DESeq 2 failes to load
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Entering edit mode
Ruggero ▴ 10
@60ecaaf7
Last seen 4 weeks ago
Italy

Does anybody know what is wrong here? I try to load the package DESeq2 from bioconductor and I get this error. I installed it using BiocManager::install("DESeq2").

BiocManager::install("DESeq2")
library("DESeq2")
Loading required package: S4Vectors
Loading required package: stats4
Loading required package: BiocGenerics

Attaching package: ‘BiocGenerics’

The following objects are masked from ‘package:stats’:

    IQR, mad, sd, var, xtabs

The following objects are masked from ‘package:base’:

    anyDuplicated, append, as.data.frame, basename, cbind, colnames, dirname, do.call,
    duplicated, eval, evalq, Filter, Find, get, grep, grepl, intersect, is.unsorted, lapply, Map,
    mapply, match, mget, order, paste, pmax, pmax.int, pmin, pmin.int, Position, rank, rbind,
    Reduce, rownames, sapply, setdiff, sort, table, tapply, union, unique, unsplit, which.max,
    which.min


Attaching package: ‘S4Vectors’

The following objects are masked from ‘package:base’:

    expand.grid, I, unname

Loading required package: IRanges
Loading required package: GenomicRanges
Loading required package: GenomeInfoDb
Loading required package: SummarizedExperiment
Loading required package: MatrixGenerics
Loading required package: matrixStats

Attaching package: ‘MatrixGenerics’

The following objects are masked from ‘package:matrixStats’:

    colAlls, colAnyNAs, colAnys, colAvgsPerRowSet, colCollapse, colCounts, colCummaxs,
    colCummins, colCumprods, colCumsums, colDiffs, colIQRDiffs, colIQRs, colLogSumExps,
    colMadDiffs, colMads, colMaxs, colMeans2, colMedians, colMins, colOrderStats, colProds,
    colQuantiles, colRanges, colRanks, colSdDiffs, colSds, colSums2, colTabulates, colVarDiffs,
    colVars, colWeightedMads, colWeightedMeans, colWeightedMedians, colWeightedSds,
    colWeightedVars, rowAlls, rowAnyNAs, rowAnys, rowAvgsPerColSet, rowCollapse, rowCounts,
    rowCummaxs, rowCummins, rowCumprods, rowCumsums, rowDiffs, rowIQRDiffs, rowIQRs,
    rowLogSumExps, rowMadDiffs, rowMads, rowMaxs, rowMeans2, rowMedians, rowMins, rowOrderStats,
    rowProds, rowQuantiles, rowRanges, rowRanks, rowSdDiffs, rowSds, rowSums2, rowTabulates,
    rowVarDiffs, rowVars, rowWeightedMads, rowWeightedMeans, rowWeightedMedians, rowWeightedSds,
    rowWeightedVars

Loading required package: Biobase
Welcome to Bioconductor

    Vignettes contain introductory material; view with 'browseVignettes()'. To cite Bioconductor,
    see 'citation("Biobase")', and for packages 'citation("pkgname")'.


Attaching package: ‘Biobase’

The following object is masked from ‘package:MatrixGenerics’:

    rowMedians

The following objects are masked from ‘package:matrixStats’:

    anyMissing, rowMedians

Error: package or namespace load failed for ‘DESeq2’ in loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]]):
 there is no package called ‘RSQLite’
In addition: Warning messages:
1: R graphics engine version 14 is not supported by this version of RStudio. The Plots tab will be disabled until a newer version of RStudio is installed. 
2: package ‘S4Vectors’ was built under R version 4.1.3 

sessionInfo( )
R version 4.1.2 (2021-11-01)
Platform: x86_64-apple-darwin17.0 (64-bit)
Running under: macOS Mojave 10.14.6

Matrix products: default
BLAS:   /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib
LAPACK: /Library/Frameworks/R.framework/Versions/4.1/Resources/lib/libRlapack.dylib

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

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

other attached packages:
[1] SummarizedExperiment_1.24.0 Biobase_2.54.0              MatrixGenerics_1.6.0       
[4] matrixStats_0.62.0          GenomicRanges_1.46.1        GenomeInfoDb_1.30.1        
[7] IRanges_2.28.0              S4Vectors_0.32.4            BiocGenerics_0.40.0        

loaded via a namespace (and not attached):
 [1] Rcpp_1.0.9             XVector_0.34.0         zlibbioc_1.40.0        BiocParallel_1.28.3   
 [5] xtable_1.8-4           lattice_0.20-45        R6_2.5.1               httr_1.4.4            
 [9] tools_4.1.2            parallel_4.1.2         grid_4.1.2             xfun_0.32             
[13] tinytex_0.41           DBI_1.1.3              yaml_2.3.5             Matrix_1.4-1          
[17] GenomeInfoDbData_1.2.7 BiocManager_1.30.18    bitops_1.0-7           RCurl_1.98-1.8        
[21] DelayedArray_0.20.0    compiler_4.1.2         XML_3.99-0.10
Bioconductor DESeq2 • 163 views
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1
Entering edit mode
Ruggero ▴ 10
@60ecaaf7
Last seen 4 weeks ago
Italy

This solved the error, in case someone else is having compilation errors from installing RSQllite:

install.packages('RSQLite', repos='http://cran.us.r-project.org', type="binary")

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