Risa package missing from Bioconductor 3.19
1
0
Entering edit mode
rkjulian • 0
@7fe7b28c
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

Results in:

Page Not Found

The page you were looking for was not found.

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

sessionInfo()

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

locale:
[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
ADD COMMENT
0
Entering edit mode
@james-w-macdonald-5106
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.

Login before adding your answer.

Traffic: 1323 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6