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xie186 / ViewBS

ViewBS - a powerful toolkit for visualization of high-throughput bisulfite sequencing data
GNU General Public License v3.0
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Conda environment conflicts #49

Closed weedcentipede closed 3 years ago

weedcentipede commented 4 years ago

Hey there,

I just ran Conda to install ViewBS and apparently there's some conflicts in the environment, listed below

Package snakemake-minimal conflicts for:
snakemake -> snakemake-minimal[version='5.10.0.*|5.9.1.*|5.8.2.*|5.8.1.*|5.7.4.*|5.7.1.*|5.7.0.*|5.6.0.*|5.5.4.*|5.5.3.*|5.5.2.*|5.5.1.*|5.5.0.*|5.4.5.*|5.4.4.*|5.4.3.*|5.4.2.*.2.2.*|5.2.1.*']
snakemake-minimal

Package datrie conflicts for:
snakemake -> datrie
snakemake-minimal -> datrie
datrie

Package markupsafe conflicts for:
jinja2 -> markupsafe[version='>=0.23']
snakemake -> jinja2 -> markupsafe[version='>=0.23']
markupsafe

Package liblapacke conflicts for:
r-base -> blas=[build=openblas] -> liblapacke==3.8.0[build='4_openblas|5_openblas|9_openblas|11_openblas|15_openblas|14_openblas|13_openblas|12_openblas|10_openblas|8_openblas|
numpy -> blas=[build=openblas] -> liblapacke==3.8.0[build='4_mkl|5_mkl|6_mkl|7_mkl|9_mkl|13_mkl|15_mkl|4_openblas|5_openblas|9_openblas|11_openblas|15_openblas|14_openblas|13_o|7_openblas|6_openblas|14_mkl|12_mkl|11_mkl|10_mkl|8_mkl']

Package perl-html-formatter conflicts for:
perl-html-formatter
perl-xml-twig -> perl-html-formatter
perl-bioperl-core -> perl-xml-twig -> perl-html-formatter
perl-bio-phylo -> perl-xml-twig -> perl-html-formatter
perl-graphviz -> perl-xml-twig -> perl-html-formatter

Package typing_extensions conflicts for:
typing_extensions
aiohttp -> typing_extensions[version='>=3.6.5']
aioeasywebdav -> aiohttp -> typing_extensions[version='>=3.6.5']

Package gitpython conflicts for:
gitpython
snakemake -> snakemake-minimal=5.10.0 -> gitpython
snakemake-minimal -> gitpython

Package perl-jcode conflicts for:
perl-spreadsheet-parseexcel -> perl-jcode
perl-jcode
perl-bioperl-core -> perl-spreadsheet-parseexcel -> perl-jcode

Package networkx conflicts for:
networkx
snakemake -> networkx[version='>=2.0']

Package multidict conflicts for:
aiohttp -> yarl[version='>=1.0,<2.0'] -> multidict[version='>=2.0|>=4.0']
multidict
aiohttp -> multidict[version='>=2.1.4|>=4.0,<5.0|>=4.5,<5.0|>=3.0.0']
aioeasywebdav -> aiohttp -> multidict[version='>=2.1.4|>=4.0,<5.0|>=4.5,<5.0|>=3.0.0']
yarl -> multidict[version='>=2.0|>=4.0']

Package r-colorspace conflicts for:
r-munsell -> r-colorspace
r-scales -> r-munsell[version='>=0.2'] -> r-colorspace
r-colorspace

Package r-ggplot2 conflicts for:
r-ggplot2
r-ggsci -> r-ggplot2[version='>=2.0.0']

Package xorg-libxcb conflicts for:
r-base -> xorg-libx11 -> xorg-libxcb=1
cairo -> xorg-libx11 -> xorg-libxcb=1

Package gitdb2 conflicts for:
gitdb2
snakemake-minimal -> gitpython -> gitdb2[version='<=3.0.0|>=3,<4']
gitpython -> gitdb2[version='<=3.0.0|>=3,<4']

Package perl-json conflicts for:
perl-json
perl-bioperl-core -> perl-bio-phylo -> perl-json
perl-bio-phylo -> perl-json
perl-data-stag -> perl-json

Package ftputil conflicts for:
ftputil
snakemake -> ftputil[version='>=3.2']

Package perl-xml-sax-expat conflicts for:
perl-xml-simple -> perl-xml-sax-expat
perl-bioperl-core -> perl-xml-simple -> perl-xml-sax-expat
perl-xml-sax-expat

