Why I can not install rTANDEM?
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0
Entering edit mode
Gilad • 0
@Gilad-24384
Last seen 9 months ago

Hi, I can not install rTANDEM and it is needed in the Mass spectrometry and proteomics data analysis (http://bioconductor.org/packages/devel/workflows/html/proteomics.html).

I run the command:

if (!requireNamespace("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install("rTANDEM")

"Warning message: package ‘rTANDEM’ is not available for this version of R"

library("rTANDEM")

Error in library("rTANDEM") : there is no package called ‘rTANDEM’

Any help or at least clarification would be appreciated. Thanks, Gilad

sessionInfo( )

R version 4.0.3 (2020-10-10)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 10 x64 (build 18363)

Matrix products: default

locale:
[1] LC_COLLATE=Hebrew_Israel.1255  LC_CTYPE=Hebrew_Israel.1255   
[3] LC_MONETARY=Hebrew_Israel.1255 LC_NUMERIC=C                  
[5] LC_TIME=Hebrew_Israel.1255    
system code page: 1252

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

loaded via a namespace (and not attached):
 [1] Rcpp_1.0.5                  AnnotationDbi_1.52.0       
 [3] XVector_0.30.0              GenomicRanges_1.42.0       
 [5] BiocGenerics_0.36.0         zlibbioc_1.36.0            
 [7] MASS_7.3-53                 IRanges_2.24.0             
 [9] bit_4.0.4                   BiocParallel_1.24.0        
[11] xtable_1.8-4                lattice_0.20-41            
[13] R6_2.5.0                    rlang_0.4.8                
[15] blob_1.2.1                  httr_1.4.2                 
[17] GenomeInfoDb_1.26.2         tools_4.0.3                
[19] SummarizedExperiment_1.20.0 parallel_4.0.3             
[21] grid_4.0.3                  Biobase_2.50.0             
[23] DBI_1.1.0                   matrixStats_0.57.0         
[25] digest_0.6.27               bit64_4.0.5                
[27] Matrix_1.2-18               GenomeInfoDbData_1.2.4     
[29] BiocManager_1.30.10         vctrs_0.3.4                
[31] S4Vectors_0.28.0            bitops_1.0-6               
[33] RCurl_1.98-1.2              memoise_1.1.0              
[35] RSQLite_2.2.1               DelayedArray_0.16.0        
[37] glmpca_0.2.0                compiler_4.0.3             
[39] MatrixGenerics_1.2.0        XML_3.99-0.5               
[41] stats4_4.0.3
MassSpectrometry Proteomics mzR • 240 views
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@laurent-gatto-5645
Last seen 4 days ago
Belgium

As the message says, rTANDEM isn't available. Indeed, it currently fails building and is marked as deprecated (which means it will be removed from Bioconductor at the next release). In other words, you won't be able to run X!Tandem from within R.

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And I'll need to update the workflow accordingly.

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Thank you for your time and clear answer.

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