Following the instructions on https://bioconductor.org/packages/devel/bioc/vignettes/goseq/inst/doc/goseq.pdf
To see what genomes are in the local database, I am told to type:
supportedOrganisms()
...which returns:
Error: could not find function "supportedOrganisms"
googling around, I find that maybe I should type the following instead:
SupportedGenomes()
...but that returns:
Error in getNodeSet(doc, "//table[@class='descTbl']")[[1L]] :
subscript out of bounds
any idea what i’m doing wrong?
Thanks
---
traceback()
4: ucscGenomes()
3: is.factor(var)
2: unfactor(ucscGenomes())
1: supportedGenomes()
---
sessionInfo()
R version 3.3.2 (2016-10-31)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: CentOS Linux 7 (Core)
locale:
[1] LC_CTYPE=en_GB.UTF-8 LC_NUMERIC=C
[3] LC_TIME=en_GB.UTF-8 LC_COLLATE=C
[5] LC_MONETARY=en_GB.UTF-8 LC_MESSAGES=en_GB.UTF-8
[7] LC_PAPER=en_GB.UTF-8 LC_NAME=C
[9] LC_ADDRESS=C LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_GB.UTF-8 LC_IDENTIFICATION=C
attached base packages:
[1] stats4 parallel stats graphics grDevices utils datasets
[8] methods base
other attached packages:
[1] Rsamtools_1.22.0 Biostrings_2.38.4 XVector_0.10.0
[4] rtracklayer_1.30.4 GenomicFeatures_1.22.13 AnnotationDbi_1.32.3
[7] Biobase_2.30.0 GenomicRanges_1.22.4 GenomeInfoDb_1.6.3
[10] IRanges_2.4.8 S4Vectors_0.8.11 BiocGenerics_0.16.1
[13] goseq_1.22.0 RSQLite_1.1-2 geneLenDataBase_1.6.0
[16] BiasedUrn_1.07
loaded via a namespace (and not attached):
[1] Rcpp_0.12.9 zlibbioc_1.16.0
[3] GenomicAlignments_1.6.3 BiocParallel_1.4.3
[5] BSgenome_1.38.0 lattice_0.20-34
[7] tools_3.3.2 grid_3.3.2
[9] SummarizedExperiment_1.0.2 nlme_3.1-131
[11] mgcv_1.8-17 DBI_0.5-1
[13] lambda.r_1.1.9 futile.logger_1.4.3
[15] digest_0.6.12 Matrix_1.2-8
[17] futile.options_1.0.0 bitops_1.0-6
[19] biomaRt_2.26.1 RCurl_1.95-4.8
[21] memoise_1.0.0 GO.db_3.2.2
[23] XML_3.98-1.5
thanks, both. useful answers. can you tell i'm an R beginner?bashing around a bit, i think the problem is that R has been updated to a version not supported by bioconductor. this meant that BiocInstaller was struggling, and while it looked (to my uneducated eye) as if it was managing to update packages, it was actually re-installing the same very old versions. does that make sense?so now the question is: do i need to install an older R version, or can i do anything useful in R3.3.2?No, the R version hasn't been updated to a version not supported by Bioconductor - all versions of R since 2003 or so have a version of Bioconductor that is specifically tailored for that version of R. What you or your system administrator have done is to install a version of goseq that was intended to be used in a much older version of R.
Both Gordon and I have tried to tell you that, but unfortunately it hasn't worked just yet. So let me be completely explicit.
source("https://www.bioconductor.org/biocLite.R") biocValid()This will test your installation, and then tell you which packages you have that are not correct. It will also tell you exactly what you need to do to fix things, which may simply be to do
which will download and install all the correct versions of packages, including goseq. Once you have done that, everything will be OK.
OK. firstly thanks again, your help is appreciated.
I’m new to all this, and don’t know as much as you.
there's a lot to get one's head around!
to my limited understanding, nothing i wrote in my last comment (wrong as it may well be) contradicts what was written in either previous comment, both of which i read and broadly understood.
I was just speculating on a cause of my problems updating.
I’m trying to be friendly and polite, and not to provoke.
so:
1. I’m glad I don’t need an older R.
2. it seems so. in what way?
