Question: error in R when installing DESeq2 package
0
gravatar for A
4.3 years ago by
A3.6k
A3.6k wrote:

sorry guys,

whenever im trying, this is the error

what does this mean please? how i can fix it?

> source("https://bioconductor.org/biocLite.R")
https:// URLs are not supported by the default method: trying "libcurl"
Bioconductor version 3.1 (BiocInstaller 1.18.4), ?biocLite for help
>

R software error • 7.3k views
ADD COMMENTlink modified 3.1 years ago by csclaros20 • written 4.3 years ago by A3.6k
2
gravatar for csclaros
3.1 years ago by
csclaros20
csclaros20 wrote:

Hi! You need to run this in your terminal before installing anything in Bioconductor/R:

sudo apt-get update
sudo apt-get install libxml2-dev
sudo apt-get install r-cran-xml
sudo apt-get install libcurl4-openssl-dev

Hope it works for you too!

ADD COMMENTlink modified 27 days ago by RamRS25k • written 3.1 years ago by csclaros20
1
gravatar for andrew.j.skelton73
4.3 years ago by
London
andrew.j.skelton735.9k wrote:
source("http://bioconductor.org/biocLite.R")

You didn't get an error, it executed. Did you even read the output you pasted here?

"https:// URLs are not supported by the default method"

secure URLs are not supported by the source function

"trying "lib curl""

It tries the lib curl library.

"Bioconductor version 3.1 (BiocInstaller 1.18.4), ?biocLite for help"

Success.

Have a go at trying to figure out the errors yourself before posting. Throwing the error into google, plus "R" brings up a number of results.

ADD COMMENTlink modified 27 days ago by RamRS25k • written 4.3 years ago by andrew.j.skelton735.9k

thanks you Andrew,

I'm trying since morning to install this package, llok at the below please

ADD REPLYlink modified 27 days ago by RamRS25k • written 4.3 years ago by A3.6k
1

This is your problem:

Error : package 'BSgenome' 1.32.0 was found, but >= 1.33.5 is required by 'BSgenome.Celegans.UCSC.ce2'

The package you are trying to install or its dependencies needs a newer version of this BSgenome. You probably had an earlier version already installed.

Try updating it first

biocLite("BSgenome")

then

biocLite("DESeq2")
ADD REPLYlink modified 27 days ago by RamRS25k • written 4.3 years ago by Lemire450

thank you

i will try

ADD REPLYlink written 4.3 years ago by A3.6k

run

biocLite()

to update all your outdated packages then

biocLite("DESeq2")

The install.packages function is for CRAN libraries, whereas DESeq2 is a Bioconductor Library.

ADD REPLYlink modified 27 days ago by RamRS25k • written 4.3 years ago by andrew.j.skelton735.9k

sorry Andrew,

I did what you said

but asked me Would you like to use a personal library instead? (y/n) and I typed y and after some time said that:

The downloaded source packages are in
    '/tmp/RtmpzRdBqS/downloaded_packages'
There were 50 or more warnings (use warnings() to see the first 50)
>

now from where I can recognize that if the package installed or not?

thank you

ADD REPLYlink modified 27 days ago by RamRS25k • written 4.3 years ago by A3.6k
1
library(DESeq2)
ADD REPLYlink modified 27 days ago by RamRS25k • written 4.3 years ago by andrew.j.skelton735.9k
> library(DESeq2)
Error in library(DESeq2) : there is no package called 'DESeq2'
>

then what can I do now?

ADD REPLYlink modified 27 days ago by RamRS25k • written 4.3 years ago by A3.6k
1

Did you run

warnings()

As it suggested?

ADD REPLYlink modified 27 days ago by RamRS25k • written 4.3 years ago by andrew.j.skelton735.9k

hi andrew,

this is my 50 error

ADD REPLYlink modified 27 days ago by RamRS25k • written 4.3 years ago by A3.6k

As @Lemire/OICR stated, from your original log:

Error : package 'BSgenome' 1.32.0 was found, but >= 1.33.5 is required by 'BSgenome.Celegans.UCSC.ce2'

Is the issue, you need to install an updated version.

ADD REPLYlink modified 27 days ago by RamRS25k • written 4.3 years ago by andrew.j.skelton735.9k

thank you,

I did the same but again the same question(would you like to your personal file) I typed y but

Error : package 'BSgenome' 1.32.0 was found, but >= 1.33.5 is required by 'BSgenome.Celegans.UCSC.ce2'
ERROR: lazy loading failed for package 'BSgenome.Celegans.UCSC.ce2'
* removing '/usr/people/home/izadi/R/x86_64-redhat-linux-gnu-library/3.2/BSgenome.Celegans.UCSC.ce2'

The downloaded source packages are in
    '/tmp/Rtmpwnc0IZ/downloaded_packages'
There were 50 or more warnings (use warnings() to see the first 50)
> library(DESeq2)
Error in library(DESeq2) : there is no package called 'DESeq2'
> library(/usr/data/nfs6/izadi/R-3.2.2/lib/DESeq2)
Error: unexpected '/' in "library(/"
ADD REPLYlink modified 27 days ago by RamRS25k • written 4.3 years ago by A3.6k

You ran

biocLite("BSgenome")

didn't you?

ADD REPLYlink modified 27 days ago by RamRS25k • written 4.3 years ago by andrew.j.skelton735.9k

I ran biocLite("BSgenome") the first then I ran (DESeq2)...but the same error...there is a file named R-3.2.2 in /usr/data/nfs6/izadi/ containing many folders then I ran the library(/usr/data/nfs6/izadi/R-3.2.2/lib/DESeq2) but again error...totally I donno how I can install this package

ADD REPLYlink modified 27 days ago by RamRS25k • written 4.3 years ago by A3.6k
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