Entering edit mode
dfhannum
▴
10
@dfhannum-15823
Last seen 6.6 years ago
I'm having issues trying to install DESeq2onto my computer. I've downloaded other packages with biocLite including edgeR, limma, and Biobase. When trying to download either limma or DESeq2 I get the same error partway through download:
> source("http://bioconductor.org/biocLite.R")
Bioconductor version 3.7 (BiocInstaller 1.30.0), ?biocLite for help
> biocLite('DESeq2')
BioC_mirror: https://bioconductor.org
Using Bioconductor 3.7 (BiocInstaller 1.30.0), R 3.5.0 (2018-04-23).
Installing package(s) ‘DESeq2’
also installing the dependencies ‘DelayedArray’, ‘snow’, ‘AnnotationDbi’, ‘annotate’, ‘SummarizedExperiment’, ‘BiocParallel’, ‘genefilter’, ‘geneplotter’, ‘RcppArmadillo’
trying URL 'https://cran.rstudio.com/bin/windows/contrib/3.5/snow_0.4-2.zip'
Content type 'application/zip' length 109323 bytes (106 KB)
downloaded 106 KB
trying URL 'https://bioconductor.org/packages/3.7/bioc/bin/windows/contrib/3.5/AnnotationDbi_1.42.1.zip'
Content type 'application/zip' length 5255772 bytes (5.0 MB)
downloaded 5.0 MB
trying URL 'https://bioconductor.org/packages/3.7/bioc/bin/windows/contrib/3.5/annotate_1.58.0.zip'
Content type 'application/zip' length 2231143 bytes (2.1 MB)
downloaded 2.1 MB
trying URL 'https://bioconductor.org/packages/3.7/bioc/bin/windows/contrib/3.5/SummarizedExperiment_1.10.1.zip'
Content type 'application/zip' length 2562175 bytes (2.4 MB)
downloaded 2.4 MB
trying URL 'https://bioconductor.org/packages/3.7/bioc/bin/windows/contrib/3.5/BiocParallel_1.14.1.zip'
Content type 'application/zip' length 1604869 bytes (1.5 MB)
downloaded 1.5 MB
trying URL 'https://bioconductor.org/packages/3.7/bioc/bin/windows/contrib/3.5/genefilter_1.62.0.zip'
Content type 'application/zip' length 1549280 bytes (1.5 MB)
downloaded 1.5 MB
trying URL 'https://bioconductor.org/packages/3.7/bioc/bin/windows/contrib/3.5/geneplotter_1.58.0.zip'
Content type 'application/zip' length 1580633 bytes (1.5 MB)
downloaded 1.5 MB
trying URL 'https://cran.rstudio.com/bin/windows/contrib/3.5/RcppArmadillo_0.8.500.0.zip'
Content type 'application/zip' length 2250156 bytes (2.1 MB)
downloaded 2.1 MB
trying URL 'https://bioconductor.org/packages/3.7/bioc/bin/windows/contrib/3.5/DESeq2_1.20.0.zip'
Content type 'application/zip' length 2524898 bytes (2.4 MB)
downloaded 2.4 MB
Error in if (any(diff)) { : missing value where TRUE/FALSE needed
I've looked multiple places online but none of the solutions work for me (I download the newest patched version of R and running it in R instead of R-Studio).
I then tried to use library(DESeq2) knowing it wouldn't work but could potentially help me trouble shoot. Each time it found a missing package I then separately downloaded it with biocLite. I got the same error message when I tried to download 'SummarizedExperiment', so maybe this is the package which is causing the problem.
Here's my sessioninfo():
R version 3.5.0 (2018-04-23) Platform: x86_64-w64-mingw32/x64 (64-bit) Running under: Windows 7 x64 (build 7601) Service Pack 1 Matrix products: default locale: [1] LC_COLLATE=English_United States.1252 LC_CTYPE=English_United States.1252 LC_MONETARY=English_United States.1252 [4] LC_NUMERIC=C LC_TIME=English_United States.1252 attached base packages: [1] stats4 parallel stats graphics grDevices utils datasets methods base other attached packages: [1] GenomicRanges_1.32.2 GenomeInfoDb_1.16.0 edgeR_3.22.1 limma_3.36.1 IRanges_2.14.8 S4Vectors_0.18.1 [7] Biobase_2.40.0 BiocGenerics_0.26.0 BiocInstaller_1.30.0 loaded via a namespace (and not attached): [1] locfit_1.5-9.1 Rcpp_0.12.16 lattice_0.20-35 bitops_1.0-6 grid_3.5.0 [6] zlibbioc_1.26.0 XVector_0.20.0 tools_3.5.0 RCurl_1.95-4.10 yaml_2.1.19 [11] compiler_3.5.0 GenomeInfoDbData_1.1.0
