missing cert.pem blocks MbedTLS and IJulia from installing, manual download fixes the issue

[janxkoci]

Solution to issue cannot be found in the documentation.

• I checked the documentation.

Issue

Installing julia with conda/mamba and trying to install IJulia using Pkg.jl leads to a bunch of errors, with the important part being:

ERROR: LoadError: InitError: SystemError: opening file "/home/jena/mambaforge/envs/julia/share/julia/cert.pem": Adresář nebo soubor neexistuje

(last part: Directory or file does not exist)

Somewhere on Julia Discourse I've read a suggestion (cannot find it now) to download Julia source from the website, unpack the cert.pam into the folder where it's missing and try again. I just did that now and it fixed the problem and I was able to start Jupyter notebook.

Installed packages

# packages in environment at /home/jena/mambaforge/envs/julia:
#
# Name                    Version                   Build  Channel
_libgcc_mutex             0.1                 conda_forge    conda-forge
_openmp_mutex             4.5                       2_gnu    conda-forge
anyio                     4.4.0              pyhd8ed1ab_0    conda-forge
argon2-cffi               23.1.0             pyhd8ed1ab_0    conda-forge
argon2-cffi-bindings      21.2.0          py311h459d7ec_4    conda-forge
arpack                    3.9.1           nompi_h77f6705_101    conda-forge
arrow                     1.3.0              pyhd8ed1ab_0    conda-forge
asttokens                 2.4.1              pyhd8ed1ab_0    conda-forge
async-lru                 2.0.4              pyhd8ed1ab_0    conda-forge
attrs                     24.2.0             pyh71513ae_0    conda-forge
babel                     2.14.0             pyhd8ed1ab_0    conda-forge
beautifulsoup4            4.12.3             pyha770c72_0    conda-forge
bleach                    6.1.0              pyhd8ed1ab_0    conda-forge
brotli-python             1.1.0           py311hb755f60_1    conda-forge
bzip2                     1.0.8                h7f98852_4    conda-forge
c-ares                    1.24.0               hd590300_0    conda-forge
ca-certificates           2024.7.4             hbcca054_0    conda-forge
cached-property           1.5.2                hd8ed1ab_1    conda-forge
cached_property           1.5.2              pyha770c72_1    conda-forge
certifi                   2024.7.4           pyhd8ed1ab_0    conda-forge
cffi                      1.17.0          py311ha8e6434_0    conda-forge
charset-normalizer        3.3.2              pyhd8ed1ab_0    conda-forge
comm                      0.2.2              pyhd8ed1ab_0    conda-forge
curl                      8.9.1                h18eb788_0    conda-forge
debugpy                   1.8.5           py311hf86e51f_0    conda-forge
decorator                 5.1.1              pyhd8ed1ab_0    conda-forge
defusedxml                0.7.1              pyhd8ed1ab_0    conda-forge
entrypoints               0.4                pyhd8ed1ab_0    conda-forge
exceptiongroup            1.2.2              pyhd8ed1ab_0    conda-forge
executing                 2.0.1              pyhd8ed1ab_0    conda-forge
fqdn                      1.5.1              pyhd8ed1ab_0    conda-forge
gettext                   0.21.1               h27087fc_0    conda-forge
git                       2.46.0          pl5321hb5640b7_0    conda-forge
gmp                       6.3.0                h59595ed_0    conda-forge
h11                       0.14.0             pyhd8ed1ab_0    conda-forge
h2                        4.1.0              pyhd8ed1ab_0    conda-forge
hpack                     4.0.0              pyh9f0ad1d_0    conda-forge
httpcore                  1.0.5              pyhd8ed1ab_0    conda-forge
httpx                     0.27.0             pyhd8ed1ab_0    conda-forge
hyperframe                6.0.1              pyhd8ed1ab_0    conda-forge
icu                       75.1                 he02047a_0    conda-forge
idna                      3.7                pyhd8ed1ab_0    conda-forge
importlib-metadata        8.2.0              pyha770c72_0    conda-forge
importlib_metadata        8.2.0                hd8ed1ab_0    conda-forge
importlib_resources       6.4.3              pyhd8ed1ab_0    conda-forge
ipykernel                 6.29.5             pyh3099207_0    conda-forge
ipython                   8.26.0             pyh707e725_0    conda-forge
ipywidgets                8.1.3              pyhd8ed1ab_0    conda-forge
isoduration               20.11.0            pyhd8ed1ab_0    conda-forge
jedi                      0.19.1             pyhd8ed1ab_0    conda-forge
jinja2                    3.1.4              pyhd8ed1ab_0    conda-forge
json5                     0.9.25             pyhd8ed1ab_0    conda-forge
jsonpointer               3.0.0           py311h38be061_0    conda-forge
jsonschema                4.23.0             pyhd8ed1ab_0    conda-forge
jsonschema-specifications 2023.12.1          pyhd8ed1ab_0    conda-forge
