Comments (5)
kdyrhage
commented on June 7, 2024
I just registered a new release (v0.1.3). See if that works.
from genomicmaps.jl.
vdejager
commented on June 7, 2024
I tested and get the following error:
(@v1.10) pkg> add GenomicMaps
Resolving package versions...
ERROR: Unsatisfiable requirements detected for package ColorTypes [3da002f7]:
ColorTypes [3da002f7] log:
├─possible versions are: 0.7.0-0.11.4 or uninstalled
├─restricted to versions * by an explicit requirement, leaving only versions: 0.7.0-0.11.4
├─restricted by compatibility requirements with QuartzImageIO [dca85d43] to versions: 0.7.0-0.9.1
│ └─QuartzImageIO [dca85d43] log:
│ ├─possible versions are: 0.5.0-0.7.4 or uninstalled
│ ├─restricted by compatibility requirements with Luxor [ae8d54c2] to versions: 0.5.0-0.6.0
│ │ └─Luxor [ae8d54c2] log:
│ │ ├─possible versions are: 0.11.0-3.8.0 or uninstalled
│ │ └─restricted by compatibility requirements with GenomicMaps [db448a0f] to versions: 0.11.0-1.12.0
│ │ └─GenomicMaps [db448a0f] log:
│ │ ├─possible versions are: 0.1.0-0.1.2 or uninstalled
│ │ └─restricted to versions * by an explicit requirement, leaving only versions: 0.1.0-0.1.2
│ └─restricted by compatibility requirements with ImageCore [a09fc81d] to versions: 0.6.0-0.7.3 or uninstalled, leaving only versions: 0.6.0
│ └─ImageCore [a09fc81d] log:
│ ├─possible versions are: 0.7.0-0.10.1 or uninstalled
│ ├─restricted by compatibility requirements with Reexport [189a3867] to versions: [0.7.0-0.8.0, 0.8.20-0.10.1] or uninstalled
│ │ └─Reexport [189a3867] log:
│ │ ├─possible versions are: 0.2.0-1.2.2 or uninstalled
│ │ └─restricted by compatibility requirements with Metal [dde4c033] to versions: 1.0.0-1.2.2
│ │ └─Metal [dde4c033] log:
│ │ ├─possible versions are: 0.0.1-0.5.1 or uninstalled
│ │ └─restricted to versions * by an explicit requirement, leaving only versions: 0.0.1-0.5.1
│ ├─restricted by compatibility requirements with ImageMagick [6218d12a] to versions: 0.7.0-0.9.4, leaving only versions: [0.7.0-0.8.0, 0.8.20-0.9.4]
│ │ └─ImageMagick [6218d12a] log:
│ │ ├─possible versions are: 0.7.0-1.3.0 or uninstalled
│ │ └─restricted by compatibility requirements with Luxor [ae8d54c2] to versions: 0.7.0-0.7.9
│ │ └─Luxor [ae8d54c2] log: see above
│ ├─restricted by compatibility requirements with FFTW [7a1cc6ca] to versions: 0.8.0-0.10.1 or uninstalled, leaving only versions: [0.8.0, 0.8.20-0.9.4]
│ │ └─FFTW [7a1cc6ca] log:
│ │ ├─possible versions are: 0.1.0-1.7.2 or uninstalled
│ │ └─restricted by compatibility requirements with Reexport [189a3867] to versions: [1.1.1, 1.3.0-1.7.2] or uninstalled
│ │ └─Reexport [189a3867] log: see above
│ └─restricted by compatibility requirements with QuartzImageIO [dca85d43] to versions: 0.7.0-0.8.22, leaving only versions: [0.8.0, 0.8.20-0.8.22]
│ └─QuartzImageIO [dca85d43] log: see above
└─restricted by compatibility requirements with Colors [5ae59095] to versions: 0.10.0-0.11.4 — no versions left
└─Colors [5ae59095] log:
├─possible versions are: 0.9.0-0.12.10 or uninstalled
├─restricted to versions * by an explicit requirement, leaving only versions: 0.9.0-0.12.10
└─restricted by compatibility requirements with Reexport [189a3867] to versions: 0.12.6-0.12.10 or uninstalled, leaving only versions: 0.12.6-0.12.10
└─Reexport [189a3867] log: see above
(@v1.10) pkg>
Maybe something with ColorTypes
from genomicmaps.jl.
kdyrhage
commented on June 7, 2024
Seems to be related to QuartzImageIO. It is not a dependency of GenomicMaps so the problem seems to be on your side, but I'll see if I can loosen some version restrictions to fix it. In the meantime you should be able to get around the problem by installing the package in a fresh environment.
from genomicmaps.jl.
kdyrhage
commented on June 7, 2024
Try v0.1.4 when it has been registered. It should also fix your original problem.
from genomicmaps.jl.
vdejager
commented on June 7, 2024
Thanks for this awesome package, it worked. However, I had to change something related to the GenomicAnnotations package:
GenomicMaps documentation in function 'addcogs':
for gene in @genes(chr, :feature == "CDS")
The documentation in https://github.com/BioJulia/GenomicAnnotations.jl suggests the following, but did not work:
for gene in @genes(chr, feature(gene) == "CDS") # Returns all coding regions
what actually worked:
for gene in @genes(chr, CDS)
Reading from https://github.com/BioJulia/GenomicAnnotations.jl/blob/master/src/macro.jl the second option should also work, but I could only use the features defined in the gene_special_cases function
from genomicmaps.jl.
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from genomicmaps.jl.