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Could not solve for environment specs #8

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mdhall272 opened this issue Feb 14, 2024 · 0 comments
Open

Could not solve for environment specs #8

mdhall272 opened this issue Feb 14, 2024 · 0 comments
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@ktmeaton
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@mdhall272
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I can't manage to install this - there are package problems after mamba env create -f workflow/envs/merge/environment.yaml, below

I fully understand if you have moved on from a place in which you have the time or inclination to fix this; in that case is there any possibility of just being given the alignment from the paper?

Could not solve for environment specs
The following packages are incompatible
├─ angsd 0.933*  does not exist (perhaps a typo or a missing channel);
├─ blast 2.10.1**  is installable with the potential options
│  ├─ blast 2.10.1 would require
│  │  ├─ perl >=5.26.2,<5.26.3.0a0 , which can be installed;
│  │  └─ zlib >=1.2.11,<1.3.0a0  with the potential options
│  │     ├─ zlib 1.2.11, which can be installed;
│  │     ├─ zlib 1.2.12 conflicts with any installable versions previously reported;
│  │     └─ zlib 1.2.13 conflicts with any installable versions previously reported;
│  └─ blast 2.10.1 would require
│     └─ perl >=5.26.2,<5.26.3.0a0 , which can be installed;
├─ gfortran_linux-64 does not exist (perhaps a typo or a missing channel);
├─ hops 0.34*  is installable and it requires
│  ├─ openjdk 8.0.144.* , which can be installed;
│  └─ r-base >=3.5  with the potential options
│     ├─ r-base [3.5.0|3.5.1|3.5.3|3.6.0|3.6.1] would require
│     │  └─ icu >=58.2,<59.0a0 , which can be installed;
│     ├─ r-base [3.5.1|3.6.1|3.6.2] would require
│     │  └─ gsl >=2.5,<2.6.0a0 , which can be installed;
│     ├─ r-base [3.6.3|4.0.0|4.0.1|4.0.2] would require
│     │  └─ gsl >=2.6,<2.7.0a0 , which can be installed;
│     ├─ r-base [3.6.3|4.0.3|...|4.2.1] would require
│     │  └─ libiconv >=1.16,<2.0.0a0 , which can be installed;
│     ├─ r-base 3.6.3 would require
│     │  ├─ icu >=67.1,<68.0a0 , which can be installed;
│     │  └─ libxml2 >=2.9.10,<3.0.0a0  with the potential options
│     │     ├─ libxml2 [2.10.0|2.10.1|...|2.9.14] would require
│     │     │  └─ libiconv [>=1.16,<2.0.0a0 |>=1.16,<2.0a0 ], which can be installed;
│     │     ├─ libxml2 2.10.2 would require
│     │     │  └─ libiconv [>=1.17,<2.0.0a0 |>=1.17,<2.0a0 ], which can be installed;
│     │     ├─ libxml2 [2.10.3|2.11.5|...|2.9.14] would require
│     │     │  ├─ libiconv >=1.17,<2.0a0 , which can be installed;
│     │     │  └─ libzlib >=1.2.13,<1.3.0a0  but there are no viable options
│     │     │     ├─ libzlib 1.2.13 would require
│     │     │     │  └─ zlib 1.2.13 *_4, which conflicts with any installable versions previously reported;
│     │     │     └─ libzlib 1.2.13 would require
│     │     │        └─ zlib 1.2.13 *_5, which conflicts with any installable versions previously reported;
│     │     ├─ libxml2 [2.10.3|2.10.4|2.11.3|2.11.4|2.11.5] would require
│     │     │  └─ icu >=72.1,<73.0a0 , which can be installed;
│     │     ├─ libxml2 2.9.10 would require
│     │     │  └─ icu >=64.2,<65.0a0 , which conflicts with any installable versions previously reported;
│     │     └─ libxml2 2.9.10 would require
│     │        └─ icu >=67.1,<68.0a0 , which can be installed;
│     ├─ r-base 4.0.2 would require
│     │  └─ icu >=67.1,<68.0a0 , which can be installed;
│     ├─ r-base [4.0.5|4.1.3|...|4.3.2] would require
│     │  ├─ libiconv >=1.17,<2.0a0 , which can be installed;
│     │  └─ libzlib >=1.2.13,<1.3.0a0 , which cannot be installed (as previously explained);
│     ├─ r-base [4.1.3|4.2.1] would require
│     │  └─ libiconv >=1.17,<2.0a0 , which can be installed;
│     ├─ r-base [4.1.3|4.2.3|4.3.0|4.3.1] would require
│     │  └─ icu >=72.1,<73.0a0 , which can be installed;
│     └─ r-base 3.5.0 would require
│        └─ icu >=58.2,<59.0a0 , which can be installed;
├─ kraken2 2.0.9beta*  is installable and it requires
│  └─ perl >=5.26.2,<5.26.3.0a0 , which can be installed;
├─ libiconv 1.15*  is not installable because it conflicts with any installable versions previously reported;
├─ nodejs 13.13.0*  is not installable because it requires
│  └─ icu >=64.2,<65.0a0 , which conflicts with any installable versions previously reported;
├─ preseq 2.0.3*  is not installable because there are no viable options
│  ├─ preseq 2.0.3 would require
│  │  ├─ gsl 2.2* , which conflicts with any installable versions previously reported;
│  │  └─ zlib 1.2.11* , which can be installed;
│  └─ preseq 2.0.3 would require
│     └─ gsl 1.16* , which conflicts with any installable versions previously reported;
├─ sequencetools 1.4.0.6*  does not exist (perhaps a typo or a missing channel);
├─ singularity 3.6.3**  does not exist (perhaps a typo or a missing channel);
├─ snakemake 5.27.4**  is installable and it requires
│  └─ imagemagick >=7.0  with the potential options
│     ├─ imagemagick [7.0.10_0|7.0.10_10|...|7.0.9_7] would require
│     │  └─ zlib >=1.2.11,<1.3.0a0  with the potential options
│     │     ├─ zlib 1.2.11, which can be installed;
│     │     ├─ zlib 1.2.12 conflicts with any installable versions previously reported;
│     │     └─ zlib 1.2.13 conflicts with any installable versions previously reported;
│     ├─ imagemagick [7.0.10_28|7.0.10_59|...|7.1.0_9] would require
│     │  └─ libglib [>=2.64.6,<3.0a0 |>=2.66.4,<3.0a0 |...|>=2.72.1,<3.0a0 ] with the potential options
│     │     ├─ libglib [2.64.6|2.66.1|...|2.72.1] would require
│     │     │  └─ libiconv >=1.16,<2.0.0a0 , which can be installed;
│     │     └─ libglib [2.74.0|2.74.1|...|2.78.3] would require
│     │        └─ libiconv >=1.17,<2.0a0 , which can be installed;
│     ├─ imagemagick [7.0.11_13|7.0.11_14|...|7.1.1_9] would require
│     │  └─ libxml2 [>=2.10.3,<3.0.0a0 |>=2.10.4,<3.0.0a0 |>=2.9.12,<3.0.0a0 ] with the potential options
│     │     ├─ libxml2 [2.10.0|2.10.1|...|2.9.14], which can be installed (as previously explained);
│     │     ├─ libxml2 2.10.2, which can be installed (as previously explained);
│     │     ├─ libxml2 [2.10.3|2.11.5|...|2.9.14], which cannot be installed (as previously explained);
│     │     └─ libxml2 [2.10.3|2.10.4|2.11.3|2.11.4|2.11.5], which can be installed (as previously explained);
│     ├─ imagemagick [7.0.6|7.0.7|...|7.0.8_7] would require
│     │  └─ perl [5.22.2.1 |5.22.2.1.* ], which conflicts with any installable versions previously reported;
│     ├─ imagemagick [7.0.8_10|7.0.8_7|7.0.8_8] would require
│     │  └─ zlib 1.2.11.* , which can be installed;
│     ├─ imagemagick 7.1.0_50 would require
│     │  └─ libglib >=2.74.0,<3.0a0 , which can be installed (as previously explained);
│     ├─ imagemagick [7.1.1_10|7.1.1_11|...|7.1.1_9] would require
│     │  └─ libxml2 [>=2.11.3,<3.0.0a0 |>=2.11.4,<3.0.0a0 |>=2.11.5,<3.0.0a0 ] with the potential options
│     │     ├─ libxml2 [2.10.3|2.11.5|...|2.9.14], which cannot be installed (as previously explained);
│     │     └─ libxml2 [2.10.3|2.10.4|2.11.3|2.11.4|2.11.5], which can be installed (as previously explained);
│     └─ imagemagick [7.1.1_21|7.1.1_22|...|7.1.1_28] would require
│        └─ libxml2 [>=2.11.6,<3.0.0a0 |>=2.12.1,<3.0.0a0 |...|>=2.12.5,<3.0a0 ], which cannot be installed (as previously explained);
├─ snippy 4.6.0**  is installable with the potential options
│  ├─ snippy 4.6.0 would require
│  │  ├─ bcftools >=1.10  with the potential options
│  │  │  ├─ bcftools [1.10|1.10.1|1.10.2] would require
│  │  │  │  └─ gsl >=2.5,<2.6.0a0 , which can be installed;
│  │  │  ├─ bcftools [1.10.2|1.11|1.12|1.13|1.14] would require
│  │  │  │  └─ gsl >=2.6,<2.7.0a0 , which can be installed;
│  │  │  ├─ bcftools [1.14|1.15|1.15.1] would require
│  │  │  │  └─ gsl >=2.7,<2.8.0a0 , which can be installed;
│  │  │  ├─ bcftools [1.15.1|1.16] would require
│  │  │  │  ├─ gsl >=2.7,<2.8.0a0 , which can be installed;
│  │  │  │  ├─ libzlib >=1.2.12,<1.3.0a0  but there are no viable options
│  │  │  │  │  ├─ libzlib 1.2.12 would require
│  │  │  │  │  │  └─ zlib 1.2.12 *_4, which conflicts with any installable versions previously reported;
│  │  │  │  │  ├─ libzlib 1.2.12 would require
│  │  │  │  │  │  └─ zlib 1.2.12 *_0, which conflicts with any installable versions previously reported;
│  │  │  │  │  ├─ libzlib 1.2.12 would require
│  │  │  │  │  │  └─ zlib 1.2.12 *_3, which conflicts with any installable versions previously reported;
│  │  │  │  │  ├─ libzlib 1.2.12 would require
│  │  │  │  │  │  └─ zlib 1.2.12 *_1, which conflicts with any installable versions previously reported;
│  │  │  │  │  ├─ libzlib 1.2.12 would require
│  │  │  │  │  │  └─ zlib 1.2.12 *_2, which conflicts with any installable versions previously reported;
│  │  │  │  │  ├─ libzlib 1.2.13, which cannot be installed (as previously explained);
│  │  │  │  │  └─ libzlib 1.2.13, which cannot be installed (as previously explained);
│  │  │  │  └─ zlib >=1.2.12,<1.3.0a0 , which conflicts with any installable versions previously reported;
│  │  │  ├─ bcftools [1.16|1.17] would require
│  │  │  │  ├─ gsl >=2.7,<2.8.0a0 , which can be installed;
│  │  │  │  ├─ libzlib >=1.2.13,<1.3.0a0 , which cannot be installed (as previously explained);
│  │  │  │  └─ zlib >=1.2.13,<1.3.0a0 , which conflicts with any installable versions previously reported;
│  │  │  └─ bcftools [1.17|1.18|1.19] would require
│  │  │     ├─ gsl >=2.7,<2.8.0a0 , which can be installed;
│  │  │     └─ libzlib >=1.2.13,<1.3.0a0 , which cannot be installed (as previously explained);
│  │  └─ perl-bioperl >=1.7.2  with the potential options
│  │     ├─ perl-bioperl 1.7.2 would require
│  │     │  └─ perl-bio-samtools with the potential options
│  │     │     ├─ perl-bio-samtools 1.43 would require
│  │     │     │  ├─ perl >=5.26.2,<5.26.3.0a0 , which can be installed;
│  │     │     │  └─ zlib >=1.2.11,<1.3.0a0  with the potential options
│  │     │     │     ├─ zlib 1.2.11, which can be installed;
│  │     │     │     ├─ zlib 1.2.12 conflicts with any installable versions previously reported;
