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
>
•
written
by
zizigolu
3 answers
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!
•
written
by
csclaros •
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.
•
written
by
andrew.j.skelton73
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to update all your outdated packages then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.
•
written
by
andrew.j.skelton73
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
library(DESeq2)
Did you run
warnings()
As it suggested?
•
written
by
andrew.j.skelton73
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.
•
written
by
andrew.j.skelton73
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(/"
You ran
biocLite("BSgenome")
didn't you?
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written
by
andrew.j.skelton73
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
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")
Some R versions have problems with biocLite in R. Try with this tutorial: 5 Ways to install DESeq2
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