Problem installing Bioconductor
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rj.innet • 0
@rjinnet-17036
Last seen 3.0 years ago

Hi,

I tried the standard procedure to install Bioconductor packages in R in my Ubuntu 18.04 64 bit but got the error message provided below-

> source("http://bioconductor.org/biocLite.R")
Error in file(filename, "r", encoding = encoding) :
  cannot open the connection to 'http://bioconductor.org/biocLite.R'
In addition: Warning message:
In file(filename, "r", encoding = encoding) :
  cannot open URL 'http://bioconductor.org/biocLite.R': HTTP status was '407 Proxy Authentication Required'

> sessionInfo()
R version 3.4.4 (2018-03-15)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 18.04.1 LTS

Matrix products: default
BLAS: /usr/lib/x86_64-linux-gnu/blas/libblas.so.3.7.1
LAPACK: /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.7.1

locale:
 [1] LC_CTYPE=en_IN       LC_NUMERIC=C         LC_TIME=en_IN       
 [4] LC_COLLATE=en_IN     LC_MONETARY=en_IN    LC_MESSAGES=en_IN   
 [7] LC_PAPER=en_IN       LC_NAME=C            LC_ADDRESS=C        
[10] LC_TELEPHONE=C       LC_MEASUREMENT=en_IN LC_IDENTIFICATION=C

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base     

loaded via a namespace (and not attached):
[1] compiler_3.4.4
>

 


I also installed the same packages in the same manner in Windows 10, 64 bit machine through the same public network but did not encounter such problem then. Could anyone give me a solution to the problem?

Thanking you

Rupjyoti

Tezpur University

biocLite • 915 views
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@martin-morgan-1513
Last seen 9 weeks ago
United States

Try using the https: url directly

source("https://bioconductor.org/biocLite.R")
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Entering edit mode

I have tried both "http" and "https" but error remains same.

Also tried doing 

export http_proxy and 
export HTTP_PROXY 
giving my proxy and port info. and then ran in R the commands 
Sys.setenv(http_proxy="http://xyz.ai:8080")(with my proxy and port) But now the error says

> source("https://bioconductor.org/biocLite.R")
Error in file(filename, "r", encoding = encoding) :
  cannot open the connection to 'https://bioconductor.org/biocLite.R'
In addition: Warning message:
In file(filename, "r", encoding = encoding) :
  URL 'https://bioconductor.org/biocLite.R': status was 'HTTP response code said error'

 

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0
Entering edit mode

Sorry, I won't really be any more help than googling; what happens when you follow the link in a browser?

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The link just opens fine in the browser.

I think the problem lies in the .Renviron file. I need to add proxy authentication in that file. But problem persist with a CA certificate and SSL connect errors now.

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