Problem while creating environment from yaml file - iphop

Question

I'm new to bioinformatics and I am trying to create an environment from a yaml file however I keep getting the following long error message and I am not certain on how to fix it.

Encountered problems while solving:

• package c-ares-1.17.2-h7f98852_0 is excluded by strict repo priority
• package rsa-4.7.2-pyh44b312d_0 is excluded by strict repo priority
• package binutils_impl_linux-64-2.35.1-h27ae35d_9 is excluded by strict repo priority
• package binutils_linux-64-2.35.1-h454624a_30 is excluded by strict repo priority
• package biopython-1.79-py37h5e8e339_0 is excluded by strict repo priority
• package gcc_impl_linux-64-9.3.0-h6df7d76_17 is excluded by strict repo priority
• package gcc_linux-64-9.3.0-h1ee779e_30 is excluded by strict repo priority
• package gfortran_impl_linux-64-9.3.0-h5abd6ed_17 is excluded by strict repo priority
• package gfortran_linux-64-9.3.0-hf47db2c_30 is excluded by strict repo priority
• package gxx_impl_linux-64-9.3.0-hbdd7822_17 is excluded by strict repo priority
• package gxx_linux-64-9.3.0-h7e70986_30 is excluded by strict repo priority
• package ld_impl_linux-64-2.35.1-h7274673_9 is excluded by strict repo priority
• package libdeflate-1.7-h7f98852_5 is excluded by strict repo priority
• package libgcc-devel_linux-64-9.3.0-hb95220a_17 is excluded by strict repo priority
• package libgfortran-ng-9.3.0-ha5ec8a7_17 is excluded by strict repo priority
• package libgfortran5-9.3.0-ha5ec8a7_17 is excluded by strict repo priority
• package libstdcxx-devel_linux-64-9.3.0-hf0c5c8d_17 is excluded by strict repo priority
• package urllib3-1.26.6-pyhd8ed1ab_0 is excluded by strict repo priority
• package google-auth-1.35.0-pyh6c4a22f_0 requires pyasn1-modules >=0.2.1, but none of the providers can be installed

I utilized the following command:

mamba env create -n iphop -f iphop.yaml

The text of the yaml file is below. Any help would be appreciated!

