Install scripts/dockerfile need to install specific versions of dependencies (R is explicitly causing trouble)

[blex-max]

all packages/dependecies installed by install scripts and the dockerfile, but especially R packages, need to be versioned. @fa8sanger if you provide me a list of versions for packages/dependencies I can make these changes

[fa8sanger]

Thank you, Alex.

I am currently using: R 3.6.1

The required packages are the following: library("Biostrings") library("data.table") library("deepSNV") library("epitools") library("GenomicRanges") library("grid") library("gridExtra") library("MASS") library("Rsamtools") library("seqinr") library("stringr") library("vcfR") library("VGAM")

These have other dependencies. Below is the full list of libraries loaded after loading the above packages, including the version numbers.

It should work with most of other versions of the packages. I mean, just install the packages without worrying too much on the version numbers.

attached base packages:
 [1] grid      splines   stats4    parallel  stats     graphics  grDevices
 [8] utils     datasets  methods   base     

other attached packages:
 [1] vcfR_1.14.0                 stringr_1.4.0              
 [3] seqinr_4.2-23               MASS_7.3-51.5              
 [5] gridExtra_2.3               epitools_0.5-10.1          
 [7] deepSNV_1.32.0              VariantAnnotation_1.32.0   
 [9] Rsamtools_2.2.3             VGAM_1.1-5                 
[11] SummarizedExperiment_1.16.1 DelayedArray_0.12.3        
[13] BiocParallel_1.20.1         matrixStats_0.63.0         
[15] Biobase_2.46.0              GenomicRanges_1.38.0       
[17] GenomeInfoDb_1.22.1         Rhtslib_1.18.1             
[19] data.table_1.14.8           Biostrings_2.54.0          
[21] XVector_0.26.0              IRanges_2.20.2             
[23] S4Vectors_0.24.4            BiocGenerics_0.32.0        

loaded via a namespace (and not attached):
 [1] httr_1.4.5               viridisLite_0.4.1        bit64_4.0.5             
 [4] assertthat_0.2.1         askpass_1.1              BiocFileCache_1.10.2    
 [7] blob_1.2.3               BSgenome_1.54.0          GenomeInfoDbData_1.2.2  
[10] progress_1.2.2           pillar_1.8.1             RSQLite_2.3.0           
[13] lattice_0.20-38          glue_1.6.2               digest_0.6.23           
[16] Matrix_1.5-3             XML_3.99-0.3             pkgconfig_2.0.3         
[19] biomaRt_2.42.1           zlibbioc_1.32.0          purrr_0.3.4             
[22] tibble_3.1.7             openssl_1.4.1            mgcv_1.8-31             
[25] generics_0.1.3           ellipsis_0.3.2           cachem_1.0.7            
[28] GenomicFeatures_1.38.2   cli_3.6.0                magrittr_2.0.3          
[31] crayon_1.5.2             memoise_2.0.1            fansi_0.4.0             
[34] nlme_3.1-143             vegan_2.6-4              tools_3.6.1             
[37] prettyunits_1.0.2        hms_1.1.2                lifecycle_1.0.0         
[40] cluster_2.1.0            AnnotationDbi_1.48.0     ade4_1.7-22             
[43] compiler_3.6.1           rlang_1.0.3              RCurl_1.98-1.10         
[46] rappdirs_0.3.3           bitops_1.0-7             gtable_0.3.1            
[49] DBI_1.1.3                curl_4.3                 R6_2.4.1                
[52] GenomicAlignments_1.22.1 pinfsc50_1.2.0           dplyr_1.0.7             
[55] rtracklayer_1.46.0       fastmap_1.1.1            bit_4.0.5               
[58] utf8_1.1.4               permute_0.9-7            ape_5.7-1               
[61] stringi_1.7.12           Rcpp_1.0.10              vctrs_0.3.8             
[64] dbplyr_2.1.1             tidyselect_1.1.1        

[blex-max]

having looked into this further, I note that some of the packages that you have listed are only installed by manualInstall.R, which is not used by the dockerfile, or not at all (e.g. Biostrings) - is this intentional? Biostrings, again for example, is loaded by some of the R scripts, but it is never installed. Perhaps it is a requisite of some of the other packages?

[fa8sanger]

I don't know about manualInstall.R, I got the list of packages from the R scripts in the repository. Meaning that all of those are required. Curiously, only the last script (snv_merge) gave you an error, even though it loads only "deepSNV"

[blex-max]

whoever coded the dockerfile (Raul?) should probably weigh in on this then. Nevertheless I'll make initial updates now.

[blex-max]

I need to know what version of bioconductor is to be used also, it's not listed in your packages

[fa8sanger]

Bioconductor version 3.10 (BiocManager 1.30.10)