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R Package installation

12 messages · Dayalan, Nithya, Jeff Newmiller, David Winsemius +2 more

Original
Dayalan, Nithya
# 
Hi Team,

We are receiving the below message while updating the package. Please help.
Warning: unable to access index for repository https://cran.fhcrc.org/src/contrib:
  cannot open URL 'https://cran.fhcrc.org/src/contrib/PACKAGES'
Warning: unable to access index for repository http://www.stats.ox.ac.uk/pub/RWin/src/contrib:
  cannot open URL 'http://www.stats.ox.ac.uk/pub/RWin/src/contrib/PACKAGES'
Warning: unable to access index for repository https://cran.fhcrc.org/bin/windows/contrib/3.2:
  cannot open URL 'https://cran.fhcrc.org/bin/windows/contrib/3.2/PACKAGES'
Warning: unable to access index for repository http://www.stats.ox.ac.uk/pub/RWin/bin/windows/contrib/3.2:
  cannot open URL 'http://www.stats.ox.ac.uk/pub/RWin/bin/windows/contrib/3.2/PACKAGES'
Warning messages:
1: package 'parallel' is not available (for R version 3.2.5)
2: package 'parallel' is a base package, and should not be updated
Thanks & Regards,
Nithya Dayalan
AMS MRL DPS | HCL @ Merck
E-mail: nithya.dayalan at merck.com<mailto:nithya.dayalan at merck.com>
Tel#+91 44 61053951| Mobile +91 8754232975

Notice:  This e-mail message, together with any attachme...{{dropped:14}}
Jeff Newmiller
# 
Choose

A

Different

Mirror
Dayalan, Nithya
# 
Yes Jeff,  I tried it with 10 mirrors.

Thanks & Regards,
Nithya Dayalan
AMS MRL DPS | HCL @ Merck
E-mail: nithya.dayalan at merck.com
Tel#+91 44 61053951| Mobile +91 8754232975

-----Original Message-----
From: Jeff Newmiller [mailto:jdnewmil at dcn.davis.ca.us] 
Sent: Friday, August 12, 2016 10:43 AM
To: Dayalan, Nithya; 'r-help at R-project.org'
Cc: Radhakrishan, Balaji
Subject: Re: [R] R Package installation

Choose

A

Different

Mirror
Dayalan, Nithya
# 
Hi Jeff,

Before selecting the mirror I am receiving the error: I can able connect internet in server and also I have already done this package installation before 2 weeks.

Error in download.file(url, destfile = f, quiet = TRUE) :
  cannot open URL 'https://cran.r-project.org/CRAN_mirrors.csv'
In addition: Warning message:
In download.file(url, destfile = f, quiet = TRUE) :
  InternetOpenUrl failed: 'A connection with the server could not be established'
Warning: unable to access index for repository https://cran.uni-muenster.de/src/contrib:
  cannot open URL 'https://cran.uni-muenster.de/src/contrib/PACKAGES'
Warning: unable to access index for repository http://www.stats.ox.ac.uk/pub/RWin/src/contrib:
  cannot open URL 'http://www.stats.ox.ac.uk/pub/RWin/src/contrib/PACKAGES'
Warning: unable to access index for repository https://cran.uni-muenster.de/bin/windows/contrib/3.2:
  cannot open URL 'https://cran.uni-muenster.de/bin/windows/contrib/3.2/PACKAGES'
Warning: unable to access index for repository http://www.stats.ox.ac.uk/pub/RWin/bin/windows/contrib/3.2:
  cannot open URL 'http://www.stats.ox.ac.uk/pub/RWin/bin/windows/contrib/3.2/PACKAGES'
Warning message:
package ?Rtsne? is not available (for R version 3.2.5)



Thanks & Regards,
Nithya Dayalan
AMS MRL DPS | HCL @ Merck
E-mail: nithya.dayalan at merck.com
Tel#+91 44 61053951| Mobile +91 8754232975


-----Original Message-----
From: Dayalan, Nithya
Sent: Friday, August 12, 2016 10:45 AM
To: 'Jeff Newmiller'; 'r-help at R-project.org'
Cc: Radhakrishan, Balaji
Subject: RE: [R] R Package installation

Yes Jeff,  I tried it with 10 mirrors.

Thanks & Regards,
Nithya Dayalan
AMS MRL DPS | HCL @ Merck
E-mail: nithya.dayalan at merck.com<mailto:nithya.dayalan at merck.com>
Tel#+91 44 61053951| Mobile +91 8754232975

-----Original Message-----
From: Jeff Newmiller [mailto:jdnewmil at dcn.davis.ca.us]
Sent: Friday, August 12, 2016 10:43 AM
To: Dayalan, Nithya; 'r-help at R-project.org'
Cc: Radhakrishan, Balaji
Subject: Re: [R] R Package installation

Choose

A

Different

Mirror
--
Sent from my phone. Please excuse my brevity.
On August 12, 2016 3:53:03 AM PDT, "Dayalan, Nithya" <nithya.dayalan at merck.com<mailto:nithya.dayalan at merck.com>> wrote:
Notice:  This e-mail message, together with any attachments, contains
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David Winsemius
# 
In most case it is the first warning or error that is most meaningful, but in this case it is the last one.

