Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Link checker cannot find dependencies for multi-output recipe in 3.28.3 #5136

Closed
carterbox opened this issue Jan 11, 2024 · 5 comments · Fixed by #5141
Closed

Link checker cannot find dependencies for multi-output recipe in 3.28.3 #5136

carterbox opened this issue Jan 11, 2024 · 5 comments · Fixed by #5141
Assignees
Labels
in-progress issue is actively being worked on locked [bot] locked due to inactivity severity::3 major; broken functionality with a workaround source::community catch-all for issues filed by community members type::bug describes erroneous operation, use severity::* to classify the type

Comments

@carterbox
Copy link
Contributor

carterbox commented Jan 11, 2024

What happened?

I believe there is an error with the link checker in conda-build version 3.28.3.

When building the libsecp256k1 recipe from this pull request, we get a missing dependency error as follows:

['  ERROR (libsecp256k1,lib/libsecp256k1.so): Needed DSO x86_64-conda-linux-gnu/sysroot/lib64/libc.so.6 not found in any CDT/compiler package, nor the whitelist?!']

It seems that the link checker cannot find libc.so.6 for the libsecp256k1 output even though the compiler jinja template is included in the build requirements section for that output.

The same requirements are used for the libsecp256k1-2 output, but the link checker can find libc there.

I was able to recproduce the issue locally, but only with conda-build 3.28.3.

conda build -m .ci_support/linux64.yaml recipes/libsecp256k1 --error-overlinking

Earlier versions of conda-build including 3.26, 3.27 did not check the links of libsecp256k1.so (because it is a symlink?), and so do not raise the error. 3.28.2 checks the links but is able to find libc.

Conda Details

conda info
active environment : base
    active env location : /home/DCHING/miniforge3
            shell level : 1
       user config file : /home/DCHING/.condarc
 populated config files : /home/DCHING/miniforge3/.condarc
                          /home/DCHING/.condarc
          conda version : 23.10.0
    conda-build version : 3.28.3
         python version : 3.10.13.final.0
       virtual packages : __archspec=1=skylake
                          __glibc=2.34=0
                          __linux=6.5.2=0
                          __unix=0=0
       base environment : /home/DCHING/miniforge3  (writable)
      conda av data dir : /home/DCHING/miniforge3/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/DCHING/miniforge3/pkgs
                          /home/DCHING/.conda/pkgs
       envs directories : /home/DCHING/miniforge3/envs
                          /home/DCHING/.conda/envs
               platform : linux-64
             user-agent : conda/23.10.0 requests/2.31.0 CPython/3.10.13 Linux/6.5.2-1.el9.elrepo.x86_64 rhel/9.2 glibc/2.34 solver/libmamba conda-libmamba-solver/23.12.0 libmambapy/1.5.3
                UID:GID : 1992:3234
             netrc file : None
           offline mode : False
conda config
==> /home/DCHING/miniforge3/.condarc <==
channels:
  - conda-forge