│  │     │     │     └─ zlib 1.2.13 conflicts with any installable versions previously reported;
│  │     │     ├─ perl-bio-samtools 1.43 would require
│  │     │     │  └─ perl >=5.22.0,<5.23.0 , which conflicts with any installable versions previously reported;
│  │     │     └─ perl-bio-samtools 1.43 would require
│  │     │        └─ perl >=5.32.1,<5.33.0a0 *_perl5, which conflicts with any installable versions previously reported;
│  │     ├─ perl-bioperl 1.7.2 would require
│  │     │  ├─ perl-bio-samtools with the potential options
│  │     │  │  ├─ perl-bio-samtools 1.43, which can be installed (as previously explained);
│  │     │  │  ├─ perl-bio-samtools 1.43, which cannot be installed (as previously explained);
│  │     │  │  └─ perl-bio-samtools 1.43, which cannot be installed (as previously explained);
│  │     │  └─ perl-bio-tools-run-alignment-tcoffee but there are no viable options
│  │     │     ├─ perl-bio-tools-run-alignment-tcoffee 1.7.4 would require
│  │     │     │  └─ t_coffee, which does not exist (perhaps a missing channel);
│  │     │     └─ perl-bio-tools-run-alignment-tcoffee 1.7.4 would require
│  │     │        └─ perl >=5.32.1,<6.0a0 *_perl5, which conflicts with any installable versions previously reported;
│  │     └─ perl-bioperl 1.7.8 would require
│  │        └─ perl-bioperl-core 1.7.8.* , which requires
│  │           └─ perl [>=5.32.1,<5.33.0a0 *_perl5|>=5.32.1,<6.0a0 *_perl5], which conflicts with any installable versions previously reported;
│  └─ snippy 4.6.0 would require
│     └─ openjdk >=11 , which conflicts with any installable versions previously reported;
├─ sqlite 3.31.1**  is installable and it requires
│  └─ zlib >=1.2.11,<1.3.0a0  with the potential options
│     ├─ zlib 1.2.11, which can be installed;
│     ├─ zlib 1.2.12 conflicts with any installable versions previously reported;
│     └─ zlib 1.2.13 conflicts with any installable versions previously reported;
├─ sra-tools 2.10.8**  does not exist (perhaps a typo or a missing channel);
└─ vcftools 0.1.16**  is installable with the potential options
   ├─ vcftools 0.1.16 would require
   │  └─ zlib >=1.2.11,<1.3.0a0  with the potential options
   │     ├─ zlib 1.2.11, which can be installed;
   │     ├─ zlib 1.2.12 conflicts with any installable versions previously reported;
   │     └─ zlib 1.2.13 conflicts with any installable versions previously reported;
   ├─ vcftools 0.1.16 would require
   │  └─ perl >=5.32.1,<5.33.0a0 *_perl5, which conflicts with any installable versions previously reported;
   ├─ vcftools 0.1.16 would require
   │  ├─ libzlib >=1.2.13,<1.3.0a0 , which cannot be installed (as previously explained);
   │  └─ zlib >=1.2.13,<1.3.0a0 , which conflicts with any installable versions previously reported;
   └─ vcftools 0.1.16 would require
      ├─ libzlib >=1.2.13,<1.3.0a0 , which cannot be installed (as previously explained);
      ├─ perl >=5.32.1,<5.33.0a0 *_perl5, which conflicts with any installable versions previously reported;
      └─ zlib with the potential options
         ├─ zlib 1.2.11, which can be installed;
         ├─ zlib 1.2.12 conflicts with any installable versions previously reported;
         ├─ zlib 1.2.13 conflicts with any installable versions previously reported;
         └─ zlib [1.2.8|1.3], which can be installed.
@mdhall272 mdhall272 added the bug Something isn't working label Feb 14, 2024
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