3. that's what I’m trying to do.
4. these are all things I’ve done already, without much success, more details below.
> source("https://www.bioconductor.org/biocLite.R")Bioconductor version 3.2 (BiocInstaller 1.20.1), ?biocLite for help
Bioconductor does not yet support R version 3.3.2
biocValid() indeed tells me to update a load of stuff.
> biocLite()Would you like to use a personal library instead? (y/n) y
trying URL 'https://bioconductor.org/packages/3.2/bioc/src/contrib/BiocInstaller_1.20.3.tar.gz'
Content type 'application/x-gzip' length 15942 bytes (15 KB)
==================================================
downloaded 15 KB
* installing *source* package ‘BiocInstaller’ ...** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** testing if installed package can be loaded
Bioconductor version 3.2 (BiocInstaller 1.20.3), ?biocLite for help
Warning: BiocInstaller version 3.2 is too old for R version 3.3.2; see
https://bioconductor.org/install/#troubleshoot-biocinstaller
* DONE (BiocInstaller)
The downloaded source packages are in‘/tmp/RtmprAkbyn/downloaded_packages’
Bioconductor version 3.2 (BiocInstaller 1.20.3), ?biocLite for help
'BiocInstaller' updated to version 1.20.3
BioC_mirror: https://bioconductor.org
Using Bioconductor 3.2 (BiocInstaller 1.20.3), R 3.3.2 (2016-10-31).
Old packages: 'DBI', 'BiocInstaller', 'DBI', 'Hmisc', 'Matrix', 'RSQLite',
'Rcpp', 'RcppArmadillo', 'XML', 'acepack', 'chron', 'colorspace',
'data.table', 'digest', 'futile.logger', 'ggplot2', 'lambda.r', 'mgcv',
'nlme', 'plyr', 'reshape2', 'scales', 'snow', 'stringi', 'stringr',
'survival'
Update all/some/none? [a/s/n]: a
trying URL 'https://cran.rstudio.com/src/contrib/DBI_0.6.tar.gz'
Content type 'application/x-gzip' length 611282 bytes (596 KB)
==================================================
downloaded 596 KB
* installing *source* package ‘DBI’ ...** package ‘DBI’ successfully unpacked and MD5 sums checked
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (DBI)
(then a whole lot of messages that seem to suggest that its installing things, ending in:)
The downloaded source packages are in‘/tmp/RtmprAkbyn/downloaded_packages’
Warning message:
BiocInstaller version 3.2 is too old for R version 3.3.2; see
https://bioconductor.org/install/#troubleshoot-biocinstaller
...and biocValid() still gives the same list of out-of-date packages.
so i follow the instructions on
https://bioconductor.org/install/#troubleshoot-biocinstaller:> remove.packages("BiocInstaller")Removing package from ‘/home/mbzdz/R/x86_64-pc-linux-gnu-library/3.3’
(as ‘lib’ is unspecified)
> remove.packages("BiocInstaller")
Removing package from ‘/home/mbzdz/R/x86_64-pc-linux-gnu-library/3.3’
(as ‘lib’ is unspecified)
Error in find.package(pkgs, lib) :
there is no package called ‘BiocInstaller’
> source("https://bioconductor.org/biocLite.R")
Bioconductor version 3.2 (BiocInstaller 1.20.1), ?biocLite for help
Bioconductor does not yet support R version 3.3.2
The reason your Bioconductor installation is broken is because each Bioc version is specifically tailored to work with a particular version of R. You have the current version of R installed, but at least some of your Bioc packages are two years old. This includes the version of the BiocInstaller package you have.
In addition, you are using the system-wide installed version of R, which means that both R and all its packages are installed in a directory for which you probably do not have write privileges. This is why you were asked if you want to use a personal directory. This is a problem for you because there appears to be a BiocInstaller package in the system-wide package library that is messing things up for you. Unless you have write privileges for that directory, you cannot upgrade!
If you don't have write privileges for the system-wide package library directory, you will have to find someone who does (usually the system administrator for your Linux computer) and have them follow the instructions for trouble-shooting the BiocInstaller (keep removing it until it's completely gone, then re-install by sourcing biocLite.R).