Question: install new package from bioconductor
0
gravatar for Tiphaine Martin
3.7 years ago by
France
Tiphaine Martin40 wrote:

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

 

ADD COMMENTlink modified 3.7 years ago by Julie Zhu4.0k • written 3.7 years ago by Tiphaine Martin40
Answer: install new package from bioconductor
1
gravatar for Tiphaine Martin
3.7 years ago by
France
Tiphaine Martin40 wrote:

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

ADD COMMENTlink written 3.7 years ago by Tiphaine Martin40

It also says:

## try http if https is not available

 

ADD REPLYlink written 3.7 years ago by Dan Tenenbaum8.2k

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

ADD REPLYlink written 3.7 years ago by Tiphaine Martin40
Answer: install new package from bioconductor
0
gravatar for Julie Zhu
3.7 years ago by
Julie Zhu4.0k
United States
Julie Zhu4.0k wrote:
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
ADD COMMENTlink written 3.7 years ago by Julie Zhu4.0k
Answer: install new package from bioconductor
0
gravatar for Julie Zhu
3.7 years ago by
Julie Zhu4.0k
United States
Julie Zhu4.0k wrote:

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

ADD COMMENTlink written 3.7 years ago by Julie Zhu4.0k

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

ADD REPLYlink written 3.7 years ago by Dan Tenenbaum8.2k
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