The `installed.packages` function can tell you which packages are in the Bases" category:

plic <- installed.packages( .Library, priority = "base")
[1] "base"      "compiler"  "datasets"  "graphics"  "grDevices" "grid"      "methods"  
 [8] "parallel"  "splines"   "stats"     "stats4"    "tcltk"     "tools"     "utils"    


Updating them requires updating your R version, which is what you should do now.
Dayalan, Nithya
# 
Hi David,

Okay thank you, but the error message receiving for other packages.
--- Please select a CRAN mirror for use in this session ---
Error in download.file(url, destfile = f, quiet = TRUE) : 
  cannot open URL 'https://cran.r-project.org/CRAN_mirrors.csv'
In addition: Warning message:
In
  InternetOpenUrl failed: 'A connection with the server could not be established'
Warning: unable to access index for repository https://cran.uni-muenster.de/src/contrib:
  cannot open URL 'https://cran.uni-muenster.de/src/contrib/PACKAGES'
Warning: unable to access index for repository http://www.stats.ox.ac.uk/pub/RWin/src/contrib:
  cannot open URL 'http://www.stats.ox.ac.uk/pub/RWin/src/contrib/PACKAGES'
Warning: unable to access index for repository https://cran.uni-muenster.de/bin/windows/contrib/3.2:
  cannot open URL 'https://cran.uni-muenster.de/bin/windows/contrib/3.2/PACKAGES'
Warning: unable to access index for repository http://www.stats.ox.ac.uk/pub/RWin/bin/windows/contrib/3.2:
  cannot open URL 'http://www.stats.ox.ac.uk/pub/RWin/bin/windows/contrib/3.2/PACKAGES'
Warning message:
package 'Rtsne' is not available (for R version 3.2.5)

Thanks & Regards,
Nithya Dayalan
AMS MRL DPS | HCL @ Merck
E-mail: nithya.dayalan at merck.com
Tel#+91 44 61053951| Mobile +91 8754232975


-----Original Message-----
From: David Winsemius [mailto:dwinsemius at comcast.net] 
Sent: Friday, August 12, 2016 10:51 AM
To: Dayalan, Nithya
Cc: r-help at R-project.org; Radhakrishan, Balaji
Subject: Re: [R] R Package installation
In most case it is the first warning or error that is most meaningful, but in this case it is the last one.

The `installed.packages` function can tell you which packages are in the Bases" category:

plic <- installed.packages( .Library, priority = "base")
[1] "base"      "compiler"  "datasets"  "graphics"  "grDevices" "grid"      "methods"  
 [8] "parallel"  "splines"   "stats"     "stats4"    "tcltk"     "tools"     "utils"    


Updating them requires updating your R version, which is what you should do now.
David Winsemius
# 
So you need to address your system access issues. Review the R Windows FAQ.

https://cran.r-project.org/bin/windows/base/rw-FAQ.html#The-Internet-download-functions-fail_002e
David Winsemius
#
David Winsemius
# 
Sorry for the blank message just now, but it appears that this is some ambiguity in your statement that you can connect to the Internet with R. The evidence below says that you _cannot_ do so. Those files exist and at least some of those mirrors have binaries of that package for the outdated version of R that you are using.

Perhaps you need to talk to your IT staff for support in getting through your corporate securioty layers, whatever they might be in whatever unstated setup you have.
John
# 
On Fri, 12 Aug 2016 06:53:03 -0400
"Dayalan, Nithya" <nithya.dayalan at merck.com> wrote:
You don't say what OS you are using, though the packages you were
trying to obtain are apparently for Windows.  You also don't say
whether you are using something like R-Studio, or whether you are on a
company network behind a firewall.

If you have a sysop, you probably should be going through him or her.
There's a very good chance that your system is lacking in permissions.
Your network's settings are problem, or Windows or a recent update may
be causing your trouble. You should also simply try opening the specific
mirror URL sans the package info to see if you can see the page.
Jeff Newmiller
# 
This may not have anything to do with the OP's problem, but if permissions are an issue then it should be mentioned. 

One problem that some windows users encounter is thinking they should "Run As"  administrator when installing or running R, rather than letting Windows UAE prompt them for privilege escalation as needed. 

The side effect of such an action is that (most? all?) files touched by R then become usable only by R running as administrator, and all sorts of weird problems ensue. It is much better to avoid ever running as administrator and updating all packages into the user-specific package library as needed, with the system-wide package library updated only when R is upgraded.
Divakar Reddy
# 
parallel is R's base package and it's already installed with base R.

 check in below location:
/usr/lib64/R/library/

Thanks,
Divakar

On Fri, Aug 12, 2016 at 3:53 AM, Dayalan, Nithya <nithya.dayalan at merck.com>
wrote: