Error At Bioconductor Installation On Mac Os X

Question

[zheboyang]

I have some problems in R installation on Mac OS X lion.

[R.app GUI 1.51 (6148) x86_64-apple-darwin9.8.0]

> source("http://bioconductor.org/biocLite.R")
BiocInstaller version 1.4.7, ?biocLite for help

> biocLite()
BioC_mirror: http://bioconductor.org
Using R version 2.15, BiocInstaller version 1.4.7.
Warning: unable to access index for repository http://brainarray.mbni.med.umich.edu/bioc/bin/macosx/leopard/contrib/2.15
Installing package(s) 'Biobase' 'IRanges' 'AnnotationDbi'
Warning: unable to access index for repository http://brainarray.mbni.med.umich.edu/bioc/bin/macosx/leopard/contrib/2.15
trying URL 'http://www.bioconductor.org/packages/2.10/bioc/bin/macosx/leopard/contrib/2.15/Biobase_2.16.0.tgz'
Content type 'application/x-gzip' length 2394691 bytes (2.3 Mb)
opened URL
============================
......

The downloaded binary packages are in
    /var/folders/0m/ptg7kg6d7szc88n7yfvpm6bm0000gn/T//RtmpDnKXiw/downloaded_packages
Warning: unable to access index for repository http://brainarray.mbni.med.umich.edu/bioc/bin/macosx/leopard/contrib/2.15

It always have the error about the repository and stop at there. I search the R/Bioconductor mail list, but I can not find any way to solve it.

Do you kniw how to install it in Mac OS??

Thank you very much!

[Vikas Bansal]

Hi! If you will simply search on Google, you will get lot of answers. One of the possible solutions can be here. (I am not sure if this question is more suitable for stackoverflow)

[zheboyang]

In fact, I find this one. It does not work.

Answer 1

[Michael]

There is no problem, you are just fine.

The packages have most likely been downloaded and installed correctly and you should be safe to ignore this warning (even though it's printed in red on the console) http://brainarray.mbni.med.umich.edu/bioc/bin/macosx/leopard/contrib/2.15 seems to be down (check with your browser) and the warning is a nuisance for sure. I do not know why biocLite() insists to look something up there, but it definitely worked nevertheless. To confirm this try:

library(Biobase)

Loading required package: BiocGenerics

Attaching package: ‘BiocGenerics’

The following object(s) are masked from ‘package:stats’:

    xtabs

The following object(s) are masked from ‘package:base’:

    anyDuplicated, cbind, colnames, duplicated, eval, Filter, Find, get, intersect, lapply, Map, mapply, mget, order,
    paste, pmax, pmax.int, pmin, pmin.int, Position, rbind, Reduce, rep.int, rownames, sapply, setdiff, table, tapply,
    union, unique

Welcome to Bioconductor

    Vignettes contain introductory material; view with 'browseVignettes()'. To cite Bioconductor, see
    'citation("Biobase")', and for packages 'citation("pkgname")'.

If that loads the package, fine! If it instead says "Error in library(UARGH) : there is no package called ‘UARGH’", then, well, it didn't work

Answer 2

[Jeremy Leipzig]

try a different mirror

chooseBioCmirror()

[zheboyang]

I try several mirror like seatle, gemerny..., no one work

Answer 3

[liats80]

I have exactly the same problem! http://brainarray.mbni.med.umich.edu/bioc/bin/macosx/leopard/contrib/2.15 does not exist. I tried ignoring the errors, but when I call a library nothing happens. So basically - it's ignoring me back :p HELP!!!

[Michael]

If you want help, post the output of the library command and your sessionInfo. No output means, it was loaded ok.

Answer 4

[robert.duvoisin]

I'm having the exact same problem. I hope someone can help. Here are the errors:

> source("http://bioconductor.org/biocLite.R")
BiocInstaller version 1.4.7, ?biocLite for help
> biocLite()
BioC_mirror: <http://bioconductor.org>
Using R version 2.15, BiocInstaller version 1.4.7.
Warning: unable to access index for repository <http://brainarray.mbni.med.umich.edu/bioc/bin/macosx/leopard/contrib/2.15>
Installing package(s) 'Biobase' 'IRanges' 'AnnotationDbi'
Warning: unable to access index for repository <http://brainarray.mbni.med.umich.edu/bioc/bin/macosx/leopard/contrib/2.15>
trying URL 'http://www.bioconductor.org/packages/2.10/bioc/bin/macosx/leopard/contrib/2.15/Biobase_2.16.0.tgz'
Content type 'application/x-gzip' length 2394691 bytes (2.3 Mb)
opened URL
==================================================
downloaded 2.3 Mb

trying URL 'http://www.bioconductor.org/packages/2.10/bioc/bin/macosx/leopard/contrib/2.15/IRanges_1.14.4.tgz'
Content type 'application/x-gzip' length 1977923 bytes (1.9 Mb)
opened URL
==================================================
downloaded 1.9 Mb

trying URL 'http://www.bioconductor.org/packages/2.10/bioc/bin/macosx/leopard/contrib/2.15/AnnotationDbi_1.18.1.tgz'
Content type 'application/x-gzip' length 5112378 bytes (4.9 Mb)
opened URL
==================================================
downloaded 4.9 Mb


The downloaded binary packages are in
    /var/folders/wM/wMD+ODwxHeGnz46GE6Y34++++TI/-Tmp-//RtmpYe7oy4/downloaded_packages
Warning: unable to access index for repository <http://brainarray.mbni.med.umich.edu/bioc/bin/macosx/leopard/contrib/2.15>
Warning message:
installed directory not writable, cannot update packages 'boot', 'class',
  'KernSmooth', 'MASS', 'mgcv', 'nnet', 'rpart', 'spatial' 
> getMonograph()
Error in biocinstall(groupName = groupName, ...) : 
  You have an outdated biocLite() function. Run 'rm(biocLite)' and try again.
>

[Michael]

No, you don't have the same problem! "You have an outdated biocLite() function. Run 'rm(biocLite)' and try again."

[robert.duvoisin]

Dear Michael,

Actually, I tried 'rm(biocLite)'. Below are the commands I type, as instructed by the vignette I'm following, and the "Bioinformatics and Computational Biology Solutions Using R and Bioconductor" book I'm using, and the /mogr page it points to. Yes, I can load Affy, so maybe most of the packages are loading despite the error messages. But I would be more confident if biocLite would stop looking for a site that apparently hasn't existed for a few months. (I've tried "chooseBioCmirror()," nothing changes.) Downloading the packages is the first thing a new user does, so a bunch of error/warning messages straight off the bat is unwelcoming.

I'd appreciate insight or fixes anyone could pass on.

Thank you, Lisa

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

biocLite() ## the slew of error messages above about brain array appear > source("http://bioconductor.org/getMonograph.R") Warning message: In safeSource() : Redefining ‘biocinstall’

getMonograph() Error in biocinstall(groupName = groupName, ...) : You have an outdated biocLite() function. Run 'rm(biocLite)' and try again.

[Michael]

In fact you have a hit a real little problem here, I guess it lies in the getMonograph.R code, which might be dated and incompatible with recent bioc code. You should post this to the bioconductor mailing list, giving the exact command sequence and the output of sessionInfo().

[Michael]

I have solved your problem, I think. I used another question to post the solution, have a look here: http://www.biostars.org/post/show/51657/error-in-getmonograph-from-bioconductor-book/#51659