Question: Problem Installing Bioconductor "Goseq" Package
1
gravatar for Travis
8.0 years ago by
Travis2.8k
USA
Travis2.8k wrote:

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] LC
TIME=enUS.UTF-8 LCCOLLATE=enUS.UTF-8
[5] LC
MONETARY=C LCMESSAGES=enUS.UTF-8
[7] LCPAPER=enUS.UTF-8 LCNAME=C
[9] LC
ADDRESS=C LCTELEPHONE=C
[11] LC
MEASUREMENT=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] GenomicFeatures
1.4.5 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)
ADD COMMENTlink modified 4.6 years ago by Naresh60 • written 8.0 years ago by Travis2.8k

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.

ADD REPLYlink written 8.0 years ago by Laurent1.6k

I am using the most recent version Laurent.

ADD REPLYlink written 8.0 years ago by Travis2.8k

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

ADD REPLYlink written 8.0 years ago by Laurent1.6k

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? ;)

ADD REPLYlink written 8.0 years ago by Michael Dondrup46k

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

ADD REPLYlink written 8.0 years ago by Travis2.8k
2
gravatar for Michael Dondrup
8.0 years ago by
Bergen, Norway
Michael Dondrup46k wrote:

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<http://bioconductor.org/biocLite.R> ") chooseBioCmirror()

or CRAN mirror; the mirror in Dortmund would be a particular good choice.

Martin

ADD COMMENTlink modified 8.0 years ago • written 8.0 years ago by Michael Dondrup46k
1

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

ADD REPLYlink written 8.0 years ago by Michael Dondrup46k
1

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

ADD REPLYlink written 8.0 years ago by Michael Dondrup46k

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

ADD REPLYlink written 8.0 years ago by Travis2.8k

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...

ADD REPLYlink written 8.0 years ago by Travis2.8k

Was it ignored there? :)

ADD REPLYlink written 8.0 years ago by Travis2.8k

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

ADD REPLYlink written 8.0 years ago by Michael Dondrup46k
1
gravatar for Travis
8.0 years ago by
Travis2.8k
USA
Travis2.8k wrote:

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.

ADD COMMENTlink written 8.0 years ago by Travis2.8k

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

ADD REPLYlink written 8.0 years ago by Michael Dondrup46k

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

ADD REPLYlink written 8.0 years ago by Travis2.8k
0
gravatar for Andrew W
8.0 years ago by
Andrew W290
Andrew W290 wrote:

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

ADD COMMENTlink written 8.0 years ago by Andrew W290

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

ADD REPLYlink written 8.0 years ago by Travis2.8k
0
gravatar for Neilfws
8.0 years ago by
Neilfws48k
Sydney, Australia
Neilfws48k wrote:

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.

ADD COMMENTlink written 8.0 years ago by Neilfws48k

I let it run overnight Neil!

ADD REPLYlink written 8.0 years ago by Travis2.8k

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

ADD REPLYlink written 8.0 years ago by Neilfws48k
0
gravatar for Naresh
4.6 years ago by
Naresh60
Korea, Republic Of
Naresh60 wrote:

> 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..

ADD COMMENTlink written 4.6 years ago by Naresh60
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