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I am attempting to create a conda environment with 3 packages and a specific python version and get the following output:
$ conda create -n testing_junk -y instrain awscli samtools python=3.8
Collecting package metadata (current_repodata.json): done
Solving environment: failed with repodata from current_repodata.json, will retry with next repodata source.
Collecting package metadata (repodata.json): done
Solving environment: |
Found conflicts! Looking for incompatible packages.
This can take several minutes. Press CTRL-C to abort.
failed \
UnsatisfiableError: The following specifications were found to be incompatible with each other:
Output in format: Requested package -> Available versions
Package ncurses conflicts for:
python=3.8 -> ncurses[version='>=6.1,<6.2.0a0|>=6.2,<7.0a0|>=6.1,<7.0a0']
awscli -> python[version='>=3.8,<3.9.0a0'] -> ncurses[version='5.9.*|5.9|>=6.1,<6.2.0a0|>=6.2,<7.0a0|>=6.1,<7.0a0|>=6.0,<7.0a0|6.0.*']
instrain -> python[version='>=3.4'] -> ncurses[version='5.9.*|5.9|>=6.1,<6.2.0a0|>=6.2,<7.0a0|>=6.1,<7.0a0|>=6.0,<7.0a0|6.0.*']
python=3.8 -> readline[version='>=7.0,<8.0a0'] -> ncurses[version='5.9.*|>=6.0,<7.0a0|6.0.*']
samtools -> ncurses[version='5.9|5.9.*|>=5.9,<5.10.0a0|>=6.1,<6.2.0a0']
Package python conflicts for:
awscli -> python[version='2.7.*|3.5.*|3.6.*|>=2.7,<2.8.0a0|>=3.6,<3.7.0a0|>=3.7,<3.8.0a0|>=3.8,<3.9.0a0|>=3.5,<3.6.0a0|3.4.*']
python=3.8
instrain -> biopython -> python[version='2.7.*|3.5.*|3.6.*|>=2.7,<2.8.0a0|>=3.6,<3.7.0a0|>=3.8,<3.9.0a0|>=3.7,<3.8.0a0|>=3.5,<3.6.0a0|3.4.*|>3|>=3.5|<3.0.0|>=3.6']
instrain -> python[version='>=3.4']
awscli -> python_abi=3.8[build=*_cp38] -> python[version='3.7.*|3.8.*']
Package ca-certificates conflicts for:
samtools -> openssl[version='>=1.1.1a,<1.1.2a'] -> ca-certificates
python=3.8 -> openssl[version='>=1.1.1g,<1.1.2a'] -> ca-certificates
awscli -> python[version='>=2.7,<2.8.0a0'] -> ca-certificates
Package setuptools conflicts for:
python=3.8 -> pip -> setuptools
instrain -> matplotlib-base -> setuptools[version='>=40.0']
Package libgcc-ng conflicts for:
samtools -> ncurses[version='>=6.1,<6.2.0a0'] -> libgcc-ng[version='>=7.2.0']
samtools -> libgcc-ng[version='>=4.9|>=7.3.0']
Package pypy3.6 conflicts for:
instrain -> numpy -> pypy3.6[version='7.3.0.*|7.3.1.*|>=7.3.1']
awscli -> python[version='>=3.6,<3.7.0a0'] -> pypy3.6[version='7.3.*|7.3.0.*|7.3.1.*']
Package bzip2 conflicts for:
samtools -> bzip2[version='1.0.*|>=1.0.6,<2.0a0|>=1.0.8,<2.0a0']
instrain -> pysam -> bzip2[version='>=1.0.6,<2.0a0|>=1.0.8,<2.0a0']
awscli -> python[version='>=3.7,<3.8.0a0'] -> bzip2[version='>=1.0.6,<2.0a0|>=1.0.8,<2.0a0']
Package zlib conflicts for:
samtools -> zlib[version='1.2.11.*|>=1.2.11,<1.3.0a0|1.2.8.*|1.2.8']
samtools -> curl[version='>=7.59.0,<8.0a0'] -> zlib[version='1.2.*|1.2.11']
Package samtools conflicts for:
samtools
instrain -> pysam -> samtools[version='1.3|1.3.1.*|1.3.1|1.5.*|1.6.*|1.7|1.7.*|1.9.*|>=1.4.1|>=1.4.1,<1.5|>=1.4,<1.5|>=1.3,<1.4|>=1.3']
Package openssl conflicts for:
samtools -> curl[version='>=7.59.0,<8.0a0'] -> openssl[version='1.0.*|>=1.0.2o,<1.0.3a|>=1.0.2m,<1.0.3a']
samtools -> openssl[version='>=1.0.2p,<1.0.3a|>=1.0.2r,<1.0.3a|>=1.1.1a,<1.1.2a']
Package _libgcc_mutex conflicts for:
samtools -> libgcc-ng[version='>=7.3.0'] -> _libgcc_mutex[version='*|0.1',build='main|conda_forge']
python=3.8 -> libgcc-ng[version='>=7.5.0'] -> _libgcc_mutex[version='*|0.1',build='main|conda_forge']The following specifications were found to be incompatible with your CUDA driver:
- feature:/linux-64::__cuda==10.2=0
- feature:|@/linux-64::__cuda==10.2=0
Your installed CUDA driver is: 10.2
I understand that there is something about the packages that conflict with each other, but I'm unable to interpret this output to understand what the problem is.
