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dariober / cnv_facets

Somatic copy variant caller (CNV) for next generation sequencing
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R dependency issue #33

Open vymao opened 3 years ago

vymao commented 3 years ago

Hi,

I tried installing cnv_facets through conda as specified, but I am running into an issue when running the calling: 

(facets) [vym1@compute-e-16-198 facets]$ cnv_facets.R -h
Error in library(argparse) : there is no package called ‘argparse’

I tried installing argparse through conda as well but I am getting an incompatability issue: 

UnsatisfiableError: The following specifications were found to be incompatible with each other:

  - bioconda/linux-64::bioconductor-biobase==2.46.0=r36h516909a_0 -> bioconductor-biocgenerics[version='>=0.32.0,<0.33.0']
  - bioconda/linux-64::bioconductor-biostrings==2.54.0=r36h516909a_0 -> bioconductor-iranges[version='>=2.20.0,<2.21.0']
  - bioconda/linux-64::bioconductor-biostrings==2.54.0=r36h516909a_0 -> bioconductor-s4vectors[version='>=0.24.0,<0.25.0'] -> bioconductor-biocgenerics[version='>=0.32.0,<0.33.0']
  - bioconda/linux-64::bioconductor-delayedarray==0.12.0=r36h516909a_0 -> bioconductor-iranges[version='>=2.20.0,<2.21.0'] -> bioconductor-biocgenerics[version='>=0.32.0,<0.33.0']
  - bioconda/linux-64::bioconductor-delayedarray==0.12.0=r36h516909a_0 -> bioconductor-iranges[version='>=2.20.0,<2.21.0'] -> bioconductor-s4vectors[version='>=0.24.0,<0.25.0']
  - bioconda/linux-64::bioconductor-genomicalignments==1.22.0=r36h516909a_0 -> bioconductor-genomicranges[version='>=1.38.0,<1.39.0'] -> bioconductor-iranges[version='>=2.20.0,<2.21.0']
  - bioconda/linux-64::bioconductor-genomicalignments==1.22.0=r36h516909a_0 -> bioconductor-genomicranges[version='>=1.38.0,<1.39.0'] -> bioconductor-s4vectors[version='>=0.24.0,<0.25.0'] -> bioconductor-biocgenerics[version='>=0.32.0,<0.33.0']
  - bioconda/linux-64::bioconductor-genomicalignments==1.22.0=r36h516909a_0 -> bioconductor-summarizedexperiment[version='>=1.16.0,<1.17.0'] -> bioconductor-biobase[version='>=2.46.0,<2.47.0']
  - bioconda/linux-64::bioconductor-genomicranges==1.38.0=r36h516909a_0 -> bioconductor-iranges[version='>=2.20.0,<2.21.0']
  - bioconda/linux-64::bioconductor-genomicranges==1.38.0=r36h516909a_0 -> bioconductor-s4vectors[version='>=0.24.0,<0.25.0'] -> bioconductor-biocgenerics[version='>=0.32.0,<0.33.0']
  - bioconda/linux-64::bioconductor-iranges==2.20.0=r36h516909a_0 -> bioconductor-biocgenerics[version='>=0.32.0,<0.33.0']
  - bioconda/linux-64::bioconductor-iranges==2.20.0=r36h516909a_0 -> bioconductor-s4vectors[version='>=0.24.0,<0.25.0']
  - bioconda/linux-64::bioconductor-rsamtools==2.2.0=r36he1b5a44_0 -> bioconductor-genomicranges[version='>=1.38.0,<1.39.0'] -> bioconductor-iranges[version='>=2.20.0,<2.21.0']
  - bioconda/linux-64::bioconductor-rsamtools==2.2.0=r36he1b5a44_0 -> bioconductor-genomicranges[version='>=1.38.0,<1.39.0'] -> bioconductor-s4vectors[version='>=0.24.0,<0.25.0'] -> bioconductor-biocgenerics[version='>=0.32.0,<0.33.0']
  - bioconda/linux-64::bioconductor-rtracklayer==1.46.0=r36h516909a_0 -> bioconductor-genomicalignments[version='>=1.22.0,<1.23.0'] -> bioconductor-summarizedexperiment[version='>=1.16.0,<1.17.0'] -> bioconductor-biobase[version='>=2.46.0,<2.47.0']
  - bioconda/linux-64::bioconductor-rtracklayer==1.46.0=r36h516909a_0 -> bioconductor-genomicranges[version='>=1.38.0,<1.39.0'] -> bioconductor-iranges[version='>=2.20.0,<2.21.0']
  - bioconda/linux-64::bioconductor-rtracklayer==1.46.0=r36h516909a_0 -> bioconductor-genomicranges[version='>=1.38.0,<1.39.0'] -> bioconductor-s4vectors[version='>=0.24.0,<0.25.0'] -> bioconductor-biocgenerics[version='>=0.32.0,<0.33.0']
  - bioconda/linux-64::bioconductor-s4vectors==0.24.0=r36h516909a_0 -> bioconductor-biocgenerics[version='>=0.32.0,<0.33.0']
  - bioconda/linux-64::bioconductor-xvector==0.26.0=r36h516909a_0 -> bioconductor-iranges[version='>=2.20.0,<2.21.0']
  - bioconda/linux-64::bioconductor-xvector==0.26.0=r36h516909a_0 -> bioconductor-s4vectors[version='>=0.24.0,<0.25.0'] -> bioconductor-biocgenerics[version='>=0.32.0,<0.33.0']
  - bioconda/noarch::bioconductor-biocgenerics==0.32.0=r36_0
  - bioconda/noarch::bioconductor-genomeinfodb==1.22.0=r36_0 -> bioconductor-iranges[version='>=2.20.0,<2.21.0']
  - bioconda/noarch::bioconductor-genomeinfodb==1.22.0=r36_0 -> bioconductor-s4vectors[version='>=0.24.0,<0.25.0'] -> bioconductor-biocgenerics[version='>=0.32.0,<0.33.0']
