install new package from bioconductor
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@tiphaine-martin-6416
Last seen 2.5 years ago
France

Hi,

I tried to install new packages and I have this error message

source("https://bioconductor.org/biocLite.R")
Error in file(filename, "r", encoding = encoding) :
  https:// URLs are not supported

I did some update of package on my version of ubuntu. I didn't think that one of them can influence this command line.

I tried to resinstall libcurl, I still have this error.

What I need to do ?

 

Regards,

Tiphaine

> sessionInfo()
R version 3.2.2 (2015-08-14)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu precise (12.04.5 LTS)

locale:
 [1] LC_CTYPE=en_GB.UTF-8       LC_NUMERIC=C               LC_TIME=en_US.UTF-8        LC_COLLATE=en_GB.UTF-8    
 [5] LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_GB.UTF-8    LC_PAPER=en_US.UTF-8       LC_NAME=C                 
 [9] LC_ADDRESS=C               LC_TELEPHONE=C             LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C       

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

other attached packages:
[1] RCurl_1.95-4.7 bitops_1.0-6  

loaded via a namespace (and not attached):
[1] tools_3.2.2

 

software error bioconductor • 14k views
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@tiphaine-martin-6416
Last seen 2.5 years ago
France

Hi Julie,

 

It works, but why is  in the page of S4Vector, the instruction to install this page ?

source("https://bioconductor.org/biocLite.R")
biocLite("S4Vectors")

I checked for my package and I have what you propose.

any way, it works. So I can carry on :)

Thanks,

Tiphaine

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It also says:

## try http if https is not available

 

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http work, but not https for me. Thank you.

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Julie Zhu ★ 4.3k
@julie-zhu-3596
Last seen 10 days ago
United States
Tiphaine, Please try source("http://bioconductor.org/biocLite.R"<https: bioconductor.org="" bioclite.r%22="">) without s after http. Best, Julie From: "Tiphaine Martin [bioc]" <noreply@bioconductor.org<mailto:noreply@bioconductor.org>> Reply-To: "reply+d4ed708d+code@bioconductor.org<mailto:reply+d4ed708d+code@bioconductor.org>" <reply+d4ed708d+code@bioconductor.org<mailto:reply+d4ed708d+code@bioconductor.org>> Date: Wednesday, October 28, 2015 2:25 PM To: Lihua Julie Zhu <julie.zhu@umassmed.edu<mailto:julie.zhu@umassmed.edu>> Subject: [bioc] install new package from bioconductor Activity on a post you are following on support.bioconductor.org<https: support.bioconductor.org=""> User Tiphaine Martin<https: support.bioconductor.org="" u="" 6416=""/> wrote Question: install new package from bioconductor<https: support.bioconductor.org="" p="" 73886=""/>: Hi, I tried to install new packages and I have this error message source("https://bioconductor.org/biocLite.R") Error in file(filename, "r", encoding = encoding) : https:// URLs are not supported I did some update of package on my version of ubuntu. I didn't think that one of them can influence this command line. I tried to resinstall libcurl, I still have this error. What I need to do ? Regards, Tiphaine > sessionInfo() R version 3.2.2 (2015-08-14) Platform: x86_64-pc-linux-gnu (64-bit) Running under: Ubuntu precise (12.04.5 LTS) locale: [1] LC_CTYPE=en_GB.UTF-8 LC_NUMERIC=C LC_TIME=en_US.UTF-8 LC_COLLATE=en_GB.UTF-8 [5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_GB.UTF-8 LC_PAPER=en_US.UTF-8 LC_NAME=C [9] LC_ADDRESS=C LC_TELEPHONE=C LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C attached base packages: [1] stats graphics grDevices utils datasets methods base other attached packages: [1] RCurl_1.95-4.7 bitops_1.0-6 loaded via a namespace (and not attached): [1] tools_3.2.2 ________________________________ Post tags: software error, bioconductor You may reply via email or visit install new package from bioconductor
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Julie Zhu ★ 4.3k
@julie-zhu-3596
Last seen 10 days ago
United States

Tiphaine, The reason is that http port is open, but https port is not open in the machine you are trying to install via https.

Best regards,

Julie

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Probably it means your version of R does not support https. 

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