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Question: Issues connecting with R 3.2.2 to source("http://bioconductor.org/biocLite.R")
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gravatar for frostbite907
2.1 years ago by
frostbite9070 wrote:

Hello,

I am trying to setup Spade for FlowJo using the following instructions.

http://docs.flowjo.com/vx/advanced-features/spade-flowjo/ 

When I run R 3.2.2 it tells me that there the current version is not supported. When I try R 3.2.1 everything seems to go fine until I test with the library(spade) command which generates 4 warning and an error about needing to use 3.2.2.

I am running this on Windows XP SP 3 32 bit.

 

> 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: 'The connection with the server was reset'
> source("http://bioconductor.org/biocLite.R")
Warning: unable to access index for repository https://bioconductor.org/packages/3.2/bioc/src/contrib
Warning: unable to access index for repository https://bioconductor.org/packages/3.2/bioc/bin/windows/contrib/3.2
'biocLite.R' failed to install 'BiocInstaller', use
  'install.packages("BiocInstaller",
  repos="https://bioconductor.org/packages/3.1/bioc")' or
  'install.packages("BiocInstaller",
  repos="http://bioconductor.org/packages/3.1/bioc")'
Warning message:
package ‘BiocInstaller’ is not available (for R version 3.2.2) 

 

ADD COMMENTlink written 2.1 years ago by frostbite9070

Does it work if you remove the 's' from 'https', as in:

source("http://bioconductor.org/biocLite.R")

?

ADD REPLYlink written 2.1 years ago by Dan Tenenbaum ♦♦ 8.2k

No, I tried both.

 


R version 3.2.2 (2015-08-14) -- "Fire Safety"
Copyright (C) 2015 The R Foundation for Statistical Computing
Platform: i386-w64-mingw32/i386 (32-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

[Previously saved workspace restored]

> source("http://bioconductor.org/biocLite.R")
Warning: unable to access index for repository https://bioconductor.org/packages/3.2/bioc/src/contrib
Warning: unable to access index for repository https://bioconductor.org/packages/3.2/bioc/bin/windows/contrib/3.2
'biocLite.R' failed to install 'BiocInstaller', use
  'install.packages("BiocInstaller",
  repos="https://bioconductor.org/packages/3.1/bioc")' or
  'install.packages("BiocInstaller",
  repos="http://bioconductor.org/packages/3.1/bioc")'
Warning message:
package ‘BiocInstaller’ is not available (for R version 3.2.2) 

ADD REPLYlink modified 2.1 years ago • written 2.1 years ago by frostbite9070

How about options(useHTTPS=FALSE, BioC_mirror="http://bioconductor.org") ? It seems like R is still trying to access the https repository.

ADD REPLYlink written 2.1 years ago by Martin Morgan ♦♦ 20k

How would I do this?

ADD REPLYlink written 2.1 years ago by frostbite9070
1

Just paste this into R:

options(useHTTPS=FALSE, BioC_mirror="http://bioconductor.org")

Then try

source("http://bioconductor.org/biocLite.R")

ADD REPLYlink written 2.1 years ago by Dan Tenenbaum ♦♦ 8.2k

I tried this but I still got the same error message.

[Previously saved workspace restored]

> options(useHTTPS=FALSE, BioC_mirror="http://bioconductor.org")
> source("http://bioconductor.org/biocLite.R")
Warning: unable to access index for repository https://bioconductor.org/packages/3.2/bioc/src/contrib
Warning: unable to access index for repository https://bioconductor.org/packages/3.2/bioc/bin/windows/contrib/3.2
'biocLite.R' failed to install 'BiocInstaller', use
  'install.packages("BiocInstaller",
  repos="https://bioconductor.org/packages/3.1/bioc")' or
  'install.packages("BiocInstaller",
  repos="http://bioconductor.org/packages/3.1/bioc")'
Warning message:
package ‘BiocInstaller’ is not available (for R version 3.2.2) 

ADD REPLYlink written 2.1 years ago by frostbite9070

The repos you pass to install.packages() should reference 3.2, not 3.1. 

You mentioned a firewall. Is it running on your machine or on your institution's network. If it's on your machine, do you open and close ports for specific apps? Can you make sure that ports 80 and 443 are open for R?

I'm assuming you can browse web pages with a browser (including the URLs above)  so the problem is not with those ports being closed to all apps, just to R. Maybe you can confirm that.

ADD REPLYlink written 2.1 years ago by Dan Tenenbaum ♦♦ 8.2k

Windows Firewall is disabled and I also disabled Norton AV on the Computer. Additionally I'm sure that port 80 and 443 are open on the firewall since they are common ports. Web browsing is fine but for some reason it keeps trying to connect over HTTPS even when I disable these options in IE. Does the version of IE I have installed have anything to do with this?

ADD REPLYlink written 2.0 years ago by frostbite9070

Is there a firewall or proxy at your institution? What's the output of sessionInfo() within R?

ADD REPLYlink written 2.1 years ago by Dan Tenenbaum ♦♦ 8.2k

There is a firewall. Any specific ports that need to be open?

 

>sessionInfo()

R version 3.2.2 (2015-08-14)
Platform: i386-w64-mingw32/i386 (32-bit)
Running under: Windows XP (build 2600) Service Pack 3

locale:
[1] LC_COLLATE=English_United States.1252 
[2] LC_CTYPE=English_United States.1252   
[3] LC_MONETARY=English_United States.1252
[4] LC_NUMERIC=C                          
[5] LC_TIME=English_United States.1252    

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

ADD REPLYlink written 2.1 years ago by frostbite9070

You could try and take biocLite out of the picture by trying

url = "http://bioconductor.org/packages/3.2/bioc/src/contrib/PACKAGES"
download.file(url, tempfile())

I guess this fails? Have you said setInternet2(TRUE) ? Can you copy the url above into your browser and have the file appear? On the help page ?download.file there are various options to the method argument; do any of these work? If so, set options(download.file.method="name-of-method-that-worked").

ADD REPLYlink written 2.1 years ago by Martin Morgan ♦♦ 20k

The above URL is accessible on the computer but the text is not formatted and is missing word wrap. It looks normal on Chrome but in IE its not spaced out properly. Not exactly sure what to do with the remaining information since I'm pretty new to this.

ADD REPLYlink written 2.0 years ago by frostbite9070
1

That's how you should be seeing the package list in the browsers.

This shouldn't be considered a fix, but I've seen

options(download.file.method="libcurl", url.method="libcurl")
source("https://www.bioconductor.org/biocLite.R")

work when R's settings for HTTPS downloading aren't quite right for some reason.

ADD REPLYlink written 2.0 years ago by Jim Java30
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