  - bioconda/noarch::bioconductor-singlecellexperiment==1.8.0=r36_0 -> bioconductor-s4vectors[version='>=0.24.0,<0.25.0'] -> bioconductor-biocgenerics[version='>=0.32.0,<0.33.0']
  - bioconda/noarch::bioconductor-singlecellexperiment==1.8.0=r36_0 -> bioconductor-summarizedexperiment[version='>=1.16.0,<1.17.0'] -> bioconductor-biobase[version='>=2.46.0,<2.47.0']
  - bioconda/noarch::bioconductor-singlecellexperiment==1.8.0=r36_0 -> bioconductor-summarizedexperiment[version='>=1.16.0,<1.17.0'] -> bioconductor-genomicranges[version='>=1.38.0,<1.39.0'] -> bioconductor-iranges[version='>=2.20.0,<2.21.0']
  - bioconda/noarch::bioconductor-summarizedexperiment==1.16.0=r36_0 -> bioconductor-biobase[version='>=2.46.0,<2.47.0']
  - bioconda/noarch::bioconductor-summarizedexperiment==1.16.0=r36_0 -> bioconductor-genomicranges[version='>=1.38.0,<1.39.0'] -> bioconductor-iranges[version='>=2.20.0,<2.21.0']
  - bioconda/noarch::bioconductor-summarizedexperiment==1.16.0=r36_0 -> bioconductor-genomicranges[version='>=1.38.0,<1.39.0'] -> bioconductor-s4vectors[version='>=0.24.0,<0.25.0'] -> bioconductor-biocgenerics[version='>=0.32.0,<0.33.0']
  - bioconda/noarch::r-brio==0.3.17=r36_0 -> bioconductor-genomicranges[version='>=1.38'] -> bioconductor-s4vectors[version='>=0.28.0,<0.29.0'] -> bioconductor-biocgenerics[version='>=0.36.0,<0.37.0']
  - bioconda/noarch::r-brio==0.3.17=r36_0 -> r-jsonlite[version='>=1.6']
  - bioconda/noarch::r-brio==0.3.17=r36_0 -> r-readxl[version='>=1.3.1'] -> r-progress -> r-r6
  - bioconda/noarch::r-brio==0.3.17=r36_0 -> r-rio[version='>=0.5.16'] -> r-curl[version='>=0.6']
  - bioconda/noarch::r-transformer==0.2.12=r36_0 -> bioconductor-genomicranges[version='>=1.38'] -> bioconductor-s4vectors[version='>=0.28.0,<0.29.0'] -> bioconductor-biocgenerics[version='>=0.36.0,<0.37.0']
  - cnv_facets -> bioconductor-rsamtools -> bioconductor-genomicranges[version='>=1.42.0,<1.43.0'] -> bioconductor-s4vectors[version='>=0.28.0,<0.29.0'] -> bioconductor-biocgenerics[version='>=0.36.0,<0.37.0']
  - conda-forge/linux-64::_openmp_mutex==4.5=1_gnu -> openmp_impl==9999
  - conda-forge/linux-64::bzip2==1.0.8=h7f98852_4 -> libgcc-ng[version='>=9.3.0'] -> _openmp_mutex[version='>=4.5'] -> llvm-openmp[version='>=9.0.1'] -> openmp[version='11.1.0|11.1.0.*']
  - conda-forge/linux-64::bzip2==1.0.8=h7f98852_4 -> libgcc-ng[version='>=9.3.0'] -> _openmp_mutex[version='>=4.5'] -> openmp_impl==9999
  - conda-forge/linux-64::fontconfig==2.13.1=hba837de_1005 -> libgcc-ng[version='>=9.3.0'] -> _openmp_mutex[version='>=4.5'] -> llvm-openmp[version='>=9.0.1'] -> openmp[version='11.1.0|11.1.0.*']
  - conda-forge/linux-64::fontconfig==2.13.1=hba837de_1005 -> libgcc-ng[version='>=9.3.0'] -> _openmp_mutex[version='>=4.5'] -> openmp_impl==9999
  - conda-forge/linux-64::freetype==2.10.4=h0708190_1 -> libgcc-ng[version='>=9.3.0'] -> _openmp_mutex[version='>=4.5'] -> llvm-openmp[version='>=9.0.1'] -> openmp[version='11.1.0|11.1.0.*']
  - conda-forge/linux-64::freetype==2.10.4=h0708190_1 -> libgcc-ng[version='>=9.3.0'] -> _openmp_mutex[version='>=4.5'] -> openmp_impl==9999
  - conda-forge/linux-64::gettext==0.19.8.1=h0b5b191_1005 -> libgcc-ng[version='>=9.3.0'] -> _openmp_mutex[version='>=4.5'] -> llvm-openmp[version='>=9.0.1'] -> openmp[version='11.1.0|11.1.0.*']
  - conda-forge/linux-64::gettext==0.19.8.1=h0b5b191_1005 -> libgcc-ng[version='>=9.3.0'] -> _openmp_mutex[version='>=4.5'] -> openmp_impl==9999
  - conda-forge/linux-64::gsl==2.6=he838d99_2 -> libgcc-ng[version='>=9.3.0'] -> _openmp_mutex[version='>=4.5'] -> llvm-openmp[version='>=9.0.1'] -> openmp[version='11.1.0|11.1.0.*']
  - conda-forge/linux-64::gsl==2.6=he838d99_2 -> libgcc-ng[version='>=9.3.0'] -> _openmp_mutex[version='>=4.5'] -> openmp_impl==9999
  - conda-forge/linux-64::libgcc-ng==9.3.0=h2828fa1_19 -> _openmp_mutex[version='>=4.5'] -> llvm-openmp[version='>=9.0.1'] -> openmp[version='11.1.0|11.1.0.*']
  - conda-forge/linux-64::libgcc-ng==9.3.0=h2828fa1_19 -> _openmp_mutex[version='>=4.5'] -> openmp_impl==9999
  - conda-forge/linux-64::libglib==2.68.1=h3e27bee_0 -> libgcc-ng[version='>=9.3.0'] -> _openmp_mutex[version='>=4.5'] -> llvm-openmp[version='>=9.0.1'] -> openmp[version='11.1.0|11.1.0.*']
  - conda-forge/linux-64::libglib==2.68.1=h3e27bee_0 -> libgcc-ng[version='>=9.3.0'] -> _openmp_mutex[version='>=4.5'] -> openmp_impl==9999
