Question: Problem installing Bioconductor
0
gravatar for rj.innet
7 months ago by
rj.innet0
rj.innet0 wrote:

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 • 212 views
ADD COMMENTlink modified 7 months ago by Martin Morgan ♦♦ 23k • written 7 months ago by rj.innet0
Answer: Problem installing Bioconductor
1
gravatar for Martin Morgan
7 months ago by
Martin Morgan ♦♦ 23k
United States
Martin Morgan ♦♦ 23k wrote:

Try using the https: url directly

source("https://bioconductor.org/biocLite.R")
ADD COMMENTlink written 7 months ago by Martin Morgan ♦♦ 23k

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'

 

ADD REPLYlink written 7 months ago by rj.innet0

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

ADD REPLYlink written 7 months ago by Martin Morgan ♦♦ 23k

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.

ADD REPLYlink written 7 months ago by rj.innet0
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