36h28b5c78_0    conda-forge
r-rpart                   4.1_15            r36h46e59ec_0  
r-spatial                 7.3_11            r36h46e59ec_4  
r-survival                2.44_1.1          r36h46e59ec_0  
r-utf8                    1.2.1             r36h28b5c78_0    conda-forge
r-uuid                    0.1_4             r36h17f1fa6_1    conda-forge
r-vctrs                   0.3.8             r36h28b5c78_1    conda-forge
readline                  7.0               hcfe32e1_1001    conda-forge
requests                  2.28.1             pyhd8ed1ab_0    conda-forge
samtools                  1.4.1                         0    bioconda
scipy                     1.3.1            py36hab3da7d_2    conda-forge
seaborn                   0.11.2               hd8ed1ab_0    conda-forge
seaborn-base              0.11.2             pyhd8ed1ab_0    conda-forge
send2trash                1.8.2              pyhd1c38e8_0    conda-forge
setuptools                49.6.0           py36h79c6626_3    conda-forge
sickle                    0.7.0              pyh9f0ad1d_0    bioconda
simplegeneric             0.8.1                      py_1    conda-forge
sip                       4.19.8           py36h0a44026_0  
six                       1.16.0             pyh6c4a22f_0    conda-forge
snakemake                 3.13.3                   py36_0    bioconda
snappy                    1.1.10               h225ccf5_0    conda-forge
sqlite                    3.28.0               h9721f7c_0    conda-forge
sra-tools                 2.8.0                         0    bioconda
stack_data                0.6.2              pyhd8ed1ab_0    conda-forge
star                      2.5.2b                        0    bioconda
statsmodels               0.12.2           py36hf14bfbd_0    conda-forge
stone                     3.3.1              pyhd8ed1ab_0    conda-forge
tapi                      1000.10.8            ha1b3eb9_0  
tbb                       2021.10.0            h1c7c39f_1    conda-forge
terminado                 0.9.4            py36hecd8cb5_0  
testpath                  0.6.0              pyhd8ed1ab_0    conda-forge
tk                        8.6.13               hef22860_0    conda-forge
tktable                   2.10                 ha166976_5    conda-forge
tornado                   6.1              py36hfa26744_1    conda-forge
traitlets                 4.3.3              pyhd8ed1ab_2    conda-forge
urllib3                   1.26.8             pyhd8ed1ab_1    conda-forge
variant_tools             3.1.3            py36h7df4a66_2    bioconda
vt                        0.57721              hfd6c91b_9    bioconda
wcwidth                   0.2.8              pyhd8ed1ab_0    conda-forge
webencodings              0.5.1              pyhd8ed1ab_2    conda-forge
wheel                     0.36.2             pyhd3deb0d_0    conda-forge
widgetsnbextension        3.3.1                    py36_1    conda-forge
wrapt                     1.12.1           py36hfa26744_3    conda-forge
xz                        5.4.2                h6c40b1e_0  
yaml                      0.2.5                h0d85af4_2    conda-forge
zeromq                    4.3.4                he49afe7_1    conda-forge
zipp                      3.6.0              pyhd3eb1b0_0  
zlib                      1.2.13               h8a1eda9_5    conda-forge
zstd                      1.5.5                h829000d_0    conda-forge

Apparently, vt is installed. However, when I run any vt command, like vt --version or vt decomposeI get the following error:

dyld: Library not loaded: @rpath/libcurl.4.dylib
  Referenced from: /Users/julia/miniconda3/envs/bioinformatics-env/bin/vt
  Reason: Incompatible library version: vt requires version 13.0.0 or later, but libcurl.4.dylib provides version 11.0.0
Abort trap: 6

I got this error before with other packages, but I could solved it either by updating all the conda packages (conda update --all) or by installing the package indicating the concrete version.

Any idea of how to solve this?

Thank you
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