name: iphop
channels:
  - bioconda
  - conda-forge
  - biocore
  - defaults
dependencies:
  - _libgcc_mutex=0.1=conda_forge
  - _openmp_mutex=4.5=1_gnu
  - _r-mutex=1.0.1=anacondar_1
  - _tflow_select=2.3.0=eigen
  - absl-py=0.13.0=pyhd8ed1ab_0
  - aiohttp=3.7.4.post0=py37h5e8e339_0
  - alsa-lib=1.2.3=h516909a_0
  - astor=0.8.1=pyh9f0ad1d_0
  - astunparse=1.6.3=pyhd8ed1ab_0
  - async-timeout=3.0.1=py_1000
  - attrs=21.2.0=pyhd8ed1ab_0
  - binutils_impl_linux-64=2.35.1=h27ae35d_9
  - binutils_linux-64=2.35.1=h454624a_30
  - biopython=1.79=py37h5e8e339_0
  - blast=2.12.0=pl5262h3289130_0
  - blinker=1.4=py_1
  - boost-cpp=1.74.0=h312852a_4
  - brotlipy=0.7.0=py37h5e8e339_1001
  - bwidget=1.9.14=ha770c72_0
  - bzip2=1.0.8=h7f98852_4
  - c-ares=1.17.2=h7f98852_0
  - ca-certificates=2021.10.8=ha878542_0
  - cachetools=4.2.2=pyhd8ed1ab_0
  - cairo=1.16.0=h6cf1ce9_1008
  - certifi=2021.10.8=py37h89c1867_2
  - cffi=1.14.6=py37hc58025e_0
  - chardet=4.0.0=py37h89c1867_1
  - click=8.0.1=py37h89c1867_0
  - crisper_recognition_tool=1.2=hdfd78af_2
  - cryptography=3.4.7=py37h5d9358c_0
  - curl=7.78.0=hea6ffbf_0
  - dataclasses=0.8=pyhc8e2a94_3
  - diamond=2.0.11=hdcc8f71_0
  - entrez-direct=13.9=pl5262he881be0_2
  - expat=2.4.1=h9c3ff4c_0
  - fasttree=2.1.10=h779adbc_5
  - font-ttf-dejavu-sans-mono=2.37=hab24e00_0
  - font-ttf-inconsolata=3.000=h77eed37_0
  - font-ttf-source-code-pro=2.038=h77eed37_0
  - font-ttf-ubuntu=0.83=hab24e00_0
  - fontconfig=2.13.1=hba837de_1005
  - fonts-conda-ecosystem=1=0
  - fonts-conda-forge=1=0
  - freetype=2.10.4=h0708190_1
  - fribidi=1.0.10=h36c2ea0_0
  - gast=0.3.3=py_0
  - gcc_impl_linux-64=9.3.0=h6df7d76_17
  - gcc_linux-64=9.3.0=h1ee779e_30
  - gettext=0.19.8.1=h0b5b191_1005
  - gfortran_impl_linux-64=9.3.0=h5abd6ed_17
  - gfortran_linux-64=9.3.0=hf47db2c_30
  - giflib=5.2.1=h36c2ea0_2
  - git-lfs=3.1.4=ha770c72_0
  - google-auth=1.35.0=pyh6c4a22f_0
  - google-auth-oauthlib=0.4.6=pyhd8ed1ab_0
  - google-pasta=0.2.0=pyh8c360ce_0
  - graphite2=1.3.13=h58526e2_1001
  - grpcio=1.38.1=py37hb27c1af_0
  - gsl=2.6=he838d99_2
  - gxx_impl_linux-64=9.3.0=hbdd7822_17
  - gxx_linux-64=9.3.0=h7e70986_30
  - h5py=2.10.0=nompi_py37ha3df211_106
  - harfbuzz=2.9.0=h83ec7ef_0
  - hdf5=1.10.6=nompi_h6a2412b_1114
  - hmmer=3.3.2=h1b792b2_1
  - icu=68.1=h58526e2_0
  - idna=2.10=pyh9f0ad1d_0
  - importlib-metadata=4.8.1=py37h89c1867_0
  - jbig=2.1=h7f98852_2003
  - joblib=1.0.1=pyhd8ed1ab_0
  - jpeg=9d=h36c2ea0_0
  - keras-preprocessing=1.1.2=pyhd8ed1ab_0
  - kernel-headers_linux-64=2.6.32=he073ed8_14
  - krb5=1.19.2=hcc1bbae_0
  - lcms2=2.12=hddcbb42_0
  - ld_impl_linux-64=2.35.1=h7274673_9
  - lerc=2.2.1=h9c3ff4c_0
  - libblas=3.9.0=11_linux64_openblas
  - libcblas=3.9.0=11_linux64_openblas
  - libcurl=7.78.0=h2574ce0_0
  - libdeflate=1.7=h7f98852_5
  - libedit=3.1.20191231=he28a2e2_2
  - libev=4.33=h516909a_1
  - libffi=3.3=h58526e2_2
  - libgcc=7.2.0=h69d50b8_2
  - libgcc-devel_linux-64=9.3.0=hb95220a_17
  - libgcc-ng=11.1.0=hc902ee8_8
  - libgfortran-ng=9.3.0=ha5ec8a7_17
  - libgfortran5=9.3.0=ha5ec8a7_17
  - libglib=2.68.4=h3e27bee_0
  - libgomp=11.1.0=hc902ee8_8
  - libiconv=1.16=h516909a_0
  - liblapack=3.9.0=11_linux64_openblas
