Problem creating new conda environment

Question

[gubrins]

Heys,

So I am trying to install a new conda environment with an .yml file but I encountered this error:

ResolvePackageNotFound: 
  - r-base==3.2.2=0

I am not sure if it is referred to the R package or which one and I am not sure how I could install it. Any help would be more than welcome!

Thanks in advance!

[DareDevil]

can you give the link to the yml file that you are using?

[gubrins]

Sure, it is from here: https://github.com/VGP/vgp-assembly/tree/master/mitoVGP

and here it is:

name: mitoVGP_pacbio
channels:
  - defaults
  - bioconda/label/cf201901
  - biobuilds
  - yuxiang
  - conda-forge
  - bioconda
dependencies:
  - _libgcc_mutex=0.1=main
  - _r-mutex=1.0.1=anacondar_1
  - alsa-lib=1.1.5=h516909a_1001
  - avro-python2=1.9.0=py_0
  - awscli=1.16.225=py27_0
  - bam2fastq=1.1.0=0
  - bcftools=1.9=ha228f0b_4
  - blast=2.5.0=hc0b0e79_3
  - boost=1.70.0=py27h9de70de_1
  - boost-cpp=1.70.0=h8e57a91_2
  - botocore=1.12.215=py_0
  - bowtie2=2.3.4.1=py27h2d50403_1
  - bzip2=1.0.8=h516909a_2
  - ca-certificates=2019.11.28=hecc5488_0
  - cairo=1.16.0=hfb77d84_1002
  - certifi=2019.11.28=py27_0
  - cffi=1.13.2=py27h8022711_0
  - chardet=3.0.4=py27_1003
  - colorama=0.3.9=py27_0
  - cryptography=2.8=py27h72c5cf5_1
  - curl=7.65.3=hf8cf82a_0
  - cython=0.29.14=py27he1b5a44_0
  - docutils=0.15.2=py27_0
  - enum34=1.1.6=py27_1002
  - fontconfig=2.13.1=h86ecdb6_1001
  - freebayes=1.0.2=0
  - freetype=2.10.0=he983fc9_1
  - fribidi=1.0.5=h516909a_1002
  - futures=3.3.0=py27_0
  - genomicconsensus=2.3.3=py27_0
  - gettext=0.19.8.1=hc5be6a0_1002
  - giflib=5.1.7=h516909a_1
  - glib=2.58.3=py27h6f030ca_1002
  - graphite2=1.3.13=hf484d3e_1000
  - h5py=2.10.0=nompi_py27h513d04c_100
  - harfbuzz=2.4.0=h9f30f68_3
  - hdf5=1.10.5=nompi_h3c11f04_1104
  - htslib=1.9=ha228f0b_7
  - icu=64.2=he1b5a44_1
  - idna=2.8=py27_1000
  - infernal=1.1.2=h14c3975_2
  - ipaddress=1.0.23=py_0
  - iso8601=0.1.12=py_1
  - java-jdk=7.0.91=1
  - jmespath=0.9.4=py_0
  - jpeg=9c=h14c3975_1001
  - krb5=1.16.3=h05b26f9_1001
  - lcms2=2.9=hbd6801e_1
  - libblas=3.8.0=14_openblas
  - libcblas=3.8.0=14_openblas
  - libcurl=7.65.3=hda55be3_0
  - libdeflate=1.0=h14c3975_1
  - libedit=3.1.20170329=hf8c457e_1001
  - libffi=3.2.1=he1b5a44_1006
  - libgcc=7.2.0=h69d50b8_2
  - libgcc-ng=9.2.0=hdf63c60_0
  - libgfortran-ng=7.3.0=hdf63c60_2
  - libiconv=1.15=h516909a_1005
  - liblapack=3.8.0=14_openblas
  - libopenblas=0.3.7=h5ec1e0e_5
  - libpng=1.6.37=hed695b0_0
  - libssh2=1.8.2=h22169c7_2
  - libstdcxx-ng=9.2.0=hdf63c60_0
  - libtiff=4.1.0=hc3755c2_1
  - libuuid=2.32.1=h14c3975_1000
  - libxcb=1.13=h14c3975_1002
  - libxml2=2.9.10=hee79883_0
  - linecache2=1.0.0=py_1