==> /home/DCHING/.condarc <==
channels:
  - conda-forge
conda list
# packages in environment at /home/DCHING/miniforge3:
#
# Name                    Version                   Build  Channel
_libgcc_mutex             0.1                 conda_forge    conda-forge
_openmp_mutex             4.5                       2_gnu    conda-forge
annotated-types           0.6.0              pyhd8ed1ab_0    conda-forge
anyio                     4.2.0              pyhd8ed1ab_0    conda-forge
archspec                  0.2.2              pyhd8ed1ab_0    conda-forge
attrs                     23.2.0             pyh71513ae_0    conda-forge
backports                 1.0                pyhd8ed1ab_3    conda-forge
backports.functools_lru_cache 2.0.0              pyhd8ed1ab_0    conda-forge
beautifulsoup4            4.12.2             pyha770c72_0    conda-forge
blinker                   1.7.0              pyhd8ed1ab_0    conda-forge
boa                       0.16.0             pyhd8ed1ab_1    conda-forge
boltons                   23.1.1             pyhd8ed1ab_0    conda-forge
boolean.py                4.0                pyhd8ed1ab_0    conda-forge
brotli-python             1.1.0           py310hc6cd4ac_1    conda-forge
bzip2                     1.0.8                hd590300_5    conda-forge
c-ares                    1.24.0               hd590300_0    conda-forge
ca-certificates           2023.11.17           hbcca054_0    conda-forge
certifi                   2023.11.17         pyhd8ed1ab_0    conda-forge
cffi                      1.16.0          py310h2fee648_0    conda-forge
cfgv                      3.3.1              pyhd8ed1ab_0    conda-forge
chardet                   5.2.0           py310hff52083_1    conda-forge
charset-normalizer        3.3.2              pyhd8ed1ab_0    conda-forge
cirun                     0.30               pyhd8ed1ab_0    conda-forge
click                     8.1.7           unix_pyh707e725_0    conda-forge
colorama                  0.4.6              pyhd8ed1ab_0    conda-forge
conda                     23.10.0         py310hff52083_1    conda-forge
conda-build               3.28.3          py310hff52083_0    conda-forge
conda-forge-pinning       2024.01.04.16.29.16      hd8ed1ab_0    conda-forge
conda-index               0.3.0              pyhd8ed1ab_1    conda-forge
conda-libmamba-solver     23.12.0            pyhd8ed1ab_0    conda-forge
conda-package-handling    2.2.0              pyh38be061_0    conda-forge
conda-package-streaming   0.9.0              pyhd8ed1ab_0    conda-forge
conda-smithy              3.30.4             pyhd8ed1ab_0    conda-forge
cryptography              41.0.7          py310hb8475ec_1    conda-forge
curl                      8.5.0                hca28451_0    conda-forge
dataclasses               0.8                pyhc8e2a94_3    conda-forge
dbus                      1.13.6               h5008d03_3    conda-forge
deprecated                1.2.14             pyh1a96a4e_0    conda-forge
distlib                   0.3.8              pyhd8ed1ab_0    conda-forge
distro                    1.9.0              pyhd8ed1ab_0    conda-forge
editables                 0.3                pyhd8ed1ab_0    conda-forge
exceptiongroup            1.2.0              pyhd8ed1ab_0    conda-forge
expat                     2.5.0                hcb278e6_1    conda-forge
filelock                  3.13.1             pyhd8ed1ab_0    conda-forge
fmt                       10.1.1               h00ab1b0_1    conda-forge
gettext                   0.21.1               h27087fc_0    conda-forge
gh                        2.40.1               ha8f183a_0    conda-forge
git                       2.43.0          pl5321h7bc287a_0    conda-forge
gitdb                     4.0.11             pyhd8ed1ab_0    conda-forge
gitpython                 3.1.40             pyhd8ed1ab_0    conda-forge
glob2                     0.7                        py_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
hatch                     1.9.1              pyhd8ed1ab_0    conda-forge
hatchling                 1.21.0             pyhd8ed1ab_0    conda-forge
hpack                     4.0.0              pyh9f0ad1d_0    conda-forge
httpcore                  1.0.2              pyhd8ed1ab_0    conda-forge
httpx                     0.26.0             pyhd8ed1ab_0    conda-forge
hyperframe                6.0.1              pyhd8ed1ab_0    conda-forge
hyperlink                 21.0.0             pyhd3deb0d_0    conda-forge
icu                       73.2                 h59595ed_0    conda-forge
identify                  2.5.33             pyhd8ed1ab_0    conda-forge
idna                      3.6                pyhd8ed1ab_0    conda-forge
importlib-metadata        7.0.1              pyha770c72_0    conda-forge
importlib_metadata        7.0.1                hd8ed1ab_0    conda-forge
importlib_resources       6.1.1              pyhd8ed1ab_0    conda-forge
isodate                   0.6.1              pyhd8ed1ab_0    conda-forge
jaraco.classes            3.3.0              pyhd8ed1ab_0    conda-forge
jeepney                   0.8.0              pyhd8ed1ab_0    conda-forge
