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PacificBiosciences / pb-CpG-tools

Collection of tools for the analysis of CpG data
BSD 3-Clause Clear License
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error installing pb-CpG-tools #34

Closed Mjaraespejo closed 1 year ago

Mjaraespejo commented 1 year ago

Hello, I am trying to install the tools using the command: conda env create -f conda_env_cpg.yaml. But I am getting this error.

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

    Traceback (most recent call last):
      File "/drives/ssd1/manuel/miniconda3/lib/python3.9/site-packages/conda/exceptions.py", line 1082, in __call__
        return func(*args, **kwargs)
      File "/drives/ssd1/manuel/miniconda3/lib/python3.9/site-packages/conda_env/cli/main.py", line 80, in do_call
        exit_code = getattr(module, func_name)(args, parser)
      File "/drives/ssd1/manuel/miniconda3/lib/python3.9/site-packages/conda_env/cli/main_create.py", line 89, in execute
        spec = specs.detect(name=name, filename=get_filename(args.file), directory=os.getcwd())
      File "/drives/ssd1/manuel/miniconda3/lib/python3.9/site-packages/conda_env/specs/__init__.py", line 43, in detect
        if spec.can_handle():
      File "/drives/ssd1/manuel/miniconda3/lib/python3.9/site-packages/conda_env/specs/yaml_file.py", line 18, in can_handle
        self._environment = env.from_file(self.filename)
      File "/drives/ssd1/manuel/miniconda3/lib/python3.9/site-packages/conda_env/env.py", line 166, in from_file
        return from_yaml(yamlstr, filename=filename)
      File "/drives/ssd1/manuel/miniconda3/lib/python3.9/site-packages/conda_env/env.py", line 143, in from_yaml
        data = yaml_safe_load(yamlstr)
      File "/drives/ssd1/manuel/miniconda3/lib/python3.9/site-packages/conda/common/serialize.py", line 67, in yaml_safe_load
        return yaml.safe_load(string, version="1.2")
      File "/drives/ssd1/manuel/miniconda3/lib/python3.9/site-packages/ruamel_yaml/main.py", line 980, in safe_load
        return load(stream, SafeLoader, version)
      File "/drives/ssd1/manuel/miniconda3/lib/python3.9/site-packages/ruamel_yaml/main.py", line 935, in load
        return loader._constructor.get_single_data()
      File "/drives/ssd1/manuel/miniconda3/lib/python3.9/site-packages/ruamel_yaml/constructor.py", line 106, in get_single_data
        node = self.composer.get_single_node()
      File "/drives/ssd1/manuel/miniconda3/lib/python3.9/site-packages/ruamel_yaml/composer.py", line 78, in get_single_node
        document = self.compose_document()
      File "/drives/ssd1/manuel/miniconda3/lib/python3.9/site-packages/ruamel_yaml/composer.py", line 104, in compose_document
        self.parser.get_event()
      File "/drives/ssd1/manuel/miniconda3/lib/python3.9/site-packages/ruamel_yaml/parser.py", line 163, in get_event
        self.current_event = self.state()
      File "/drives/ssd1/manuel/miniconda3/lib/python3.9/site-packages/ruamel_yaml/parser.py", line 239, in parse_document_end
        token = self.scanner.peek_token()
      File "/drives/ssd1/manuel/miniconda3/lib/python3.9/site-packages/ruamel_yaml/scanner.py", line 182, in peek_token
        self.fetch_more_tokens()
      File "/drives/ssd1/manuel/miniconda3/lib/python3.9/site-packages/ruamel_yaml/scanner.py", line 282, in fetch_more_tokens
        return self.fetch_value()
      File "/drives/ssd1/manuel/miniconda3/lib/python3.9/site-packages/ruamel_yaml/scanner.py", line 651, in fetch_value
        raise ScannerError(
    ruamel_yaml.scanner.ScannerError: mapping values are not allowed here
      in "<unicode string>", line 29, column 66:
         ... le" content="{&quot;groups&quot;: [], &quot;environmentKey&quot; ... 
                                             ^ (line: 29)