  - conda-forge/linux-64::libssh2==1.9.0=ha56f1ee_6 -> libgcc-ng[version='>=9.3.0'] -> _openmp_mutex[version='>=4.5'] -> llvm-openmp[version='>=9.0.1'] -> openmp[version='11.1.0|11.1.0.*']
  - conda-forge/linux-64::libssh2==1.9.0=ha56f1ee_6 -> libgcc-ng[version='>=9.3.0'] -> _openmp_mutex[version='>=4.5'] -> openmp_impl==9999
  - conda-forge/linux-64::libtiff==4.2.0=hdc55705_1 -> libgcc-ng[version='>=9.3.0'] -> _openmp_mutex[version='>=4.5'] -> llvm-openmp[version='>=9.0.1'] -> openmp[version='11.1.0|11.1.0.*']
  - conda-forge/linux-64::libtiff==4.2.0=hdc55705_1 -> libgcc-ng[version='>=9.3.0'] -> _openmp_mutex[version='>=4.5'] -> openmp_impl==9999
  - conda-forge/linux-64::libuuid==2.32.1=h7f98852_1000 -> libgcc-ng[version='>=9.3.0'] -> _openmp_mutex[version='>=4.5'] -> llvm-openmp[version='>=9.0.1'] -> openmp[version='11.1.0|11.1.0.*']
  - conda-forge/linux-64::libuuid==2.32.1=h7f98852_1000 -> libgcc-ng[version='>=9.3.0'] -> _openmp_mutex[version='>=4.5'] -> openmp_impl==9999
  - conda-forge/linux-64::libwebp-base==1.2.0=h7f98852_2 -> libgcc-ng[version='>=9.3.0'] -> _openmp_mutex[version='>=4.5'] -> llvm-openmp[version='>=9.0.1'] -> openmp[version='11.1.0|11.1.0.*']
  - conda-forge/linux-64::libwebp-base==1.2.0=h7f98852_2 -> libgcc-ng[version='>=9.3.0'] -> _openmp_mutex[version='>=4.5'] -> openmp_impl==9999
  - conda-forge/linux-64::libxcb==1.13=h7f98852_1003 -> libgcc-ng[version='>=9.3.0'] -> _openmp_mutex[version='>=4.5'] -> llvm-openmp[version='>=9.0.1'] -> openmp[version='11.1.0|11.1.0.*']
  - conda-forge/linux-64::libxcb==1.13=h7f98852_1003 -> libgcc-ng[version='>=9.3.0'] -> _openmp_mutex[version='>=4.5'] -> openmp_impl==9999
  - conda-forge/linux-64::lz4-c==1.9.3=h9c3ff4c_0 -> libgcc-ng[version='>=9.3.0'] -> _openmp_mutex[version='>=4.5'] -> llvm-openmp[version='>=9.0.1'] -> openmp[version='11.1.0|11.1.0.*']
  - conda-forge/linux-64::lz4-c==1.9.3=h9c3ff4c_0 -> libgcc-ng[version='>=9.3.0'] -> _openmp_mutex[version='>=4.5'] -> openmp_impl==9999
  - conda-forge/linux-64::r-backports==1.2.1=r36hcfec24a_0 -> libgcc-ng[version='>=9.3.0'] -> _openmp_mutex[version='>=4.5'] -> llvm-openmp[version='>=9.0.1'] -> openmp[version='11.1.0|11.1.0.*']
  - conda-forge/linux-64::r-backports==1.2.1=r36hcfec24a_0 -> libgcc-ng[version='>=9.3.0'] -> _openmp_mutex[version='>=4.5'] -> openmp_impl==9999
  - conda-forge/linux-64::r-bitops==1.0_7=r36hcfec24a_0 -> libgcc-ng[version='>=9.3.0'] -> _openmp_mutex[version='>=4.5'] -> llvm-openmp[version='>=9.0.1'] -> openmp[version='11.1.0|11.1.0.*']
  - conda-forge/linux-64::r-bitops==1.0_7=r36hcfec24a_0 -> libgcc-ng[version='>=9.3.0'] -> _openmp_mutex[version='>=4.5'] -> openmp_impl==9999
  - conda-forge/linux-64::r-curl==4.3=r36hcfec24a_1 -> libgcc-ng[version='>=9.3.0'] -> _openmp_mutex[version='>=4.5'] -> llvm-openmp[version='>=9.0.1'] -> openmp[version='11.1.0|11.1.0.*']
  - conda-forge/linux-64::r-curl==4.3=r36hcfec24a_1 -> libgcc-ng[version='>=9.3.0'] -> _openmp_mutex[version='>=4.5'] -> openmp_impl==9999
  - conda-forge/linux-64::r-data.table==1.14.0=r36hcfec24a_0 -> libgcc-ng[version='>=9.3.0'] -> _openmp_mutex[version='>=4.5'] -> llvm-openmp[version='>=9.0.1'] -> openmp[version='11.1.0|11.1.0.*']
  - conda-forge/linux-64::r-data.table==1.14.0=r36hcfec24a_0 -> libgcc-ng[version='>=9.3.0'] -> _openmp_mutex[version='>=4.5'] -> openmp_impl==9999
  - conda-forge/linux-64::r-diffobj==0.3.3=r36hcfec24a_0 -> libgcc-ng[version='>=9.3.0'] -> _openmp_mutex[version='>=4.5'] -> llvm-openmp[version='>=9.0.1'] -> openmp[version='11.1.0|11.1.0.*']
  - conda-forge/linux-64::r-diffobj==0.3.3=r36hcfec24a_0 -> libgcc-ng[version='>=9.3.0'] -> _openmp_mutex[version='>=4.5'] -> openmp_impl==9999
  - conda-forge/linux-64::r-fansi==0.4.2=r36hcfec24a_0 -> libgcc-ng[version='>=9.3.0'] -> _openmp_mutex[version='>=4.5'] -> llvm-openmp[version='>=9.0.1'] -> openmp[version='11.1.0|11.1.0.*']
  - conda-forge/linux-64::r-fansi==0.4.2=r36hcfec24a_0 -> libgcc-ng[version='>=9.3.0'] -> _openmp_mutex[version='>=4.5'] -> openmp_impl==9999
  - conda-forge/linux-64::r-farver==2.1.0=r36h03ef668_0 -> libgcc-ng[version='>=9.3.0'] -> _openmp_mutex[version='>=4.5'] -> llvm-openmp[version='>=9.0.1'] -> openmp[version='11.1.0|11.1.0.*']
  - conda-forge/linux-64::r-farver==2.1.0=r36h03ef668_0 -> libgcc-ng[version='>=9.3.0'] -> _openmp_mutex[version='>=4.5'] -> openmp_impl==9999
  - conda-forge/linux-64::r-glue==1.4.2=r36hcfec24a_0 -> libgcc-ng[version='>=9.3.0'] -> _openmp_mutex[version='>=4.5'] -> llvm-openmp[version='>=9.0.1'] -> openmp[version='11.1.0|11.1.0.*']