jinja2                    3.1.2              pyhd8ed1ab_1    conda-forge
joblib                    1.3.2              pyhd8ed1ab_0    conda-forge
json5                     0.9.14             pyhd8ed1ab_0    conda-forge
jsonpatch                 1.33               pyhd8ed1ab_0    conda-forge
jsonpointer               2.4             py310hff52083_3    conda-forge
jsonschema                4.20.0             pyhd8ed1ab_0    conda-forge
jsonschema-specifications 2023.12.1          pyhd8ed1ab_0    conda-forge
keyring                   24.3.0          py310hff52083_0    conda-forge
keyutils                  1.6.1                h166bdaf_0    conda-forge
krb5                      1.21.2               h659d440_0    conda-forge
ld_impl_linux-64          2.40                 h41732ed_0    conda-forge
libarchive                3.7.2                h2aa1ff5_1    conda-forge
libcurl                   8.5.0                hca28451_0    conda-forge
libedit                   3.1.20191231         he28a2e2_2    conda-forge
libev                     4.33                 hd590300_2    conda-forge
libexpat                  2.5.0                hcb278e6_1    conda-forge
libffi                    3.4.2                h7f98852_5    conda-forge
libgcc-ng                 13.2.0               h807b86a_3    conda-forge
libglib                   2.78.3               h783c2da_0    conda-forge
libgomp                   13.2.0               h807b86a_3    conda-forge
libiconv                  1.17                 hd590300_2    conda-forge
liblief                   0.12.3               h27087fc_0    conda-forge
libmamba                  1.5.3                had39da4_2    conda-forge
libmambapy                1.5.3           py310h39ff949_2    conda-forge
libnghttp2                1.58.0               h47da74e_1    conda-forge
libnsl                    2.0.1                hd590300_0    conda-forge
libsodium                 1.0.18               h36c2ea0_1    conda-forge
libsolv                   0.7.27               hfc55251_0    conda-forge
libsqlite                 3.44.2               h2797004_0    conda-forge
libssh2                   1.11.0               h0841786_0    conda-forge
libstdcxx-ng              13.2.0               h7e041cc_3    conda-forge
libuuid                   2.38.1               h0b41bf4_0    conda-forge
libxcrypt                 4.4.36               hd590300_1    conda-forge
libxml2                   2.12.3               h232c23b_0    conda-forge
libzlib                   1.2.13               hd590300_5    conda-forge
license-expression        30.1.1             pyhd8ed1ab_0    conda-forge
lz4-c                     1.9.4                hcb278e6_0    conda-forge
lzo                       2.10              h516909a_1000    conda-forge
mamba                     1.5.3           py310h51d5547_2    conda-forge
markdown-it-py            3.0.0              pyhd8ed1ab_0    conda-forge
markupsafe                2.1.3           py310h2372a71_1    conda-forge
mdurl                     0.1.2              pyhd8ed1ab_0    conda-forge
menuinst                  2.0.1           py310hff52083_0    conda-forge
more-itertools            10.1.0             pyhd8ed1ab_0    conda-forge
moreutils                 0.67                 h166bdaf_0    conda-forge
msrest                    0.6.21             pyh44b312d_0    conda-forge
ncurses                   6.4                  h59595ed_2    conda-forge
nodeenv                   1.8.0              pyhd8ed1ab_0    conda-forge
oauthlib                  3.2.2              pyhd8ed1ab_0    conda-forge
openssl                   3.2.0                hd590300_1    conda-forge
packaging                 23.2               pyhd8ed1ab_0    conda-forge
patch                     2.7.6             h7f98852_1002    conda-forge
patchelf                  0.17.2               h58526e2_0    conda-forge
pathspec                  0.12.1             pyhd8ed1ab_0    conda-forge
pcre2                     10.42                hcad00b1_0    conda-forge
perl                      5.32.1          7_hd590300_perl5    conda-forge
pexpect                   4.8.0              pyh1a96a4e_2    conda-forge
pip                       23.3.2             pyhd8ed1ab_0    conda-forge
pkginfo                   1.9.6              pyhd8ed1ab_0    conda-forge
pkgutil-resolve-name      1.3.10             pyhd8ed1ab_1    conda-forge
platformdirs              4.1.0              pyhd8ed1ab_0    conda-forge
pluggy                    1.3.0              pyhd8ed1ab_0    conda-forge
pre-commit                3.6.0              pyha770c72_0    conda-forge
prompt-toolkit            3.0.42             pyha770c72_0    conda-forge
prompt_toolkit            3.0.42               hd8ed1ab_0    conda-forge
psutil                    5.9.7           py310h2372a71_0    conda-forge
ptyprocess                0.7.0              pyhd3deb0d_0    conda-forge
py-lief                   0.12.3          py310hd8f1fbe_0    conda-forge
pybind11-abi              4                    hd8ed1ab_3    conda-forge
pycosat                   0.6.6           py310h2372a71_0    conda-forge
