'ZygosityPredictor's dependency 'datastructures' missing in R 4.3.0
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Marc • 0
@2f4b9c03
Last seen 13 months ago
Germany

When trying to install ZygosityPredictor in R3.4.0 we get the error below.

The datastructures package was removed from CRAN, stating:

Package 'datastructures' was removed from the CRAN repository. Formerly available versions can be obtained from the archive. Archived on 2023-05-05 as issues were not corrected in time. A summary of the most recent check results can be obtained from the check results archive.

I have filed an issue on their GitHub page.

The package can be manually installed from GitHub via devtools until the dependency issue is resolved in ZygosityPredictor:

BiocManager::install("ZygosityPredictor")
ERROR: dependency 'datastructures' is not available for package 'ZygosityPredictor'

devtools::install_github("dirmeier/datastructures", ref="tags/v0.2.9")
BiocManager::install("ZygosityPredictor")

sessionInfo()
R version 4.3.0 (2023-04-21)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: CentOS Linux 7 (Core)

Matrix products: default
BLAS/LAPACK: /usr/lib64/libopenblas-r0.3.3.so;  LAPACK version 3.8.0

locale:
 [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C              
 [3] LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8    
 [5] LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8   
 [7] LC_PAPER=en_US.UTF-8       LC_NAME=C                 
 [9] LC_ADDRESS=C               LC_TELEPHONE=C            
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C       

time zone: Europe/Berlin
tzcode source: system (glibc)

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
[1] ZygosityPredictor_1.0.0

loaded via a namespace (and not attached):
 [1] KEGGREST_1.40.0             SummarizedExperiment_1.30.1
 [3] rjson_0.2.21                Biobase_2.60.0             
 [5] lattice_0.21-8              vctrs_0.6.2                
 [7] tools_4.3.0                 bitops_1.0-7               
 [9] generics_0.1.3              curl_5.0.0                 
[11] stats4_4.3.0                parallel_4.3.0             
[13] tibble_3.2.1                fansi_1.0.4                
[15] AnnotationDbi_1.62.1        RSQLite_2.3.1              
[17] blob_1.2.4                  pkgconfig_2.0.3            
[19] Matrix_1.5-4                BSgenome_1.68.0            
[21] dbplyr_2.3.2                S4Vectors_0.38.1           
[23] lifecycle_1.0.3             GenomeInfoDbData_1.2.10    
[25] compiler_4.3.0              stringr_1.5.0              
[27] Rsamtools_2.16.0            Biostrings_2.68.0          
[29] progress_1.2.2              codetools_0.2-19           
[31] GenomeInfoDb_1.36.0         yaml_2.3.7                 
[33] RCurl_1.98-1.12             pillar_1.9.0               
[35] crayon_1.5.2                BiocParallel_1.34.1        
[37] DelayedArray_0.26.2         cachem_1.0.8               
[39] tidyselect_1.2.0            digest_0.6.31              
[41] stringi_1.7.12              purrr_1.0.1                
[43] restfulr_0.0.15             dplyr_1.1.2                
[45] VariantAnnotation_1.46.0    biomaRt_2.56.0             
[47] fastmap_1.1.1               grid_4.3.0                 
[49] cli_3.6.1                   magrittr_2.0.3             
[51] S4Arrays_1.0.4              GenomicFeatures_1.52.0     
[53] XML_3.99-0.14               utf8_1.2.3                 
[55] rappdirs_0.3.3              filelock_1.0.2             
[57] prettyunits_1.1.1           bit64_4.0.5                
[59] XVector_0.40.0              httr_1.4.5                 
[61] matrixStats_0.63.0          bit_4.0.5                  
[63] png_0.1-8                   hms_1.1.3                  
[65] memoise_2.0.1               BiocIO_1.10.0              
[67] GenomicRanges_1.52.0        IRanges_2.34.0             
[69] BiocFileCache_2.8.0         rtracklayer_1.60.0         
[71] datastructures_0.2.9        rlang_1.1.1                
[73] Rcpp_1.0.10                 glue_1.6.2                 
[75] DBI_1.1.3                   xml2_1.3.4                 
[77] BiocGenerics_0.46.0         R6_2.5.1                   
[79] MatrixGenerics_1.12.0       GenomicAlignments_1.36.0   
[81] zlibbioc_1.46.0
ZygosityPredictor • 348 views
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