jsonschema-with-format-nongpl 4.23.0               hd8ed1ab_0    conda-forge
julia                     1.10.4               hf18f99d_1    conda-forge
jupyter                   1.0.0             pyhd8ed1ab_10    conda-forge
jupyter-lsp               2.2.5              pyhd8ed1ab_0    conda-forge
jupyter_client            8.6.2              pyhd8ed1ab_0    conda-forge
jupyter_console           6.6.3              pyhd8ed1ab_0    conda-forge
jupyter_core              5.7.2           py311h38be061_0    conda-forge
jupyter_events            0.10.0             pyhd8ed1ab_0    conda-forge
jupyter_server            2.14.2             pyhd8ed1ab_0    conda-forge
jupyter_server_terminals  0.5.3              pyhd8ed1ab_0    conda-forge
jupyterlab                4.2.4              pyhd8ed1ab_0    conda-forge
jupyterlab_pygments       0.3.0              pyhd8ed1ab_1    conda-forge
jupyterlab_server         2.27.3             pyhd8ed1ab_0    conda-forge
jupyterlab_widgets        3.0.11             pyhd8ed1ab_0    conda-forge
keyutils                  1.6.1                h166bdaf_0    conda-forge
krb5                      1.21.3               h659f571_0    conda-forge
ld_impl_linux-64          2.40                 hf3520f5_7    conda-forge
libblas                   3.9.0           16_linux64_openblas    conda-forge
libcblas                  3.9.0           16_linux64_openblas    conda-forge
libcurl                   8.9.1                hdb1bdb2_0    conda-forge
libedit                   3.1.20191231         he28a2e2_2    conda-forge
libev                     4.33                 h516909a_1    conda-forge
libexpat                  2.6.2                h59595ed_0    conda-forge
libffi                    3.4.2                h7f98852_5    conda-forge
libgcc-ng                 12.2.0              h65d4601_19    conda-forge
libgfortran-ng            13.2.0               h69a702a_0    conda-forge
libgfortran5              13.2.0               ha4646dd_0    conda-forge
libgit2                   1.8.1                he8d1d4c_1    conda-forge
libgomp                   12.2.0              h65d4601_19    conda-forge
libhwloc                  2.11.1          default_hecaa2ac_1000    conda-forge
libiconv                  1.17                 h166bdaf_0    conda-forge
liblapack                 3.9.0           16_linux64_openblas    conda-forge
libnghttp2                1.58.0               h47da74e_1    conda-forge
libnsl                    2.0.0                h7f98852_0    conda-forge
libopenblas               0.3.21          pthreads_h78a6416_3    conda-forge
libopenblas-ilp64         0.3.23          pthreads_h5c82d6a_0    conda-forge
libopenlibm4              0.8.1                hd590300_1    conda-forge
libsodium                 1.0.18               h36c2ea0_1    conda-forge
libsqlite                 3.46.0               hde9e2c9_0    conda-forge
libssh2                   1.11.0               h0841786_0    conda-forge
libstdcxx-ng              12.2.0              h46fd767_19    conda-forge
libunwind                 1.6.2                h9c3ff4c_0    conda-forge
libutf8proc               2.8.0                h166bdaf_0    conda-forge
libuuid                   2.38.1               h0b41bf4_0    conda-forge
libxml2                   2.12.7               he7c6b58_4    conda-forge
libzlib                   1.3.1                h4ab18f5_1    conda-forge
markupsafe                2.1.5           py311h459d7ec_0    conda-forge
matplotlib-inline         0.1.7              pyhd8ed1ab_0    conda-forge
mbedtls                   3.3.0                hcb278e6_0    conda-forge
metis                     5.1.0             h58526e2_1006    conda-forge
mistune                   3.0.2              pyhd8ed1ab_0    conda-forge
mpfr                      4.2.1                h9458935_0    conda-forge
nbclient                  0.10.0             pyhd8ed1ab_0    conda-forge
nbconvert                 7.16.4               hd8ed1ab_1    conda-forge
nbconvert-core            7.16.4             pyhd8ed1ab_1    conda-forge
nbconvert-pandoc          7.16.4               hd8ed1ab_1    conda-forge
nbformat                  5.10.4             pyhd8ed1ab_0    conda-forge
ncurses                   6.3                  h27087fc_1    conda-forge
nest-asyncio              1.6.0              pyhd8ed1ab_0    conda-forge
notebook                  7.2.1              pyhd8ed1ab_0    conda-forge
notebook-shim             0.2.4              pyhd8ed1ab_0    conda-forge
openblas-ilp64            0.3.23          pthreads_h3d04fff_0    conda-forge
openlibm                  0.8.1                h7f98852_0    conda-forge
openssl                   3.3.1                h4bc722e_2    conda-forge
overrides                 7.7.0              pyhd8ed1ab_0    conda-forge
p7zip                     16.02             h9c3ff4c_1001    conda-forge
packaging                 24.1               pyhd8ed1ab_0    conda-forge
pandoc                    3.3                  ha770c72_0    conda-forge