pycparser                 2.21               pyhd8ed1ab_0    conda-forge
pycryptodome              3.19.1          py310hb0f0acc_0    conda-forge
pydantic                  2.5.3              pyhd8ed1ab_0    conda-forge
pydantic-core             2.14.6          py310hcb5633a_1    conda-forge
pygithub                  2.1.1              pyhd8ed1ab_0    conda-forge
pygments                  2.17.2             pyhd8ed1ab_0    conda-forge
pyjwt                     2.8.0              pyhd8ed1ab_0    conda-forge
pynacl                    1.5.0           py310h2372a71_3    conda-forge
pyopenssl                 23.3.0             pyhd8ed1ab_0    conda-forge
pyperclip                 1.8.2              pyhd8ed1ab_2    conda-forge
pysocks                   1.7.1              pyha2e5f31_6    conda-forge
python                    3.10.13         hd12c33a_0_cpython    conda-forge
python-dateutil           2.8.2              pyhd8ed1ab_0    conda-forge
python-libarchive-c       5.0             py310hff52083_2    conda-forge
python_abi                3.10                    4_cp310    conda-forge
pytz                      2023.3.post1       pyhd8ed1ab_0    conda-forge
pyyaml                    6.0.1           py310h2372a71_1    conda-forge
readline                  8.2                  h8228510_1    conda-forge
referencing               0.32.0             pyhd8ed1ab_0    conda-forge
reproc                    14.2.4.post0         hd590300_1    conda-forge
reproc-cpp                14.2.4.post0         h59595ed_1    conda-forge
requests                  2.31.0             pyhd8ed1ab_0    conda-forge
requests-oauthlib         1.3.1              pyhd8ed1ab_0    conda-forge
rich                      13.7.0             pyhd8ed1ab_0    conda-forge
ripgrep                   14.0.3               he8a937b_1    conda-forge
rpds-py                   0.16.2          py310hcb5633a_0    conda-forge
ruamel.yaml               0.17.40         py310h2372a71_0    conda-forge
ruamel.yaml.clib          0.2.7           py310h2372a71_2    conda-forge
scrypt                    0.8.20          py310hd2d1899_1    conda-forge
secretstorage             3.3.3           py310hff52083_2    conda-forge
setuptools                69.0.3             pyhd8ed1ab_0    conda-forge
shellingham               1.5.4              pyhd8ed1ab_0    conda-forge
six                       1.16.0             pyh6c4a22f_0    conda-forge
smmap                     5.0.0              pyhd8ed1ab_0    conda-forge
sniffio                   1.3.0              pyhd8ed1ab_0    conda-forge
soupsieve                 2.5                pyhd8ed1ab_1    conda-forge
tk                        8.6.13          noxft_h4845f30_101    conda-forge
tomli                     2.0.1              pyhd8ed1ab_0    conda-forge
tomli-w                   1.0.0              pyhd8ed1ab_0    conda-forge
tomlkit                   0.12.3             pyha770c72_0    conda-forge
toolz                     0.12.0             pyhd8ed1ab_0    conda-forge
tqdm                      4.66.1             pyhd8ed1ab_0    conda-forge
trove-classifiers         2023.11.29         pyhd8ed1ab_0    conda-forge
truststore                0.8.0              pyhd8ed1ab_0    conda-forge
typer                     0.9.0              pyhd8ed1ab_0    conda-forge
typing-extensions         4.9.0                hd8ed1ab_0    conda-forge
typing_extensions         4.9.0              pyha770c72_0    conda-forge
tzdata                    2023d                h0c530f3_0    conda-forge
ukkonen                   1.0.1           py310hd41b1e2_4    conda-forge
urllib3                   2.1.0              pyhd8ed1ab_0    conda-forge
userpath                  1.7.0              pyhd8ed1ab_0    conda-forge
virtualenv                20.25.0            pyhd8ed1ab_0    conda-forge
vsts-python-api           0.1.25             pyhd8ed1ab_1    conda-forge
watchgod                  0.7                pyhd8ed1ab_0    conda-forge
wcwidth                   0.2.12             pyhd8ed1ab_0    conda-forge
wheel                     0.42.0             pyhd8ed1ab_0    conda-forge
wrapt                     1.16.0          py310h2372a71_0    conda-forge
xz                        5.2.6                h166bdaf_0    conda-forge
yaml                      0.2.5                h7f98852_2    conda-forge
yaml-cpp                  0.8.0                h59595ed_0    conda-forge
yapf                      0.40.1             pyhd8ed1ab_0    conda-forge
zipp                      3.17.0             pyhd8ed1ab_0    conda-forge
zstandard                 0.22.0          py310h1275a96_0    conda-forge
zstd                      1.5.5                hfc55251_0    conda-forge
@carterbox carterbox added the type::bug describes erroneous operation, use severity::* to classify the type label Jan 11, 2024
@github-project-automation github-project-automation bot moved this to 🆕 New in 🧭 Planning Jan 11, 2024
carterbox added a commit to MementoRC/staged-recipes that referenced this issue Jan 12, 2024
This version of conda-build was not able to correctly
locate libc for satisfying links in as multioutput
recipe.

