Question: DESeq2 install problem
0
gravatar for bikashten
13 months 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)

 

R is free software and comes with ABSOLUTELY NO WARRANTY.

You are welcome to redistribute it under certain conditions.

Type 'license()' or 'licence()' for distribution details.

 

R is a collaborative project with many contributors.

Type 'contributors()' for more information and

'citation()' on how to cite R or R packages in publications.

 

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

deseq • 959 views
ADD COMMENTlink modified 13 months ago by Michael Love26k • written 13 months ago by bikashten0
Answer: DESeq2 install problem
0
gravatar for Michael Love
13 months ago by
Michael Love26k
United States
Michael Love26k 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 13 months ago by Michael Love26k

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 13 months ago by bikashten0

Can you try what I said?

ADD REPLYlink written 13 months ago by Michael Love26k

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 13 months 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 13 months ago by Michael Love26k

NP Michael. Thank you so much for your time.

 

Thanks,

Bikash

ADD REPLYlink written 13 months 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 13 months ago by Martin Morgan ♦♦ 24k
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