  - libnghttp2=1.43.0=h812cca2_0
  - libopenblas=0.3.17=pthreads_h8fe5266_1
  - libpng=1.6.37=h21135ba_2
  - libprotobuf=3.17.2=h780b84a_1
  - libssh2=1.10.0=ha56f1ee_0
  - libstdcxx-devel_linux-64=9.3.0=hf0c5c8d_17
  - libstdcxx-ng=11.1.0=h56837e0_8
  - libtiff=4.3.0=hf544144_1
  - libuuid=2.32.1=h7f98852_1000
  - libwebp-base=1.2.1=h7f98852_0
  - libxcb=1.13=h7f98852_1003
  - libxml2=2.9.12=h72842e0_0
  - lz4-c=1.9.3=h9c3ff4c_1
  - make=4.3=hd18ef5c_1
  - markdown=3.3.4=pyhd8ed1ab_0
  - multidict=5.1.0=py37h5e8e339_1
  - ncurses=6.2=h58526e2_4
  - numpy=1.21.2=py37h31617e3_0
  - oauthlib=3.1.1=pyhd8ed1ab_0
  - openjdk=11.0.9.1=h5cc2fde_1
  - openssl=1.1.1o=h166bdaf_0
  - opt_einsum=3.3.0=pyhd8ed1ab_1
  - pandas=1.3.2=py37he8f5f7f_0
  - pango=1.48.9=hb8ff022_0
  - pcre=8.45=h9c3ff4c_0
  - pcre2=10.37=h032f7d1_0
  - perl=5.26.2=h36c2ea0_1008
  - perl-app-cpanminus=1.7044=pl526_1
  - perl-archive-tar=2.32=pl526_0
  - perl-base=2.23=pl526_1
  - perl-bioperl=1.6.924=4
  - perl-business-isbn=3.004=pl526_0
  - perl-business-isbn-data=20140910.003=pl526_0
  - perl-carp=1.38=pl526_3
  - perl-common-sense=3.74=pl526_2
  - perl-compress-raw-bzip2=2.087=pl526he1b5a44_0
  - perl-compress-raw-zlib=2.087=pl526hc9558a2_0
  - perl-constant=1.33=pl526_1
  - perl-data-dumper=2.173=pl526_0
  - perl-digest-hmac=1.03=pl526_3
  - perl-digest-md5=2.55=pl526_0
  - perl-encode=2.88=pl526_1
  - perl-encode-locale=1.05=pl526_6
  - perl-exporter=5.72=pl526_1
  - perl-exporter-tiny=1.002001=pl526_0
  - perl-extutils-makemaker=7.36=pl526_1
  - perl-file-listing=6.04=pl526_1
  - perl-file-path=2.16=pl526_0
  - perl-file-temp=0.2304=pl526_2
  - perl-html-parser=3.72=pl526h6bb024c_5
  - perl-html-tagset=3.20=pl526_3
  - perl-html-tree=5.07=pl526_1
  - perl-http-cookies=6.04=pl526_0
  - perl-http-daemon=6.01=pl526_1
  - perl-http-date=6.02=pl526_3
  - perl-http-message=6.18=pl526_0
  - perl-http-negotiate=6.01=pl526_3
  - perl-io-compress=2.087=pl526he1b5a44_0
  - perl-io-html=1.001=pl526_2
  - perl-io-socket-ssl=2.066=pl526_0
  - perl-io-zlib=1.10=pl526_2
  - perl-json=4.02=pl526_0
  - perl-json-xs=2.34=pl526h6bb024c_3
  - perl-libwww-perl=6.39=pl526_0
  - perl-list-moreutils=0.428=pl526_1
  - perl-list-moreutils-xs=0.428=pl526_0
  - perl-lwp-mediatypes=6.04=pl526_0
  - perl-lwp-protocol-https=6.07=pl526_4
  - perl-mime-base64=3.15=pl526_1
  - perl-mozilla-ca=20180117=pl526_1
  - perl-net-http=6.19=pl526_0
  - perl-net-ssleay=1.88=pl526h90d6eec_0
  - perl-ntlm=1.09=pl526_4
  - perl-parent=0.236=pl526_1
  - perl-pathtools=3.75=pl526h14c3975_1
  - perl-scalar-list-utils=1.52=pl526h516909a_0
  - perl-socket=2.027=pl526_1
  - perl-storable=3.15=pl526h14c3975_0
  - perl-test-requiresinternet=0.05=pl526_0
  - perl-threaded=5.26.0=0
  - perl-time-local=1.28=pl526_1
  - perl-try-tiny=0.30=pl526_1
  - perl-types-serialiser=1.0=pl526_2
  - perl-uri=1.76=pl526_0
  - perl-www-robotrules=6.02=pl526_3
  - perl-xml-namespacesupport=1.12=pl526_0
  - perl-xml-parser=2.44=4
  - perl-xml-sax=1.02=pl526_0
  - perl-xml-sax-base=1.09=pl526_0
  - perl-xml-sax-expat=0.51=pl526_3
  - perl-xml-simple=2.25=pl526_1
  - perl-xsloader=0.24=pl526_0
  - perl-yaml=1.29=pl526_0
