AntunesLab / crossdome

A tool for predicting cross-reactivity risk using immunopeptidomics databases
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Issue during installation #1

Open mauriciomr1985 opened 7 months ago

mauriciomr1985 commented 7 months ago

Hi,

I'm having an issue during crossdome installation:

Input devtools::install_github("antuneslab/crossdome", build_vignettes = TRUE)

Output Downloading GitHub repo antuneslab/crossdome@HEAD Skipping 9 packages ahead of CRAN: BiocGenerics, zlibbioc, GenomeInfoDbData, GenomeInfoDb, XVector, IRanges, S4Vectors, MatrixGenerics, Biostrings ── R CMD build ─────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────── ✔ checking for file ‘/tmp/RtmpL0nx6O/remotes460221a67fe4/AntunesLab-crossdome-05b8da5/DESCRIPTION’ ... ─ preparing ‘crossdome’: ✔ checking DESCRIPTION meta-information ... ─ installing the package to build vignettes E creating vignettes (1m 3.4s) --- re-building ‘Example_01.Rmd’ using rmarkdown

Quitting from lines at lines 68-72 [substitution] (Example_01.Rmd) Error: processing vignette 'Example_01.Rmd' failed with diagnostics: only ACDEFGHIKLMNPQRSTVWY are accepted for AA --- failed re-building ‘Example_01.Rmd’

--- re-building ‘Example_02.Rmd’ using rmarkdown

Quitting from lines at lines 48-52 [subs_crystal] (Example_02.Rmd) Error: processing vignette 'Example_02.Rmd' failed with diagnostics: only ACDEFGHIKLMNPQRSTVWY are accepted for AA --- failed re-building ‘Example_02.Rmd’

SUMMARY: processing the following files failed: ‘Example_01.Rmd’ ‘Example_02.Rmd’

Error: Vignette re-building failed. Execution halted Error: Failed to install 'crossdome' from GitHub: ! System command 'R' `failed``


I thought the problem was related to setting build_vignettes = TRUE. If I set it to "FALSE", all works fine, until I need to use cross_substitution_matrix:

Input database <- cross_background(off_targets = 'ESDPIVAQY', allele = "HLA-A*01:01") result <- cross_compose(query = 'EVDPIGHLY', background = database)

result <- cross_substitution_matrix(result) cross_substitution_plot(object = result)'

Output

result <- cross_substitution_matrix(result) Error in universalmotif::create_motif(peptides, type = "PPM") : only ACDEFGHIKLMNPQRSTVWY are accepted for AA

martielafreitas commented 3 months ago

Hello,

Looks like we're having some issues with the libraries and your R version. Would please install the library currently in the following link: https://www.dropbox.com/scl/fi/q9sh1se9abdkxr79qii7l/library.tar.gz?rlkey=ogb87dpc5ke24136ii0rer6vs&st=q82ffj8o&dl=0

You can import the full file through Tools → Install Packages. Select Package Archive File (.tar.gz) in the "Install from slot" OR "Install package(s) from local zip files". Find the corresponding file on the local machine, and click Open, then click Install.

Please let me know if this solution works for you.

Thanks for using CrossDome.