conda-forge.github.io: openssl incompatibility
% conda list | grep ssl
openssl 1.1.1a h14c3975_1000 conda-forge
pyopenssl 18.0.0 py27_0
% conda update --all
The following packages will be UPDATED:
asn1crypto: 0.24.0-py27_0 --> 0.24.0-py27_1003 conda-forge
cffi: 1.11.5-py27he75722e_1 --> 1.11.5-py27h9745a5d_1001 conda-forge
chardet: 3.0.4-py27_1 --> 3.0.4-py27_1003 conda-forge
conda-env: 2.6.0-1 --> 2.6.0-1 conda-forge
cryptography: 2.4.2-py27h1ba5d50_0 --> 2.5-py27hb7f436b_0 conda-forge
enum34: 1.1.6-py27_1 --> 1.1.6-py27_1001 conda-forge
futures: 3.2.0-py27_0 --> 3.2.0-py27_1000 conda-forge
idna: 2.8-py27_0 --> 2.8-py27_1000 conda-forge
ipaddress: 1.0.22-py27_0 --> 1.0.22-py_1 conda-forge
libedit: 3.1.20170329-h6b74fdf_2 --> 3.1.20170329-hf8c457e_1001 conda-forge
libffi: 3.2.1-hd88cf55_4 --> 3.2.1-hf484d3e_1005 conda-forge
ncurses: 6.1-he6710b0_1 --> 6.1-hf484d3e_1002 conda-forge
pip: 18.1-py27_0 --> 19.0.1-py27_0 conda-forge
pycosat: 0.6.3-py27h14c3975_0 --> 0.6.3-py27h14c3975_1001 conda-forge
pycparser: 2.19-py27_0 --> 2.19-py_0 conda-forge
pyopenssl: 18.0.0-py27_0 --> 19.0.0-py27_0 conda-forge
pysocks: 1.6.8-py27_0 --> 1.6.8-py27_1002 conda-forge
python: 2.7.15-h9bab390_6 --> 2.7.15-h938d71a_1006 conda-forge
readline: 7.0-h7b6447c_5 --> 7.0-hf8c457e_1001 conda-forge
ruamel_yaml: 0.15.46-py27h14c3975_0 --> 0.15.71-py27h14c3975_1000 conda-forge
setuptools: 40.6.3-py27_0 --> 40.7.1-py27_0 conda-forge
six: 1.12.0-py27_0 --> 1.12.0-py27_1000 conda-forge
sqlite: 3.26.0-h7b6447c_0 --> 3.26.0-h67949de_1000 conda-forge
tk: 8.6.8-hbc83047_0 --> 8.6.9-h84994c4_1000 conda-forge
wheel: 0.32.3-py27_0 --> 0.32.3-py27_0 conda-forge
yaml: 0.1.7-had09818_2 --> 0.1.7-h14c3975_1001 conda-forge
zlib: 1.2.11-h7b6447c_3 --> 1.2.11-h14c3975_1004 conda-forge
The following packages will be DOWNGRADED:
conda: 4.6.2-py27_0 conda-forge --> 4.5.12-py27_1000 conda-forge
libgcc-ng: 8.2.0-hdf63c60_1 --> 7.3.0-hdf63c60_0 conda-forge
libstdcxx-ng: 8.2.0-hdf63c60_1 --> 7.3.0-hdf63c60_0 conda-forge
openssl: 1.1.1a-h14c3975_1000 conda-forge --> 1.0.2p-h14c3975_1002 conda-forge
requests: 2.21.0-py27_0 --> 2.13.0-py27_0 conda-forge
urllib3: 1.24.1-py27_0 --> 1.12-py27_0 bioconda
So updating causes openssl to downgrade from 1.1.1a to 1.0.2p. The problem is that those versions of openssl are binary incompatible. So all those packages that are upgraded need to be rebuilt with the latest openssl, including pyopenssl and maybe python.
This is causing endless troubles in bioconda now.
About this issue
- Original URL
- State: closed
- Created 5 years ago
- Reactions: 3
- Comments: 20 (8 by maintainers)
Commits related to this issue
- Maybe this should depend on openssl explicitly Maybe the whole problem was that it was being built against system openssl. I do not see where openssl-1.1.1 is being specified in Bioconda. In theory, ... — committed to bio-nim/bioconda-recipes by deleted user 5 years ago
- Maybe this should depend on openssl explicitly (#13518) Maybe the whole problem was that it was being built against system openssl. I do not see where openssl-1.1.1 is being specified in Bioconda. ... — committed to bioconda/bioconda-recipes by deleted user 5 years ago
- Ucsc update (#13722) * Fixed missing file PLEK.range for PLEK receipe. (#13389) * Add new recipe for Alder (#13390) New recipe for Alder software * Apply fix to bash script to detect correct... — committed to bioconda/bioconda-recipes by dpryan79 5 years ago
- Merge bioconductor packages back into master (#16953) * add gsl * try to build mzr * add sklearn as deps * Various updates (#12677) * remove mzr dependent packages from blacklist * add... — committed to bioconda/bioconda-recipes by dpryan79 5 years ago
- Bulk (#16979) * build bumps * Bulk update 241218 (#12795) [BULK] Bulk update 241218 * increase build numbers * bump build number * bump * blacklist a few more * Bump karyoploteR ... — committed to bioconda/bioconda-recipes by dpryan79 5 years ago
- Bulk (#17316) * bump build number * bump * blacklist a few more * Bump karyoploteR as seen in https://github.com/bioconda/bioconda-recipes/pull/12732, thanks @dpryan79 and @bgruening. (#1280... — committed to bioconda/bioconda-recipes by dpryan79 5 years ago
- Noarch generic bulk (#17783) * bump build numbers again * a few updates (#12927) * updates (#12930) * updates * Update build.sh * Update build.sh * build bumps and openmp * Bulk ... — committed to bioconda/bioconda-recipes by dpryan79 5 years ago
- Bulk (#18029) * bbn * update the blacklist (#12862) * various bulk updates (#12863) * fix gviz (#12864) * a few updates, modify blacklist (#12865) * a few updates (#12866) * Add a f... — committed to bioconda/bioconda-recipes by dpryan79 5 years ago
- Bulk (#18260) * bulk updates (#12887) * more updates (#12888) * more updates * update mageckflute * Bulk update 030119a (#12896) * bulk updates * a couple more updates * Bulk upd... — committed to bioconda/bioconda-recipes by dpryan79 5 years ago
- Bulk (#18362) * Bulk update 130119c (#13062) * Update a few recipes * These will fail * Updates (#13064) * Ucsc update (#13722) * Fixed missing file PLEK.range for PLEK receipe. (#1338... — committed to bioconda/bioconda-recipes by dpryan79 5 years ago
In
~/.condarc:seems to have fixed the problem. In one environment, with a particular miniconda,
conda install pb-assemblytried to “upgrade” openssl to 1.1.1, but afterstrict, that same command did the right thing.