Question: Installing DESeq2 error: missing value where TRUE/FALSE needed
1
gravatar for dfhannum
11 months ago by
dfhannum10
dfhannum10 wrote:

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

 

 

biocinstaller deseq2 error • 199 views
ADD COMMENTlink modified 11 months ago by Martin Morgan ♦♦ 23k • written 11 months ago by dfhannum10
Answer: Installing DESeq2 error: missing value where TRUE/FALSE needed
0
gravatar for Martin Morgan
11 months ago by
Martin Morgan ♦♦ 23k
United States
Martin Morgan ♦♦ 23k wrote:

My guess is that this occurs when R tries to validate the 'md5sums' of the downloaded packages. I think you should try to isolate this problem by trying to install the individual packages, starting with

biocLite("snow")

It might also help to see the output of

.libPaths()
tempdir()

and to make sure that each of these locations have a reasonable amount of free disk space.

ADD COMMENTlink written 11 months ago by Martin Morgan ♦♦ 23k
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