Code:
library(devtools)
library(crisprScore)
data(scoringMethodsInfo)
print(scoringMethodsInfo)
spacer <- "ATCGATGCTGATGCTAGATA" #20bp
pam <- "AGG" #3bp
input <- paste0(spacer, pam)
results <- getDeepHFScores(input)
Error:
> results <- getDeepHFScores(input)
snapshotDate(): 2022-10-31
see ?crisprScoreData and browseVignettes('crisprScoreData') for documentation
loading from cache
+ '/Users/arjanhada/Library/Caches/org.R-project.R/R/basilisk/1.10.2/0/bin/conda' 'create' '--yes' '--prefix' '/Users/arjanhada/Library/Caches/org.R-project.R/R/basilisk/1.10.2/crisprScore/1.3.1/deephf_basilisk' 'python=3.6' '--quiet' '-c' 'conda-forge' '-c' 'bioconda'
Collecting package metadata (current_repodata.json): ...working... done
Solving environment: ...working... failed with repodata from current_repodata.json, will retry with next repodata source.
Collecting package metadata (repodata.json): ...working... done
Solving environment: ...working... failed
PackagesNotFoundError: The following packages are not available from current channels:
- python=3.6
Current channels:
- https://conda.anaconda.org/conda-forge/osx-arm64
- https://conda.anaconda.org/conda-forge/noarch
- https://conda.anaconda.org/bioconda/osx-arm64
- https://conda.anaconda.org/bioconda/noarch
- https://repo.anaconda.com/pkgs/main/osx-arm64
- https://repo.anaconda.com/pkgs/main/noarch
- https://repo.anaconda.com/pkgs/r/osx-arm64
- https://repo.anaconda.com/pkgs/r/noarch
To search for alternate channels that may provide the conda package you're
looking for, navigate to
https://anaconda.org
and use the search bar at the top of the page.
Error: Error creating conda environment '/Users/arjanhada/Library/Caches/org.R-project.R/R/basilisk/1.10.2/crisprScore/1.3.1/deephf_basilisk' [exit code 1]
In addition: Warning message:
In for (Cl in classes) if (is(object, Cl)) return(object) :
closing unused connection 3 (<-localhost:11214)
>
> sessionInfo()
R version 4.2.3 (2023-03-15)
Platform: aarch64-apple-darwin20 (64-bit)
Running under: macOS Ventura 13.2.1
Matrix products: default
LAPACK: /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/lib/libRlapack.dylib
locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
attached base packages:
[1] stats4 stats graphics grDevices utils datasets methods base
other attached packages:
[1] reticulate_1.28 crisprScore_1.3.1 crisprScoreData_1.3.0 ExperimentHub_2.6.0
[5] AnnotationHub_3.6.0 BiocFileCache_2.6.1 dbplyr_2.3.2 devtools_2.4.5
[9] usethis_2.1.6 crisprDesign_1.0.0 crisprBase_1.2.0 BSgenome_1.66.3
[13] rtracklayer_1.58.0 Biostrings_2.66.0 XVector_0.38.0 GenomicRanges_1.50.2
[17] GenomeInfoDb_1.34.9 IRanges_2.32.0 S4Vectors_0.36.2 BiocGenerics_0.44.0
loaded via a namespace (and not attached):
[1] rjson_0.2.21 ellipsis_0.3.2 Rbowtie_1.38.0
[4] fs_1.6.1 rstudioapi_0.14 remotes_2.4.2
[7] bit64_4.0.5 interactiveDisplayBase_1.36.0 AnnotationDbi_1.60.2
[10] fansi_1.0.4 xml2_1.3.3 codetools_0.2-19
[13] cachem_1.0.7 pkgload_1.3.2 jsonlite_1.8.4
[16] Rsamtools_2.14.0 png_0.1-8 shiny_1.7.4
[19] BiocManager_1.30.20 readr_2.1.4 compiler_4.2.3
[22] httr_1.4.5 basilisk_1.10.2 Matrix_1.5-3
[25] fastmap_1.1.1 cli_3.6.1 later_1.3.0
[28] htmltools_0.5.5 prettyunits_1.1.1 tools_4.2.3
[31] glue_1.6.2 GenomeInfoDbData_1.2.9 crisprBowtie_1.2.0
[34] dplyr_1.1.1 rappdirs_0.3.3 Rcpp_1.0.10
[37] Biobase_2.58.0 vctrs_0.6.1 stringr_1.5.0
[40] ps_1.7.3 mime_0.12 miniUI_0.1.1.1
[43] lifecycle_1.0.3 restfulr_0.0.15 XML_3.99-0.14
[46] zlibbioc_1.44.0 basilisk.utils_1.10.0 VariantAnnotation_1.44.1
[49] hms_1.1.3 promises_1.2.0.1 MatrixGenerics_1.10.0
[52] parallel_4.2.3 SummarizedExperiment_1.28.0 yaml_2.3.7
[55] curl_5.0.0 memoise_2.0.1 biomaRt_2.54.1
[58] stringi_1.7.12 RSQLite_2.3.0 BiocVersion_3.16.0
[61] BiocIO_1.8.0 randomForest_4.7-1.1 GenomicFeatures_1.50.4
[64] filelock_1.0.2 pkgbuild_1.4.0 BiocParallel_1.32.6
[67] rlang_1.1.0 pkgconfig_2.0.3 matrixStats_0.63.0
[70] bitops_1.0-7 lattice_0.20-45 purrr_1.0.1
[73] GenomicAlignments_1.34.1 htmlwidgets_1.6.2 bit_4.0.5
[76] tidyselect_1.2.0 processx_3.8.0 magrittr_2.0.3
[79] R6_2.5.1 generics_0.1.3 profvis_0.3.7
[82] DelayedArray_0.24.0 DBI_1.1.3 withr_2.5.0
[85] pillar_1.9.0 KEGGREST_1.38.0 RCurl_1.98-1.10
[88] tibble_3.2.1 dir.expiry_1.6.0 crayon_1.5.2
[91] utf8_1.2.3 urlchecker_1.0.1 tzdb_0.3.0
[94] progress_1.2.2 grid_4.2.3 blob_1.2.4
[97] callr_3.7.3 digest_0.6.31 xtable_1.8-4
[100] httpuv_1.6.9