Question: Any Experiences/Solutions For Problems With The Last R Update?
5
gravatar for Chris Evelo
6.1 years ago by
Chris Evelo9.9k
Maastricht, The Netherlands
Chris Evelo9.9k wrote:

We ran into some serious problem with our R/Bioconductor pipelines for Affymetrix gene expression arrays at arrayanalysis.org (and some others in the developer version) after the last R update from (2.13 -> 2.14)

First of all we used to use Rshell to run these procedures. Somehow that does no longer work. When run from Rshell Bioconductor is not able to read the .cel files. We changed to another shell. That helped.

But we also have problems with core Bioconductor packages which a.o. leads to annotations being wrong. The release notes mention something related to package environment changes, we are still investigating that.

Did anyone experience the same problems and find a generic solution or specific solutions for specific packages?

In any case this should serve as a warning. If you regularly run Bioconductor procedures and recently updated R do double check the output!

Update

The code used can be downloaded from arrayanalysis.org (click the yellow tab that says download source).

We try to tackle problems one by one.

First we were not able to run the pipeline from the server at all. That was solved by moving away from Rshell as mentioned above.

Next thing is that we need the right annotations to build the genesets for RMA. When the custom cdf's are not yet installed, it should get them, and that doesn't work. If we run the script directly from R, (so not as php invoked server code) all seems to go well. As soon as the custom cdf's are installed everything works and if we skip the step loading these cdfs the original cdf works fine. (We were told by another group that automatically getting the cdf's also causes problems for GCRMA where it tries to reinstall custom cdf's that are already there).

I am traveling. But I got an email explaining that the problem with standard cdf's after a custom cdf failed to load (I described that as a second problem earlier) was in fact a regular bug and not related to the update.

Apart from that there also are downstream procedures which don't work at all, or provide erroneous output. But we are not there yet.

R bioconductor • 1.5k views
ADD COMMENTlink modified 6.1 years ago by Chris Miller19k • written 6.1 years ago by Chris Evelo9.9k
1

What versions were involved? Was this 2.13 -> 2.14?

ADD REPLYlink written 6.1 years ago by Neilfws47k

Yes, that is right correct.

ADD REPLYlink written 6.1 years ago by Chris Evelo9.9k

Can you provide some more information, like a simple reproducible example? Sometimes creating the simple example helps to understand what the problem is.

ADD REPLYlink written 6.1 years ago by Martin Morgan1.5k

Downloading the source code isn't good enough for a reproducible example -- what specifically am I supposed to do to trigger the errors you're seeing? When you say "When the custom cdf's are not yet installed, it should get them, and that doesn't work" can you give an example of the code in that part of the script, show the R commands and the errors that they produce? I'm not sure that Biostar is the right forum for this sort of trouble-shooting; have you thought of posting to the Bioconductor mailing list http://bioconductor.org/help/mailing-list/ ?

ADD REPLYlink written 6.1 years ago by Martin Morgan1.5k

Martin you are right. I will try to get the isolated code part that causes the problems for the installation of the custom cdf files. We really have no clue what part of the code causes the problems with the default cdf as we can only see that from the output. The strange thing is both only happen when invoked from php on the server. I am traveling to New York at the moment. So getting that might take a while. My question was not meant to trouble-shoot our specific code, just to hear other experiences. Chris Miller's answer was very helpful in that respect.

ADD REPLYlink written 6.1 years ago by Chris Evelo9.9k

@Chris: sessionInfo() is also a good idea to include when asking R-related questions.

ADD REPLYlink written 6.1 years ago by Sean Davis24k
7
gravatar for Chris Miller
6.1 years ago by
Chris Miller19k
Washington University in St. Louis, MO
Chris Miller19k wrote:

R 2.14 enforces some new rules about namespaces that have many package maintainers scrambling to get fixes in. I spent a couple of hours the other night working on the package I maintain. The fix wasn't difficult, but to someone without detailed knowledge of the internals of R namespaces, it took a little while to wrap my head around.

Here are some links I found useful:

ADD COMMENTlink written 6.1 years ago by Chris Miller19k
1
gravatar for Neilfws
6.1 years ago by
Neilfws47k
Sydney, Australia
Neilfws47k wrote:

I have not done much work since upgrading to 2.14, but have not noticed any problems so far.

Here's the upgrade procedure that I use:

# in shell
cp -r ~/R/x86_64-pc-linux-gnu-library/2.13 ~/R/x86_64-pc-linux-gnu-library/2.14
# then in R
source("http://bioconductor.org/biocLite.R")
update.packages(repos=biocinstallRepos(), ask=FALSE, checkBuilt=TRUE)
# back to shell
rm -rf ~/R/x86_64-pc-linux-gnu-library/2.13

Here's a brief session that I just ran using some CEL files from GEO (GSE7275, platform Affymetrix Mouse Genome 430 2.0 Array), without problems:

> library(simpleaffy)
Loading required package: affy
Loading required package: Biobase

Welcome to Bioconductor

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

Loading required package: genefilter
Loading required package: gcrma
> cel <- read.affy()
> cel.rma <- rma(cel)
Loading required package: AnnotationDbi

Background correcting
Normalizing
Calculating Expression
ADD COMMENTlink written 6.1 years ago by Neilfws47k
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