`$ /drives/ssd1/manuel/miniconda3/bin/conda-env create -f conda_env_cpg.yaml`

  environment variables:
                 CIO_TEST=<not set>
  CONDA_AUTO_UPDATE_CONDA=false
   CONDA_BACKUP_ADDR2LINE=/drives/ssd1/manuel/miniconda3/envs/r4-base/bin/x86_64-conda-linux-
                          gnu-addr2line
          CONDA_BACKUP_AR=/drives/ssd1/manuel/miniconda3/envs/r4-base/bin/x86_64-conda-linux-
                          gnu-ar
          CONDA_BACKUP_AS=/drives/ssd1/manuel/miniconda3/envs/r4-base/bin/x86_64-conda-linux-
                          gnu-as
       CONDA_BACKUP_BUILD=x86_64-conda-linux-gnu
          CONDA_BACKUP_CC=/drives/ssd1/manuel/miniconda3/envs/r4-base/bin/x86_64-conda-linux-
                          gnu-cc
CONDA_BACKUP_CC_FOR_BUILD=/drives/ssd1/manuel/miniconda3/envs/r4-base/bin/x86_64-conda-linux-
                          gnu-cc
      CONDA_BACKUP_CFLAGS=-march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-
                          strong -fno-plt -O2 -ffunction-sections -pipe -isystem
                          /drives/ssd1/manuel/miniconda3/envs/r4-base/include
CONDA_BACKUP_CMAKE_PREFIX_PATH=/drives/ssd1/manuel/miniconda3/envs/r4-base:/drives/ssd1/manuel/minico
                          nda3/envs/r4-base/x86_64-conda-linux-gnu/sysroot/usr
CONDA_BACKUP_CONDA_BUILD_SYSROOT=/drives/ssd1/manuel/miniconda3/envs/r4-base/x86_64-conda-linux-
                          gnu/sysroot
         CONDA_BACKUP_CPP=/drives/ssd1/manuel/miniconda3/envs/r4-base/bin/x86_64-conda-linux-
                          gnu-cpp
    CONDA_BACKUP_CPPFLAGS=-DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem
                          /drives/ssd1/manuel/miniconda3/envs/r4-base/include
         CONDA_BACKUP_CXX=/drives/ssd1/manuel/miniconda3/envs/r4-base/bin/x86_64-conda-linux-
                          gnu-c++
     CONDA_BACKUP_CXXFILT=/drives/ssd1/manuel/miniconda3/envs/r4-base/bin/x86_64-conda-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
                          /drives/ssd1/manuel/miniconda3/envs/r4-base/include
CONDA_BACKUP_CXX_FOR_BUILD=/drives/ssd1/manuel/miniconda3/envs/r4-base/bin/x86_64-conda-linux-
                          gnu-c++
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
                          /drives/ssd1/manuel/miniconda3/envs/r4-base/include
CONDA_BACKUP_DEBUG_CPPFLAGS=-D_DEBUG -D_FORTIFY_SOURCE=2 -Og -isystem
                          /drives/ssd1/manuel/miniconda3/envs/r4-base/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
                          /drives/ssd1/manuel/miniconda3/envs/r4-base/include
CONDA_BACKUP_DEBUG_FFLAGS=-fopenmp -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-
                          protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem
                          /drives/ssd1/manuel/miniconda3/envs/r4-base/include
CONDA_BACKUP_DEBUG_FORTRANFLAGS=-fopenmp -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-
                          protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem
                          /drives/ssd1/manuel/miniconda3/envs/r4-base/include
     CONDA_BACKUP_ELFEDIT=/drives/ssd1/manuel/miniconda3/envs/r4-base/bin/x86_64-conda-linux-
                          gnu-elfedit
         CONDA_BACKUP_F77=/drives/ssd1/manuel/miniconda3/envs/r4-base/bin/x86_64-conda-linux-
                          gnu-gfortran
         CONDA_BACKUP_F90=/drives/ssd1/manuel/miniconda3/envs/r4-base/bin/x86_64-conda-linux-
                          gnu-gfortran
         CONDA_BACKUP_F95=/drives/ssd1/manuel/miniconda3/envs/r4-base/bin/x86_64-conda-linux-
                          gnu-f95
          CONDA_BACKUP_FC=/drives/ssd1/manuel/miniconda3/envs/r4-base/bin/x86_64-conda-linux-
                          gnu-gfortran
      CONDA_BACKUP_FFLAGS=-fopenmp -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-
                          protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem
                          /drives/ssd1/manuel/miniconda3/envs/r4-base/include
CONDA_BACKUP_FORTRANFLAGS=-fopenmp -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-
                          protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem
                          /drives/ssd1/manuel/miniconda3/envs/r4-base/include
         CONDA_BACKUP_GCC=/drives/ssd1/manuel/miniconda3/envs/r4-base/bin/x86_64-conda-linux-
                          gnu-gcc
      CONDA_BACKUP_GCC_AR=/drives/ssd1/manuel/miniconda3/envs/r4-base/bin/x86_64-conda-linux-
                          gnu-gcc-ar
      CONDA_BACKUP_GCC_NM=/drives/ssd1/manuel/miniconda3/envs/r4-base/bin/x86_64-conda-linux-