Package perl-cache-cache conflicts for:
perl-bioperl-core -> perl-aceperl -> perl-cache-cache
perl-aceperl -> perl-cache-cache

Package perl-types-serialiser conflicts for:
perl-json-xs -> perl-types-serialiser
perl-json -> perl-json-xs[version='<3'] -> perl-types-serialiser

Package pycrypto conflicts for:
paramiko -> pycrypto[version='>=2.1,!=2.4,<3.0']
pysftp -> paramiko[version='>=1.7.7'] -> pycrypto[version='>=2.1,!=2.4,<3.0']

Package filechunkio conflicts for:
filechunkio
snakemake -> filechunkio[version='>=1.6']

Package perl-spreadsheet-writeexcel conflicts for:
perl-spreadsheet-parseexcel -> perl-spreadsheet-writeexcel
perl-bioperl-core -> perl-spreadsheet-parseexcel -> perl-spreadsheet-writeexcel
perl-spreadsheet-writeexcel

Package perl-template-toolkit conflicts for:
perl-bio-phylo -> perl-template-toolkit
perl-template-toolkit
perl-bioperl-core -> perl-bio-phylo -> perl-template-toolkit

Package boto3 conflicts for:
snakemake -> boto3
boto3
snakemake -> moto[version='>=0.4.14'] -> boto3[version='>=1.2.1|>=1.2.1,<1.8.0|>=1.6.15|>=1.9.201|>=1.9.86,<1.9.197|>=1.9.86,<=1.9.197|>=1.9.86']

Package httplib2 conflicts for:
google-cloud-core -> google-auth-httplib2 -> httplib2
google-cloud-core -> httplib2[version='>=0.9.1']

Package paramiko conflicts for:
pysftp -> paramiko[version='>=1.17.0|>=1.7.7']
snakemake -> pysftp[version='>=0.2.8'] -> paramiko[version='>=1.17.0|>=1.7.7']
paramiko

Package mkl_fft conflicts for:
pandas -> numpy[version='>=1.14.6,<2.0a0'] -> mkl_fft[version='>=1.0.4|>=1.0.6,<2.0a0']
numpy -> mkl_fft[version='>=1.0.4|>=1.0.6,<2.0a0']

EDIT:

Even installing a "mild" version of the environment the conflicts persist


(meths-illumina) larteagafi@bf2i-galaxy:~/meths/longipes$ conda create -n viewbs bioconda::htslib anaconda::perl r::r-ggplot2 bioconda::r-pheatmap r::r-reshape2 conda-forge::r-cowplot bioconda::perl-cpan-shell
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.                                                                                                                                                                   failed

