Question

error in installing bioconductor

1

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farahqureshi5 • 0

@farahqureshi5-12184

Last seen 7.3 years ago

greetings!!

source("https://bioconductor.org/biocLite.R")
Error in file(filename, "r", encoding = encoding) :
cannot open the connection
In addition: Warning message:
In file(filename, "r", encoding = encoding) :
InternetOpenUrl failed: 'A connection with the server could not be established'

how to debug the error. when i have already many times used the bioconductor packages.

installation • 2.0k views

ADD COMMENT • link updated 7.8 years ago by b.nota ▴ 370 • written 7.8 years ago by farahqureshi5 • 0

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The same command is working for me the moment I write this, so the problem is on your side, and not with the Bioconductor servers. So check again, check whether you can browse the internet at all, restart your PC, etc....

ADD REPLY • link 7.8 years ago Guido Hooiveld ★ 4.1k

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Does the link open in a browser? Experiment with different values for download.file argument 'method', e.g., options(download.file.method="libcurl").

ADD REPLY • link 7.8 years ago Martin Morgan 25k

score 0 · Answer 1 · 2017-03-15

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farahqureshi5 • 0

@farahqureshi5-12184

Last seen 7.3 years ago

is there any way, so that i can include the package from library once and use it again and again

ADD COMMENT • link 7.8 years ago farahqureshi5 • 0

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The biocLite() function is in the BiocInstaller package. Once BiocInstaller is installed you can either call library(BiocInstaller) in an R session or put library(BiocInstaller) in your .Rprofile to automatically load the package (which makes biocLite() available) when you start R.

Valerie

ADD REPLY • link 7.8 years ago Valerie Obenchain ★ 6.8k

score 0 · Answer 2 · 2017-03-15

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b.nota ▴ 370

@bnota-7379

Last seen 4.3 years ago

Netherlands

Did you try http instead of https?

ADD COMMENT • link 7.8 years ago b.nota ▴ 370