warning in R

Question

[zizigolu]

Hey friends,

I opened Rstudio and typed source ("http://bioconductor.org/biocLite.R") in console part but says that

A new version of Bioconductor is available after installing the most recent
 version of R; see http://bioconductor.org/install
Bioconductor version 2.11 (BiocInstaller 1.8.3), ?biocLite for help

I have already installed R 3.2.0 and 2.15.0, and when I typed biocLite() it said that:

BioC_mirror: http://bioconductor.org
Using Bioconductor version 2.11 (BiocInstaller 1.8.3), R version 2.15.
Installing package(s) 'Biobase' 'IRanges' 'AnnotationDbi'
Warning: unable to access index for repository http://brainarray.mbni.med.umich.edu/bioc/src/contrib

Then why warning yet?

Answer 1

[iraun]

The warning is because the current release of Bioconductor is version 3.1. So once R is updated to version 3.2.0, you can download the latest version of Bioconductor typing:

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

[alolex]

Are you using RStudio? If so check to make sure it is that latest version. When I updated my R it was not very compatible with the older RStudio. Then I had to reinstall all my Bioconductor packages with the new R and RStudio versions.

[zizigolu]

Thank you alolex for your attention. I don't know how I know whether my Rstudio is the latest version or not.

May I ask another question which I got bad confused about specially with sporadic searching and tremendous pages.

I downloaded an array experiment (GSE33964), I am interesting in knowing which genes expressing in this experiment is correlated with my genes (genes involved in sterol biosynthesis pathway in citrus sinensis), something like Co-Expression Network Analysis using Pearson's correlation coefficient or another way. Do you think please my idea has any sense or I am wasting time? Especially I am fighting with R to process the data and I am just a beginner. If possible give me some advice.

Thank you

[alolex]

Please post this as a new question as it is not related to the original question on this page. Also, if you could provide some more details about your data (time points, replicates, conditions etc) that would help answer your question.

With regards to the RStudio version you can type R.Version() to get the version information. When I do this in my RStudio I get the following output:

> R.Version()
$platform
[1] "x86_64-apple-darwin13.4.0"

$arch
[1] "x86_64"

$os
[1] "darwin13.4.0"

$system
[1] "x86_64, darwin13.4.0"

$status
[1] ""

$major
[1] "3"

$minor
[1] "2.0"

$year
[1] "2015"

$month
[1] "04"

$day
[1] "16"

$`svn rev`
[1] "68180"

$language
[1] "R"

$version.string
[1] "R version 3.2.0 (2015-04-16)"

$nickname
[1] "Full of Ingredients"

[zizigolu]

Thank you

My data are like this:

GSM839728    Epithelial cells at 28mm, biological rep1
GSM839729    Epithelial cells at 28mm, biological rep2
GSM839730    Epithelial cells at 28mm, biological rep3
GSM839731    Parenchyma cells at 28mm, biological rep1
GSM839732    Parenchyma cells at 28mm, biological rep2
GSM839733    Parenchyma cells at 28mm, biological rep3
GSM839734    Epithelial cells at 41mm, biological rep1
GSM839735    Epithelial cells at 41mm, biological rep2
GSM839736    Epithelial cells at 41mm, biological rep3
GSM839737    Parenchyma cells at 41mm, biological rep1
GSM839738    Parenchyma cells at 41mm, biological rep2
GSM839739    Parenchyma cells at 41mm, biological rep3

About my Rstudio

R.Version()

$platform
[1] "x86_64-w64-mingw32"

$arch
[1] "x86_64"

$os
[1] "mingw32"

$system
[1] "x86_64, mingw32"

$status
[1] ""

$major
[1] "3"

$minor
[1] "2.0"

$year
[1] "2015"

$month
[1] "04"

$day
[1] "16"

$`svn rev`
[1] "68180"

$language
[1] "R"

$version.string
[1] "R version 3.2.0 (2015-04-16)"

$nickname
[1] "Full of Ingredients"

[alolex]

OK, sorry, that was actually the R version info, which it looks like you are using the most current, but bioconductor is seeing your old version for some reason. Try the following few suggestions, and make sure you restart RStudio.