pandocfilters             1.5.0              pyhd8ed1ab_0    conda-forge
parso                     0.8.4              pyhd8ed1ab_0    conda-forge
pcre2                     10.44                hba22ea6_2    conda-forge
perl                      5.32.1          2_h7f98852_perl5    conda-forge
pexpect                   4.9.0              pyhd8ed1ab_0    conda-forge
pickleshare               0.7.5                   py_1003    conda-forge
pip                       24.2               pyhd8ed1ab_0    conda-forge
pkgutil-resolve-name      1.3.10             pyhd8ed1ab_1    conda-forge
platformdirs              4.2.2              pyhd8ed1ab_0    conda-forge
prometheus_client         0.20.0             pyhd8ed1ab_0    conda-forge
prompt-toolkit            3.0.47             pyha770c72_0    conda-forge
prompt_toolkit            3.0.47               hd8ed1ab_0    conda-forge
psutil                    6.0.0           py311h331c9d8_0    conda-forge
ptyprocess                0.7.0              pyhd3deb0d_0    conda-forge
pure_eval                 0.2.3              pyhd8ed1ab_0    conda-forge
pycparser                 2.22               pyhd8ed1ab_0    conda-forge
pygments                  2.18.0             pyhd8ed1ab_0    conda-forge
pysocks                   1.7.1              pyha2e5f31_6    conda-forge
python                    3.11.3          h2755cc3_0_cpython    conda-forge
python-dateutil           2.9.0              pyhd8ed1ab_0    conda-forge
python-fastjsonschema     2.20.0             pyhd8ed1ab_0    conda-forge
python-json-logger        2.0.7              pyhd8ed1ab_0    conda-forge
python_abi                3.11                    5_cp311    conda-forge
pytz                      2024.1             pyhd8ed1ab_0    conda-forge
pyyaml                    6.0.2           py311h61187de_0    conda-forge
pyzmq                     26.1.0          py311h759c1eb_0    conda-forge
qtconsole-base            5.5.2              pyha770c72_0    conda-forge
qtpy                      2.4.1              pyhd8ed1ab_0    conda-forge
readline                  8.2                  h8228510_1    conda-forge
referencing               0.35.1             pyhd8ed1ab_0    conda-forge
requests                  2.32.3             pyhd8ed1ab_0    conda-forge
rfc3339-validator         0.1.4              pyhd8ed1ab_0    conda-forge
rfc3986-validator         0.1.1              pyh9f0ad1d_0    conda-forge
rpds-py                   0.20.0          py311hb3a8bbb_0    conda-forge
send2trash                1.8.3              pyh0d859eb_0    conda-forge
setuptools                72.1.0             pyhd8ed1ab_0    conda-forge
six                       1.16.0             pyh6c4a22f_0    conda-forge
sniffio                   1.3.1              pyhd8ed1ab_0    conda-forge
soupsieve                 2.5                pyhd8ed1ab_1    conda-forge
stack_data                0.6.2              pyhd8ed1ab_0    conda-forge
suitesparse               7.8.1                h41f34aa_0    conda-forge
tbb                       2021.12.0            h434a139_3    conda-forge
terminado                 0.18.1             pyh0d859eb_0    conda-forge
tinycss2                  1.3.0              pyhd8ed1ab_0    conda-forge
tk                        8.6.13          noxft_h4845f30_101    conda-forge
tomli                     2.0.1              pyhd8ed1ab_0    conda-forge
tornado                   6.4.1           py311h331c9d8_0    conda-forge
traitlets                 5.14.3             pyhd8ed1ab_0    conda-forge
types-python-dateutil     2.9.0.20240316     pyhd8ed1ab_0    conda-forge
typing-extensions         4.12.2               hd8ed1ab_0    conda-forge
typing_extensions         4.12.2             pyha770c72_0    conda-forge
typing_utils              0.1.0              pyhd8ed1ab_0    conda-forge
tzdata                    2024a                h0c530f3_0    conda-forge
uri-template              1.3.0              pyhd8ed1ab_0    conda-forge
urllib3                   2.2.2              pyhd8ed1ab_1    conda-forge
wcwidth                   0.2.13             pyhd8ed1ab_0    conda-forge
webcolors                 24.8.0             pyhd8ed1ab_0    conda-forge
webencodings              0.5.1              pyhd8ed1ab_2    conda-forge
websocket-client          1.8.0              pyhd8ed1ab_0    conda-forge
wheel                     0.44.0             pyhd8ed1ab_0    conda-forge
widgetsnbextension        4.0.11             pyhd8ed1ab_0    conda-forge
xz                        5.2.6                h166bdaf_0    conda-forge
yaml                      0.2.5                h7f98852_2    conda-forge
zeromq                    4.3.5                h75354e8_4    conda-forge
zipp                      3.20.0             pyhd8ed1ab_0    conda-forge
zlib                      1.3.1                h4ab18f5_1    conda-forge
zstandard                 0.23.0          py311h5cd10c7_0    conda-forge
zstd                      1.5.6                ha6fb4c9_0    conda-forge

