Problem Installing Bioconductor "Goseq" Package

Question

[Travis]

Hi,

I am trying to install the GOSeq package for GO analysis of RNASeq data but am hitting a problem. The install process tries to download a file called geneLenDataBase_0.99.7.tar.gz from http://bioconductor.org/packages/2.8/data/experiment/src/contrib/

The file downloads approximately 70% and then freezes.

Can anyone else confirm or deny the existence of this problem? I need to figure out if it is a general or a local problem. Perhaps this should go to the bioconductor mailing list but I am having problems mailing it and admin will not respond.

Thanks in advance.

sessionInfo() output:

sessionInfo()

R version 2.13.1 (2011-07-08)

Platform: x86_64-pc-linux-gnu (64-bit)

locale:

[1] LCCTYPE=enUS.UTF-8 LCNUMERIC=C
[3] LCTIME=enUS.UTF-8 LCCOLLATE=enUS.UTF-8
[5] LCMONETARY=C LCMESSAGES=enUS.UTF-8
[7] LCPAPER=enUS.UTF-8 LCNAME=C
[9] LCADDRESS=C LCTELEPHONE=C
[11] LCMEASUREMENT=enUS.UTF-8 LCIDENTIFICATION=C

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

other attached packages:

[1] edgeR2.2.6 Rsamtools1.4.3 Biostrings2.20.4
[4] GenomicFeatures1.4.5 GenomicRanges1.4.8 IRanges1.10.6

loaded via a namespace (and not attached):

[1] biomaRt2.8.1 BSgenome1.20.1 DBI0.2-5 limma3.8.3
[5] RCurl1.6-10 RSQLite0.10.0 rtracklayer1.12.5 tcltk2.13.1
[9] tools2.13.1 XML3.4-3

biocLite("geneLenDataBase") output:

biocLite("geneLenDataBase") Using R version 2.13.1, biocinstall version 2.8.4. Installing Bioconductor version 2.8 packages:

[1] "geneLenDataBase" Please wait...

Installing package(s) into ‘/home/goliver/R/x8664-pc-linux-gnu-library/2.13’ (as ‘lib’ is unspecified) trying URL 'http://bioconductor.statistik.tu-dortmund.de/packages/2.8/data/experiment/src/contrib/geneLenDataBase0.99.7.tar.gz' Content type 'application/x-gzip' length 100445668 bytes (95.8 Mb)

opened URL==================================

(freezes at this point)

[Laurent]

Although this is not going to help your downloading issue, you might consider upgrading to most recent R/Bioconductor versions to benefit from the latest fixes/features.

[Travis]

I am using the most recent version Laurent.

[Laurent]

Ok, then. Thought not, as you seem to be downloading a data package from Bioc 2.8...

[Michael]

It must have to do something with your local setup or internet connection. But please edit your question and provide the whole output in the places I edited. And btw, it's not that your disk partition is full, is it? ;)

[Travis]

The disk has a few hundred spare GB Michael :) Question has been edited as you requested.

Answer 1

[Michael]

Try:

chooseBioCmirror()

and select a mirror site, then run biocLite("goseq") again.

Edit: the same problem was also reported on the Bioconductor mailing list, they seem to propose almost the same, but in addition to use a different source for the BiocLite script. Citing a mail there:

Hi Claudia -- you might try an alternative Bioconductor

source("http://bioconductor.org/biocLite.R") chooseBioCmirror() or CRAN mirror; the mirror in Dortmund would be a particular good choice.

Martin

[Michael]

I have just installed it successfully. What happens when you do: biocLite("geneLenDataBase") ?

[Michael]

Following the BioC mailling list, the same error was reported.

[Travis]

I have tried a couple of mirrors now and the download always seems to halt at the same point. Strange!

[Travis]

The install freezes at exactly the same point Michael. The progress bar stops moving and the cursor stops flashing.

Does Laurent (above) have a point about the versions?

biocLite("geneLenDataBase") Using R version 2.13.1, biocinstall version 2.8.4. Installing Bioconductor version 2.8 packages: [1] "geneLenDataBase" Please wait...

[Travis]

Was it ignored there? :)

[Michael]

No, it seemingly worked for the poster, as described.

Answer 2

[Travis]

I got around the problem by downloading the database file manually:

wget http://bioconductor.org/packages/2.8/data/experiment/src/contrib/geneLenDataBase_0.99.7.tar.gz

and installing manually:

R CMD INSTALL geneLenDataBase_0.99.7.tar.gz

before returning to my R environment and installing GOSeq as normal:

biocLite("goseq")

I am still unsure why the database download was freezing in R. I wonder if there is some environment variable causing the download to cut-off at a given point? Problem solved regardless.

[Michael]

This is a good way to solve it. However, I am still unable to reproduce the problem.

[Travis]

Me neither Michael! I'm clueless. Very new to R/Bioconductor which doesn't help either. I appreciate all of your input.

Answer 3

[Andrew W]

If it's any help, I am able to download it from http://bioconductor.case.edu/bioconductor/2.8/data/experiment/src/contrib/.

[Travis]

My own download via wget just completed but the download via R is still frozen.

Answer 4

[Neilfws]

I'm attempting the install using biocLite("goseq") right now. I'm seeing plenty of network activity during the download of geneLenDataBase, which is 95.8 MB.

I often find that Bioconductor downloads of tens of megabytes run quite slowly (but not days - 30 mins maybe at most). My advice is just to let it run and go do something else until it completes.

[Travis]

I let it run overnight Neil!

[Neilfws]

Well, my point was that it's not taking overnight for me. Try again and follow Michael's advice about choosing a mirror.

Answer 5

[Naresh]

> biocLite("geneLenDataBase")
BioC_mirror: http://bioconductor.org
Using Bioconductor version 3.0 (BiocInstaller 1.16.2), R
  version 3.1.2.
Installing package(s) 'geneLenDataBase'
trying URL 'http://bioconductor.org/packages/3.0/data/experiment/bin/windows/contrib/3.1/geneLenDataBase_1.1.1.zip'
Content type 'application/zip' length 201604709 bytes (192.3 Mb)
opened URL
downloaded 192.3 Mb

package 'geneLenDataBase' successfully unpacked and MD5 sums checked..