Risa package missing from Bioconductor 3.19
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rkjulian • 0
Last seen 21 days ago
United States

The Risa package for reading ISA files is listed as active for 3.19 and in development for 3.20, however it appears missing from the repository.

I managed to install it from source from the archive version of 3.18, so the old code works with 3.19 and R 4.4.1

On the download stats page, there is a note:

Download stats for software package Risa Data as of Wed. 26 Jun 2024 Package Risa is not in the current release of Bioconductor. It was last seen in 3.18.

The PDF link: https://www.bioconductor.org/packages/release/bioc/manuals/Risa/man/Risa.pdf

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Risa should be included in Bioconductor and be able to be installed


R version 4.4.1 (2024-06-14)
Platform: aarch64-apple-darwin20
Running under: macOS Sonoma 14.5

Matrix products: default
BLAS:   /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib 
LAPACK: /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/lib/libRlapack.dylib;  LAPACK version 3.12.0

[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8

time zone: America/Indiana/Indianapolis
tzcode source: internal

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

other attached packages:
 [1] knitrProgressBar_1.1.0 fpCompare_0.2.4        pander_0.6.5           xcms_4.2.2            
 [5] Spectra_1.14.1         BiocParallel_1.38.0    MSnbase_2.30.1         ProtGenerics_1.36.0   
 [9] S4Vectors_0.42.0       mzR_2.38.0             Rcpp_1.0.12            Biobase_2.64.0        
[13] BiocGenerics_0.50.0    lubridate_1.9.3        forcats_1.0.0          stringr_1.5.1         
[17] dplyr_1.1.4            purrr_1.0.2            readr_2.1.5            tidyr_1.3.1           
[21] tibble_3.2.1           ggplot2_3.5.1          tidyverse_2.0.0       

loaded via a namespace (and not attached):
  [1] DBI_1.2.3                   rlang_1.1.4                 magrittr_2.0.3             
  [4] clue_0.3-65                 MassSpecWavelet_1.70.0      matrixStats_1.3.0          
  [7] compiler_4.4.1              vctrs_0.6.5                 reshape2_1.4.4             
 [10] pkgconfig_2.0.3             MetaboCoreUtils_1.12.0      crayon_1.5.3               
 [13] fastmap_1.2.0               XVector_0.44.0              labeling_0.4.3             
 [16] utf8_1.2.4                  rmarkdown_2.27              tzdb_0.4.0                 
 [19] UCSC.utils_1.0.0            preprocessCore_1.66.0       bit_4.0.5                  
 [22] xfun_0.45                   MultiAssayExperiment_1.30.2 zlibbioc_1.50.0            
 [25] GenomeInfoDb_1.40.1         jsonlite_1.8.8              progress_1.2.3             
 [28] DelayedArray_0.30.1         prettyunits_1.2.0           parallel_4.4.1             
 [31] cluster_2.1.6               R6_2.5.1                    RColorBrewer_1.1-3         
 [34] stringi_1.8.4               limma_3.60.3                GenomicRanges_1.56.1       
 [37] iterators_1.0.14            bookdown_0.39               SummarizedExperiment_1.34.0
 [40] knitr_1.47                  IRanges_2.38.0              Matrix_1.7-0               
 [43] igraph_2.0.3                timechange_0.3.0            tidyselect_1.2.1           
 [46] rstudioapi_0.16.0           abind_1.4-5                 yaml_2.3.8                 
 [49] doParallel_1.0.17           codetools_0.2-20            affy_1.82.0                
 [52] lattice_0.22-6              plyr_1.8.9                  withr_3.0.0                
 [55] evaluate_0.24.0             pillar_1.9.0                affyio_1.74.0              
 [58] BiocManager_1.30.23         MatrixGenerics_1.16.0       foreach_1.5.2              
 [61] MALDIquant_1.22.2           ncdf4_1.22                  generics_0.1.3             
 [64] vroom_1.6.5                 hms_1.1.3                   munsell_0.5.1              
 [67] scales_1.3.0                MsExperiment_1.6.0          glue_1.7.0                 
 [70] MsFeatures_1.12.0           lazyeval_0.2.2              tools_4.4.1                
 [73] mzID_1.42.0                 QFeatures_1.14.1            vsn_3.72.0                 
 [76] fs_1.6.4                    XML_3.99-0.17               grid_4.4.1                 
 [79] impute_1.78.0               MsCoreUtils_1.16.0          colorspace_2.1-0           
 [82] GenomeInfoDbData_1.2.12     PSMatch_1.8.0               cli_3.6.3                  
 [85] fansi_1.0.6                 viridisLite_0.4.2           S4Arrays_1.4.1             
 [88] AnnotationFilter_1.28.0     pcaMethods_1.96.0           gtable_0.3.5               
 [91] R.methodsS3_1.8.2           digest_0.6.36               SparseArray_1.4.8          
 [94] farver_2.1.2                R.oo_1.26.0                 htmltools_0.5.8.1          
 [97] lifecycle_1.0.4             httr_1.4.7                  statmod_1.5.0              
[100] bit64_4.0.5                 MASS_7.3-61
3.19 Risa • 131 views
Entering edit mode
Last seen 2 hours ago
United States

It should be, but is not being built due to a failure to pass check, due apparently to errors in one of the help files. It looks like Risa needs to import some functions from BiocParallel. Ideally the maintainers of Risa are following any tags for their package and will respond/fix the issue, but otherwise you could ping them directly.

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