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=Cattached 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 IRanges1.10.6loaded 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)
5 answers
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
•
written
by
Michael Dondrup
I have just installed it successfully. What happens when you do: biocLite("geneLenDataBase") ?
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...
Following the BioC mailling list, the same error was reported.
No, it seemingly worked for the poster, as described.
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.
This is a good way to solve it. However, I am still unable to reproduce the problem.
If it's any help, I am able to download it from http://bioconductor.case.edu/bioconductor/2.8/data/experiment/src/contrib/.
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.
> 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..
Log in to answer this question.
-
Facing problem when trying to install a new packages in R version 3.4.3 (2017-11-30 through latest …
written by Pijush Das •
-
DEXSeq install problem
written by bartosovic.marek •
-
Installing Bioconductor On Centos6
written by syrup16g_TO •
-
Deseq Handle Samples Without Replicates
written by camelbbs
-
Problem With Hypergtest On Hgu133Plus2 Data
written by juulia.suvilehto •
-
Bioconductor - Mogene10Stv1Mmensgcdf Not Available -Rma(Affybatchobject)
written by Agatha •
-
Goseq With Mouse Gene Id'S, Does It Work For Anyone?
written by ethanford •
-
Bioconductor Problem With Maketranscriptdbfrombiomart (Genomicfeatures Package)
written by Travis
-
Using Postform() And Readhtmltable()
written by Avoks •
-
Cannot Install Latest Version Of Deseq
written by Pasta •
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.
I am using the most recent version Laurent.
Ok, then. Thought not, as you seem to be downloading a data package from Bioc 2.8...
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? ;)
The disk has a few hundred spare GB Michael :) Question has been edited as you requested.