Installation error

[Ella Sieradzki]

It’s yelling at me. Why is it yelling at me?

(iphop_env) [esieradz@prepost-cascade bin]$ mamba install -c conda-forge -c bioconda iphop

Looking for: ['iphop']

conda-forge/linux-64 Using cache
conda-forge/noarch Using cache
bioconda/linux-64 Using cache
bioconda/noarch Using cache
pkgs/r/linux-64 No change
pkgs/main/linux-64 No change
pkgs/main/noarch No change
pkgs/r/noarch No change
ursky/noarch No change
ursky/linux-64 No change

Pinned packages:

• python 3.8.*

warning libmamba Problem type not implemented SOLVER_RULE_STRICT_REPO_PRIORITY
warning libmamba Problem type not implemented SOLVER_RULE_STRICT_REPO_PRIORITY
warning libmamba Problem type not implemented SOLVER_RULE_STRICT_REPO_PRIORITY
warning libmamba Problem type not implemented SOLVER_RULE_STRICT_REPO_PRIORITY
warning libmamba Problem type not implemented SOLVER_RULE_STRICT_REPO_PRIORITY
warning libmamba Problem type not implemented SOLVER_RULE_STRICT_REPO_PRIORITY
warning libmamba Problem type not implemented SOLVER_RULE_STRICT_REPO_PRIORITY
warning libmamba Problem type not implemented SOLVER_RULE_STRICT_REPO_PRIORITY
warning libmamba Problem type not implemented SOLVER_RULE_STRICT_REPO_PRIORITY
warning libmamba Problem type not implemented SOLVER_RULE_STRICT_REPO_PRIORITY
Could not solve for environment specs
The following packages are incompatible
└─ iphop is not installable because there are no viable options
├─ iphop [1.0.0|1.1.0] would require
│ ├─ perl 5.26.* , which can be installed;
│ └─ perl-bioperl 1.6.924.* but there are no viable options
│ ├─ perl-bioperl 1.6.924 would require
│ │ └─ perl >=5.22.0,<5.23.0 , which conflicts with any installable versions previously reported;
│ └─ perl-bioperl 1.6.924 would require
│ └─ perl 5.22.0* , which conflicts with any installable versions previously reported;
├─ iphop [1.1.0|1.2.0] would require
│ ├─ blast 2.12.0.* , which requires
│ │ └─ perl-json with the potential options
│ │ ├─ perl-json [2.90|2.97001|4.00|4.02] would require
│ │ │ └─ perl-json-xs <3 with the potential options
│ │ │ ├─ perl-json-xs 2.34 would require
│ │ │ │ └─ perl-common-sense with the potential options
│ │ │ │ ├─ perl-common-sense 3.75 would require
│ │ │ │ │ └─ perl >=5.32.1,<6.0a0 *_perl5, which can be installed;
│ │ │ │ └─ perl-common-sense [3.74|3.75] conflicts with any installable versions previously reported;
│ │ │ ├─ perl-json-xs 2.34 would require
│ │ │ │ ├─ libstdcxx-ng >=12 , which can be installed;
│ │ │ │ └─ perl >=5.32.1,<5.33.0a0 *_perl5, which can be installed;
│ │ │ └─ perl-json-xs 2.34 would require
│ │ │ └─ perl >=5.32.1,<5.33.0a0 _perl5, which can be installed;
│ │ └─ perl-json [4.02|4.05|...|4.10] would require
│ │ └─ perl >=5.32.1,<6.0a0 _perl5, which can be installed;
│ ├─ libstdcxx-ng 11.2.0. , which conflicts with any installable versions previously reported;
│ └─ perl-bioperl <=1.7 , which cannot be installed (as previously explained);
└─ iphop [1.3.0|1.3.1|1.3.2] would require
├─ blast 2.12. , which can be installed (as previously explained);
└─ perl-bioperl <=1.7 , which cannot be installed (as previously explained).

[Simon Roux]

Hmm I’m not entirely sure. Are you trying this install on a Mac by any chance ? Or on an “exotic” linux ? (it doesn’t look like it, but ..)

The other option I would try would be to create an environment from scratch, i.e.:

$ mamba create -n iphop_test -c bioconda -c conda-forge iphop

Just in case some of the packages installed when you originally created the environment are causing the issue

[Ella Sieradzki]

Yeah, sorry, I think it’s just a typical French linux. Works fine when I install on an American linux.

[Simon Roux]

What about the installation via github, i.e.:

$ git clone https://[e-mail]/srouxjgi/iphop.git
$ mamba env create -f iphop_environment.yml

?

[Ella Sieradzki]

I’ll give it a try. Otherwise you’ll have to fly to France and talk to the sys admin.