  - lz4-c=1.8.3=he1b5a44_1001
  - minimap2=2.17=h8b12597_1
  - mummer=3.23=pl526_8
  - muscle=3.8.1551=h6bb024c_4
  - ncurses=6.1=hf484d3e_1002
  - numpy=1.16.5=py27h95a1406_0
  - openjdk=11.0.1=h46a85a0_1017
  - openssl=1.1.1d=h516909a_0
  - pango=1.42.4=ha030887_1
  - pbbam=0.23.0=h88345a9_0
  - pbcommand=1.1.1=py_3
  - pbcopper=0.4.2=h3f2a3d2_1
  - pbcore=1.7.1=py27_0
  - pbcoretools=0.2.4=py27_4
  - pbgcpp=1.9.0=0
  - pbmm2=1.0.0=ha888412_0
  - pcre=8.43=he1b5a44_0
  - perl=5.26.2=h516909a_1006
  - picard=2.20.6=0
  - pip=19.3.1=py27_0
  - pixman=0.38.0=h516909a_1003
  - pthread-stubs=0.4=h14c3975_1001
  - pyasn1=0.4.8=py_0
  - pycparser=2.19=py27_1
  - pyopenssl=19.1.0=py27_0
  - pysam=0.15.3=py27hda2845c_1
  - pysocks=1.7.1=py27_0
  - python=2.7.15=h5a48372_1009
  - python-consensuscore=1.1.1=py27h3f2a3d2_3
  - python-consensuscore2=3.4.1=py27_0
  - python-dateutil=2.8.1=py_0
  - pytz=2019.3=py_0
  - pyyaml=5.2=py27h516909a_0
  - r-base=3.2.2=0
  - readline=8.0=hf8c457e_0
  - requests=2.22.0=py27_1
  - rsa=3.4.2=py_1
  - s3transfer=0.2.1=py27_0
  - samtools=1.9=h8571acd_11
  - setuptools=42.0.2=py27_0
  - six=1.13.0=py27_0
  - sqlite=3.30.1=hcee41ef_0
  - tbb=2019.9=hc9558a2_1
  - tk=8.6.10=hed695b0_0
  - traceback2=1.4.0=py27_0
  - trnascan-se=2.0=pl526h470a237_1
  - unittest2=1.1.0=py_0
  - urllib3=1.25.7=py27_0
  - wheel=0.33.6=py27_0
  - xorg-fixesproto=5.0=h14c3975_1002
  - xorg-inputproto=2.3.2=h14c3975_1002
  - xorg-kbproto=1.0.7=h14c3975_1002
  - xorg-libice=1.0.10=h516909a_0
  - xorg-libsm=1.2.3=h84519dc_1000
  - xorg-libx11=1.6.9=h516909a_0
  - xorg-libxau=1.0.9=h14c3975_0
  - xorg-libxdmcp=1.1.3=h516909a_0
  - xorg-libxext=1.3.4=h516909a_0
  - xorg-libxfixes=5.0.3=h516909a_1004
  - xorg-libxi=1.7.10=h516909a_0
  - xorg-libxrender=0.9.10=h516909a_1002
  - xorg-libxtst=1.2.3=h516909a_1002
  - xorg-recordproto=1.14.2=h516909a_1002
  - xorg-renderproto=0.11.1=h14c3975_1002
  - xorg-xextproto=7.3.0=h14c3975_1002
  - xorg-xproto=7.0.31=h14c3975_1007
  - xz=5.2.4=h14c3975_1001
  - yaml=0.2.2=h516909a_1
  - zlib=1.2.11=h516909a_1006
  - zstd=1.4.4=h3b9ef0a_1

[Ma]

Thank you so much, your post solved my problem very well, I tried it on my server in 20 Feb 2023 and still work.

Answer 1

[zorbax]

That's because the 3.2.2 version is not available any longer on the r channel from conda. The last version available to install is 3.3.1, however, it is available through the biobuilds channel. Change the channel order in your yaml file and try again.

[gubrins]

Thanks! What do you mean by changing the channel order? I put biobuilds as the first channel and I changed r-base to version 3.3.1 but I am having the same error message:

ResolvePackageNotFound: 
  - r-base==3.3.1=0