Where downloaded data are stored?
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@arman-shahrisa-7713
Last seen 2.8 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 • 755 views
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Andrzej Oleś ▴ 750
@andrzej-oles-5540
Last seen 10 months 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

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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.

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@arman-shahrisa-7713
Last seen 2.8 years ago

Thanks! Thanks a lot! It worked! I was able to execute library command! It works!!!!!!!!!!!!

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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().

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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.

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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.

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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.

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Hi Arman,

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

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