  - conda-forge/linux-64::r-glue==1.4.2=r36hcfec24a_0 -> libgcc-ng[version='>=9.3.0'] -> _openmp_mutex[version='>=4.5'] -> openmp_impl==9999
  - conda-forge/linux-64::r-haven==2.4.1=r36h2713e49_0 -> libgcc-ng[version='>=9.3.0'] -> _openmp_mutex[version='>=4.5'] -> llvm-openmp[version='>=9.0.1'] -> openmp[version='11.1.0|11.1.0.*']
  - conda-forge/linux-64::r-haven==2.4.1=r36h2713e49_0 -> libgcc-ng[version='>=9.3.0'] -> _openmp_mutex[version='>=4.5'] -> openmp_impl==9999
  - conda-forge/linux-64::r-isoband==0.2.4=r36h03ef668_0 -> libgcc-ng[version='>=9.3.0'] -> _openmp_mutex[version='>=4.5'] -> llvm-openmp[version='>=9.0.1'] -> openmp[version='11.1.0|11.1.0.*']
  - conda-forge/linux-64::r-isoband==0.2.4=r36h03ef668_0 -> libgcc-ng[version='>=9.3.0'] -> _openmp_mutex[version='>=4.5'] -> openmp_impl==9999
  - conda-forge/linux-64::r-jsonlite==1.7.2=r36hcfec24a_0 -> libgcc-ng[version='>=9.3.0'] -> _openmp_mutex[version='>=4.5'] -> llvm-openmp[version='>=9.0.1'] -> openmp[version='11.1.0|11.1.0.*']
  - conda-forge/linux-64::r-jsonlite==1.7.2=r36hcfec24a_0 -> libgcc-ng[version='>=9.3.0'] -> _openmp_mutex[version='>=4.5'] -> openmp_impl==9999
  - conda-forge/linux-64::r-lattice==0.20_41=r36hcfec24a_3 -> libgcc-ng[version='>=9.3.0'] -> _openmp_mutex[version='>=4.5'] -> llvm-openmp[version='>=9.0.1'] -> openmp[version='11.1.0|11.1.0.*']
  - conda-forge/linux-64::r-lattice==0.20_41=r36hcfec24a_3 -> libgcc-ng[version='>=9.3.0'] -> _openmp_mutex[version='>=4.5'] -> openmp_impl==9999
  - conda-forge/linux-64::r-magrittr==2.0.1=r36hcfec24a_1 -> libgcc-ng[version='>=9.3.0'] -> _openmp_mutex[version='>=4.5'] -> llvm-openmp[version='>=9.0.1'] -> openmp[version='11.1.0|11.1.0.*']
  - conda-forge/linux-64::r-magrittr==2.0.1=r36hcfec24a_1 -> libgcc-ng[version='>=9.3.0'] -> _openmp_mutex[version='>=4.5'] -> openmp_impl==9999
  - conda-forge/linux-64::r-mass==7.3_53.1=r36hcfec24a_0 -> libgcc-ng[version='>=9.3.0'] -> _openmp_mutex[version='>=4.5'] -> llvm-openmp[version='>=9.0.1'] -> openmp[version='11.1.0|11.1.0.*']
  - conda-forge/linux-64::r-mass==7.3_53.1=r36hcfec24a_0 -> libgcc-ng[version='>=9.3.0'] -> _openmp_mutex[version='>=4.5'] -> openmp_impl==9999
  - conda-forge/linux-64::r-matrix==1.3_2=r36he454529_0 -> libgcc-ng[version='>=9.3.0'] -> _openmp_mutex[version='>=4.5'] -> llvm-openmp[version='>=9.0.1'] -> openmp[version='11.1.0|11.1.0.*']
  - conda-forge/linux-64::r-matrix==1.3_2=r36he454529_0 -> libgcc-ng[version='>=9.3.0'] -> _openmp_mutex[version='>=4.5'] -> openmp_impl==9999
  - conda-forge/linux-64::r-matrixstats==0.58.0=r36hcfec24a_0 -> libgcc-ng[version='>=9.3.0'] -> _openmp_mutex[version='>=4.5'] -> llvm-openmp[version='>=9.0.1'] -> openmp[version='11.1.0|11.1.0.*']
  - conda-forge/linux-64::r-matrixstats==0.58.0=r36hcfec24a_0 -> libgcc-ng[version='>=9.3.0'] -> _openmp_mutex[version='>=4.5'] -> openmp_impl==9999
  - conda-forge/linux-64::r-mgcv==1.8_34=r36he454529_0 -> libgcc-ng[version='>=9.3.0'] -> _openmp_mutex[version='>=4.5'] -> llvm-openmp[version='>=9.0.1'] -> openmp[version='11.1.0|11.1.0.*']
  - conda-forge/linux-64::r-mgcv==1.8_34=r36he454529_0 -> libgcc-ng[version='>=9.3.0'] -> _openmp_mutex[version='>=4.5'] -> openmp_impl==9999
  - conda-forge/linux-64::r-pkgload==1.2.1=r36h03ef668_0 -> libgcc-ng[version='>=9.3.0'] -> _openmp_mutex[version='>=4.5'] -> llvm-openmp[version='>=9.0.1'] -> openmp[version='11.1.0|11.1.0.*']
  - conda-forge/linux-64::r-pkgload==1.2.1=r36h03ef668_0 -> libgcc-ng[version='>=9.3.0'] -> _openmp_mutex[version='>=4.5'] -> openmp_impl==9999
  - conda-forge/linux-64::r-pkgload==1.2.1=r36h03ef668_0 -> r-desc -> r-r6
  - conda-forge/linux-64::r-processx==3.5.1=r36hcfec24a_0 -> libgcc-ng[version='>=9.3.0'] -> _openmp_mutex[version='>=4.5'] -> llvm-openmp[version='>=9.0.1'] -> openmp[version='11.1.0|11.1.0.*']
  - conda-forge/linux-64::r-processx==3.5.1=r36hcfec24a_0 -> libgcc-ng[version='>=9.3.0'] -> _openmp_mutex[version='>=4.5'] -> openmp_impl==9999
  - conda-forge/linux-64::r-processx==3.5.1=r36hcfec24a_0 -> r-r6
  - conda-forge/linux-64::r-ps==1.6.0=r36hcfec24a_0 -> libgcc-ng[version='>=9.3.0'] -> _openmp_mutex[version='>=4.5'] -> llvm-openmp[version='>=9.0.1'] -> openmp[version='11.1.0|11.1.0.*']
  - conda-forge/linux-64::r-ps==1.6.0=r36hcfec24a_0 -> libgcc-ng[version='>=9.3.0'] -> _openmp_mutex[version='>=4.5'] -> openmp_impl==9999