For example, in looking at the first block of conflicts (related to ncurses), shouldn't version 6.1 satisfy all requirements listed?
Additionally, for the block about package setuptools, I don't see any problem at all?
Any insight into how to interpret these conflicts so that I can attempt to address them would be much appreciated.
846
With conda, you can create, export, list, remove, and update environments that have different versions of Python and/or packages installed in them. Switching or moving between environments is called activating the environment. You can also share an environment file.
@Quantum7's answer gives a fine literal interpretation of Conda's conflict reporting. However, I wanted to offer a more practical take, which is that this "feature" from Conda is too non-specific to be useful in most non-trivial environments. And sometimes it won't even include the underlying conflict. Don't waste your time with it!
On the face of it, Conda attempts to report all possible sources of conflict. That is, all sets of paths in the dependency graph that begin from the explicit specifications and end in the same package. This amounts to most of what is reported being innocuous and frankly distracting. For example, the zlib "conflicts":
Package zlib conflicts for:
samtools -> zlib[version='1.2.11.*|>=1.2.11,<1.3.0a0|1.2.8.*|1.2.8']
samtools -> curl[version='>=7.59.0,<8.0a0'] -> zlib[version='1.2.*|1.2.11']
Since samtools depends on zlib both directly and indirectly (mediated through curl), this comes up as two alternate paths that lead to constraints. The problem is that the intersection of the final constraints are not empty, such that there is nothing incompatible here.
Furthermore, there are cases where none of what is reported is in conflict (e.g., this question or this one), which means parsing through the output could be a complete waste of time.
Instead, if one is actually concerned with resolving conflicts, I find Mamba to be more effective to work with, both in speed and precision.
# install mamba
conda install -n base conda-forge::mamba
# use 'mamba' just like 'conda'
mamba create -n foo instrain awscli samtools python=3.8
Unfortunately, this example simply works now. However, there are other questions where Conda and Mamba unsatisfiability reporting is compared, e.g., this question.
82
The package version specification is described here, but the important parts are:
, represents AND and has the highest precedence| represents OR and has second precedenceAs an example, consider the first line of the ncurses group:
python=3.8 -> ncurses[version='>=6.1,<6.2.0a0|>=6.2,<7.0a0|>=6.1,<7.0a0']
This indicates that your requested python=3.8 depends on ncurses with the following versions:
>=6.1,<6.2.0a0 version 6.1*>=6.2,<7.0a0 version 6.2*>=6.1,<7.0a0 (redundantly) at least 6.1 but not as high as 7.0The lists are difficult to read since they include many unnecessary constraints. However, also didn't see any real conflicts with your versions. Not trusting my own ability to check package specifications, I found the conda package that does it directly:
>>> from conda.models import version as cv
>>> cv.VersionSpec(">=6.1,<6.2.0a0|>=6.2,<7.0a0|>=6.1,<7.0a0").match("6.1")
True
Running this on all the conflicts you reported, I was a able to find versions that satisfied all the stated version requirements: https://gist.github.com/sbliven/aab43e1f0bce1f4ac63aaaaa718df0b3
The only part I can't test is the cuda part, but it does look like you have a graphics card that supports CUDA 10.2.
When I started this answer I was preparing an explanation about how SAT solvers like the one used in conda add constraints iteratively and how that could lead to seemingly valid constraints being output as conflicts. However, there should always be some conflict, so I think your issue must lie elsewhere
Since samtools seems to have been removed from conda-forge I'm unable to reproduce the example myself, so I'm left confused about the exact error you're seeing. Hopefully understanding the version strings helps in the future.