conda/conda-build#5136
@carterbox
Copy link
Contributor Author

@conda-forge/help-c-cpp, I discovered this bug while reviewing on staged-recipes. Pinging y'all for awareness.

@minrk
Copy link
Contributor

minrk commented Jan 16, 2024

This is fixed by #5138

@kenodegard kenodegard added the in-progress issue is actively being worked on label Jan 16, 2024
@kenodegard kenodegard moved this from 🆕 New to 🏗️ In Progress in 🧭 Planning Jan 16, 2024
@kenodegard kenodegard added severity::3 major; broken functionality with a workaround and removed severity::1 blocker; broken functionality with no workaround labels Jan 16, 2024
@kenodegard kenodegard added this to the 24.1.x milestone Jan 16, 2024
@kenodegard
Copy link
Contributor

kenodegard commented Jan 16, 2024

lowered severity since there are workarounds like adding overlinking_ignore_patterns to the recipe

there are currently two candidate fixes, so for those interested please take a look and leave feedback:

the fix will be included in the January release (conda-build 24.1.0)

@carterbox
Copy link
Contributor Author

Thanks, @kenodegard @minrk ! I appreciate your quick attention.

@kenodegard kenodegard linked a pull request Jan 17, 2024 that will close this issue
3 tasks
kenodegard added a commit that referenced this issue Jan 17, 2024
* Add test for deleted files in which_package
* Add which_package case-insensitivity test on Win
* Restore pre-3.28 behavior for which_package
* Add regression test for #5136

---------

Signed-off-by: Marcel Bargull <marcel.bargull@udo.edu>
Co-authored-by: Ken Odegard <kodegard@anaconda.com>
@kenodegard kenodegard removed this from the 24.1.x milestone Jan 18, 2024
@kenodegard
Copy link
Contributor

thanks to @minrk and @mbargull for helping to debug and proposing fixes

#5141 has been merged and we're now working on a patch release (conda-build 3.28.4)

@github-project-automation github-project-automation bot moved this from 🏗️ In Progress to 🏁 Done in 🧭 Planning Jan 18, 2024
@github-actions github-actions bot added the locked [bot] locked due to inactivity label Aug 20, 2024
@github-actions github-actions bot locked as resolved and limited conversation to collaborators Aug 20, 2024
Sign up for free to subscribe to this conversation on GitHub. Already have an account? Sign in.
Labels
in-progress issue is actively being worked on locked [bot] locked due to inactivity severity::3 major; broken functionality with a workaround source::community catch-all for issues filed by community members type::bug describes erroneous operation, use severity::* to classify the type
Projects
Archived in project
3 participants