To see your RStudio version:

> library(rstudio)
> versionInfo()
$version
[1] '0.98.1103'

$mode
[1] "desktop"

They actually just posted a newer version of RStudio a few days ago, 0.99.441 here: http://www.rstudio.com/products/rstudio/download/

So you could try to install that version, then try your bioconductor installation again. If that doesn't work, try installing bioconductor through a vanilla session of R in the terminal (Command Prompt on Windows I think)--don't go through RStudio.

> R --vanilla

Did the suggestions from @Deepak and @airan work? If you are still having problems it would help if you could post all your command line input and output up to the error you are getting.

[zizigolu]

Thank you

$version
[1] '0.98.1103'

$mode
[1] "desktop"

Unfortunately tips from Deepak and Airan didn't work.

[alolex]

Looks like you are all up-to-date. Try installing Bioconductor and packages using the R --vanilla approach, then go back to using RStudio. If that doesn't work I'm not sure I have any other suggestions :( as I have a mac and not windows. You can post this problem to the Bioconductor forum (https://support.bioconductor.org), and they may be able to help. As a complete last resort you can always completely uninstall R and RStudio, then reinstall them and start from scratch. I hope you figure it out!

[zizigolu]

Thank you

I opened cmd and typed R --vanilla

but said that:

Microsoft Windows [Version 6.1.7600]
Copyright (c) 2009 Microsoft Corporation. All rights reserved.

C:\Users\yang>>> R --vanilla
'--vanilla' is not recognized as an internal or external command, operable program or batch file.

C:\Users\yang>

Anyway I am thankful...

[zizigolu]

Thank you alolex I went through your tip (https://support.bioconductor.org/) and I could download my packages from this link: https://support.bioconductor.org/p/68201/#68206

[alolex]

Great! Thanks for letting me know the solution. I'm glad you found someone who could help and that you got it working :) I know how frustrating things like that are!

[zizigolu]

Thank you

I typed, something is downloading

[iraun]

Bioconductor in particular is that "something" :) Glad to help.

[zizigolu]

Sorry Airan,

After downloading finished, I closed Rstudio and opended again and typed source("http://bioconductor.org/biocLite.R") and clicked Enter

It said in red that:

A new version of Bioconductor is available after installing the most recent version of R; see http://bioconductor.org/install
Bioconductor version 2.11 (BiocInstaller 1.8.3), ?biocLite for help

:( :(

[iraun]

Mmm...that's weird. If you type sessionInfo(), which R version do you have?

[zizigolu]

I have R 3.2.0

[zizigolu]

R version 3.2.0 (2015-04-16)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 7 x64 (build 7600)

locale:

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

attached base packages:

[1] stats     graphics  grDevices utils     datasets  methods

loaded via a namespace (and not attached):

[1] tools_3.2.0

[zizigolu]

Sorry, I have to install package whenever I launch Rstudio?

[iraun]

OK. Take a look to these two posts, specially the first one, and check if you can fix the problems:

• https://support.bioconductor.org/p/66799/
• http://nebc.nerc.ac.uk/nebc_website_frozen/nebc.nerc.ac.uk//tools/bioinformatics-docs/other-bioinf/r-and-bioconductor

[zizigolu]

OK thanks :)

Answer 2

[Deepak Tanwar]

Try this

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

[zizigolu]

Thank you Deepak,

I tried:

source("http://bioconductor.org/biocLite.R")
Bioconductor version 3.1 (BiocInstaller 1.18.2), ?biocLite for help

biocLite("BiocInstaller")
BioC_mirror: http://bioconductor.org
Using Bioconductor version 3.1 (BiocInstaller 1.18.2), R version 3.2.0.
Installing package(s) 'BiocInstaller'
Warning: package 'BiocInstaller' is in use and will not be installed
 in addition when I tried to download with CRAN, my packages like "GEOquery" are not in the list

:(

[Deepak Tanwar]

Restart your Rstudio.

Try again. GEOquery is not a CRAN package. It's a Bioconductor package. So, you have to install in through biocLite() command

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

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

[zizigolu]

Deepak,

My R is RGui (32 bit) but my windows is 64, do you think if it is the problem?

[Deepak Tanwar]

I don't think so, that would be a problem.

[zizigolu]

OK, thank you