Edit: Of course, samtools is from bioconda not conda-forge! The following command worked for me:
conda create -n testing_junk -c bioconda -y instrain awscli samtools python=3.8
It resolved to these package versions (maybe something was fixed since your question posted):
The following packages will be downloaded:
package | build
---------------------------|-----------------
asteval-0.9.16 | pyh5ca1d4c_0 18 KB conda-forge
awscli-1.18.221 | py38h50d1736_0 1.8 MB conda-forge
biopython-1.74 | py38h0b31af3_0 2.5 MB conda-forge
blas-2.14 | openblas 10 KB conda-forge
boost-1.70.0 | py38hbf1eeb5_1 347 KB conda-forge
boost-cpp-1.70.0 | hef959ae_3 18.9 MB conda-forge
botocore-1.19.61 | pyhd8ed1ab_0 4.5 MB conda-forge
brotlipy-0.7.0 |py38h5406a74_1001 357 KB conda-forge
c-ares-1.11.0 | 0 73 KB bioconda
capnproto-0.6.1 | h0ceac7d_2 2.4 MB conda-forge
cffi-1.14.4 | py38h979bc6b_1 219 KB conda-forge
colorama-0.4.3 | py_0 17 KB conda-forge
cryptography-3.3.1 | py38h6b4ec92_1 614 KB conda-forge
docutils-0.15.2 | py38h50d1736_1 739 KB conda-forge
drep-3.0.0 | py_2 59 KB bioconda
fastani-1.32 | he69ab0f_0 151 KB bioconda
future-0.18.2 | py38h50d1736_3 715 KB conda-forge
hdf5-1.10.6 |nompi_h34ad4e8_1111 3.0 MB conda-forge
htslib-1.11 | h422799e_1 1.5 MB bioconda
idna-3.1 | pyhd3deb0d_0 52 KB conda-forge
instrain-1.4.0 | py_0 380 KB bioconda
jmespath-0.10.0 | pyh9f0ad1d_0 21 KB conda-forge
joblib-1.0.0 | pyhd8ed1ab_0 206 KB conda-forge
kiwisolver-1.3.1 | py38hd9c93a9_1 57 KB conda-forge
libblas-3.8.0 | 14_openblas 10 KB conda-forge
libcblas-3.8.0 | 14_openblas 10 KB conda-forge
libdeflate-1.6 | h0b31af3_0 61 KB conda-forge
liblapack-3.8.0 | 14_openblas 10 KB conda-forge
liblapacke-3.8.0 | 14_openblas 10 KB conda-forge
libnghttp2-1.41.0 | h8a08a2b_1 736 KB conda-forge
libopenblas-0.3.7 | h3d69b6c_4 8.2 MB conda-forge
llvm-openmp-8.0.1 | h770b8ee_0 253 KB conda-forge
llvmlite-0.34.0 | py38h3707e27_2 247 KB conda-forge
lmfit-1.0.1 | py_1 69 KB conda-forge
mash-2.2.2 | h194473e_2 449 KB bioconda
matplotlib-base-3.3.4 | py38hb24f337_0 6.8 MB conda-forge
mummer4-4.0.0rc1 | pl526h4a8c4bd_0 699 KB bioconda
numba-0.51.2 | py38h6be0db6_0 3.5 MB conda-forge
openmp-8.0.1 | 0 8 KB conda-forge
pandas-1.2.1 | py38he9f00de_0 10.6 MB conda-forge
pillow-8.1.0 | py38hc1d52f7_1 646 KB conda-forge
pluggy-0.13.1 | py38h50d1736_4 29 KB conda-forge
prodigal-2.6.3 | h01d97ff_2 397 KB bioconda
psutil-5.8.0 | py38h5406a74_1 350 KB conda-forge
pyasn1-0.4.8 | py_0 53 KB conda-forge
pysam-0.16.0.1 | py38hb3e8b06_1 2.1 MB bioconda
pysocks-1.7.1 | py38h50d1736_3 27 KB conda-forge
pytest-6.2.2 | py38h50d1736_0 432 KB conda-forge
pyyaml-5.3.1 | py38h5406a74_2 173 KB conda-forge
rsa-4.4.1 | pyh9f0ad1d_0 27 KB conda-forge
s3transfer-0.3.4 | pyhd8ed1ab_0 51 KB conda-forge
samtools-1.11 | h725deca_0 381 KB bioconda
scikit-learn-0.22.1 | py38hebd9d1a_0 4.7 MB
scipy-1.5.3 | py38h352ea5d_0 19.1 MB conda-forge
seaborn-0.11.1 | hd8ed1ab_1 4 KB conda-forge
seaborn-base-0.11.1 | pyhd8ed1ab_1 217 KB conda-forge
statsmodels-0.12.1 | py38hc7193ba_2 10.5 MB conda-forge
tornado-6.1 | py38h5406a74_1 643 KB conda-forge
uncertainties-3.1.5 | pyhd8ed1ab_0 75 KB conda-forge
------------------------------------------------------------
Total: 110.1 MB
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