# >>>>>>>>>>>>>>>>>>>>>> ERROR REPORT <<<<<<<<<<<<<<<<<<<<<<

    Traceback (most recent call last):
      File "/home/data/larteagafi/miniconda3/lib/python3.7/site-packages/conda/exceptions.py", line 1079, in __call__
        return func(*args, **kwargs)
      File "/home/data/larteagafi/miniconda3/lib/python3.7/site-packages/conda/cli/main.py", line 84, in _main
        exit_code = do_call(args, p)
      File "/home/data/larteagafi/miniconda3/lib/python3.7/site-packages/conda/cli/conda_argparse.py", line 82, in do_call
        return getattr(module, func_name)(args, parser)
      File "/home/data/larteagafi/miniconda3/lib/python3.7/site-packages/conda/cli/main_create.py", line 37, in execute
        install(args, parser, 'create')
      File "/home/data/larteagafi/miniconda3/lib/python3.7/site-packages/conda/cli/install.py", line 265, in install
        should_retry_solve=(_should_retry_unfrozen or repodata_fn != repodata_fns[-1]),
      File "/home/data/larteagafi/miniconda3/lib/python3.7/site-packages/conda/core/solve.py", line 117, in solve_for_transaction
        should_retry_solve)
      File "/home/data/larteagafi/miniconda3/lib/python3.7/site-packages/conda/core/solve.py", line 158, in solve_for_diff
        force_remove, should_retry_solve)
      File "/home/data/larteagafi/miniconda3/lib/python3.7/site-packages/conda/core/solve.py", line 281, in solve_final_state
        ssc = self._run_sat(ssc)
      File "/home/data/larteagafi/miniconda3/lib/python3.7/site-packages/conda/common/io.py", line 88, in decorated
        return f(*args, **kwds)
      File "/home/data/larteagafi/miniconda3/lib/python3.7/site-packages/conda/core/solve.py", line 808, in _run_sat
        should_retry_solve=ssc.should_retry_solve
      File "/home/data/larteagafi/miniconda3/lib/python3.7/site-packages/conda/common/io.py", line 88, in decorated
        return f(*args, **kwds)
      File "/home/data/larteagafi/miniconda3/lib/python3.7/site-packages/conda/resolve.py", line 1318, in solve
        self.find_conflicts(specs, specs_to_add, history_specs)
      File "/home/data/larteagafi/miniconda3/lib/python3.7/site-packages/conda/resolve.py", line 347, in find_conflicts
        bad_deps = self.build_conflict_map(specs, specs_to_add, history_specs)
      File "/home/data/larteagafi/miniconda3/lib/python3.7/site-packages/conda/resolve.py", line 507, in build_conflict_map
        root, search_node, dep_graph, num_occurances)
      File "/home/data/larteagafi/miniconda3/lib/python3.7/site-packages/conda/resolve.py", line 369, in breadth_first_search_for_dep_graph
        last_spec = MatchSpec.union((path[-1], target_paths[-1][-1]))[0]
      File "/home/data/larteagafi/miniconda3/lib/python3.7/site-packages/conda/models/match_spec.py", line 481, in union
        return cls.merge(match_specs, union=True)
      File "/home/data/larteagafi/miniconda3/lib/python3.7/site-packages/conda/models/match_spec.py", line 475, in merge
        reduce(lambda x, y: x._merge(y, union), group) if len(group) > 1 else group[0]
      File "/home/data/larteagafi/miniconda3/lib/python3.7/site-packages/conda/models/match_spec.py", line 475, in <lambda>
        reduce(lambda x, y: x._merge(y, union), group) if len(group) > 1 else group[0]
      File "/home/data/larteagafi/miniconda3/lib/python3.7/site-packages/conda/models/match_spec.py", line 502, in _merge
        final = this_component.union(that_component)
      File "/home/data/larteagafi/miniconda3/lib/python3.7/site-packages/conda/models/match_spec.py", line 764, in union
        return '|'.join(options)
    TypeError: sequence item 0: expected str instance, Channel found

`$ /home/data/larteagafi/miniconda3/bin/conda create -n viewbs bioconda::htslib anaconda::perl r::r-ggplot2 bioconda::r-pheatmap r::r-reshape2 conda-forge::r-cowplot bioconda::perl-cpan-shell`

