Where downloaded data are stored?
2
0
Entering edit mode
@arman-shahrisa-7713
Last seen 6.1 years ago

I can't download "BSgenome.Hsapiens.UCSC.hg19_1.4.0" through R due to limitations in my network. I have manually downloaded the file. Where should I put the downloaded file? I mean where R stores downloaded bioconductor packages befor installation? I want to execute "biocLite" after that and the script only decompress and install it. I mean I don't want it to start downloading again.
R • 1.7k views
ADD COMMENT •
1
Entering edit mode
Andrzej Oleś ▴ 750
@andrzej-oles-5540
Last seen 4.1 years ago
Heidelberg, Germany

You can install the package manually from your terminal (not R!) by typing

R CMD INSTALL filename

where filename is the package file name you downloaded.

Cheers,

Andrzej
ADD COMMENT •
3
Entering edit mode

Or alternatively (and especially if you are on Windows), by doing

install.packages(<path to file>, repos = NULL)

depending on what you downloaded, you may also need to add source = TRUE.

ADD REPLY •
0
Entering edit mode
@arman-shahrisa-7713
Last seen 6.1 years ago

Thanks! Thanks a lot! It worked! I was able to execute library command! It works!!!!!!!!!!!!
ADD COMMENT •
1
Entering edit mode

You need to give us more information. Rather than describing what you think is happening, try running biocLite() and showing the output that you get.

library(BiocInstaller)
biocLite("BSgenome.Hsapiens.UCSC.hg19")

If this fails, show us the output, what you get after running traceback(), and what you get after running sessionInfo().

ADD REPLY •
0
Entering edit mode

I think Shahrisa said earlier that biocLite won't work at their institution due to network limitations, so the question is how to install a package downloaded by other means.

ADD REPLY •
2
Entering edit mode

Indeed. Which is why both Andrzej and I gave her suggestions to accomplish that. But then she said

Is there any chance I can prevent downloading? I moved the file to certain temp folders associated with downloaded files but at the best shot I got only error that package is not available as separate binary package! Is there any chance I can force the bioconductor to instal the predownloaded file?

Which she subsequently edited. But this original text indicated to me that perhaps she was confused and might not actually be diagnosing her problem correctly, in which case some R output might have been enlightening.

ADD REPLY •
0
Entering edit mode

I'm a man! Shahrisa is my family name! My name is Arman! Yes, I mistakenly edited my message when you were answering. By the way,your answers were perfect! I have installed multiple new packages with that command. My network connection is very restricted and unstable to HTTPS connection. That is why I can't install bioconductor packages directly. I can download packages with download managers faster even without using proxy or vpn.

ADD REPLY •
0
Entering edit mode

Hi Arman,

Sorry about that. But I am glad you have things working now.

ADD REPLY •

Login before adding your answer.

Similar Posts
Loading Similar Posts
Traffic: 966 users visited in the last hour
Content Search
Users
Tags
Badges
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6