Environment info

active environment : julia
    active env location : /home/jena/mambaforge/envs/julia
            shell level : 2
       user config file : /home/jena/.condarc
 populated config files : /home/jena/mambaforge/.condarc
                          /home/jena/.condarc
          conda version : 23.3.1
    conda-build version : not installed
         python version : 3.10.12.final.0
       virtual packages : __archspec=1=x86_64
                          __glibc=2.35=0
                          __linux=6.8.0=0
                          __unix=0=0
       base environment : /home/jena/mambaforge  (writable)
      conda av data dir : /home/jena/mambaforge/etc/conda
  conda av metadata url : None
           channel URLs : https://conda.anaconda.org/conda-forge/linux-64
                          https://conda.anaconda.org/conda-forge/noarch
          package cache : /home/jena/mambaforge/pkgs
                          /home/jena/.conda/pkgs
       envs directories : /home/jena/mambaforge/envs
                          /home/jena/.conda/envs
               platform : linux-64
             user-agent : conda/23.3.1 requests/2.31.0 CPython/3.10.12 Linux/6.8.0-40-generic elementary/7.1 glibc/2.35 solver/libmamba conda-libmamba-solver/23.3.0 libmambapy/1.4.2
                UID:GID : 1000:1000
             netrc file : None
           offline mode : False

[mkitti]

Is this on Linux only?

[janxkoci]

I only use Linux, so hard to say. I recall on the Julia Discourse they were also mentioning Linux (Arch, etc).

PS: I think this is the Discourse thread, although it does not include the aforementioned suggestion to get the missing cert from source tarball (either I read between the lines or found it somewhere else). Anyway, the thread discusses how different Linux distro maintainers fail to include the certificate (usually by providing different mbedtls library). It does not mention conda, but in principle the issue can still apply, as conda is just another distribution of packages.

[mkitti]

By the way, if you are in a bind, you could also just get the official binaries from https://prefix.dev/channels/julia-forge

[janxkoci]

Found the suggestion in a thread linked from the thread I previously mentioned.

if you are in a bind

I don't know what is "bind". If it means I need to solve this quickly, then I just did that with manually unpacking the cert in the right location, as mentioned above and in the link.

I'm actually new to Julia and want to learn it, which is why I want to use IJulia. I usually use R + jupyter and conda for installing most of my software and packages, as conda provides the least painful way to install R packages on Linux (I dunno why it's so painful, but it is). I thought to manage my Julia installation the same way, but somehow Julia is not playing so nicely with Jupyter when installed by conda - I only had luck when using the official installation method. But it gets outdated easily, so I prefer something like conda. (Actually, I use mamba almost exclusively now.)