  - conda-forge/linux-64::r-rcpp==1.0.6=r36h03ef668_0 -> libgcc-ng[version='>=9.3.0'] -> _openmp_mutex[version='>=4.5'] -> llvm-openmp[version='>=9.0.1'] -> openmp[version='11.1.0|11.1.0.*']
  - conda-forge/linux-64::r-rcpp==1.0.6=r36h03ef668_0 -> libgcc-ng[version='>=9.3.0'] -> _openmp_mutex[version='>=4.5'] -> openmp_impl==9999
  - conda-forge/linux-64::r-readr==1.4.0=r36h1b71b39_0 -> r-r6
  - conda-forge/linux-64::r-readxl==1.3.1=r36hde08347_4 -> r-progress -> r-r6
  - conda-forge/linux-64::r-rlang==0.4.10=r36hcfec24a_0 -> libgcc-ng[version='>=9.3.0'] -> _openmp_mutex[version='>=4.5'] -> llvm-openmp[version='>=9.0.1'] -> openmp[version='11.1.0|11.1.0.*']
  - conda-forge/linux-64::r-rlang==0.4.10=r36hcfec24a_0 -> libgcc-ng[version='>=9.3.0'] -> _openmp_mutex[version='>=4.5'] -> openmp_impl==9999
  - conda-forge/linux-64::r-stringi==1.5.3=r36hca8494e_0 -> libgcc-ng[version='>=9.3.0'] -> _openmp_mutex[version='>=4.5'] -> llvm-openmp[version='>=9.0.1'] -> openmp[version='11.1.0|11.1.0.*']
  - conda-forge/linux-64::r-stringi==1.5.3=r36hca8494e_0 -> libgcc-ng[version='>=9.3.0'] -> _openmp_mutex[version='>=4.5'] -> openmp_impl==9999
  - conda-forge/linux-64::r-testthat==3.0.2=r36h03ef668_0 -> libgcc-ng[version='>=9.3.0'] -> _openmp_mutex[version='>=4.5'] -> llvm-openmp[version='>=9.0.1'] -> openmp[version='11.1.0|11.1.0.*']
  - conda-forge/linux-64::r-testthat==3.0.2=r36h03ef668_0 -> libgcc-ng[version='>=9.3.0'] -> _openmp_mutex[version='>=4.5'] -> openmp_impl==9999
  - conda-forge/linux-64::r-testthat==3.0.2=r36h03ef668_0 -> r-processx -> r-r6
  - conda-forge/linux-64::r-tibble==3.1.1=r36hcfec24a_0 -> libgcc-ng[version='>=9.3.0'] -> _openmp_mutex[version='>=4.5'] -> llvm-openmp[version='>=9.0.1'] -> openmp[version='11.1.0|11.1.0.*']
  - conda-forge/linux-64::r-tibble==3.1.1=r36hcfec24a_0 -> libgcc-ng[version='>=9.3.0'] -> _openmp_mutex[version='>=4.5'] -> openmp_impl==9999
  - conda-forge/linux-64::r-utf8==1.2.1=r36hcfec24a_0 -> libgcc-ng[version='>=9.3.0'] -> _openmp_mutex[version='>=4.5'] -> llvm-openmp[version='>=9.0.1'] -> openmp[version='11.1.0|11.1.0.*']
  - conda-forge/linux-64::r-utf8==1.2.1=r36hcfec24a_0 -> libgcc-ng[version='>=9.3.0'] -> _openmp_mutex[version='>=4.5'] -> openmp_impl==9999
  - conda-forge/linux-64::r-vctrs==0.3.7=r36hcfec24a_0 -> libgcc-ng[version='>=9.3.0'] -> _openmp_mutex[version='>=4.5'] -> llvm-openmp[version='>=9.0.1'] -> openmp[version='11.1.0|11.1.0.*']
  - conda-forge/linux-64::r-vctrs==0.3.7=r36hcfec24a_0 -> libgcc-ng[version='>=9.3.0'] -> _openmp_mutex[version='>=4.5'] -> openmp_impl==9999
  - conda-forge/linux-64::r-yaml==2.2.1=r36hcfec24a_1 -> libgcc-ng[version='>=9.3.0'] -> _openmp_mutex[version='>=4.5'] -> llvm-openmp[version='>=9.0.1'] -> openmp[version='11.1.0|11.1.0.*']
  - conda-forge/linux-64::r-yaml==2.2.1=r36hcfec24a_1 -> libgcc-ng[version='>=9.3.0'] -> _openmp_mutex[version='>=4.5'] -> openmp_impl==9999
  - conda-forge/linux-64::readline==8.1=h46c0cb4_0 -> libgcc-ng[version='>=9.3.0'] -> _openmp_mutex[version='>=4.5'] -> llvm-openmp[version='>=9.0.1'] -> openmp[version='11.1.0|11.1.0.*']
  - conda-forge/linux-64::readline==8.1=h46c0cb4_0 -> libgcc-ng[version='>=9.3.0'] -> _openmp_mutex[version='>=4.5'] -> openmp_impl==9999
  - conda-forge/linux-64::sqlite==3.35.5=h74cdb3f_0 -> libgcc-ng[version='>=9.3.0'] -> _openmp_mutex[version='>=4.5'] -> llvm-openmp[version='>=9.0.1'] -> openmp[version='11.1.0|11.1.0.*']
  - conda-forge/linux-64::sqlite==3.35.5=h74cdb3f_0 -> libgcc-ng[version='>=9.3.0'] -> _openmp_mutex[version='>=4.5'] -> openmp_impl==9999
  - conda-forge/linux-64::xorg-kbproto==1.0.7=h7f98852_1002 -> libgcc-ng[version='>=9.3.0'] -> _openmp_mutex[version='>=4.5'] -> llvm-openmp[version='>=9.0.1'] -> openmp[version='11.1.0|11.1.0.*']
  - conda-forge/linux-64::xorg-kbproto==1.0.7=h7f98852_1002 -> libgcc-ng[version='>=9.3.0'] -> _openmp_mutex[version='>=4.5'] -> openmp_impl==9999
  - conda-forge/linux-64::xorg-libice==1.0.10=h7f98852_0 -> libgcc-ng[version='>=9.3.0'] -> _openmp_mutex[version='>=4.5'] -> llvm-openmp[version='>=9.0.1'] -> openmp[version='11.1.0|11.1.0.*']
  - conda-forge/linux-64::xorg-libice==1.0.10=h7f98852_0 -> libgcc-ng[version='>=9.3.0'] -> _openmp_mutex[version='>=4.5'] -> openmp_impl==9999
  - conda-forge/linux-64::xorg-libsm==1.2.3=hd9c2040_1000 -> libgcc-ng[version='>=9.3.0'] -> _openmp_mutex[version='>=4.5'] -> llvm-openmp[version='>=9.0.1'] -> openmp[version='11.1.0|11.1.0.*']