  environment variables:
                 CIO_TEST=<not set>
   CONDA_BACKUP_ADDR2LINE=/home/data/larteagafi/miniconda3/bin/x86_64-conda_cos6-linux-gnu-
                          addr2line
          CONDA_BACKUP_AR=/home/data/larteagafi/miniconda3/bin/x86_64-conda_cos6-linux-gnu-ar
          CONDA_BACKUP_AS=/home/data/larteagafi/miniconda3/bin/x86_64-conda_cos6-linux-gnu-as
          CONDA_BACKUP_CC=/home/data/larteagafi/miniconda3/bin/x86_64-conda_cos6-linux-gnu-cc
      CONDA_BACKUP_CFLAGS=-march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-
                          strong -fno-plt -O2 -ffunction-sections -pipe -isystem
                          /home/data/larteagafi/miniconda3/include
CONDA_BACKUP_CMAKE_PREFIX_PATH=/home/data/larteagafi/miniconda3:/home/data/larteagafi/miniconda3/x86_
                          64-conda_cos6-linux-gnu/sysroot/usr
CONDA_BACKUP_CONDA_BUILD_SYSROOT=/home/data/larteagafi/miniconda3/x86_64-conda_cos6-linux-gnu/sysroot
         CONDA_BACKUP_CPP=/home/data/larteagafi/miniconda3/bin/x86_64-conda_cos6-linux-gnu-cpp
    CONDA_BACKUP_CPPFLAGS=-DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem
                          /home/data/larteagafi/miniconda3/include
         CONDA_BACKUP_CXX=/home/data/larteagafi/miniconda3/bin/x86_64-conda_cos6-linux-gnu-c++
     CONDA_BACKUP_CXXFILT=/home/data/larteagafi/miniconda3/bin/x86_64-conda_cos6-linux-
                          gnu-c++filt
    CONDA_BACKUP_CXXFLAGS=-fvisibility-inlines-hidden -std=c++17 -fmessage-length=0
                          -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-
                          strong -fno-plt -O2 -ffunction-sections -pipe -isystem
                          /home/data/larteagafi/miniconda3/include
CONDA_BACKUP_DEBUG_CFLAGS=-march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-
                          all -fno-plt -Og -g -Wall -Wextra -fvar-tracking-assignments
                          -ffunction-sections -pipe -isystem
                          /home/data/larteagafi/miniconda3/include
CONDA_BACKUP_DEBUG_CPPFLAGS=-D_DEBUG -D_FORTIFY_SOURCE=2 -Og -isystem
                          /home/data/larteagafi/miniconda3/include
CONDA_BACKUP_DEBUG_CXXFLAGS=-fvisibility-inlines-hidden -std=c++17 -fmessage-length=0
                          -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-
                          all -fno-plt -Og -g -Wall -Wextra -fvar-tracking-assignments
                          -ffunction-sections -pipe -isystem
                          /home/data/larteagafi/miniconda3/include
CONDA_BACKUP_DEBUG_FFLAGS=-fopenmp -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-
                          protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem
                          /home/data/larteagafi/miniconda3/include
CONDA_BACKUP_DEBUG_FORTRANFLAGS=-fopenmp -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-
                          protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem
                          /home/data/larteagafi/miniconda3/include
     CONDA_BACKUP_ELFEDIT=/home/data/larteagafi/miniconda3/bin/x86_64-conda_cos6-linux-gnu-
                          elfedit
         CONDA_BACKUP_F77=/home/data/larteagafi/miniconda3/bin/x86_64-conda_cos6-linux-gnu-
                          gfortran
         CONDA_BACKUP_F90=/home/data/larteagafi/miniconda3/bin/x86_64-conda_cos6-linux-gnu-
                          gfortran
         CONDA_BACKUP_F95=/home/data/larteagafi/miniconda3/bin/x86_64-conda_cos6-linux-gnu-f95
          CONDA_BACKUP_FC=/home/data/larteagafi/miniconda3/bin/x86_64-conda_cos6-linux-gnu-
                          gfortran
      CONDA_BACKUP_FFLAGS=-fopenmp -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-
                          protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem
                          /home/data/larteagafi/miniconda3/include
CONDA_BACKUP_FORTRANFLAGS=-fopenmp -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-
                          protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem
                          /home/data/larteagafi/miniconda3/include
         CONDA_BACKUP_GCC=/home/data/larteagafi/miniconda3/bin/x86_64-conda_cos6-linux-gnu-gcc
      CONDA_BACKUP_GCC_AR=/home/data/larteagafi/miniconda3/bin/x86_64-conda_cos6-linux-gnu-gcc-
                          ar
      CONDA_BACKUP_GCC_NM=/home/data/larteagafi/miniconda3/bin/x86_64-conda_cos6-linux-gnu-gcc-
                          nm
  CONDA_BACKUP_GCC_RANLIB=/home/data/larteagafi/miniconda3/bin/x86_64-conda_cos6-linux-gnu-gcc-
                          ranlib
    CONDA_BACKUP_GFORTRAN=/home/data/larteagafi/miniconda3/bin/x86_64-conda_cos6-linux-gnu-
                          gfortran
       CONDA_BACKUP_GPROF=/home/data/larteagafi/miniconda3/bin/x86_64-conda_cos6-linux-gnu-gprof
         CONDA_BACKUP_GXX=/home/data/larteagafi/miniconda3/bin/x86_64-conda_cos6-linux-gnu-g++
        CONDA_BACKUP_HOST=x86_64-conda_cos6-linux-gnu
   CONDA_BACKUP_JAVA_HOME=/usr/lib/jvm/java-8-oracle
CONDA_BACKUP_JAVA_LD_LIBRARY_PATH=
          CONDA_BACKUP_LD=/home/data/larteagafi/miniconda3/bin/x86_64-conda_cos6-linux-gnu-ld
     CONDA_BACKUP_LDFLAGS=-Wl,-O2 -Wl,--sort-common -Wl,--as-needed -Wl,-z,relro -Wl,-z,now -Wl,
                          --disable-new-dtags -Wl,--gc-sections
                          -Wl,-rpath,/home/data/larteagafi/miniconda3/lib -Wl,-rpath-
                          link,/home/data/larteagafi/miniconda3/lib
                          -L/home/data/larteagafi/miniconda3/lib
     CONDA_BACKUP_LD_GOLD=/home/data/larteagafi/miniconda3/bin/x86_64-conda_cos6-linux-gnu-
                          ld.gold
          CONDA_BACKUP_NM=/home/data/larteagafi/miniconda3/bin/x86_64-conda_cos6-linux-gnu-nm
     CONDA_BACKUP_OBJCOPY=/home/data/larteagafi/miniconda3/bin/x86_64-conda_cos6-linux-gnu-
                          objcopy
     CONDA_BACKUP_OBJDUMP=/home/data/larteagafi/miniconda3/bin/x86_64-conda_cos6-linux-gnu-
                          objdump
      CONDA_BACKUP_RANLIB=/home/data/larteagafi/miniconda3/bin/x86_64-conda_cos6-linux-gnu-
                          ranlib
     CONDA_BACKUP_READELF=/home/data/larteagafi/miniconda3/bin/x86_64-conda_cos6-linux-gnu-
                          readelf
        CONDA_BACKUP_SIZE=/home/data/larteagafi/miniconda3/bin/x86_64-conda_cos6-linux-gnu-size
     CONDA_BACKUP_STRINGS=/home/data/larteagafi/miniconda3/bin/x86_64-conda_cos6-linux-gnu-
                          strings
       CONDA_BACKUP_STRIP=/home/data/larteagafi/miniconda3/bin/x86_64-conda_cos6-linux-gnu-strip
CONDA_BACKUP__CONDA_PYTHON_SYSCONFIGDATA_NAME=_sysconfigdata_x86_64_conda_cos6_linux_gnu
        CONDA_DEFAULT_ENV=meths-illumina
                CONDA_EXE=/home/data/larteagafi/miniconda3/bin/conda
             CONDA_PREFIX=/home/data/larteagafi/miniconda3/envs/meths-illumina
           CONDA_PREFIX_1=/home/data/larteagafi/miniconda3
    CONDA_PROMPT_MODIFIER=(meths-illumina)
         CONDA_PYTHON_EXE=/home/data/larteagafi/miniconda3/bin/python
               CONDA_ROOT=/home/data/larteagafi/miniconda3
              CONDA_SHLVL=2
     JAVA_LD_LIBRARY_PATH=/home/data/larteagafi/miniconda3/envs/meths-
                          illumina/jre/lib/amd64/server
                     PATH=/home/data/larteagafi/miniconda3/bin:/home/data/larteagafi/miniconda3/
                          envs/meths-illumina/bin:/home/data/larteagafi/miniconda3/bin:/home/dat
                          a/larteagafi/miniconda3/bin:/home/data/larteagafi/miniconda3/condabin:
                          /usr/local/bin:/usr/bin:/bin:/usr/local/games:/usr/games:/usr/lib/jvm/
                          java-8-oracle/bin:/usr/lib/jvm/java-8-oracle/db/bin:/usr/lib/jvm/java-
                          8-oracle/jre/bin:/usr/local/bin/kentUtils:/home/data/larteagafi/apps/m
                          irdeep2-0.1.3/bin
       REQUESTS_CA_BUNDLE=<not set>
            SSL_CERT_FILE=<not set>