                          gnu-gcc-nm
  CONDA_BACKUP_GCC_RANLIB=/drives/ssd1/manuel/miniconda3/envs/r4-base/bin/x86_64-conda-linux-
                          gnu-gcc-ranlib
    CONDA_BACKUP_GFORTRAN=/drives/ssd1/manuel/miniconda3/envs/r4-base/bin/x86_64-conda-linux-
                          gnu-gfortran
       CONDA_BACKUP_GPROF=/drives/ssd1/manuel/miniconda3/envs/r4-base/bin/x86_64-conda-linux-
                          gnu-gprof
         CONDA_BACKUP_GXX=/drives/ssd1/manuel/miniconda3/envs/r4-base/bin/x86_64-conda-linux-
                          gnu-g++
        CONDA_BACKUP_HOST=x86_64-conda-linux-gnu
          CONDA_BACKUP_LD=/drives/ssd1/manuel/miniconda3/envs/r4-base/bin/x86_64-conda-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,/drives/ssd1/manuel/miniconda3/envs/r4-base/lib -Wl,-rpath-
                          link,/drives/ssd1/manuel/miniconda3/envs/r4-base/lib
                          -L/drives/ssd1/manuel/miniconda3/envs/r4-base/lib
     CONDA_BACKUP_LD_GOLD=/drives/ssd1/manuel/miniconda3/envs/r4-base/bin/x86_64-conda-linux-
                          gnu-ld.gold
          CONDA_BACKUP_NM=/drives/ssd1/manuel/miniconda3/envs/r4-base/bin/x86_64-conda-linux-
                          gnu-nm
     CONDA_BACKUP_OBJCOPY=/drives/ssd1/manuel/miniconda3/envs/r4-base/bin/x86_64-conda-linux-
                          gnu-objcopy
     CONDA_BACKUP_OBJDUMP=/drives/ssd1/manuel/miniconda3/envs/r4-base/bin/x86_64-conda-linux-
                          gnu-objdump
      CONDA_BACKUP_RANLIB=/drives/ssd1/manuel/miniconda3/envs/r4-base/bin/x86_64-conda-linux-
                          gnu-ranlib
     CONDA_BACKUP_READELF=/drives/ssd1/manuel/miniconda3/envs/r4-base/bin/x86_64-conda-linux-
                          gnu-readelf
        CONDA_BACKUP_SIZE=/drives/ssd1/manuel/miniconda3/envs/r4-base/bin/x86_64-conda-linux-
                          gnu-size
     CONDA_BACKUP_STRINGS=/drives/ssd1/manuel/miniconda3/envs/r4-base/bin/x86_64-conda-linux-
                          gnu-strings
       CONDA_BACKUP_STRIP=/drives/ssd1/manuel/miniconda3/envs/r4-base/bin/x86_64-conda-linux-
                          gnu-strip
 CONDA_BACKUP_build_alias=x86_64-conda-linux-gnu
  CONDA_BACKUP_host_alias=x86_64-conda-linux-gnu
        CONDA_DEFAULT_ENV=base
                CONDA_EXE=/drives/ssd1/manuel/miniconda3/bin/conda
             CONDA_PREFIX=/drives/ssd1/manuel/miniconda3
    CONDA_PROMPT_MODIFIER=(base)
         CONDA_PYTHON_EXE=/drives/ssd1/manuel/miniconda3/bin/python
               CONDA_ROOT=/drives/ssd1/manuel/miniconda3
              CONDA_SHLVL=1
           CURL_CA_BUNDLE=<not set>
     JAVA_LD_LIBRARY_PATH=/drives/ssd1/manuel/miniconda3/lib/server
                     PATH=/drives/ssd1/manuel/miniconda3/bin:/drives/ssd1/manuel/miniconda3/bin:
                          /drives/ssd1/manuel/miniconda3/envs/gapfilling/bin:/drives/ssd1/manuel
                          /miniconda3/envs/py27/bin:/home/zoo/zool2528/meme/bin:/home/zoo/zool25
                          28/meme/libexec/meme-5.4.1:/drives/ssd1/manuel/miniconda3/condabin:/us
                          r/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/
                          usr/local/games:/snap/bin:/drives/raid/AboobakerLab/software/bedtools2
                          /bin:/home/zoo/zool2528/.local/bin:/drives/raid/AboobakerLab/software/
                          ViennaRNA-2.4.18/src/bin:/drives/raid/AboobakerLab/software/ncbi-blast
                          -2.12.0+/bin:/drives/raid/AboobakerLab/software/bedops/bin:/drives/rai
                          d/AboobakerLab/software/SalmonTE:/drives/raid/AboobakerLab/software/sa
                          lmon-1.5.2_linux_x86_64/bin:/drives/raid/AboobakerLab/software/SalmonT
                          E/salmon/darwin/lib:/drives/raid/AboobakerLab/software/STAR-2.7.9a/bin
                          /Linux_x86_64:/drives/raid/AboobakerLab/software/STAR-2.7.9a/bin/Linux
                          _x86_64:/drives/raid/AboobakerLab/software/canu-2.2/bin:/drives/raid/A
                          boobakerLab/software/LR_Gapcloser/src:/drives/raid/AboobakerLab/softwa
                          re/LTR_FINDER_parallel/bin/LTR_FINDER.x86_64-1.0.7:/drives/raid/Abooba
                          kerLab/software/LTR_FINDER_parallel:/drives/raid/AboobakerLab/software
                          /seqtk:/drives/raid/AboobakerLab/software/standard-RAxML:/drives/raid/
                          AboobakerLab/software/quast:/drives/raid/AboobakerLab/software/gapless
                          :/drives/raid/AboobakerLab/software/hisat2/
       REQUESTS_CA_BUNDLE=<not set>
            SSL_CERT_FILE=<not set>