  - conda-forge/linux-64::xorg-libsm==1.2.3=hd9c2040_1000 -> libgcc-ng[version='>=9.3.0'] -> _openmp_mutex[version='>=4.5'] -> openmp_impl==9999
  - conda-forge/linux-64::xorg-libx11==1.7.0=h7f98852_0 -> libgcc-ng[version='>=9.3.0'] -> _openmp_mutex[version='>=4.5'] -> llvm-openmp[version='>=9.0.1'] -> openmp[version='11.1.0|11.1.0.*']
  - conda-forge/linux-64::xorg-libx11==1.7.0=h7f98852_0 -> libgcc-ng[version='>=9.3.0'] -> _openmp_mutex[version='>=4.5'] -> openmp_impl==9999
  - conda-forge/linux-64::xorg-libxau==1.0.9=h7f98852_0 -> libgcc-ng[version='>=9.3.0'] -> _openmp_mutex[version='>=4.5'] -> llvm-openmp[version='>=9.0.1'] -> openmp[version='11.1.0|11.1.0.*']
  - conda-forge/linux-64::xorg-libxau==1.0.9=h7f98852_0 -> libgcc-ng[version='>=9.3.0'] -> _openmp_mutex[version='>=4.5'] -> openmp_impl==9999
  - conda-forge/linux-64::xorg-libxdmcp==1.1.3=h7f98852_0 -> libgcc-ng[version='>=9.3.0'] -> _openmp_mutex[version='>=4.5'] -> llvm-openmp[version='>=9.0.1'] -> openmp[version='11.1.0|11.1.0.*']
  - conda-forge/linux-64::xorg-libxdmcp==1.1.3=h7f98852_0 -> libgcc-ng[version='>=9.3.0'] -> _openmp_mutex[version='>=4.5'] -> openmp_impl==9999
  - conda-forge/linux-64::xorg-libxext==1.3.4=h7f98852_1 -> libgcc-ng[version='>=9.3.0'] -> _openmp_mutex[version='>=4.5'] -> llvm-openmp[version='>=9.0.1'] -> openmp[version='11.1.0|11.1.0.*']
  - conda-forge/linux-64::xorg-libxext==1.3.4=h7f98852_1 -> libgcc-ng[version='>=9.3.0'] -> _openmp_mutex[version='>=4.5'] -> openmp_impl==9999
  - conda-forge/linux-64::xorg-libxrender==0.9.10=h7f98852_1003 -> libgcc-ng[version='>=9.3.0'] -> _openmp_mutex[version='>=4.5'] -> llvm-openmp[version='>=9.0.1'] -> openmp[version='11.1.0|11.1.0.*']
  - conda-forge/linux-64::xorg-libxrender==0.9.10=h7f98852_1003 -> libgcc-ng[version='>=9.3.0'] -> _openmp_mutex[version='>=4.5'] -> openmp_impl==9999
  - conda-forge/linux-64::xorg-renderproto==0.11.1=h7f98852_1002 -> libgcc-ng[version='>=9.3.0'] -> _openmp_mutex[version='>=4.5'] -> llvm-openmp[version='>=9.0.1'] -> openmp[version='11.1.0|11.1.0.*']
  - conda-forge/linux-64::xorg-renderproto==0.11.1=h7f98852_1002 -> libgcc-ng[version='>=9.3.0'] -> _openmp_mutex[version='>=4.5'] -> openmp_impl==9999
  - conda-forge/linux-64::xorg-xextproto==7.3.0=h7f98852_1002 -> libgcc-ng[version='>=9.3.0'] -> _openmp_mutex[version='>=4.5'] -> llvm-openmp[version='>=9.0.1'] -> openmp[version='11.1.0|11.1.0.*']
  - conda-forge/linux-64::xorg-xextproto==7.3.0=h7f98852_1002 -> libgcc-ng[version='>=9.3.0'] -> _openmp_mutex[version='>=4.5'] -> openmp_impl==9999
  - conda-forge/linux-64::xorg-xproto==7.0.31=h7f98852_1007 -> libgcc-ng[version='>=9.3.0'] -> _openmp_mutex[version='>=4.5'] -> llvm-openmp[version='>=9.0.1'] -> openmp[version='11.1.0|11.1.0.*']
  - conda-forge/linux-64::xorg-xproto==7.0.31=h7f98852_1007 -> libgcc-ng[version='>=9.3.0'] -> _openmp_mutex[version='>=4.5'] -> openmp_impl==9999
  - conda-forge/linux-64::zstd==1.4.9=ha95c52a_0 -> libgcc-ng[version='>=9.3.0'] -> _openmp_mutex[version='>=4.5'] -> llvm-openmp[version='>=9.0.1'] -> openmp[version='11.1.0|11.1.0.*']
  - conda-forge/linux-64::zstd==1.4.9=ha95c52a_0 -> libgcc-ng[version='>=9.3.0'] -> _openmp_mutex[version='>=4.5'] -> openmp_impl==9999
  - conda-forge/noarch::r-callr==3.7.0=r36hc72bb7e_0 -> r-r6
  - conda-forge/noarch::r-desc==1.3.0=r36hc72bb7e_0 -> r-r6
  - conda-forge/noarch::r-ggplot2==3.3.3=r36hc72bb7e_0 -> r-scales[version='>=0.5.0'] -> r-r6
  - conda-forge/noarch::r-lifecycle==1.0.0=r36hc72bb7e_0 -> r-rlang[version='>=0.4.10'] -> libgcc-ng[version='>=9.3.0'] -> _openmp_mutex[version='>=4.5'] -> llvm-openmp[version='>=9.0.1'] -> openmp[version='11.1.0|11.1.0.*']
  - conda-forge/noarch::r-lifecycle==1.0.0=r36hc72bb7e_0 -> r-rlang[version='>=0.4.10'] -> libgcc-ng[version='>=9.3.0'] -> _openmp_mutex[version='>=4.5'] -> openmp_impl==9999
  - conda-forge/noarch::r-progress==1.2.2=r36h6115d3f_2 -> r-r6
  - conda-forge/noarch::r-r6==2.5.0=r36hc72bb7e_0
  - conda-forge/noarch::r-rio==0.5.26=r36hc72bb7e_0 -> r-curl[version='>=0.6']
  - conda-forge/noarch::r-scales==1.1.1=r36h6115d3f_0 -> r-r6
  - python_abi -> pypy3.7=7.3 -> libgcc-ng[version='>=9.3.0'] -> _openmp_mutex[version='>=4.5'] -> llvm-openmp[version='>=9.0.1'] -> openmp[version='11.1.0|11.1.0.*']
  - python_abi -> pypy3.7=7.3 -> libgcc-ng[version='>=9.3.0'] -> _openmp_mutex[version='>=4.5'] -> openmp_impl==9999
  - python_abi -> pypy3.7=7.3 -> pypy3.5==99999999999
  - python_abi -> pypy[version='<0a0']