     active environment : meths-illumina
    active env location : /home/data/larteagafi/miniconda3/envs/meths-illumina
            shell level : 2
       user config file : /home/data/larteagafi/.condarc
 populated config files : /home/data/larteagafi/.condarc
          conda version : 4.8.2
    conda-build version : not installed
         python version : 3.7.4.final.0
       virtual packages : __glibc=2.28
       base environment : /home/data/larteagafi/miniconda3  (writable)
           channel URLs : https://repo.anaconda.com/pkgs/main/linux-64
                          https://repo.anaconda.com/pkgs/main/noarch
                          https://repo.anaconda.com/pkgs/r/linux-64
                          https://repo.anaconda.com/pkgs/r/noarch
          package cache : /home/data/larteagafi/miniconda3/pkgs
                          /home/data/larteagafi/.conda/pkgs
       envs directories : /home/data/larteagafi/miniconda3/envs
                          /home/data/larteagafi/.conda/envs
               platform : linux-64
             user-agent : conda/4.8.2 requests/2.22.0 CPython/3.7.4 Linux/4.19.0-6-amd64 debian/10 glibc/2.28
                UID:GID : 1016:1019
             netrc file : None
           offline mode : False

An unexpected error has occurred. Conda has prepared the above report.

Cheers, Luis Alfonso.