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Question: DESeq2 install problem
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gravatar for bikashten
6 days ago by
bikashten0
bikashten0 wrote:

Hi all, I am trying to install the DESeq2, but I keep getting error message. Here is a code:

R version 3.5.1 (2018-07-02) -- "Feather Spray"

Copyright (C) 2018 The R Foundation for Statistical Computing

Platform: x86_64-w64-mingw32/x64 (64-bit)

 

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Type 'contributors()' for more information and

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Type 'demo()' for some demos, 'help()' for on-line help, or

'help.start()' for an HTML browser interface to help.

Type 'q()' to quit R.

 

[Workspace loaded from ~/.RData]

 

> source("https://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 3.5.1 (2018-07-02).

Installing package(s) ‘DESeq2’

Warning: unable to access index for repository https://cran.rstudio.com/src/contrib:

  cannot open URL 'https://cran.rstudio.com/src/contrib/PACKAGES'

Warning: dependencies ‘locfit’, ‘RcppArmadillo’ are not available

Warning: unable to access index for repository https://cran.rstudio.com/bin/windows/contrib/3.5:

  cannot open URL 'https://cran.rstudio.com/bin/windows/contrib/3.5/PACKAGES'

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

 

package ‘DESeq2’ successfully unpacked and MD5 sums checked

 

The downloaded binary packages are in

C:\Users\b0bhan02\AppData\Local\Temp\RtmpsrxmSY\downloaded_packages

Warning: unable to access index for repository https://cran.rstudio.com/src/contrib:

  cannot open URL 'https://cran.rstudio.com/src/contrib/PACKAGES'

> library("DESeq2")

Loading required package: S4Vectors

Loading required package: stats4

Loading required package: BiocGenerics

Loading required package: parallel

 

Attaching package: ‘BiocGenerics’

 

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

 

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ, clusterExport, clusterMap, parApply, parCapply, parLapply, parLapplyLB, parRapply,

    parSapply, parSapplyLB

 

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, colMeans, colnames, colSums, dirname, do.call, duplicated, eval, evalq, Filter, Find, get,

    grep, grepl, intersect, is.unsorted, lapply, lengths, Map, mapply, match, mget, order, paste, pmax, pmax.int, pmin, pmin.int, Position, rank, rbind,

    Reduce, rowMeans, rownames, rowSums, sapply, setdiff, sort, table, tapply, union, unique, unsplit, which, which.max, which.min

 

 

Attaching package: ‘S4Vectors’

 

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

 

    expand.grid

 

Loading required package: IRanges

 

Attaching package: ‘IRanges’

 

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

 

    windows

 

Loading required package: GenomicRanges

Loading required package: GenomeInfoDb

Error: package or namespace load failed for ‘GenomeInfoDb’ in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]):

 there is no package called ‘RCurl’

Error: package ‘GenomeInfoDb’ could not be loaded

ADD COMMENTlink modified 6 days ago by Michael Love19k • written 6 days ago by bikashten0
0
gravatar for Michael Love
6 days ago by
Michael Love19k
United States
Michael Love19k wrote:

The first warning is your clue what's going on.

I wonder, can you access this URL from your computer:

https://cran.rstudio.com/src/contrib/PACKAGES

ADD COMMENTlink written 6 days ago by Michael Love19k

Hi Michael,

I just downloaded the r and rstudio, but it keep popping up same error. Is there any way to fix this problem?

 

Thanks,

Bikash

ADD REPLYlink written 6 days ago by bikashten0

Can you try what I said?

ADD REPLYlink written 6 days ago by Michael Love19k

Hi Michael,

Yes, I can. If I click this link from my computer, it leads to lots of packages. The first package is

Package: A3
Version: 1.0.0
Depends: R (>= 2.15.0), xtable, pbapply
Suggests: randomForest, e1071
License: GPL (>= 2)
NeedsCompilation: no

 

Thanks,

Bikash

ADD REPLYlink written 5 days ago by bikashten0

I’m not sure why R can’t access that URL if you can from eg a web browser. Sorry can’t help much more

ADD REPLYlink written 5 days ago by Michael Love19k

NP Michael. Thank you so much for your time.

 

Thanks,

Bikash

ADD REPLYlink written 5 days ago by bikashten0

Have you restarted your R session? Can you use get available.packages() to work on the rstudio url, perhaps with the argument ignore_repo_cache = TRUE?

ADD REPLYlink written 5 days ago by Martin Morgan ♦♦ 22k
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