[Ella Sieradzki]

Nope. I get all kinds of interesting errors. I think it’s just a local issue to address with the sys admin. Probably worth leaving in issues in case somebody else has this problem though.

Looking for: ['iphop']

warning libmamba Cache file "/home/ampere/esieradz/bin/miniconda3/pkgs/cache/ffeee55f.json" was modified by another program
warning libmamba Cache file "/home/ampere/esieradz/bin/miniconda3/pkgs/cache/2a957770.json" was modified by another program
warning libmamba Cache file "/home/ampere/esieradz/bin/miniconda3/pkgs/cache/497deca9.json" was modified by another program
warning libmamba Cache file "/home/ampere/esieradz/bin/miniconda3/pkgs/cache/09cdf8bf.json" was modified by another program
warning libmamba Could not parse state file: Could not load cache state: [json.exception.type_error.302] type must be string, but is null
warning libmamba Could not parse state file: Could not load cache state: [json.exception.type_error.302] type must be string, but is null
warning libmamba Cache file "/home/ampere/esieradz/bin/miniconda3/pkgs/cache/47929eba.json" was modified by another program
warning libmamba Cache file "/home/ampere/esieradz/bin/miniconda3/pkgs/cache/3e39a7aa.json" was modified by another program
warning libmamba Cache file "/home/ampere/esieradz/bin/miniconda3/pkgs/cache/2ce54b42.json" was modified by another program
warning libmamba Cache file "/home/ampere/esieradz/bin/miniconda3/pkgs/cache/4ea078d6.json" was modified by another program
ursky/linux-64 4.6kB @ 15.5kB/s 0.3s
ursky/noarch 135.0 B @ 275.0 B/s 0.2s
pkgs/r/linux-64 1.4MB @ 1.6MB/s 0.4s
bioconda/noarch 4.6MB @ 4.3MB/s 1.2s
pkgs/r/noarch 1.3MB @ 1.1MB/s 0.4s
bioconda/linux-64 5.1MB @ 4.1MB/s 1.4s
pkgs/main/noarch 852.1kB @ 580.4kB/s 0.2s
pkgs/main/linux-64 6.0MB @ 2.4MB/s 1.5s
conda-forge/noarch 13.6MB @ 4.4MB/s 3.3s
conda-forge/linux-64 33.4MB @ 5.0MB/s 7.3s
warning libmamba Problem type not implemented SOLVER_RULE_STRICT_REPO_PRIORITY
warning libmamba Problem type not implemented SOLVER_RULE_STRICT_REPO_PRIORITY
warning libmamba Problem type not implemented SOLVER_RULE_STRICT_REPO_PRIORITY
warning libmamba Problem type not implemented SOLVER_RULE_STRICT_REPO_PRIORITY
warning libmamba Problem type not implemented SOLVER_RULE_STRICT_REPO_PRIORITY
warning libmamba Problem type not implemented SOLVER_RULE_STRICT_REPO_PRIORITY
warning libmamba Problem type not implemented SOLVER_RULE_STRICT_REPO_PRIORITY
warning libmamba Problem type not implemented SOLVER_RULE_STRICT_REPO_PRIORITY
warning libmamba Problem type not implemented SOLVER_RULE_STRICT_REPO_PRIORITY
warning libmamba Problem type not implemented SOLVER_RULE_STRICT_REPO_PRIORITY
warning libmamba Problem type not implemented SOLVER_RULE_STRICT_REPO_PRIORITY
warning libmamba Problem type not implemented SOLVER_RULE_STRICT_REPO_PRIORITY
warning libmamba Problem type not implemented SOLVER_RULE_STRICT_REPO_PRIORITY
warning libmamba Problem type not implemented SOLVER_RULE_STRICT_REPO_PRIORITY
warning libmamba Problem type not implemented SOLVER_RULE_STRICT_REPO_PRIORITY
warning libmamba Problem type not implemented SOLVER_RULE_STRICT_REPO_PRIORITY
warning libmamba Problem type not implemented SOLVER_RULE_STRICT_REPO_PRIORITY
warning libmamba Problem type not implemented SOLVER_RULE_STRICT_REPO_PRIORITY
warning libmamba Problem type not implemented SOLVER_RULE_STRICT_REPO_PRIORITY
warning libmamba Problem type not implemented SOLVER_RULE_STRICT_REPO_PRIORITY
warning libmamba Problem type not implemented SOLVER_RULE_STRICT_REPO_PRIORITY
warning libmamba Problem type not implemented SOLVER_RULE_STRICT_REPO_PRIORITY
warning libmamba Problem type not implemented SOLVER_RULE_STRICT_REPO_PRIORITY
Could not solve for environment specs
The following package could not be installed
└─ iphop is uninstallable because it requires
└─ biopython 1.79.* , which conflicts with any installable versions previously reported.