DESeq 2 failes to load
1
0
Entering edit mode
Ruggero ▴ 10
@60ecaaf7
Last seen 19 months 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 • 703 views
ADD COMMENT
1
Entering edit mode
Ruggero ▴ 10
@60ecaaf7
Last seen 19 months 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")

ADD COMMENT

Login before adding your answer.

Traffic: 739 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