Is there a proper way to install this?

dariober commented 3 years ago

Hi- Sorry about that. Can you show the commands you used to install cnv_facets?

The documentation has:

conda create -n my_project
conda activate my_project
conda install -c bioconda -c conda-forge cnv_facets

And it should work. However, I should update it and recommend to install mamba first and then use mamba install ... instead of conda install .... Mamba is a lot better than conda install so I would suggest that regardless of cnv_facets.

So install with something like:

# Install mamba in base environment
conda install mamba 

# As per bioconda https://bioconda.github.io/user/install.html#set-up-channels
conda config --add channels defaults
conda config --add channels bioconda
conda config --add channels conda-forge

conda create -n my_project
conda activate my_project
mamba install cnv_facets

Having said that, I tested it just now and it works for me. However, I'm slightly surprised that argparse is installed at all since the recipe for cnv_facets doesn't list r-argparse at the moment. (I'll investigate...). (Update: r-argparse is installed by build.sh)

See also issue https://github.com/dariober/cnv_facets/issues/35

pinunQ commented 2 years ago

I have tried the same command line as you suggested to download the CNV_facets and there is no activity in the system it just gets stuck at the solving environment state.

`Collecting package metadata (current_repodata.json): done Solving environment: failed with initial frozen solve. Retrying with flexible solve. Solving environment: failed with repodata from current_repodata.json, will retry with next repodata source.

Collecting package metadata (repodata.json): done`

The command line used for the purpose of installing CNV_facets is the conda create -n my_project conda activate my_project conda install -c bioconda -c conda-forge cnv_facets

Please help with this.

jgarces02 commented 1 year ago

Nope, it doesn't work either... 

Collecting package metadata (current_repodata.json): done
Solving environment: done

==> WARNING: A newer version of conda exists. <==
  current version: 4.7.10
  latest version: 23.5.0

Please update conda by running

    $ conda update -n base -c defaults conda

## Package Plan ##

  environment location: /home/jgarces/.conda/envs/cnv_facets

  added / updated specs:
    - mamba

The following NEW packages will be INSTALLED:

  _libgcc_mutex      conda-forge/linux-64::_libgcc_mutex-0.1-conda_forge
  _openmp_mutex      conda-forge/linux-64::_openmp_mutex-4.5-2_gnu
  boltons            conda-forge/noarch::boltons-23.0.0-pyhd8ed1ab_0
  brotli             conda-forge/linux-64::brotli-1.0.9-h166bdaf_8
  brotli-bin         conda-forge/linux-64::brotli-bin-1.0.9-h166bdaf_8
  bzip2              conda-forge/linux-64::bzip2-1.0.8-h7f98852_4
  c-ares             conda-forge/linux-64::c-ares-1.19.1-hd590300_0
  ca-certificates    conda-forge/linux-64::ca-certificates-2023.5.7-hbcca054_0
  certifi            conda-forge/noarch::certifi-2023.5.7-pyhd8ed1ab_0
  cffi               conda-forge/linux-64::cffi-1.15.1-py310h255011f_3
  charset-normalizer conda-forge/noarch::charset-normalizer-3.1.0-pyhd8ed1ab_0
  colorama           conda-forge/noarch::colorama-0.4.6-pyhd8ed1ab_0
  conda              conda-forge/linux-64::conda-23.3.1-py310hff52083_0
  conda-package-han~ conda-forge/noarch::conda-package-handling-2.0.2-pyh38be061_0
  conda-package-str~ conda-forge/noarch::conda-package-streaming-0.8.0-pyhd8ed1ab_0
  cryptography       conda-forge/linux-64::cryptography-40.0.2-py310h34c0648_0
  fmt                conda-forge/linux-64::fmt-9.1.0-h924138e_0
  icu                conda-forge/linux-64::icu-72.1-hcb278e6_0
  idna               conda-forge/noarch::idna-3.4-pyhd8ed1ab_0
  jsonpatch          conda-forge/noarch::jsonpatch-1.32-pyhd8ed1ab_0
  jsonpointer        conda-forge/noarch::jsonpointer-2.0-py_0
  keyutils           conda-forge/linux-64::keyutils-1.6.1-h166bdaf_0
  krb5               conda-forge/linux-64::krb5-1.20.1-h81ceb04_0
  ld_impl_linux-64   conda-forge/linux-64::ld_impl_linux-64-2.40-h41732ed_0
  libarchive         conda-forge/linux-64::libarchive-3.6.2-h039dbb9_1
  libbrotlicommon    conda-forge/linux-64::libbrotlicommon-1.0.9-h166bdaf_8
  libbrotlidec       conda-forge/linux-64::libbrotlidec-1.0.9-h166bdaf_8
  libbrotlienc       conda-forge/linux-64::libbrotlienc-1.0.9-h166bdaf_8
  libcurl            conda-forge/linux-64::libcurl-8.1.1-h409715c_0
  libedit            conda-forge/linux-64::libedit-3.1.20191231-he28a2e2_2
  libev              conda-forge/linux-64::libev-4.33-h516909a_1
  libffi             conda-forge/linux-64::libffi-3.4.2-h7f98852_5
  libgcc-ng          conda-forge/linux-64::libgcc-ng-12.2.0-h65d4601_19
  libgomp            conda-forge/linux-64::libgomp-12.2.0-h65d4601_19
  libiconv           conda-forge/linux-64::libiconv-1.17-h166bdaf_0
  libmamba           conda-forge/linux-64::libmamba-1.4.2-hcea66bb_0
  libmambapy         conda-forge/linux-64::libmambapy-1.4.2-py310h1428755_0
  libnghttp2         conda-forge/linux-64::libnghttp2-1.52.0-h61bc06f_0
  libnsl             conda-forge/linux-64::libnsl-2.0.0-h7f98852_0
  libsolv            conda-forge/linux-64::libsolv-0.7.23-h3eb15da_0
  libsqlite          conda-forge/linux-64::libsqlite-3.42.0-h2797004_0
  libssh2            conda-forge/linux-64::libssh2-1.10.0-hf14f497_3
  libstdcxx-ng       conda-forge/linux-64::libstdcxx-ng-12.2.0-h46fd767_19
  libuuid            conda-forge/linux-64::libuuid-2.38.1-h0b41bf4_0
  libxml2            conda-forge/linux-64::libxml2-2.11.4-h0d562d8_0
  libzlib            conda-forge/linux-64::libzlib-1.2.13-h166bdaf_4
  lz4-c              conda-forge/linux-64::lz4-c-1.9.4-hcb278e6_0
  lzo                conda-forge/linux-64::lzo-2.10-h516909a_1000
  mamba              conda-forge/linux-64::mamba-1.4.2-py310h51d5547_0
  ncurses            conda-forge/linux-64::ncurses-6.3-h27087fc_1
  openssl            conda-forge/linux-64::openssl-3.1.0-hd590300_3
  packaging          conda-forge/noarch::packaging-23.1-pyhd8ed1ab_0
  pip                conda-forge/noarch::pip-23.1.2-pyhd8ed1ab_0
  pluggy             conda-forge/noarch::pluggy-1.0.0-pyhd8ed1ab_5
  pybind11-abi       conda-forge/noarch::pybind11-abi-4-hd8ed1ab_3
  pycosat            conda-forge/linux-64::pycosat-0.6.4-py310h5764c6d_1
  pycparser          conda-forge/noarch::pycparser-2.21-pyhd8ed1ab_0
  pyopenssl          conda-forge/noarch::pyopenssl-23.1.1-pyhd8ed1ab_0
  pysocks            conda-forge/linux-64::pysocks-1.7.1-py310hff52083_5
  python             conda-forge/linux-64::python-3.10.11-he550d4f_0_cpython
  python_abi         conda-forge/linux-64::python_abi-3.10-3_cp310
  readline           conda-forge/linux-64::readline-8.2-h8228510_1
  reproc             conda-forge/linux-64::reproc-14.2.4-h0b41bf4_0
  reproc-cpp         conda-forge/linux-64::reproc-cpp-14.2.4-hcb278e6_0
  requests           conda-forge/noarch::requests-2.31.0-pyhd8ed1ab_0
  ruamel.yaml        conda-forge/linux-64::ruamel.yaml-0.17.27-py310h2372a71_0
  ruamel.yaml.clib   conda-forge/linux-64::ruamel.yaml.clib-0.2.7-py310h1fa729e_1
  setuptools         conda-forge/noarch::setuptools-67.7.2-pyhd8ed1ab_0
  tk                 conda-forge/linux-64::tk-8.6.12-h27826a3_0
  toolz              conda-forge/noarch::toolz-0.12.0-pyhd8ed1ab_0
  tqdm               conda-forge/noarch::tqdm-4.65.0-pyhd8ed1ab_1
  tzdata             conda-forge/noarch::tzdata-2023c-h71feb2d_0
  urllib3            conda-forge/noarch::urllib3-2.0.2-pyhd8ed1ab_0
  wheel              conda-forge/noarch::wheel-0.40.0-pyhd8ed1ab_0
  xz                 conda-forge/linux-64::xz-5.2.6-h166bdaf_0
  yaml-cpp           conda-forge/linux-64::yaml-cpp-0.7.0-h27087fc_2
  zstandard          conda-forge/linux-64::zstandard-0.19.0-py310hdeb6495_1
  zstd               conda-forge/linux-64::zstd-1.5.2-h3eb15da_6

Proceed ([y]/n)?

Preparing transaction: done
Verifying transaction: done
Executing transaction: done
ERROR conda.core.link:_execute(656): An error occurred while installing package 'conda-forge::pip-23.1.2-pyhd8ed1ab_0'.
Rolling back transaction: done

[Errno 2] No such file or directory: '/home/jgarces/.conda/envs/cnv_facets/lib/python3.1/site-packages/pip/_vendor/tenacity/__init__.py'
(FileNotFoundError(2, 'No such file or directory'), FileNotFoundError(2, 'No such file or directory'))