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rietho / IPO

A Tool for automated Optimization of XCMS Parameters
http://bioconductor.org/packages/IPO/
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Unable install any packages in R-3.2.2 version #30

Closed anupb08 closed 8 years ago

anupb08 commented 8 years ago

After updating to R-3.2.2, I am unable to install any package. It saying the error:

install.packages("ggplot2") Installing package into ‘/home/drishti/R/x86_64-redhat-linux-gnu-library/3.2’ (as ‘lib’ is unspecified) --- Please select a CRAN mirror for use in this session --- Error in download.file(url, destfile = f, quiet = TRUE) : unsupported URL scheme Warning: unable to access index for repository https://mirrors.nics.utk.edu/cran/src/contrib Warning message: package ‘ggplot2’ is not available (for R version 3.2.2)

In fact, i tried to install other package, problem is same. the repository link is accessible from my browser, but i dont know why this error is giving. Please help.

glibiseller commented 8 years ago

Hi!

Sry for the late reply! Did you find a solution to your problem? Have you tried the latest R-version?

best regards Gunnar

anupb08 commented 8 years ago

Hi Gunnar, Thanks for reply. Yes I am able to install packages in latest R version.

Regards, Anup

On Mon, Oct 12, 2015 at 2:18 PM, Gunnar Libiseller <notifications@github.com

wrote:

Hi!

Sry for the late reply! Did you find a solution to your problem? Have you tried the latest R-version?

best regards Gunnar

— Reply to this email directly or view it on GitHub https://github.com/glibiseller/IPO/issues/30#issuecomment-147331145.

glibiseller commented 8 years ago

Thanks for the reply.

shlomita commented 8 years ago

Hi,

I have same problem, I cannot install any package in R-3.2.2. How did you solved the problem?

Thanks.

anupb08 commented 8 years ago

Hi, I dont know what exact problem you are facing during package installation. I can tell you how I installed packages. After typing install.packages("ggplot") in R console, one popup will be shown. In the poup, there will be shown some mirrors. I selected bottom most "HTTP mirrors". After selecting this mirror, there will be shown lots of mirrors. Then you can select any of them, if that fail you have to try other one.

-Anup

On Tue, Oct 13, 2015 at 11:51 AM, shlomita notifications@github.com wrote:

Hi,

I have same problem, I cannot install any package in R-3.2.2. How did you solved the problem?

Thanks.

— Reply to this email directly or view it on GitHub https://github.com/glibiseller/IPO/issues/30#issuecomment-147616926.

glibiseller commented 8 years ago

If you are using R-Studio you can change the mirror in Tools->Global Options...->Packages

shlomita commented 8 years ago

I successfully install it with the command: install.packages("randomForest", repos="http://cran.cnr.berkeley.edu")

Just: install.packages("randomForest") Did not worked and give error like above in the first message.

Thanks a lot!

mitrarath commented 8 years ago

I faced the same issue with R-3.2.2. But after googling a bit found that it requires libcurl suppport in order to be able toh deal with https websites. If you select the mirror which is http....then it would have no issues.

johanjordaan commented 8 years ago

Hi. I had the same issue. Doing this: sudo apt-get install libcurl4-gnutls-dev Fixed it for me on ubuntu 15.1.

Just for reference and to help other ppl :)

rietho commented 8 years ago

Thank you very much for the information!

shun1024 commented 8 years ago

the answer from @shlomita is CORRECT and useful. Thanks a lot .

But I still dont know why it does work. Might be some errors in other repos for this version?

vicruiser commented 8 years ago

Hey there, I've tried everything you've posted here but didn't work. I'm using R 3.2.3 and ubuntu 14.04. Finally I found the solution so that's why I'm posting here an alternative. http://packages.ubuntu.com/trusty/gnu-r/r-cran-ggplot2 I've installed every package of that website manually but not in R terminal, in ubuntu terminal. Then I runned R and "library(ggplot2)" worked perfectly.

Hope this help someone. Best wishes!

bandhakavi commented 8 years ago

i just changed the mirror from a https one to a http. Used the menu option: Packages->Set CRAN mirror... option

harshilsaini commented 8 years ago

please help guys non of the method is working for me i am using ubuntu 16.04LTS R version is 3.2.3

rietho commented 8 years ago

@harshilsaini It's diffiucult to help you without more information (how do you run R, why did the other proposed solutions not work). As your issue is not IPO-related I'd suggest to post your question with more details at Stackoverflow or if it's rather Ubuntu related on Ask Ubuntu

venkat01 commented 7 years ago

When selecting the mirrors for install.packages("ggplot2"), choose the http and not the https as that is the issue that i had.

Jeet1994 commented 7 years ago

Hello all,

type the following in RStudio :options(download.file.method="libcurl")

And then try installing.

Solved the same problem for me.

Regards.

sriprad commented 5 years ago

Hi, I am unable to install tidytext in 3.2.2 . any clue?

Sangeetha-Dns commented 4 years ago

Hello all,

type the following in RStudio :options(download.file.method="libcurl")

And then try installing.

Solved the same problem for me.

Regards.

Thank you very much this is the only solution that really fixed my package installation issue!! perhaps after going through all other listed solutions on web-pages which did not help fix the repository access issue!

lecorguille commented 4 years ago

An alternative could be to install IPO using Conda/Miniconda https://anaconda.org/bioconda/r-ipo