DROP_1.3.3.yaml package update required?

[chrisodhams]

Hi,

I've installed DROP v1.3.3 as per: mamba env create -f DROP_1.3.3.yaml taken from: https://www.cmm.in.tum.de/public/paper/drop_analysis/DROP_1.3.3.yaml

When running the demo, OUTRIDER throws an error in the pvalsOutrider.R script at the line ods <- computePvalues(ods, subsets=subsets_final).

I believe this is because the OUTRIDER version specified in DROP_1.3.3.yaml uses v1.16.0 (bioconductor-outrider=1.16.0=r42hc247a5b_0) and at this version I don't believe the subsets argument has been implemented yet (thus the error unused argument subsets get's thrown).

> ods <- computePvalues(ods, subsets=subsets_final) Error in .local(object, ...) : unused argument (subsets = NULL)

Note - no error thrown when removing subsets: ods <- computePvalues(ods)

Was this change was implemented in 1.16.1?

CHANGES IN VERSION 1.16.1

o Add option to restrict FDR correction to sets of genes of interest
o Add opttion to retrieve results based on those FDR values on subsets of 
  genes

Unfortunately, if I point to the latest version of OUTRIDER (bioconductor-outrider-1.18.1-r43hf17093f_0.tar.bz2) - it causes many package conflicts with the existing packages in the YAML. Note that 1.18.1 is the only later version of OUTRIDER available on bioconda.

Is there anyway this can be circumvented or the YAML updated? The FRASER version may also need to be looked into if new features in drop are implemented but not reflected in the package version.

Cheers,

Chris

> sessionInfo()
R version 4.2.2 (2022-10-31)
Platform: x86_64-conda-linux-gnu (64-bit)
Running under: Debian GNU/Linux 11 (bullseye)

Matrix products: default
BLAS/LAPACK: /opt/conda/lib/libopenblasp-r0.3.21.so

locale:
 [1] LC_CTYPE=C.UTF-8       LC_NUMERIC=C           LC_TIME=C.UTF-8       
 [4] LC_COLLATE=C.UTF-8     LC_MONETARY=C.UTF-8    LC_MESSAGES=C.UTF-8   
 [7] LC_PAPER=C.UTF-8       LC_NAME=C              LC_ADDRESS=C          
[10] LC_TELEPHONE=C         LC_MEASUREMENT=C.UTF-8 LC_IDENTIFICATION=C   

attached base packages:
[1] tools     stats4    stats     graphics  grDevices utils     datasets 
[8] methods   base     

other attached packages:
 [1] yaml_2.3.7                  magrittr_2.0.3             
 [3] dplyr_1.1.2                 ggplot2_3.4.2              
 [5] OUTRIDER_1.16.0             data.table_1.14.8          
 [7] SummarizedExperiment_1.28.0 MatrixGenerics_1.10.0      
 [9] matrixStats_0.63.0          GenomicFeatures_1.50.2     
[11] AnnotationDbi_1.60.0        Biobase_2.58.0             
[13] GenomicRanges_1.50.0        GenomeInfoDb_1.34.9        
[15] IRanges_2.32.0              S4Vectors_0.36.0           
[17] BiocGenerics_0.44.0         BiocParallel_1.32.5        

loaded via a namespace (and not attached):
  [1] bitops_1.0-7             bit64_4.0.5              filelock_1.0.2          
  [4] webshot_0.5.4            RColorBrewer_1.1-3       progress_1.2.2          
  [7] PRROC_1.3.1              httr_1.4.5               backports_1.4.1         
 [10] utf8_1.2.3               R6_2.5.1                 lazyeval_0.2.2          
 [13] DBI_1.1.3                colorspace_2.1-0         withr_2.5.0             
 [16] tidyselect_1.2.0         gridExtra_2.3            prettyunits_1.1.1       
 [19] DESeq2_1.38.0            bit_4.0.5                curl_4.3.3              
 [22] compiler_4.2.2           cli_3.6.1                TSP_1.2-4               
 [25] xml2_1.3.3               DelayedArray_0.24.0      plotly_4.10.1           
 [28] rtracklayer_1.58.0       scales_1.2.1             checkmate_2.1.0         
 [31] genefilter_1.80.0        rappdirs_0.3.3           stringr_1.5.0           
 [34] digest_0.6.31            Rsamtools_2.14.0         ca_0.71.1               
 [37] XVector_0.38.0           pkgconfig_2.0.3          htmltools_0.5.5         
 [40] dbplyr_2.3.2             fastmap_1.1.1            htmlwidgets_1.6.2       
 [43] rlang_1.1.0              RSQLite_2.3.1            BBmisc_1.13             
 [46] BiocIO_1.8.0             generics_0.1.3           jsonlite_1.8.4          
 [49] dendextend_1.17.1        RCurl_1.98-1.10          GenomeInfoDbData_1.2.9  
 [52] Matrix_1.5-4             Rcpp_1.0.10              munsell_0.5.0           
 [55] fansi_1.0.4              viridis_0.6.2            lifecycle_1.0.3         
 [58] stringi_1.7.12           zlibbioc_1.44.0          plyr_1.8.8              
 [61] BiocFileCache_2.6.0      grid_4.2.2               blob_1.2.4              
 [64] parallel_4.2.2           crayon_1.5.2             lattice_0.21-8          
 [67] Biostrings_2.66.0        splines_4.2.2            annotate_1.76.0         
 [70] hms_1.1.3                KEGGREST_1.38.0          locfit_1.5-9.7          
 [73] pillar_1.9.0             rjson_0.2.21             reshape2_1.4.4          
 [76] geneplotter_1.76.0       codetools_0.2-19         biomaRt_2.54.0          
 [79] XML_3.99-0.14            glue_1.6.2               pcaMethods_1.90.0       
 [82] foreach_1.5.2            png_0.1-8                vctrs_0.6.2             
 [85] tidyr_1.3.0              purrr_1.0.1              gtable_0.3.3            
 [88] heatmaply_1.4.2          assertthat_0.2.1         cachem_1.0.7            
 [91] xtable_1.8-4             restfulr_0.0.15          survival_3.5-5          
 [94] viridisLite_0.4.1        pheatmap_1.0.12          seriation_1.4.2         
 [97] tibble_3.2.1             iterators_1.0.14         registry_0.5-1          
[100] GenomicAlignments_1.34.0 memoise_2.0.1 

[ischeller]

Hi @chrisodhams , thanks for pointing this out and the provided information. I will have a look at what is going on and try to provide an updated yaml file to fix this.

[chrisodhams]

Thanks @ischeller , Just an additional note - that the drop installation also requires unzip i.e.: unzip=6.0=h4e0d66e_3 as it breaks if this is not included in the YAML. Cheers,

[chrisodhams]

Hi @ischeller , Wondering if you have any updates on this? Best,

[vyepez88]

Hi @chrisodhams , sorry, we were on holidays. We've now resumed to check this, but it's not straightforward as it seems some packages have conflicts. We'll keep you updated

[neverov-am]

Hi @chrisodhams ,

we uploaded an updated DROP_1.3.3.yaml to our public server. Could you kindly give it a try and let us know, if it fixes the issue?

Thanks again for pointing this out

[chrisodhams]

Hi @neverov-am @vyepez88 - it seems that the drop bioconda package is not in the yaml. It was there before (drop=1.3.3=pyhdfd78af_0). Cheers,

[neverov-am]

Hi @chrisodhams ,

I apologise for this bug, there was an issue with exporting the environment. I have updated the DROP_1.3.3.yaml, could you try it?

[vyepez88]

Hi @chrisodhams , we have updated now DROP including its dependencies. Can you please try with 1.4.0?