     active environment : base
    active env location : /drives/ssd1/manuel/miniconda3
            shell level : 1
       user config file : /home/zoo/zool2528/.condarc
 populated config files : /home/zoo/zool2528/.condarc
          conda version : 4.12.0
    conda-build version : not installed
         python version : 3.9.5.final.0
       virtual packages : __linux=5.15.0=0
                          __glibc=2.31=0
                          __unix=0=0
                          __archspec=1=x86_64
       base environment : /drives/ssd1/manuel/miniconda3  (writable)
      conda av data dir : /drives/ssd1/manuel/miniconda3/etc/conda
  conda av metadata url : None
           channel URLs : https://conda.anaconda.org/conda-forge/linux-64
                          https://conda.anaconda.org/conda-forge/noarch
                          https://conda.anaconda.org/bioconda/linux-64
                          https://conda.anaconda.org/bioconda/noarch
                          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 : /drives/ssd1/manuel/miniconda3/pkgs
                          /home/zoo/zool2528/.conda/pkgs
       envs directories : /drives/ssd1/manuel/miniconda3/envs
                          /home/zoo/zool2528/.conda/envs
               platform : linux-64
             user-agent : conda/4.12.0 requests/2.27.1 CPython/3.9.5 Linux/5.15.0-52-generic ubuntu/20.04.4 glibc/2.31
                UID:GID : 1792830678:1792800513
             netrc file : None
           offline mode : False

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

If submitted, this report will be used by core maintainers to improve
future releases of conda.
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ctsa commented 1 year ago

Hi @Mjaraespejo , The python method has just been updated with a new compiled binary v2.1.0 release today to help better manage these package and conda issues:

https://github.com/PacificBiosciences/pb-CpG-tools/releases/latest

If you're still interested, can you give this a try instead?

ctsa commented 1 year ago

Closing as no longer applicable. Please open a new issue if you're having any trouble with v2.