  - piler-cr=1.06=h7d875b9_1
  - pip=21.2.4=pyhd8ed1ab_0
  - pixman=0.40.0=h36c2ea0_0
  - prodigal=2.6.3=h779adbc_3
  - protobuf=3.17.2=py37hcd2ae1e_0
  - pthread-stubs=0.4=h36c2ea0_1001
  - pyasn1=0.4.8=py_0
  - pycparser=2.20=pyh9f0ad1d_2
  - pyjwt=2.1.0=pyhd8ed1ab_0
  - pyopenssl=20.0.1=pyhd8ed1ab_0
  - pysocks=1.7.1=py37h89c1867_3
  - python=3.7.10=hffdb5ce_100_cpython
  - python-dateutil=2.8.2=pyhd8ed1ab_0
  - python_abi=3.7=2_cp37m
  - pytz=2021.1=pyhd8ed1ab_0
  - pyu2f=0.1.5=pyhd8ed1ab_0
  - r-base=4.0.5=hb67fd72_2
  - r-lattice=0.20_44=r40hcfec24a_0
  - r-matrix=1.3_4=r40he454529_0
  - r-ranger=0.13.1=r40h03ef668_0
  - r-rcpp=1.0.7=r40h03ef668_0
  - r-rcppeigen=0.3.3.9.1=r40h306847c_0
  - readline=8.1=h46c0cb4_0
  - requests=2.25.1=pyhd3deb0d_0
  - requests-oauthlib=1.3.0=pyh9f0ad1d_0
  - rsa=4.7.2=pyh44b312d_0
  - scikit-learn=0.22=py37hcdab131_1
  - scipy=1.6.3=py37h29e03ee_0
  - sed=4.8=he412f7d_0
  - setuptools=57.4.0=py37h89c1867_0
  - six=1.16.0=pyh6c4a22f_0
  - sqlite=3.36.0=h9cd32fc_0
  - sysroot_linux-64=2.12=he073ed8_14
  - tensorboard=2.6.0=pyhd8ed1ab_1
  - tensorboard-data-server=0.6.0=py37hf1a17b8_0
  - tensorboard-plugin-wit=1.8.0=pyh44b312d_0
  - termcolor=1.1.0=py_2
  - threadpoolctl=3.0.0=pyh8a188c0_0
  - tk=8.6.11=h27826a3_1
  - tktable=2.10=hb7b940f_3
  - typing-extensions=3.10.0.0=hd8ed1ab_0
  - typing_extensions=3.10.0.0=pyha770c72_0
  - urllib3=1.26.6=pyhd8ed1ab_0
  - werkzeug=2.0.1=pyhd8ed1ab_0
  - wrapt=1.12.1=py37h5e8e339_3
  - xorg-fixesproto=5.0=h7f98852_1002
  - xorg-inputproto=2.3.2=h7f98852_1002
  - xorg-kbproto=1.0.7=h7f98852_1002
  - xorg-libice=1.0.10=h7f98852_0
  - xorg-libsm=1.2.3=hd9c2040_1000
  - xorg-libx11=1.7.2=h7f98852_0
  - xorg-libxau=1.0.9=h7f98852_0
  - xorg-libxdmcp=1.1.3=h7f98852_0
  - xorg-libxext=1.3.4=h7f98852_1
  - xorg-libxfixes=5.0.3=h7f98852_1004
  - xorg-libxi=1.7.10=h7f98852_0
  - xorg-libxrender=0.9.10=h7f98852_1003
  - xorg-libxt=1.2.1=h7f98852_2
  - xorg-libxtst=1.2.3=h7f98852_1002
  - xorg-recordproto=1.14.2=h7f98852_1002
  - xorg-renderproto=0.11.1=h7f98852_1002
  - xorg-xextproto=7.3.0=h7f98852_1002
  - xorg-xproto=7.0.31=h7f98852_1007
  - xz=5.2.5=h516909a_1
  - yarl=1.6.3=py37h5e8e339_2
  - zipp=3.5.0=pyhd8ed1ab_0
  - zlib=1.2.11=h516909a_1010
  - zstd=1.5.0=ha95c52a_0
  - pip:
    - flatbuffers==2.0
    - keras==2.7.0
    - libclang==12.0.0
    - pyasn1-modules==0.2.8
    - tensorflow==2.7.0
    - tensorflow-decision-forests==0.2.2
    - tensorflow-estimator==2.7.0
    - tensorflow-io-gcs-filesystem==0.22.0
    - wheel==0.37.1
    - wurlitzer==3.0.2
prefix: /global/cfs/cdirs/pkmeco/virus/.conda/envs/iphop

Answer 1

I'm only guessing here:

excluded by strict repo priority

suggests your conda is configured in such way that packages from some channels are excluded. Look at the output of conda config --show. If the entry channel_priority: is strict try setting it to flexible.

Another option could be to edit the yaml file to have the exact package versions but not the package builds. E.g. use:

- absl-py=0.13.0

instead of:

- absl-py=0.13.0=pyhd8ed1ab_0

in this way you give the solver more flexibility but you still get the exact package versions of the original environment.